From bd09171a1354112f5b400c461657db144e76471d Mon Sep 17 00:00:00 2001 From: Luan Garcia Date: Sat, 6 Apr 2024 23:58:08 -0300 Subject: [PATCH] started odk --- .github/workflows/qc.yml | 33 + .gitignore | 47 + CODE_OF_CONDUCT.md | 46 + CONTRIBUTING.md | 95 + GeoReservoirOntology.owl | 1016 -------- KarooChannelLeveeCaseStudy.owl | 583 ----- LICENSE => LICENSE.md | 0 README.md | 34 +- catalog-v001.xml | 12 - geores-base.obo | 356 +++ geores-base.owl | 1347 +++++++++++ geores-full.obo | 781 ++++++ geores-full.owl | 2130 +++++++++++++++++ geores-simple.obo | 414 ++++ geores-simple.owl | 1268 ++++++++++ geores.obo | 781 ++++++ geores.owl | 2130 +++++++++++++++++ imports/GeoCoreOntology.owl | 469 ---- .../GeologicalSpatialRelationsOntology.owl | 527 ---- issue_template.md | 21 + src/metadata/README.md | 24 + src/metadata/geores.md | 45 + src/metadata/geores.yml | 28 + src/ontology/Makefile | 660 +++++ src/ontology/README-editors.md | 27 + src/ontology/catalog-v001.xml | 10 + src/ontology/geores-edit.owl | 681 ++++++ src/ontology/geores-idranges.owl | 53 + src/ontology/geores-odk.yaml | 22 + src/ontology/geores.Makefile | 7 + src/ontology/imports/bfo2020_import.owl | 273 +++ src/ontology/imports/bfo2020_terms.txt | 3 + src/ontology/imports/geocore_import.owl | 471 ++++ src/ontology/imports/geocore_terms.txt | 9 + src/ontology/imports/iao_import.owl | 1182 +++++++++ src/ontology/imports/iao_terms.txt | 0 src/ontology/run.bat | 1 + src/ontology/run.sh | 107 + src/ontology/tmp/.gitkeep | 0 src/scripts/run-command.sh | 4 + src/scripts/update_repo.sh | 31 + src/scripts/validate_id_ranges.sc | 75 + src/sparql/README.md | 32 + src/sparql/basic-report.sparql | 12 + src/sparql/dc-properties-violation.sparql | 11 + src/sparql/edges.sparql | 18 + src/sparql/geores_terms.sparql | 7 + src/sparql/inject-subset-declaration.ru | 11 + src/sparql/inject-synonymtype-declaration.ru | 11 + src/sparql/iri-range-violation.sparql | 19 + src/sparql/label-with-iri-violation.sparql | 9 + src/sparql/labels.sparql | 9 + .../multiple-replaced_by-violation.sparql | 12 + src/sparql/obsoletes.sparql | 14 + .../owldef-self-reference-violation.sparql | 12 + src/sparql/postprocess-module.ru | 16 + src/sparql/preprocess-module.ru | 22 + src/sparql/simple-seed.sparql | 13 + src/sparql/subsets-labeled.sparql | 13 + src/sparql/synonyms.sparql | 26 + src/sparql/terms.sparql | 15 + src/sparql/xrefs.sparql | 8 + 62 files changed, 13465 insertions(+), 2628 deletions(-) create mode 100644 .github/workflows/qc.yml create mode 100644 .gitignore create mode 100644 CODE_OF_CONDUCT.md create mode 100644 CONTRIBUTING.md delete mode 100644 GeoReservoirOntology.owl delete mode 100644 KarooChannelLeveeCaseStudy.owl rename LICENSE => LICENSE.md (100%) delete mode 100644 catalog-v001.xml create mode 100644 geores-base.obo create mode 100644 geores-base.owl create mode 100644 geores-full.obo create mode 100644 geores-full.owl create mode 100644 geores-simple.obo create mode 100644 geores-simple.owl create mode 100644 geores.obo create mode 100644 geores.owl delete mode 100644 imports/GeoCoreOntology.owl delete mode 100644 imports/GeologicalSpatialRelationsOntology.owl create mode 100644 issue_template.md create mode 100644 src/metadata/README.md create mode 100644 src/metadata/geores.md create mode 100644 src/metadata/geores.yml create mode 100644 src/ontology/Makefile create mode 100644 src/ontology/README-editors.md create mode 100644 src/ontology/catalog-v001.xml create mode 100644 src/ontology/geores-edit.owl create mode 100644 src/ontology/geores-idranges.owl create mode 100644 src/ontology/geores-odk.yaml create mode 100644 src/ontology/geores.Makefile create mode 100644 src/ontology/imports/bfo2020_import.owl create mode 100644 src/ontology/imports/bfo2020_terms.txt create mode 100644 src/ontology/imports/geocore_import.owl create mode 100644 src/ontology/imports/geocore_terms.txt create mode 100644 src/ontology/imports/iao_import.owl create mode 100644 src/ontology/imports/iao_terms.txt create mode 100644 src/ontology/run.bat create mode 100644 src/ontology/run.sh create mode 100644 src/ontology/tmp/.gitkeep create mode 100644 src/scripts/run-command.sh create mode 100644 src/scripts/update_repo.sh create mode 100644 src/scripts/validate_id_ranges.sc create mode 100644 src/sparql/README.md create mode 100644 src/sparql/basic-report.sparql create mode 100644 src/sparql/dc-properties-violation.sparql create mode 100644 src/sparql/edges.sparql create mode 100644 src/sparql/geores_terms.sparql create mode 100644 src/sparql/inject-subset-declaration.ru create mode 100644 src/sparql/inject-synonymtype-declaration.ru create mode 100644 src/sparql/iri-range-violation.sparql create mode 100644 src/sparql/label-with-iri-violation.sparql create mode 100644 src/sparql/labels.sparql create mode 100644 src/sparql/multiple-replaced_by-violation.sparql create mode 100644 src/sparql/obsoletes.sparql create mode 100644 src/sparql/owldef-self-reference-violation.sparql create mode 100644 src/sparql/postprocess-module.ru create mode 100644 src/sparql/preprocess-module.ru create mode 100644 src/sparql/simple-seed.sparql create mode 100644 src/sparql/subsets-labeled.sparql create mode 100644 src/sparql/synonyms.sparql create mode 100644 src/sparql/terms.sparql create mode 100644 src/sparql/xrefs.sparql diff --git a/.github/workflows/qc.yml b/.github/workflows/qc.yml new file mode 100644 index 0000000..77b4c72 --- /dev/null +++ b/.github/workflows/qc.yml @@ -0,0 +1,33 @@ +# Basic ODK workflow + +name: CI + +# Controls when the action will run. +on: + # Triggers the workflow on push or pull request events but only for the master branch + push: + branches: [ master ] + pull_request: + branches: [ master ] + + # Allows you to run this workflow manually from the Actions tab + workflow_dispatch: + +# A workflow run is made up of one or more jobs that can run sequentially or in parallel +jobs: + # This workflow contains a single job called "ontology_qc" + ontology_qc: + # The type of runner that the job will run on + runs-on: ubuntu-latest + container: obolibrary/odkfull:v1.5 + + # Steps represent a sequence of tasks that will be executed as part of the job + steps: + # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it + - uses: actions/checkout@v3 + + - name: Run ontology QC checks + env: + DEFAULT_BRANCH: master + run: cd src/ontology && make ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G' test IMP=false PAT=false MIR=false + diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..6720e05 --- /dev/null +++ b/.gitignore @@ -0,0 +1,47 @@ +.DS_Store +semantic.cache +bin/ + +*.tmp +*.tmp.obo +*.tmp.owl +*.tmp.json + +.github/token.txt + +src/ontology/mirror +src/ontology/mirror/* +src/ontology/reports/* +!src/ontology/reports/release-diff.md +src/ontology/geores.owl +src/ontology/geores.obo +src/ontology/geores.json +src/ontology/geores-base.* +src/ontology/geores-basic.* +src/ontology/geores-full.* +src/ontology/geores-simple.* +src/ontology/geores-simple-non-classified.* +src/ontology/geores-edit.properties + +src/ontology/seed.txt +src/ontology/dosdp-tools.log +src/ontology/ed_definitions_merged.owl +src/ontology/ontologyterms.txt +src/ontology/simple_seed.txt +src/ontology/patterns +src/ontology/merged-geores-edit.owl + +src/ontology/target/ +src/ontology/tmp/* +!src/ontology/tmp/.gitkeep +!src/ontology/tmp/README.md + +src/ontology/run.sh.conf +src/ontology/run.sh.env + +src/ontology/imports/*_terms_combined.txt + +src/patterns/data/**/*.ofn +src/patterns/data/**/*.txt +src/patterns/pattern_owl_seed.txt +src/patterns/all_pattern_terms.txt \ No newline at end of file diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..b547f39 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,46 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to make participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment include: + +* Using welcoming and inclusive language +* Being respectful of differing viewpoints and experiences +* Gracefully accepting constructive criticism +* Focusing on what is best for the community +* Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +* The use of sexualized language or imagery and unwelcome sexual attention or advances +* Trolling, insulting/derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or electronic address, without explicit permission +* Other conduct which could reasonably be considered inappropriate in a professional setting + +## Our Responsibilities + +Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior. + +Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. + +## Scope + +This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by [contacting the project team](contact.md). All complaints will be reviewed and investigated and will result in a response that is deemed necessary and appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately. + +Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership. + +## Attribution + +This code of conduct has been derived from the excellent code of conduct of the [ATOM project](https://github.com/atom/atom/blob/master/CODE_OF_CONDUCT.md) which in turn is adapted from the [Contributor Covenant][homepage], version 1.4, available at [https://contributor-covenant.org/version/1/4][version] + +[homepage]: https://contributor-covenant.org +[version]: https://contributor-covenant.org/version/1/4/ diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..0078ee1 --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,95 @@ +# Contributing to GeoReservoir Ontology + +:+1: First of all: Thank you for taking the time to contribute! + +The following is a set of guidelines for contributing to GEORES. +These guidelines are not strict rules. Use your best judgment, and feel free to propose +changes to this document in a pull request. + +## Table Of Contents + +- [Code of Conduct](#code-of-conduct) +- [Guidelines for Contributions and Requests](#contributions) + * [Reporting problems with the ontology](#reporting-bugs) + * [Requesting new terms](#requesting-terms) + * [Adding new terms by yourself](#adding-terms) +- [Best practices](#best-practices) + * [How to write a great issue?](#great-issues) + * [How to create a great pull/merge request?](#great-pulls) + + + +## Code of Conduct + +The GeoReservoir Ontology team strives to create a +welcoming environment for editors, users and other contributors. +Please carefully read our [Code of Conduct](CODE_OF_CONDUCT.md). + + + +## Guidelines for Contributions and Requests + + + +### Reporting problems with the ontology + +Please use our [Issue Tracker](https://github.com/BDI-UFRGS/GeoReservoirOntology/issues/) for reporting problems with the ontology. +To learn how to write a good issue [see here](#great-issues). + + + +### Requesting new terms + +Before you write a new request, please consider the following: + +- **Does the term already exist?** Before submitting suggestions for new ontology terms, check whether the term exist, +either as a primary term or a synonym term. You can search for your term using [OLS](http://www.ebi.ac.uk/ols/ontologies/geores). +- **Can you provide a definition for the term?** It should be very clear what the term means, and you should be +able to provide a concise definition, ideally with a scientific reference. +- **Is the ontology in scope for the term?** Sometimes, it is hard to tell whether a term "belongs" in +and ontology. A rule of thumb is "if a similar term already exists, the new term is probably in scope." +It can be very helpful to mention a very similar concept as part of the term request! + +#### Who can request a term? + +Anyone can request new terms. However, there is not guarantee that your term will be added automatically. Since this is a +community resource, it is often necessary to do at least some of the work of adding the term yourself, see below. + +#### How to write a new term request + +Request a new term _via_ the GitHub [Issue Tracker](https://github.com/BDI-UFRGS/GeoReservoirOntology/issues/). + +It is important to remember that it takes a lot of time for curators to process issues submitted to the tracker. +To make this work easier, please always use issue templates if they are available (https://github.com/BDI-UFRGS/GeoReservoirOntology/issues/new/choose). + +For how to write a good term request, please read the [best practices carefully](#great-issues). + + + +### How to add a new term + +If you have never editted this ontology before, first follow a [general tutorial](https://oboacademy.github.io/obook/lesson/contributing-to-obo-ontologies) + +**Process**: + +1. Clone the repository (In case you are not an offical team member, create a fork first) +1. Create new branch in git, for example `git checkout -b issue123` +1. Open src/ontology/geores-edit.owl in your favourite editor, i.e. [Protege](https://protege.stanford.edu/). **Careful:** double check you are editing the correct file. There are many ontology files in this repository, but only one _editors file_! +1. Perform your edit and save your changes +1. Commit changes to branch +1. Push changes upstream +1. Create pull request + +## Best Practices + + + +### How to write great issues? + +Please refer to the [OBO Academy term request guide](https://oboacademy.github.io/obook/howto/term-request/). + + + +### How to create a great pull/merge request? + +Please refer to the [OBO Academy best practices](https://oboacademy.github.io/obook/howto/github-create-pull-request/) \ No newline at end of file diff --git a/GeoReservoirOntology.owl b/GeoReservoirOntology.owl deleted file mode 100644 index 509f306..0000000 --- a/GeoReservoirOntology.owl +++ /dev/null @@ -1,1016 +0,0 @@ - - - - - - - - - https://www.inf.ufrgs.br/bdi/ontologies/geocoreontology - https://www.inf.ufrgs.br/bdi/ontologies/geologicalspatialrelationsontology - - - Fabrício Henrique Rodrigues - - - - Fernando Cicconeto - - - - Joel Luis Carbonera - - - - Luan Fonseca Garcia - - - - Lucas Valadares Vieira - - - - Mara Abel - - - - Renata dos Santos Alvarenga - - - - Tiago Agne de Oliveira - - - - Yuanwei Qu - - - - This work is distributed under Creative Commons Attribution License CC BY 4.0 <https://creativecommons.org/licenses/by/4.0/legalcode> - - - - Cited references: - -1. Abel, M., Perrin, M., Carbonera, J.L.: Ontological analysis for information integration in geomodeling. Earth Science Informatics 8, 21–36 (2015) -2. Arp, R., Smith, B., Spear, A.D.: Building Ontologies with Basic Formal Ontology. The MIT Press, Cambridge, MA (2015) -3. Carbonera, J.L., Abel, M., Scherer, C.M.S.: Visual interpretation of events in petroleum exploration: An approach supported by well-founded ontologies. Expert Systems With Applications 42, 2749–2763 (2015) -4. Cullis, S., Colombera, L., Patacci, M., McCaffrey, W.D.: Hierarchical classifications of the sedimentary architecture of deep-marine depositional systems. Earth-Science Reviews 179, 38–71 (2018) -5. De Ros, L.F., Goldberg, K.: Reservoir petrofacies: A tool for quality characterization and prediction. In: AAPG Annual Conference and Exhibition. Long Beach (2007) -6. Garcia, L.F., Abel, M., Perrin, M., Alvarenga, R.S.: The geocore ontology: A core ontology for general use in geology. Computers & Geosciences 135 (2020) -7. Garcia, L.F., Carbonera, J.L., Rodrigues, F.H., Antunes, C.R., Abel, M.: What rocks are made of: Towards an ontological pattern for material constitution in the geological domain. In: Laender, A.H.F., Pernici, B., Lim, E.P., Oliveira, J.P.M. (eds.) ER: 38th International Conference on Conceptual Modeling. pp. 275–286. Springer, Cham (2019) -8. Guarino, N., Welty, C.A.: An overview of ontoclean. In: Staab, S., Studer, R. (eds.) Handbook on Ontologies, pp. 151–171. Springer, Berlin, Heidelberg (2004) -9. McHargue, T., Pyrcz, M.J., Sullivan, M.D., Clark, J.D., Fildani, A., Romans, B.W., Covault, J.A., Levy, M., Posamentier, H.W., Drinkwater, N.J.: Architecture of turbidite channel systems on the continental slope: Patterns and predictions. Marine and Petroleum Geology 28, 728–743 (2011) -10. Middleton, G.V.: Johannes walther’s law of the correlation of facies. Bulletin of the Geological Society of America 84, 979–988 (1973) -11. Nichols, G.: Sedimentology and Stratigraphy. Wiley-Blackwell, Chichester, 2nd edn. (2009) -12. Rovetto, R.: The shape of shapes: An ontological exploration. In: Hastings, J., Kutz, O., Bhatt, M., Borgo, S. (eds.) Proceedings of the First Interdisciplinary Workshop on SHAPES. Karlsruhe (2011), http://ceur-ws.org/Vol-812/ -13. Walker, R.G., James, N.P.: Facies Models: Response to Sea Level Change. Geological Association of Canada, St. John’s (1992) - - - - GeoReservoir is an ontology to support the description of the geometry and the lithology of deep-marine deposits. The GeoReservoir ontology provides formal and clear definitions of deep-marine depositional system entities, creating an unambiguous terminology for geometrical and lithological properties of the deposits in the scale of outcrop and seismic sections. These definitions are independent of tasks, geological interpretations, and process inferences. We created this language to make it possible to formally and uniformly describe any deep-marine occurrence in the world with an adequate level of detail for sedimentological studies and computer processing. - - - - We acknowledge the Brazilian funding agencies CNPq and CAPES for financing this work and the Research Centre of Petrobras (CENPES) for collaborating on this project. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - channel - - - - - - - - - - - - lobe - - - - - - - - - - - - mound - - - - - - - - - - - - - - - - - - - - - - - - - wedge - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - channel - irregular - lens - lobe - mound - scour - sheet - sigmoid - waveform - wedge - wing - - - - - - - - - channel - irregular - lens - lobe - mound - scour - sheet - sigmoid - waveform - wedge - wing - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - http://purl.obolibrary.org/obo/RO_0010001 - Genetic information generically depend on molecules of DNA. - - - - http://purl.obolibrary.org/obo/RO_0010001 - The novel *War and Peace* generically depends on this copy of the novel. - - - - http://purl.obolibrary.org/obo/RO_0010001 - The pattern shared by chess boards generically depends on any chess board. - - - - http://purl.obolibrary.org/obo/RO_0010001 - The score of a symphony g-depends on a copy of the score. - - - - http://purl.obolibrary.org/obo/RO_0010001 - This pdf file generically depends on this server. - - - - http://purl.obolibrary.org/obo/RO_0010001 - A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*. - - - - http://purl.obolibrary.org/obo/RO_0010001 - [072-ISO] - - - - http://purl.obolibrary.org/obo/RO_0010001 - generically depends on - - - - #UFRGS:GeoReservoirOntology_channel_geometry - A synonym for Geometry with “channel” value - - - - #UFRGS:GeoReservoirOntology_channel_geometry - channel geometry - - - - #UFRGS:GeoReservoirOntology_channel_surface - A Geological Boundary that forms the basis of a Channel Unit, having a concave-up shape unless truncated by overlying depositional units. - - - - #UFRGS:GeoReservoirOntology_channel_surface - channel surface - - - - #UFRGS:GeoReservoirOntology_channel_surface - R+ I+ O- U+ ED- - - - - #UFRGS:GeoReservoirOntology_channel_unit - An elongated Depositional Unit having some Channel Surface as its boundary and constituted by some Sediment or Sedimentary Rock that fills it (McHargue et al., 2011). - - - - #UFRGS:GeoReservoirOntology_channel_unit - In stratigraphic terms, a channel unit is constituted by the sediments or sedimentary rocks that fill a channel. It is important to notice that, in more general terms, a channel is a passageway for fluids or sediments, i.e., an immaterial entity. If one elaborates about the erosion and deposition processes that generate these units (McHargue et al., 2011), it is essential to have this disambiguation. - - - - #UFRGS:GeoReservoirOntology_channel_unit - In this work, we decided not to model the named hierarchical scales as entities (e.g., Channel Element, Channel Complex, Channel Complex Set - McHargue et al., 2011) because there exists a wide variety of hierarchical schemes in the literature, and they are not necessarily interoperable (Cullis et al., 2018). Instead, we focus on the fact that depositional units can be fractally nested: a unit can be a Proper Spatial Part Of another unit, which can be a Proper Spatial Part Of another unit, and so forth. This approach solves the problem of supporting the repeated geological objects' description in multiple scales. As so, a Channel Unit can be decomposed in other Channel Units many times as necessary, keeping the representation structure. - - - - #UFRGS:GeoReservoirOntology_channel_unit - channel unit - - - - #UFRGS:GeoReservoirOntology_channel_unit - R+ I+ O- U+ ED- - - - - #UFRGS:GeoReservoirOntology_depositional_system - An Object Aggregate whose members are mereotopologically connected Depositional Units. - - - - #UFRGS:GeoReservoirOntology_depositional_system - depositional system - - - - #UFRGS:GeoReservoirOntology_depositional_system - R+ I+ O+ U+ ED- - - - - #UFRGS:GeoReservoirOntology_depositional_unit - A Sedimentary Geological Object having a dimension of at least 1 m in at least one of its extents (width, length, or thickness). - - - - #UFRGS:GeoReservoirOntology_depositional_unit - A Depositional Unit is recognizable in a mapping scale of at least 1:1000. - - - - #UFRGS:GeoReservoirOntology_depositional_unit - depositional unit - - - - #UFRGS:GeoReservoirOntology_depositional_unit - R+ I+ O- U+ ED- - - - - #UFRGS:GeoReservoirOntology_dimension - A Quality that inheres in an Independent Continuant by virtue of one of its one-dimensional extents. It is a category that includes at least the three dimensions defined in this ontology: Width, Length, and Thickness. All dimensions are expressed by a real number indicating its value and a literal string indicating its measurement unit. - - - - #UFRGS:GeoReservoirOntology_dimension - dimension - - - - #UFRGS:GeoReservoirOntology_facies - A pattern of properties of Geological Objects. - - - - #UFRGS:GeoReservoirOntology_facies - Considering facies as generically dependent continuants is a controversial issue. We are taking in account that geologists consider structures as patterns that can be recognized in several distinct deposits, such as a cross stratification pattern that indicates tractive depositional currents. Naturally this pattern will be materialized in a specific particular rock as a specific dependent continuant that concretizes the generic one (Arp et al., 2015). For an extensive discussion on this issue, see Garcia et al. (2020). - - - - #UFRGS:GeoReservoirOntology_facies - This entity is defined in the literature as a combination of features that differentiates a geological object from its adjacent geological objects (Walker and James, 1992). However, a Facies does not describe a single Geological Object’s features: it might repeat in several objects as a pattern. This particular aspect matches the definition of Generically Dependent Continuant in BFO. Another important aspect is that the features that compose facies vary depending on the research context, e.g., Sedimentary Facies, Petrofacies (De Ros and Goldberg, 2007), Lithofacies, Ichnofacies, and Biofacies (Nichols, 2009). - - - - #UFRGS:GeoReservoirOntology_facies - facies - - - - #UFRGS:GeoReservoirOntology_facies_association - A Generically Dependent Continuant that consists of an aggregate of Facies. - - - - #UFRGS:GeoReservoirOntology_facies_association - It usually describes the Facies that are typically found in specific regions or sub-environments. For example, the Channel Axis Association (McHargue et al., 2011) describes Sedimentary Facies typically found at the center part of channels (in a cross-section point of view). - - - - #UFRGS:GeoReservoirOntology_facies_association - facies association - - - - #UFRGS:GeoReservoirOntology_geometry - A Quality that inheres in a Depositional Unit by virtue of its external three-dimensional shape. It does not reflect the exact mathematical specifications of a geometric shape but abstracts and simplifies these specifications (Rovetto, 2011). - - - - #UFRGS:GeoReservoirOntology_geometry - geometry - - - - #UFRGS:GeoReservoirOntology_has_measurement_unit - A relation between a Quality and a literal string that represents its measurement unit. - - - - #UFRGS:GeoReservoirOntology_has_measurement_unit - has measurement unit - - - - #UFRGS:GeoReservoirOntology_has_quality_value - A relation between a Quality and its value. - - - - #UFRGS:GeoReservoirOntology_has_quality_value - has quality value - - - - #UFRGS:GeoReservoirOntology_length - A Dimension that inheres in an Independent Continuant by virtue of the distance between its two extremes along its longest side. - - - - #UFRGS:GeoReservoirOntology_length - length - - - - #UFRGS:GeoReservoirOntology_levee_unit - A Depositional Unit having Wedge Geometry and forming a bank or ridge geomorphology associated with some Channel Unit. - - - - #UFRGS:GeoReservoirOntology_levee_unit - This term is not consensual as some authors refer to these units as the wedge-shape embankments around channels, which is the definition that we adopt here, while other authors refer to them as not necessarily being these embankments and possibly having wing shapes, among other definitions. - - - - #UFRGS:GeoReservoirOntology_levee_unit - This term refers to the geomorphological association of some wegde-shaped unit with some channel unit, even if the channel does not exist at the moment of the observation by the geologist and the levee is probabilistically identified by tendencies (e.g., typical facies). In other words, the term "levee" ontologicallly denotes this relation even if it cannot be deterministically observed. - - - - #UFRGS:GeoReservoirOntology_levee_unit - levee unit - - - - #UFRGS:GeoReservoirOntology_levee_unit - R~ I+ O- U+ ED- - - - - #UFRGS:GeoReservoirOntology_lobe_geometry - A synonym for Geometry with “lobe” value - - - - #UFRGS:GeoReservoirOntology_lobe_geometry - lobe geometry - - - - #UFRGS:GeoReservoirOntology_lobe_unit - A Depositional Unit having some Lobe Geometry. - - - - #UFRGS:GeoReservoirOntology_lobe_unit - For Lobe Unit hierarchical scales, we adopted the same approach as in Channel Unit. - - - - #UFRGS:GeoReservoirOntology_lobe_unit - These depositional units are usually found at deep-water depositional system terminal regions, or at channel laterals as Overbank Units. - - - - #UFRGS:GeoReservoirOntology_lobe_unit - lobe unit - - - - #UFRGS:GeoReservoirOntology_lobe_unit - R+ I+ O- U+ ED- - - - - #UFRGS:GeoReservoirOntology_metaproperties - For metaproperties, we use the following notation (Guarino and Welty, 2004; Abel et al., 2015): - -– R+ / R- / R~: rigid / not rigid / anti-rigid; -– I+ / I-: carries / does not carry identity; -– O+ / O-: provides / does not provide identity; -– U+ / U-: carries / does not carry unity; -– ED+ / ED-: existentially dependent / independent. - - - - #UFRGS:GeoReservoirOntology_metaproperties - metaproperties - - - - #UFRGS:GeoReservoirOntology_mound_geometry - A synonym for Geometry with “mound” value - - - - #UFRGS:GeoReservoirOntology_mound_geometry - mound geometry - - - - #UFRGS:GeoReservoirOntology_mound_unit - A Depositional Unit having Mound Geometry with an irregular top surface and internal chaotic facies. - - - - #UFRGS:GeoReservoirOntology_mound_unit - mound unit - - - - #UFRGS:GeoReservoirOntology_mound_unit - R+ I+ O- U+ ED- - - - - #UFRGS:GeoReservoirOntology_overbank_unit - A Depositional Unit found at some overbank area, which is geomorphologically associated with some Channel Unit or Levee Unit. - - - - #UFRGS:GeoReservoirOntology_overbank_unit - This term refers to the units that usually result from the sedimentary current overflows and have geometries such as lobate or waveform. In the same way that occurs with Levee Unit, this term refers to a geomorphological association with some other unit that may not exist at the observation moment. - - - - #UFRGS:GeoReservoirOntology_overbank_unit - overbank unit - - - - #UFRGS:GeoReservoirOntology_overbank_unit - R~ I+ O- U+ ED- - - - - #UFRGS:GeoReservoirOntology_sediment - An Unconsolidated Earth Material constituted by some collection of sedimentary grains or particles (Garcia et al., 2019). - - - - #UFRGS:GeoReservoirOntology_sediment - sediment - - - - #UFRGS:GeoReservoirOntology_sediment - R+ I+ O- U- ED- - - - - #UFRGS:GeoReservoirOntology_sedimentary_facies - A Facies consisting of the sum of the sedimentological characteristics of Depositional Units (Middleton, 1973, Nichols, 2009, Carbonera et al., 2015). - - - - #UFRGS:GeoReservoirOntology_sedimentary_facies - As an example, if we would model Cross-bedded Sandstone (Nichols, 2009), it would be an entity subsumed by Sedimentary Facies having the following relations: (1) Generically Depends On some (Constituted By some Sandstone (a)); and (2) Has Part some Cross-bedding Structure (b). (a): Sandstone would be an entity subsumed by Sedimentary Rock. (b): Cross-bedding Structure would be an entity subsumed by Sedimentary Structure. - - - - #UFRGS:GeoReservoirOntology_sedimentary_facies - sedimentary facies - - - - #UFRGS:GeoReservoirOntology_sedimentary_geological_object - A Geological Object constituted by some Sedimentary Rock or Sediment. - - - - #UFRGS:GeoReservoirOntology_sedimentary_geological_object - sedimentary geological object - - - - #UFRGS:GeoReservoirOntology_sedimentary_geological_object - R+ I+ O- U+ ED- - - - - #UFRGS:GeoReservoirOntology_sedimentary_rock - A Rock constituted by some collection of sedimentary grains or particles (Garcia et al., 2019). - - - - #UFRGS:GeoReservoirOntology_sedimentary_rock - sedimentary rock - - - - #UFRGS:GeoReservoirOntology_sedimentary_rock - R+ I+ O- U- ED- - - - - #UFRGS:GeoReservoirOntology_sedimentary_structure - A Geological Structure consisting of a pattern of the internal arrangement of Depositional Units. - - - - #UFRGS:GeoReservoirOntology_sedimentary_structure - An example would be Cross-bedding Structure as noted in the Sedimentary Facies entity definition. - - - - #UFRGS:GeoReservoirOntology_sedimentary_structure - sedimentary structure - - - - #UFRGS:GeoReservoirOntology_sinuosity - A Quality that inheres in a Channel Unit by virtue of how wavy it is across its length. It is expressed by a real number given by its curved length divided by its length in a straight line. - - - - #UFRGS:GeoReservoirOntology_sinuosity - sinuosity - - - - #UFRGS:GeoReservoirOntology_thickness - A Dimension that inheres in an Independent Continuant by virtue of the distance between its two extremes perpendicularly to its width and length. - - - - #UFRGS:GeoReservoirOntology_thickness - thickness - - - - #UFRGS:GeoReservoirOntology_wedge_geometry - A synonym for Geometry with “wedge” value. - - - - #UFRGS:GeoReservoirOntology_wedge_geometry - wedge geometry - - - - #UFRGS:GeoReservoirOntology_width - A Dimension that inheres in an Independent Continuant by virtueof the distance between its two lateral extremes. - - - - #UFRGS:GeoReservoirOntology_width - width - - - - - - - diff --git a/KarooChannelLeveeCaseStudy.owl b/KarooChannelLeveeCaseStudy.owl deleted file mode 100644 index e9f8d05..0000000 --- a/KarooChannelLeveeCaseStudy.owl +++ /dev/null @@ -1,583 +0,0 @@ - - - - - - - - - https://www.inf.ufrgs.br/bdi/ontologies/geocoreontology - https://www.inf.ufrgs.br/bdi/ontologies/geologicalspatialrelationsontology - https://www.inf.ufrgs.br/bdi/ontologies/georeservoirontology - - - Fabrício Henrique Rodrigues - - - - Fernando Cicconeto - - - - Joel Luis Carbonera - - - - Luan Fonseca Garcia - - - - Lucas Valadares Vieira - - - - Mara Abel - - - - Renata dos Santos Alvarenga - - - - Tiago Agne de Oliveira - - - - Yuanwei Qu - - - - This work is distributed under Creative Commons Attribution License CC BY 4.0 <https://creativecommons.org/licenses/by/4.0/legalcode> - - - - Cited references: - -- Hodgson, D.M., Di Celma, C.N., Brunt, R.L., Flint, S.S.: Submarine slope degradation and aggradation and the stratigraphic evolution of channel-levee systems. Journal of the Geological Society 168, 625–628 (2011) - - - - This is the implementation of a GeoReservoir ontology application case study conducted to evaluate the adequacy and limitations in describing the domain entities. It describes a subset of geological data from the Karoo Basin, which was extracted from the study of an area near Laingsburg, South Africa, where two seismic-scale deep-water channel-levee systems are exposed (Hodgson et al., 2011). - - - - We acknowledge the Brazilian funding agencies CNPq and CAPES for financing this work and the Research Centre of Petrobras (CENPES) for collaborating on this project. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #UFRGS:KarooChannelLeveeCaseStudy_cc1 - cc1 - - - - #UFRGS:KarooChannelLeveeCaseStudy_ch1 - ch1 - - - - #UFRGS:KarooChannelLeveeCaseStudy_ch2 - ch2 - - - - #UFRGS:KarooChannelLeveeCaseStudy_ch3 - ch3 - - - - #UFRGS:KarooChannelLeveeCaseStudy_channelized - channelized - - - - #UFRGS:KarooChannelLeveeCaseStudy_du1 - du1 - - - - #UFRGS:KarooChannelLeveeCaseStudy_du2 - du2 - - - - #UFRGS:KarooChannelLeveeCaseStudy_du3 - du3 - - - - #UFRGS:KarooChannelLeveeCaseStudy_el1 - el1 - - - - #UFRGS:KarooChannelLeveeCaseStudy_massive - massive - - - - #UFRGS:KarooChannelLeveeCaseStudy_massive_sandstone - massive sandstone - - - - #UFRGS:KarooChannelLeveeCaseStudy_non_channelized - non-channelized - - - - #UFRGS:KarooChannelLeveeCaseStudy_sandstone - sandstone - - - - #UFRGS:KarooChannelLeveeCaseStudy_siltstone - siltstone - - - - #UFRGS:KarooChannelLeveeCaseStudy_thin_bedded - thin bedded - - - - #UFRGS:KarooChannelLeveeCaseStudy_thin_bedded_sand_siltstone - thin bedded sand/siltstone - - - - #UFRGS:KarooChannelLeveeCaseStudy_unit_c - Unit C - - - - - - - diff --git a/LICENSE b/LICENSE.md similarity index 100% rename from LICENSE rename to LICENSE.md diff --git a/README.md b/README.md index 7fb6982..82cc46e 100644 --- a/README.md +++ b/README.md @@ -1,36 +1,28 @@ + +![Build Status](https://github.com/BDI-UFRGS/GeoReservoirOntology/actions/workflows/qc.yml/badge.svg) # GeoReservoir Ontology GeoReservoir is an ontology to support the description of the geometry and the lithology of deep-marine deposits. The GeoReservoir ontology provides formal and clear definitions of deep-marine depositional system entities, creating an unambiguous terminology for geometrical and lithological properties of the deposits in the scale of outcrop and seismic sections. These definitions are independent of tasks, geological interpretations, and process inferences. We created this language to make it possible to formally and uniformly describe any deep-marine occurrence in the world with an adequate level of detail for sedimentological studies and computer processing. -To open and visualize the GeoReservoir ontology, we recommend using the [Protégé editor](https://protege.stanford.edu/). See section [Project structure](#project-structure) for more details. +## Cite + +https://doi.org/10.1016/j.cageo.2021.105005 -## Project structure +### Stable release versions -To download the GeoReservoir ontology files, go to the [Releases](https://github.com/BDI-UFRGS/GeoReservoirOntology/releases) section. +The latest version of the ontology can always be found at: -The project is organized as follows: +https://www.inf.ufrgs.br/bdi/ontologies/geores.owl -- GeoReservoirOntology.owl - The main GeoReservoir ontology file -- KarooChannelLeveeCaseStudy.owl - A case study containing a usage example -- ./imports - Folder containing the local copies of imported ontologies -- catalog-v001.xml - Protégé catalog pointing to the local copies of imported ontologies -## Contributors +### Editors' version -- [Fernando Cicconeto](mailto:fcicconeto@gmail.com) (corresponding author, [BDI/UFRGS](https://www.inf.ufrgs.br/bdi/about-us-2/)) -- Fabrício Henrique Rodrigues (BDI/UFRGS) -- Joel Luis Carbonera (BDI/UFRGS) -- Luan Fonseca Garcia (BDI/UFRGS) -- Lucas Valadares Vieira (CENPES/Petrobras) -- Mara Abel (BDI/UFRGS) -- Renata dos Santos Alvarenga (BDI/UFRGS) -- Tiago Agne de Oliveira (CENPES/Petrobras) -- Yuanwei Qu (Department of Geoscience/UiO) +Editors of this ontology should use the edit version, [src/ontology/geores-edit.owl](src/ontology/geores-edit.owl) -## How to contribute +## Contact -We accept the opening of issues and pull requests in this repository. +Please use this GitHub repository's [Issue tracker](https://github.com/BDI-UFRGS/GeoReservoirOntology/issues) to request new terms/classes or report errors or specific concerns related to the ontology. ## Acknowledgements -We acknowledge the Brazilian funding agencies CNPq and CAPES for financing this project in part and the Research Centre of Petrobras (CENPES) for collaborating on this project. +This ontology repository was created using the [Ontology Development Kit (ODK)](https://github.com/INCATools/ontology-development-kit). \ No newline at end of file diff --git a/catalog-v001.xml b/catalog-v001.xml deleted file mode 100644 index 4516030..0000000 --- a/catalog-v001.xml +++ /dev/null @@ -1,12 +0,0 @@ - - - - - - - - - - - - diff --git a/geores-base.obo b/geores-base.obo new file mode 100644 index 0000000..63fcd19 --- /dev/null +++ b/geores-base.obo @@ -0,0 +1,356 @@ +format-version: 1.2 +data-version: https://www.inf.ufrgs.br/bdi/ontologies/geores/releases/2024-04-07/geores-base.owl +remark: Cited references:\n\n1. Abel, M., Perrin, M., Carbonera, J.L.: Ontological analysis for information integration in geomodeling. Earth Science Informatics 8, 21–36 (2015)\n2. Carbonera, J.L., Abel, M., Scherer, C.M.S.: Visual interpretation of events in petroleum exploration: An approach supported by well-founded ontologies. Expert Systems With Applications 42, 2749–2763 (2015)\n3. Cullis, S., Colombera, L., Patacci, M., McCaffrey, W.D.: Hierarchical classifications of the sedimentary architecture of deep-marine depositional systems. Earth-Science Reviews 179, 38–71 (2018)\n4. De Ros, L.F., Goldberg, K.: Reservoir petrofacies: A tool for quality characterization and prediction. In: AAPG Annual Conference and Exhibition. Long Beach (2007)\n5. Garcia, L.F., Carbonera, J.L., Rodrigues, F.H., Antunes, C.R., Abel, M.: What rocks are made of: Towards an ontological pattern for material constitution in the geological domain. In: Laender, A.H.F., Pernici, B., Lim, E.P., Oliveira, J.P.M. (eds.) ER: 38th International Conference on Conceptual Modeling. pp. 275–286. Springer, Cham (2019)\n6. Guarino, N., Welty, C.A.: An overview of ontoclean. In: Staab, S., Studer, R. (eds.) Handbook on Ontologies, pp. 151–171. Springer, Berlin, Heidelberg (2004)\n7. McHargue, T., Pyrcz, M.J., Sullivan, M.D., Clark, J.D., Fildani, A., Romans, B.W., Covault, J.A., Levy, M., Posamentier, H.W., Drinkwater, N.J.: Architecture of turbidite channel systems on the continental slope: Patterns and predictions. Marine and Petroleum Geology 28, 728–743 (2011)\n8. Middleton, G.V.: Johannes walther’s law of the correlation of facies. Bulletin of the Geological Society of America 84, 979–988 (1973)\n9. Nichols, G.: Sedimentology and Stratigraphy. Wiley-Blackwell, Chichester, 2nd edn. (2009)\n10. Rovetto, R.: The shape of shapes: An ontological exploration. In: Hastings, J., Kutz, O., Bhatt, M., Borgo, S. (eds.) Proceedings of the First Interdisciplinary Workshop on SHAPES. Karlsruhe (2011), http://ceur-ws.org/Vol-812/\n11. Walker, R.G., James, N.P.: Facies Models: Response to Sea Level Change. Geological Association of Canada, St. John’s (1992) +remark: We acknowledge the Brazilian funding agencies CNPq and CAPES for financing this work and the Research Centre of Petrobras (CENPES) for collaborating on this project. +ontology: https://www.inf.ufrgs.br/bdi/ontologies/geores/geores-base.owl +property_value: http://purl.org/dc/elements/1.1/contributor "Alcides Lopes" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Fabrício Henrique Rodrigues" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Fernando Cicconeto" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Joel Luis Carbonera" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Luan Fonseca Garcia" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Lucas Valadares Vieira" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Mara Abel" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Renata dos Santos Alvarenga" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Tiago Agne de Oliveira" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Yuanwei Qu" xsd:string +property_value: http://purl.org/dc/elements/1.1/type IAO:8000001 +property_value: http://purl.org/dc/terms/description "GeoReservoir is an ontology to support the description of the geometry and the lithology of deep-marine deposits. The GeoReservoir ontology provides formal and clear definitions of deep-marine depositional system entities, creating an unambiguous terminology for geometrical and lithological properties of the deposits in the scale of outcrop and seismic sections. These definitions are independent of tasks, geological interpretations, and process inferences. We created this language to make it possible to formally and uniformly describe any deep-marine occurrence in the world with an adequate level of detail for sedimentological studies and computer processing." xsd:string +property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by-nc/4.0/" xsd:string +property_value: http://purl.org/dc/terms/title "GeoReservoir Ontology" xsd:string +property_value: owl:versionInfo "2024-04-07" xsd:string + +[Term] +id: GEORES:0000001 +name: body of rock +is_a: GEOCORE:0000001 +intersection_of: GEOCORE:0000001 +intersection_of: GEOCORE:0000017 GEOCORE:0000008 +relationship: BFO:0000101 GEOCORE:0000004 +relationship: BFO:0000129 GEORES:0000020 ! depositional system +relationship: BFO:0000129 GEORES:0000021 ! sedimentary environment +relationship: GEOCORE:0000017 GEOCORE:0000008 +property_value: altLabel "corpo de rocha" xsd:string +property_value: definition "'body of rock' is a 'geological object' that is 'constituted by' some 'amount of rock'" xsd:string + +[Term] +id: GEORES:0000002 +name: stratigraphic unit +comment: Os diferentes elementos arquiteturais ocorrem dentro de uma unidade com uma idade definida que é a unidade estratigráfica.\n\nAinda não sabemos se poderia ser uma unidade litoestratigráfica. +is_a: GEORES:0000001 ! body of rock +property_value: altLabel "unidade estratigráfica" xsd:string + +[Term] +id: GEORES:0000003 +name: lithostratigraphic unit +is_a: GEORES:0000001 ! body of rock +property_value: altLabel "unidade litoestratigráfica" xsd:string + +[Term] +id: GEORES:0000004 +name: formation +is_a: GEORES:0000003 ! lithostratigraphic unit +relationship: BFO:0000129 GEORES:0000019 ! group +property_value: altLabel "formação" xsd:string + +[Term] +id: GEORES:0000005 +name: member +is_a: GEORES:0000003 ! lithostratigraphic unit +relationship: BFO:0000176 GEORES:0000004 ! formation +property_value: altLabel "membro" xsd:string + +[Term] +id: GEORES:0000006 +name: architectural element +comment: A restrição de partes de escala menores ainda não foi implementada. +comment: Luan: Elementos arquiteturais são os objetos básicos que os geólogos vão reconhecer e descrever. Eles podem ocorrer em diversas escalas.\nUm elemento pode ter outro elemento como parte, desde que de uma escala menor. +is_a: GEORES:0000001 ! body of rock +relationship: BFO:0000196 GEORES:0000023 ! geometry +property_value: altLabel "elemento arquitetural" xsd:string + +[Term] +id: GEORES:0000007 +name: build up unit +is_a: GEORES:0000006 ! architectural element +disjoint_from: GEORES:0000008 ! channel unit +property_value: altLabel "edifício" xsd:string + +[Term] +id: GEORES:0000008 +name: channel unit +def: "An elongated Depositional Unit having some Channel Surface as its boundary and constituted by some Sediment or Sedimentary Rock that fills it (McHargue et al., 2011)." [] +comment: In stratigraphic terms, a channel unit is constituted by the sediments or sedimentary rocks that fill a channel. It is important to notice that, in more general terms, a channel is a passageway for fluids or sediments, i.e., an immaterial entity. If one elaborates about the erosion and deposition processes that generate these units (McHargue et al., 2011), it is essential to have this disambiguation. +comment: In this work, we decided not to model the named hierarchical scales as entities (e.g., Channel Element, Channel Complex, Channel Complex Set - McHargue et al., 2011) because there exists a wide variety of hierarchical schemes in the literature, and they are not necessarily interoperable (Cullis et al., 2018). Instead, we focus on the fact that units can be fractally nested: a unit can be a Proper Spatial Part Of another unit, which can be a Proper Spatial Part Of another unit, and so forth. We consider that this approach solves the problem of implementing a solution for the repeatability of the geological objects in multiple scales. As so, a Channel Unit can be decomposed in other Channel Units many times as necessary, keeping the representation structure. In the future, we can study the integration of hierarchical schemes and try to infer scales from the spatial relations. +is_a: GEORES:0000006 ! architectural element +disjoint_from: GEORES:0000013 ! levee unit +property_value: altLabel "canal" xsd:string +property_value: GEORES:0000050 "R+ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000009 +name: dome unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "domo" xsd:string + +[Term] +id: GEORES:0000010 +name: dune unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "duna" xsd:string + +[Term] +id: GEORES:0000011 +name: intrusive dike +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "dique intrusivo" xsd:string + +[Term] +id: GEORES:0000012 +name: intrusive sill unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "soleira intrusiva" xsd:string + +[Term] +id: GEORES:0000013 +name: levee unit +def: "A Depositional Unit having Wedge Geometry and forming a bank or ridge geomorphology associated with some Channel Unit." [] +comment: This term is not consensual as some authors refer to these units as the wedge-shape embankments around channels, which is the definition that we adopt here, while other authors refer to them as not necessarily being these embankments and possibly having wing shapes, among other definitions. +comment: This term refers to the geomorphological association of some wegde-shaped unit with some channel unit, even if the channel does not exist at the moment of the observation by the geologist and the levee is probabilistically identified by tendencies (e.g., typical facies). In other words, the term "levee" ontologicallly denotes this relation even though it cannot be deterministically observed. +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "dique" xsd:string +property_value: GEORES:0000050 "R~ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000014 +name: lobe unit +def: "A Depositional Unit having some Lobe Geometry." [] +comment: For Lobe Unit hierarchical scales, we adopted the same approach as in Channel Unit. +comment: These depositional units are usually found at deep-water depositional system terminal regions, or at channel laterals as Overbank Units. +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "lobo" xsd:string +property_value: GEORES:0000050 "R+ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000015 +name: mound unit +def: "A Depositional Unit having Mound Geometry with an irregular top surface and internal chaotic facies." [] +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "monte" xsd:string +property_value: GEORES:0000050 "R+ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000016 +name: olistrostomes unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "olistrostomas" xsd:string +property_value: IAO:0000118 "megaclast" xsd:string +property_value: IAO:0000118 "megaclasto" xsd:string + +[Term] +id: GEORES:0000017 +name: sheet unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "lençol" xsd:string + +[Term] +id: GEORES:0000018 +name: fossil +is_a: GEOCORE:0000001 +property_value: altLabel "fóssil" xsd:string + +[Term] +id: GEORES:0000019 +name: group +is_a: BFO:0000027 +relationship: BFO:0000115 GEORES:0000004 {all_only="true"} ! formation +property_value: altLabel "grupo" xsd:string + +[Term] +id: GEORES:0000020 +name: depositional system +def: "An Object Aggregate whose members are mereotopologically-linked Depositional Units." [] +is_a: BFO:0000027 +property_value: altLabel "sistema deposicional" xsd:string +property_value: GEORES:0000050 "R+ I+ O+ U+ ED-" xsd:string + +[Term] +id: GEORES:0000021 +name: sedimentary environment +def: "The sedimentary environment is the specific depositional setting of a particular sedimentary rock and is unique in terms of physical, chemical, and biological characteristics." [] +is_a: BFO:0000027 +property_value: altLabel "ambiente de sedimentação" xsd:string +property_value: IAO:0000119 "Britannica\nhttps://www.britannica.com/science/sedimentary-rock/Sedimentary-environments" xsd:string + +[Term] +id: GEORES:0000022 +name: dimension +def: "A Quality that inheres in an Independent Continuant by virtue of one of its one-dimensional extents. It is a category that includes at least the three dimensions defined in this ontology: Width, Length, and Thickness. All dimensions are expressed by a real number indicating its value and a literal string indicating its measurement unit." [] +is_a: BFO:0000019 + +[Term] +id: GEORES:0000023 +name: geometry +def: "A Quality that inheres in a Depositional Unit by virtue of its external three-dimensional shape. It does not reflect the exact mathematical specifications of a geometric shape but abstracts and simplifies these specifications (Rovetto, 2011)." [] +is_a: BFO:0000019 +relationship: GEORES:0000046 GEORES:0000042 {minCardinality="1"} ! has geometry type geometry type +property_value: altLabel "geometria" xsd:string + +[Term] +id: GEORES:0000024 +name: lithology +is_a: BFO:0000019 +property_value: altLabel "litologia" xsd:string + +[Term] +id: GEORES:0000025 +name: statigraphic contact +is_a: GEOCORE:0000012 +property_value: altLabel "contato estratigráfico" xsd:string + +[Term] +id: GEORES:0000026 +name: bed contact +is_a: GEOCORE:0000012 +relationship: GEORES:0000044 GEORES:0000041 {cardinality="1"} ! has contact position contact position +relationship: GEORES:0000045 GEORES:0000043 {cardinality="1"} ! has contact type contact type +property_value: altLabel "contato de camada" xsd:string + +[Term] +id: GEORES:0000027 +name: sinuosity +def: "A Quality that inheres in a Channel Unit by virtue of how wavy it is across its length. It is expressed by a real number given by its curved length divided by its length in a straight line." [] +is_a: BFO:0000019 +relationship: BFO:0000197 GEORES:0000008 {cardinality="1"} ! channel unit + +[Term] +id: GEORES:0000028 +name: facies +def: "A pattern of properties of Geological Objects." [] +comment: This entity is defined in the literature as a combination of features that differentiates a geological object from its adjacent geological objects (Walker and James, 1992). However, a Facies does not describe a single Geological Object’s features: it might repeat in several objects as a pattern. This particular aspect matches the definition of Generically Dependent Continuant in BFO. Another important aspect is that the features that compose facies vary depending on the research context, e.g., Sedimentary Facies, Petrofacies (De Ros and Goldberg, 2007), Lithofacies, Ichnofacies, and Biofacies (Nichols, 2009). +is_a: BFO:0000031 +relationship: BFO:0000084 GEORES:0000001 ! body of rock +property_value: altLabel "fácies" xsd:string + +[Term] +id: GEORES:0000029 +name: sedimentary facies +def: "A Facies consisting of the sum of the sedimentological characteristics of Depositional Units (Middleton, 1973, Nichols, 2009, Carbonera et al., 2015)." [] +comment: As an example, if we would model Cross-bedded Sandstone (Nichols, 2009), it would be an entity subsumed by Sedimentary Facies having the following relations: (1) Generically Depends On some (Constituted By some Sandstone (a)); and (2) Has Part some Cross-bedding Structure (b). (a): Sandstone would be an entity subsumed by Sedimentary Rock. (b): Cross-bedding Structure would be an entity subsumed by Sedimentary Structure. +is_a: GEORES:0000028 ! facies +property_value: altLabel "fácies sedimentar" xsd:string + +[Term] +id: GEORES:0000030 +name: facies association +def: "A Generically Dependent Continuant that consists of an aggregate of Facies." [] +comment: It usually describes the Facies that are typically found in specific regions or sub-environments. For example, the Channel Axis Association (McHargue et al., 2011) describes Sedimentary Facies typically found at the center part of channels (in a cross-section point of view). +is_a: BFO:0000031 +relationship: BFO:0000178 GEORES:0000028 {minCardinality="2"} ! facies +property_value: altLabel "associação de facies" xsd:string + +[Term] +id: GEORES:0000031 +name: sediment +def: "An Unconsolidated Earth Material constituted by some collection of sedimentary grains or particles (Garcia et al., 2019)." [] +is_a: GEOCORE:0000010 +property_value: GEORES:0000050 "R+ I+ O- U- ED-" xsd:string + +[Term] +id: GEORES:0000032 +name: sedimentary rock +def: "'sedimentary rock' is an 'amount of rock' constituted by some collection of sedimentary grains or particles (Garcia et al., 2019)." [] +is_a: GEOCORE:0000008 +disjoint_from: GEORES:0000033 ! igneous rock +property_value: altLabel "rocha sedimentar" xsd:string +property_value: GEORES:0000050 "R+ I+ O- U- ED-" xsd:string + +[Term] +id: GEORES:0000033 +name: igneous rock +is_a: GEOCORE:0000008 +property_value: altLabel "rocha ígnea" xsd:string +property_value: definition "'igneous rock' is an 'amount of rock' generated by the cooling and solidification of molten 'earth material'." xsd:string +property_value: isDefinedBy "https://www.britannica.com/science/igneous-rock" xsd:string + +[Term] +id: GEORES:0000034 +name: metamorphic rock +is_a: GEOCORE:0000008 +property_value: altLabel "rocha metamórfica" xsd:string +property_value: definition "'metamorphic rock' is an 'amount of rock' generated by the alteration of preexisting rocks in response to changing environmental conditions, such as variations in temperature, pressure, and mechanical stress, and the addition or subtraction of chemical components." xsd:string +property_value: isDefinedBy "Adapted from Brittanica.\nhttps://www.britannica.com/science/metamorphic-rock" xsd:string + +[Term] +id: GEORES:0000035 +name: complex architectural element +is_a: GEORES:0000001 ! body of rock +disjoint_from: GEORES:0000036 ! composite architectural element + +[Term] +id: GEORES:0000036 +name: composite architectural element +is_a: GEORES:0000001 ! body of rock + +[Term] +id: GEORES:0000037 +name: individual architectural element + +[Term] +id: GEORES:0000038 +name: channel surface +def: "A Geological Boundary that forms the basis of a Channel Unit, having a concave-up shape unless truncated by overlying depositional units." [] +is_a: GEOCORE:0000011 +property_value: GEORES:0000050 "R+ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000039 +name: basin +is_a: BFO:0000029 +property_value: altLabel "bacia" xsd:string + +[Term] +id: GEORES:0000040 +name: geological site +comment: Epistemologicamente não é possível determinar os limites deste site e, portanto, cada geólogo pode posicionar sua área de interesse em uma localização e limites distintos, o que torna muito difícil tratar computacionalmente a identidade do sítio geológico. Esse problema acontece com outras entidades do tipo site: Região da Serra Gaúcha, Litoral Norte, etc, cuja delimitação é problemática, mas existe uma identidade consensual. +is_a: BFO:0000029 +property_value: altLabel "sítio geológico" xsd:string + +[Term] +id: GEORES:0000041 +name: contact position +property_value: altLabel "posição do contato" xsd:string + +[Term] +id: GEORES:0000042 +name: geometry type +comment: Luan: Talvez tipo de Geometria seja uma classe de segunda ordem, mas em primeiro momento não utilizaremos punning para representar isto. A classe geometry tem uma relação de 'has geometry type' com um 'geometry type' e as instâncias dessa classe é que definem o tipo de geometria de fato. Caso seja necessário criar alguma subclasse de um 'body of rock' que tenha um 'geometry type' específico é possível utilizar a primitiva do owl value para isto.\n\nNão sabemos ainda como classificar esta classe. Do que ela seria subclasse? +property_value: altLabel "tipo de geometria" xsd:string + +[Term] +id: GEORES:0000043 +name: contact type +property_value: altLabel "tipo de contato" xsd:string + +[Typedef] +id: GEORES:0000044 +name: has contact position + +[Typedef] +id: GEORES:0000045 +name: has contact type + +[Typedef] +id: GEORES:0000046 +name: has geometry type +comment: Luan: Geometry Type talvez seja uma classe de segunda ordem cuja as instâncias são os diferentes tipos de Geometria. Por exemplo, é errado dizer que Geometria Lenticular é subtipo da Quality Geometria. Lenticular é na realidade um subtipo de Tipo de Geometria e não de Geometria. + +[Typedef] +id: GEORES:0000047 +name: has base geometry +is_a: GEORES:0000046 ! has geometry type + +[Typedef] +id: GEORES:0000048 +name: has top geometry +is_a: GEORES:0000046 ! has geometry type + diff --git a/geores-base.owl b/geores-base.owl new file mode 100644 index 0000000..397697b --- /dev/null +++ b/geores-base.owl @@ -0,0 +1,1347 @@ + + + + + Alcides Lopes + Fabrício Henrique Rodrigues + Fernando Cicconeto + Joel Luis Carbonera + Luan Fonseca Garcia + Lucas Valadares Vieira + Mara Abel + Renata dos Santos Alvarenga + Tiago Agne de Oliveira + Yuanwei Qu + + GeoReservoir is an ontology to support the description of the geometry and the lithology of deep-marine deposits. The GeoReservoir ontology provides formal and clear definitions of deep-marine depositional system entities, creating an unambiguous terminology for geometrical and lithological properties of the deposits in the scale of outcrop and seismic sections. These definitions are independent of tasks, geological interpretations, and process inferences. We created this language to make it possible to formally and uniformly describe any deep-marine occurrence in the world with an adequate level of detail for sedimentological studies and computer processing. + https://creativecommons.org/licenses/by-nc/4.0/ + GeoReservoir Ontology + Cited references: + +1. Abel, M., Perrin, M., Carbonera, J.L.: Ontological analysis for information integration in geomodeling. Earth Science Informatics 8, 21–36 (2015) +2. Carbonera, J.L., Abel, M., Scherer, C.M.S.: Visual interpretation of events in petroleum exploration: An approach supported by well-founded ontologies. Expert Systems With Applications 42, 2749–2763 (2015) +3. Cullis, S., Colombera, L., Patacci, M., McCaffrey, W.D.: Hierarchical classifications of the sedimentary architecture of deep-marine depositional systems. Earth-Science Reviews 179, 38–71 (2018) +4. De Ros, L.F., Goldberg, K.: Reservoir petrofacies: A tool for quality characterization and prediction. In: AAPG Annual Conference and Exhibition. Long Beach (2007) +5. Garcia, L.F., Carbonera, J.L., Rodrigues, F.H., Antunes, C.R., Abel, M.: What rocks are made of: Towards an ontological pattern for material constitution in the geological domain. In: Laender, A.H.F., Pernici, B., Lim, E.P., Oliveira, J.P.M. (eds.) ER: 38th International Conference on Conceptual Modeling. pp. 275–286. Springer, Cham (2019) +6. Guarino, N., Welty, C.A.: An overview of ontoclean. In: Staab, S., Studer, R. (eds.) Handbook on Ontologies, pp. 151–171. Springer, Berlin, Heidelberg (2004) +7. McHargue, T., Pyrcz, M.J., Sullivan, M.D., Clark, J.D., Fildani, A., Romans, B.W., Covault, J.A., Levy, M., Posamentier, H.W., Drinkwater, N.J.: Architecture of turbidite channel systems on the continental slope: Patterns and predictions. Marine and Petroleum Geology 28, 728–743 (2011) +8. Middleton, G.V.: Johannes walther’s law of the correlation of facies. Bulletin of the Geological Society of America 84, 979–988 (1973) +9. Nichols, G.: Sedimentology and Stratigraphy. Wiley-Blackwell, Chichester, 2nd edn. (2009) +10. Rovetto, R.: The shape of shapes: An ontological exploration. In: Hastings, J., Kutz, O., Bhatt, M., Borgo, S. (eds.) Proceedings of the First Interdisciplinary Workshop on SHAPES. Karlsruhe (2011), http://ceur-ws.org/Vol-812/ +11. Walker, R.G., James, N.P.: Facies Models: Response to Sea Level Change. Geological Association of Canada, St. John’s (1992) + We acknowledge the Brazilian funding agencies CNPq and CAPES for financing this work and the Research Centre of Petrobras (CENPES) for collaborating on this project. + 2024-04-07 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + For metaproperties, we use the following notation (Guarino and Welty, 2004; Abel et al., 2015): + +– R+ / R- / R~: rigid / not rigid / anti-rigid; +– I+ / I-: carries / does not carry identity; +– O+ / O-: provides / does not provide identity; +– U+ / U-: carries / does not carry unity; +– ED+ / ED-: existentially dependent / independent. + metaproperties + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + has contact position + + + + + + + + + has contact type + + + + + + + + Luan: Geometry Type talvez seja uma classe de segunda ordem cuja as instâncias são os diferentes tipos de Geometria. Por exemplo, é errado dizer que Geometria Lenticular é subtipo da Quality Geometria. Lenticular é na realidade um subtipo de Tipo de Geometria e não de Geometria. + has geometry type + + + + + + + + + has base geometry + + + + + + + + + has top geometry + + + + + + + + + + + + + + A relation between a Quality and its values. + O objetivo desta data property é conectar em níveL de implementação uma qualidade com o valor em seu espaço de qualiades. Por exemplo, a qualidade dimensão tem um espaço de qualidade que é um valor real positivo para sua largura. + +A IAO possui uma propriedade has measurement datum cujo domínio é um measurement datum. Porém, o problema de usar tal propriedade é acrescentar a necessidade de criar uma instância de measurement datum. + has value + + + + + + + + + has dimension value + + + + + + + + + has lenght value + + + + + + + + + A relation between a Quality and a literal string that represents its measurement unit. + has measurement unit + + + + + + + + + has thickness value + + + + + + + + + has width value + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + body of rock + corpo de rocha + 'body of rock' is a 'geological object' that is 'constituted by' some 'amount of rock' + + + + + + + + + Os diferentes elementos arquiteturais ocorrem dentro de uma unidade com uma idade definida que é a unidade estratigráfica. + +Ainda não sabemos se poderia ser uma unidade litoestratigráfica. + stratigraphic unit + unidade estratigráfica + + + + + + + + + lithostratigraphic unit + unidade litoestratigráfica + + + + + + + + + + + + + + + formation + formação + + + + + + + + + + + + + + + member + membro + + + + + + + + + + + + + + + A restrição de partes de escala menores ainda não foi implementada. + Luan: Elementos arquiteturais são os objetos básicos que os geólogos vão reconhecer e descrever. Eles podem ocorrer em diversas escalas. +Um elemento pode ter outro elemento como parte, desde que de uma escala menor. + architectural element + elemento arquitetural + + + + + + + + + build up unit + edifício + + + + + + + + + An elongated Depositional Unit having some Channel Surface as its boundary and constituted by some Sediment or Sedimentary Rock that fills it (McHargue et al., 2011). + In stratigraphic terms, a channel unit is constituted by the sediments or sedimentary rocks that fill a channel. It is important to notice that, in more general terms, a channel is a passageway for fluids or sediments, i.e., an immaterial entity. If one elaborates about the erosion and deposition processes that generate these units (McHargue et al., 2011), it is essential to have this disambiguation. + In this work, we decided not to model the named hierarchical scales as entities (e.g., Channel Element, Channel Complex, Channel Complex Set - McHargue et al., 2011) because there exists a wide variety of hierarchical schemes in the literature, and they are not necessarily interoperable (Cullis et al., 2018). Instead, we focus on the fact that units can be fractally nested: a unit can be a Proper Spatial Part Of another unit, which can be a Proper Spatial Part Of another unit, and so forth. We consider that this approach solves the problem of implementing a solution for the repeatability of the geological objects in multiple scales. As so, a Channel Unit can be decomposed in other Channel Units many times as necessary, keeping the representation structure. In the future, we can study the integration of hierarchical schemes and try to infer scales from the spatial relations. + channel unit + canal + R+ I+ O- U+ ED- + + + + + + + + + dome unit + domo + + + + + + + + + dune unit + duna + + + + + + + + + intrusive dike + dique intrusivo + + + + + + + + + intrusive sill unit + soleira intrusiva + + + + + + + + + A Depositional Unit having Wedge Geometry and forming a bank or ridge geomorphology associated with some Channel Unit. + This term is not consensual as some authors refer to these units as the wedge-shape embankments around channels, which is the definition that we adopt here, while other authors refer to them as not necessarily being these embankments and possibly having wing shapes, among other definitions. + This term refers to the geomorphological association of some wegde-shaped unit with some channel unit, even if the channel does not exist at the moment of the observation by the geologist and the levee is probabilistically identified by tendencies (e.g., typical facies). In other words, the term "levee" ontologicallly denotes this relation even though it cannot be deterministically observed. + levee unit + dique + R~ I+ O- U+ ED- + + + + + + + + + A Depositional Unit having some Lobe Geometry. + For Lobe Unit hierarchical scales, we adopted the same approach as in Channel Unit. + These depositional units are usually found at deep-water depositional system terminal regions, or at channel laterals as Overbank Units. + lobe unit + lobo + R+ I+ O- U+ ED- + + + + + + + + + A Depositional Unit having Mound Geometry with an irregular top surface and internal chaotic facies. + mound unit + monte + R+ I+ O- U+ ED- + + + + + + + + + megaclast + megaclasto + olistrostomes unit + olistrostomas + + + + + + + + + sheet unit + lençol + + + + + + + + + fossil + fóssil + + + + + + + + + + + + + + + group + grupo + + + + + + + + + An Object Aggregate whose members are mereotopologically-linked Depositional Units. + depositional system + sistema deposicional + R+ I+ O+ U+ ED- + + + + + + + + + The sedimentary environment is the specific depositional setting of a particular sedimentary rock and is unique in terms of physical, chemical, and biological characteristics. + Britannica +https://www.britannica.com/science/sedimentary-rock/Sedimentary-environments + sedimentary environment + ambiente de sedimentação + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A Quality that inheres in an Independent Continuant by virtue of one of its one-dimensional extents. It is a category that includes at least the three dimensions defined in this ontology: Width, Length, and Thickness. All dimensions are expressed by a real number indicating its value and a literal string indicating its measurement unit. + dimension + + + + + + + + + + + + 1 + + + + A Quality that inheres in a Depositional Unit by virtue of its external three-dimensional shape. It does not reflect the exact mathematical specifications of a geometric shape but abstracts and simplifies these specifications (Rovetto, 2011). + geometry + geometria + + + + + + + + + lithology + litologia + + + + + + + + + statigraphic contact + contato estratigráfico + + + + + + + + + + + + 1 + + + + + + + 1 + + + + bed contact + contato de camada + + + + + + + + + + + + 1 + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + 1 + + + + + + + A Quality that inheres in a Channel Unit by virtue of how wavy it is across its length. It is expressed by a real number given by its curved length divided by its length in a straight line. + sinuosity + + + + + + + + + + + + + + + A pattern of properties of Geological Objects. + This entity is defined in the literature as a combination of features that differentiates a geological object from its adjacent geological objects (Walker and James, 1992). However, a Facies does not describe a single Geological Object’s features: it might repeat in several objects as a pattern. This particular aspect matches the definition of Generically Dependent Continuant in BFO. Another important aspect is that the features that compose facies vary depending on the research context, e.g., Sedimentary Facies, Petrofacies (De Ros and Goldberg, 2007), Lithofacies, Ichnofacies, and Biofacies (Nichols, 2009). + facies + fácies + + + + + + + + + A Facies consisting of the sum of the sedimentological characteristics of Depositional Units (Middleton, 1973, Nichols, 2009, Carbonera et al., 2015). + As an example, if we would model Cross-bedded Sandstone (Nichols, 2009), it would be an entity subsumed by Sedimentary Facies having the following relations: (1) Generically Depends On some (Constituted By some Sandstone (a)); and (2) Has Part some Cross-bedding Structure (b). (a): Sandstone would be an entity subsumed by Sedimentary Rock. (b): Cross-bedding Structure would be an entity subsumed by Sedimentary Structure. + sedimentary facies + fácies sedimentar + + + + + + + + + + + + 2 + + + + A Generically Dependent Continuant that consists of an aggregate of Facies. + It usually describes the Facies that are typically found in specific regions or sub-environments. For example, the Channel Axis Association (McHargue et al., 2011) describes Sedimentary Facies typically found at the center part of channels (in a cross-section point of view). + facies association + associação de facies + + + + + + + + + An Unconsolidated Earth Material constituted by some collection of sedimentary grains or particles (Garcia et al., 2019). + sediment + R+ I+ O- U- ED- + + + + + + + + + 'sedimentary rock' is an 'amount of rock' constituted by some collection of sedimentary grains or particles (Garcia et al., 2019). + sedimentary rock + rocha sedimentar + R+ I+ O- U- ED- + + + + + + + + + https://www.britannica.com/science/igneous-rock + igneous rock + rocha ígnea + 'igneous rock' is an 'amount of rock' generated by the cooling and solidification of molten 'earth material'. + + + + + + + + + Adapted from Brittanica. +https://www.britannica.com/science/metamorphic-rock + metamorphic rock + rocha metamórfica + 'metamorphic rock' is an 'amount of rock' generated by the alteration of preexisting rocks in response to changing environmental conditions, such as variations in temperature, pressure, and mechanical stress, and the addition or subtraction of chemical components. + + + + + + + + + + + + + + + + + + + + + + + + + + + complex architectural element + + + + + + + + + + + + + + + + + + + + composite architectural element + + + + + + + + + + + + + + + + + + + + + + + individual architectural element + + + + + + + + + A Geological Boundary that forms the basis of a Channel Unit, having a concave-up shape unless truncated by overlying depositional units. + channel surface + R+ I+ O- U+ ED- + + + + + + + + + basin + bacia + + + + + + + + + Epistemologicamente não é possível determinar os limites deste site e, portanto, cada geólogo pode posicionar sua área de interesse em uma localização e limites distintos, o que torna muito difícil tratar computacionalmente a identidade do sítio geológico. Esse problema acontece com outras entidades do tipo site: Região da Serra Gaúcha, Litoral Norte, etc, cuja delimitação é problemática, mas existe uma identidade consensual. + geological site + sítio geológico + + + + + + + + + + + + + + + + + contact position + posição do contato + + + + + + + + + + + + + + + + + + + + + + Luan: Talvez tipo de Geometria seja uma classe de segunda ordem, mas em primeiro momento não utilizaremos punning para representar isto. A classe geometry tem uma relação de 'has geometry type' com um 'geometry type' e as instâncias dessa classe é que definem o tipo de geometria de fato. Caso seja necessário criar alguma subclasse de um 'body of rock' que tenha um 'geometry type' específico é possível utilizar a primitiva do owl value para isto. + +Não sabemos ainda como classificar esta classe. Do que ela seria subclasse? + geometry type + tipo de geometria + + + + + + + + + + + + + + + + + + + + + + contact type + tipo de contato + + + + + + + + + + + + + + amalgamated contact + contato amalgamado + + + + + + + + + base position contact + contato de base + + + + + + + + + cryptic/covered contact + contato críptico/encoberto + + + + + + + + + conformable contact + contato concordante + + + + + + + + + erosive contact + contato erosivo + + + + + + + + + faulted contact + contato de falha + + + + + + + + + gradational contact + contato gradacional + + + + + + + + + intrusive contact + contato intrusivo + + + + + + + + + sharp contact + contato abrupto + + + + + + + + + irregular geometry + geometria irregular + + + + + + + + + lenticular convex top flatbed geometry + geometria lenticular topo convexo base plana + + + + + + + + + lenticular concave convex geometry + geometria lenticular côncavo convexa + + + + + + + + + lateral position contact + contato lateral + + + + + + + + + lenticular flattop concave base geometry + geometria lenticular topo plano base convexa + + + + + + + + + sheet geometry + geometria lençoidal + + + + + + + + + sigmoidal geometry + geometria sigmoidal + + + + + + + + + tabular geometry + geometria tabular + + + + + + + + + top position contact + contato de topo + + + + + + + + + wedge shape geometry + geometria de cunha + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/geores-full.obo b/geores-full.obo new file mode 100644 index 0000000..eed6305 --- /dev/null +++ b/geores-full.obo @@ -0,0 +1,781 @@ +format-version: 1.2 +data-version: https://www.inf.ufrgs.br/bdi/ontologies/geores/releases/2024-04-07/geores-full.owl +remark: Cited references:\n\n1. Abel, M., Perrin, M., Carbonera, J.L.: Ontological analysis for information integration in geomodeling. Earth Science Informatics 8, 21–36 (2015)\n2. Carbonera, J.L., Abel, M., Scherer, C.M.S.: Visual interpretation of events in petroleum exploration: An approach supported by well-founded ontologies. Expert Systems With Applications 42, 2749–2763 (2015)\n3. Cullis, S., Colombera, L., Patacci, M., McCaffrey, W.D.: Hierarchical classifications of the sedimentary architecture of deep-marine depositional systems. Earth-Science Reviews 179, 38–71 (2018)\n4. De Ros, L.F., Goldberg, K.: Reservoir petrofacies: A tool for quality characterization and prediction. In: AAPG Annual Conference and Exhibition. Long Beach (2007)\n5. Garcia, L.F., Carbonera, J.L., Rodrigues, F.H., Antunes, C.R., Abel, M.: What rocks are made of: Towards an ontological pattern for material constitution in the geological domain. In: Laender, A.H.F., Pernici, B., Lim, E.P., Oliveira, J.P.M. (eds.) ER: 38th International Conference on Conceptual Modeling. pp. 275–286. Springer, Cham (2019)\n6. Guarino, N., Welty, C.A.: An overview of ontoclean. In: Staab, S., Studer, R. (eds.) Handbook on Ontologies, pp. 151–171. Springer, Berlin, Heidelberg (2004)\n7. McHargue, T., Pyrcz, M.J., Sullivan, M.D., Clark, J.D., Fildani, A., Romans, B.W., Covault, J.A., Levy, M., Posamentier, H.W., Drinkwater, N.J.: Architecture of turbidite channel systems on the continental slope: Patterns and predictions. Marine and Petroleum Geology 28, 728–743 (2011)\n8. Middleton, G.V.: Johannes walther’s law of the correlation of facies. Bulletin of the Geological Society of America 84, 979–988 (1973)\n9. Nichols, G.: Sedimentology and Stratigraphy. Wiley-Blackwell, Chichester, 2nd edn. (2009)\n10. Rovetto, R.: The shape of shapes: An ontological exploration. In: Hastings, J., Kutz, O., Bhatt, M., Borgo, S. (eds.) Proceedings of the First Interdisciplinary Workshop on SHAPES. Karlsruhe (2011), http://ceur-ws.org/Vol-812/\n11. Walker, R.G., James, N.P.: Facies Models: Response to Sea Level Change. Geological Association of Canada, St. John’s (1992) +remark: We acknowledge the Brazilian funding agencies CNPq and CAPES for financing this work and the Research Centre of Petrobras (CENPES) for collaborating on this project. +ontology: https://www.inf.ufrgs.br/bdi/ontologies/geores/geores-full.owl +property_value: http://purl.org/dc/elements/1.1/contributor "Alcides Lopes" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Fabrício Henrique Rodrigues" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Fernando Cicconeto" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Joel Luis Carbonera" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Luan Fonseca Garcia" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Lucas Valadares Vieira" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Mara Abel" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Renata dos Santos Alvarenga" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Tiago Agne de Oliveira" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Yuanwei Qu" xsd:string +property_value: http://purl.org/dc/terms/description "GeoReservoir is an ontology to support the description of the geometry and the lithology of deep-marine deposits. The GeoReservoir ontology provides formal and clear definitions of deep-marine depositional system entities, creating an unambiguous terminology for geometrical and lithological properties of the deposits in the scale of outcrop and seismic sections. These definitions are independent of tasks, geological interpretations, and process inferences. We created this language to make it possible to formally and uniformly describe any deep-marine occurrence in the world with an adequate level of detail for sedimentological studies and computer processing." xsd:string +property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by-nc/4.0/" xsd:string +property_value: http://purl.org/dc/terms/title "GeoReservoir Ontology" xsd:string +property_value: owl:versionInfo "2024-04-07" xsd:string + +[Term] +id: BFO:0000001 +name: entity +property_value: definition "(Elucidation) An entity is anything that exists or has existed or will exist" xsd:string +property_value: example "Julius Caesar; the Second World War; your body mass index; Verdi's Requiem" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "001-BFO" xsd:string + +[Term] +id: BFO:0000002 +name: continuant +is_a: BFO:0000001 ! entity +disjoint_from: BFO:0000003 ! occurrent +relationship: BFO:0000176 BFO:0000002 {all_only="true"} ! continuant part of continuant +property_value: definition "(Elucidation) A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity" xsd:string +property_value: example "A human being; a tennis ball; a cave; a region of space; someone's temperature" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "008-BFO" xsd:string + +[Term] +id: BFO:0000003 +name: occurrent +is_a: BFO:0000001 ! entity +property_value: definition "(Elucidation) An occurrent is an entity that unfolds itself in time or it is the start or end of such an entity or it is a temporal or spatiotemporal region" xsd:string +property_value: example "As for process, history, process boundary, spatiotemporal region, zero-dimensional temporal region, one-dimensional temporal region, temporal interval, temporal instant." xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "077-BFO" xsd:string + +[Term] +id: BFO:0000004 +name: independent continuant +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000020 ! specifically dependent continuant +relationship: BFO:0000176 BFO:0000004 {all_only="true"} ! continuant part of independent continuant +property_value: definition "b is an independent continuant =Def b is a continuant & there is no c such that b specifically depends on c or b generically depends on c" xsd:string +property_value: example "An atom; a molecule; an organism; a heart; a chair; the bottom right portion of a human torso; a leg; the interior of your mouth; a spatial region; an orchestra" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "017-BFO" xsd:string + +[Term] +id: BFO:0000006 +name: spatial region +is_a: BFO:0000141 ! immaterial entity +disjoint_from: BFO:0000029 ! site +relationship: BFO:0000176 BFO:0000006 {all_only="true"} ! continuant part of spatial region +property_value: definition "(Elucidation) A spatial region is a continuant entity that is a continuant part of the spatial projection of a portion of spacetime at a given time" xsd:string +property_value: example "As for zero-dimensional spatial region, one-dimensional spatial region, two-dimensional spatial region, three-dimensional spatial region" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "035-BFO" xsd:string + +[Term] +id: BFO:0000008 +name: temporal region +is_a: BFO:0000003 ! occurrent +disjoint_from: BFO:0000011 ! spatiotemporal region +property_value: definition "(Elucidation) A temporal region is an occurrent over which processes can unfold" xsd:string +property_value: example "As for zero-dimensional temporal region and one-dimensional temporal region" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "100-BFO" xsd:string + +[Term] +id: BFO:0000011 +name: spatiotemporal region +is_a: BFO:0000003 ! occurrent +property_value: definition "(Elucidation) A spatiotemporal region is an occurrent that is an occurrent part of spacetime" xsd:string +property_value: example "The spatiotemporal region occupied by the development of a cancer tumour; the spatiotemporal region occupied by an orbiting satellite" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "095-BFO" xsd:string +property_value: scopeNote "'Spacetime' here refers to the maximal instance of the universal spatiotemporal region." xsd:string + +[Term] +id: BFO:0000015 +name: process +is_a: BFO:0000003 ! occurrent +property_value: altLabel "event" xsd:string +property_value: definition "(Elucidation) p is a process means p is an occurrent that has some temporal proper part and for some time t, p has some material entity as participant" xsd:string +property_value: example "An act of selling; the life of an organism; a process of sleeping; a process of cell-division; a beating of the heart; a process of meiosis; the taxiing of an aircraft; the programming of a computer" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "083-BFO" xsd:string + +[Term] +id: BFO:0000019 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant +property_value: definition "(Elucidation) A quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized" xsd:string +property_value: example "The colour of a tomato; the ambient temperature of this portion of air; the length of the circumference of your waist; the shape of your nose; the shape of your nostril; the mass of this piece of gold" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "055-BFO" xsd:string + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +is_a: BFO:0000002 ! continuant +property_value: definition "b is a specifically dependent continuant =Def b is a continuant & there is some independent continuant c which is not a spatial region & which is such that b specifically depends on c" xsd:string +property_value: example "(with multiple bearers) John's love for Mary; the ownership relation between John and this statue; the relation of authority between John and his subordinates" xsd:string +property_value: example "(with one bearer) The mass of this tomato; the pink colour of a medium rare piece of grilled filet mignon at its centre; the smell of this portion of mozzarella; the disposition of this fish to decay; the role of being a doctor; the function of this heart to pump blood; the shape of this hole" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "050-BFO" xsd:string + +[Term] +id: BFO:0000027 +name: object aggregate +is_a: BFO:0000040 ! material entity +property_value: definition "(Elucidation) An object aggregate is a material entity consisting exactly of a plurality (≥1) of objects as member parts which together form a unit" xsd:string +property_value: example "The aggregate of the musicians in a symphony orchestra and their instruments; the aggregate of bearings in a constant velocity axle joint; the nitrogen atoms in the atmosphere; a collection of cells in a blood biobank" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "025-BFO" xsd:string +property_value: scopeNote "'Exactly' means that there are no parts of the object aggregate other than its member parts." xsd:string +property_value: scopeNote "The unit can, at certain times, consist of exactly one object, for example, when a wolf litter loses all but one of its pups, but it must at some time have a plurality of member parts." xsd:string + +[Term] +id: BFO:0000029 +name: site +is_a: BFO:0000141 ! immaterial entity +property_value: definition "(Elucidation) A site is a three-dimensional immaterial entity whose boundaries either (partially or wholly) coincide with the boundaries of one or more material entities or have locations determined in relation to some material entity" xsd:string +property_value: example "A hole in a portion of cheese; a rabbit hole; the Grand Canyon; the Piazza San Marco; the kangaroo-joey-containing hole of a kangaroo pouch; your left nostril (a fiat part - the opening - of your left nasal cavity); the lumen of your gut; the hold of a ship; the interior of the trunk of your car; hole in an engineered floor joist" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "034-BFO" xsd:string + +[Term] +id: BFO:0000030 +name: object +is_a: BFO:0000040 ! material entity +property_value: definition "(Elucidation) An object is a material entity which manifests causal unity & is of a type instances of which are maximal relative to the sort of causal unity manifested" xsd:string +property_value: example "An organism; a fish tank; a planet; a laptop; a valve; a block of marble; an ice cube" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "024-BFO" xsd:string +property_value: scopeNote "A description of three primary sorts of causal unity is provided in Basic Formal Ontology 2.0. Specification and User Guide" xsd:string + +[Term] +id: BFO:0000031 +name: generically dependent continuant +is_a: BFO:0000002 ! continuant +property_value: altLabel "g-dependent continuant" xsd:string +property_value: definition "(Elucidation) A generically dependent continuant is an entity that exists in virtue of the fact that there is at least one of what may be multiple copies which is the content or the pattern that multiple copies would share" xsd:string +property_value: example "The pdf file on your laptop; the pdf file that is a copy thereof on my laptop; the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule; the content that is shared by a string of dots and dashes written on a page and the transmitted Morse code signal; the content of a sentence; an engineering blueprint" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "074-BFO" xsd:string + +[Term] +id: BFO:0000035 +name: process boundary +is_a: BFO:0000003 ! occurrent +property_value: definition "p is a process boundary =Def p is a temporal part of a process & p has no proper temporal parts" xsd:string +property_value: example "The boundary between the 2nd and 3rd year of your life" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "084-BFO" xsd:string + +[Term] +id: BFO:0000038 +name: one-dimensional temporal region +is_a: BFO:0000008 ! temporal region +property_value: definition "(Elucidation) A one-dimensional temporal region is a temporal region that is a whole that has a temporal interval and zero or more temporal intervals and temporal instants as parts" xsd:string +property_value: example "The temporal region during which a process occurs" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "103-BFO" xsd:string + +[Term] +id: BFO:0000040 +name: material entity +is_a: BFO:0000004 ! independent continuant +disjoint_from: BFO:0000141 ! immaterial entity +relationship: BFO:0000176 BFO:0000040 {all_only="true"} ! continuant part of material entity +property_value: definition "(Elucidation) A material entity is an independent continuant has some portion of matter as continuant part" xsd:string +property_value: example "A human being; the undetached arm of a human being; an aggregate of human beings" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "019-BFO" xsd:string + +[Term] +id: BFO:0000140 +name: continuant fiat boundary +is_a: BFO:0000141 ! immaterial entity +relationship: BFO:0000178 BFO:0000140 {all_only="true"} ! has continuant part continuant fiat boundary +property_value: definition "(Elucidation) A continuant fiat boundary b is an immaterial entity that is of zero, one or two dimensions & such that there is no time t when b has a spatial region as continuant part & whose location is determined in relation to some material entity" xsd:string +property_value: example "As for fiat point, fiat line, fiat surface" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "029-BFO" xsd:string + +[Term] +id: BFO:0000141 +name: immaterial entity +is_a: BFO:0000004 ! independent continuant +property_value: definition "b is an immaterial entity =Def b is an independent continuant which is such that there is no time t when it has a material entity as continuant part" xsd:string +property_value: example "As for fiat point, fiat line, fiat surface, site" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "028-BFO" xsd:string + +[Term] +id: BFO:0000145 +name: relational quality +is_a: BFO:0000019 ! quality +property_value: definition "b is a relational quality =Def b is a quality & there exists c and d such that c and d are not identical & b specifically depends on c & b specifically depends on d" xsd:string +property_value: example "A marriage bond; an instance of love; an obligation between one person and another" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "057-BFO" xsd:string + +[Term] +id: BFO:0000146 +name: fiat surface +is_a: BFO:0000140 ! continuant fiat boundary +property_value: definition "(Elucidation) A fiat surface is a two-dimensional continuant fiat boundary that is self-connected" xsd:string +property_value: example "The surface of the Earth; the plane separating the smoking from the non-smoking zone in a restaurant" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "033-BFO" xsd:string + +[Term] +id: GEOCORE:0000001 +name: geological object +def: "An object that is 'generated by' some 'geological process' and has at least one part 'constituted by' some 'earth material' that is not an 'earth fluid'." [] +is_a: BFO:0000030 ! object +disjoint_from: GEOCORE:0000006 ! earth material +relationship: BFO:0000196 GEORES:0000022 ! bearer of dimension +relationship: GEOCORE:0000015 GEOCORE:0000003 ! has age geological age +property_value: altLabel "objeto geológico" xsd:string +property_value: IAO:0000116 "A geological object is a naturally occurring entity because a geological process\ngenerates it, and some earth material constitutes it. Thus, we can differentiate geological objects from artificial objects, such as a well-core, because even though some earth material constitutes artificial objects, they are human-made rather than generated by some geological process. Furthermore, Geological Objects are specializations of BFO Objects, meaning they must necessarily have some unity criteria. The unity is what differentiates geological objects from Earth Materials." xsd:string + +[Term] +id: GEOCORE:0000002 +name: geological process +def: "It is a physical, or chemical, or biological, naturally occurring process that occurs on the Earth’s surface or subsurface and occupies some 'geological time interval'" [] +is_a: BFO:0000015 ! process +relationship: BFO:0000199 GEOCORE:0000005 ! occupies temporal region geological time interval +property_value: altLabel "processo geológico" xsd:string +property_value: IAO:0000112 "Examples are the process of deposition, the process of folding, a tectonic process, a sedimentary process." xsd:string +property_value: IAO:0000116 "Geological processes are macro processes that generate, transform, deform, transport, or destroy geological objects and earth materials. These processes are not necessarily atomic and may have other geological processes as parts." xsd:string + +[Term] +id: GEOCORE:0000003 +name: geological age +def: "It is a quality that 'inheres in' a 'geological object' or 'earth material' that corresponds to the 'geological time interval' in which the 'geological process' that it was 'generated by' occupied." [] +is_a: BFO:0000019 ! quality +property_value: altLabel "idade geológica" xsd:string + +[Term] +id: GEOCORE:0000004 +name: geological structure +def: "It is a 'generically dependent continuant' that is the pattern of a non-atomic 'geological object''s internal arrangement." [] +is_a: BFO:0000031 ! generically dependent continuant +relationship: BFO:0000084 GEOCORE:0000001 ! generically depends on geological object +property_value: altLabel "estrutura geológica" xsd:string +property_value: IAO:0000116 "Geological structures are general material patterns repeated in many geological\nobjects. The pattern comprises the material configuration and the mutual relationships of the object’s different parts. Structures result from one or a series of geological processes that generated or transformed the geological object they generically depend on. Thus, there is some historical dependence relation between the structure and this geological process, but what concretizes the structure is some complex quality inhering in the object, not the process." xsd:string + +[Term] +id: GEOCORE:0000005 +name: geological time interval +def: "It is a BFO temporal interval that corresponds to a time interval within the Geological Time Scale." [] +is_a: BFO:0000038 ! one-dimensional temporal region +property_value: altLabel "intervalo de tempo geológico" xsd:string + +[Term] +id: GEOCORE:0000006 +name: earth material +def: "It is a natural amount of matter 'generated by' some 'geological process'." [] +is_a: BFO:0000040 ! material entity +relationship: GEOCORE:0000015 GEOCORE:0000003 ! has age geological age +property_value: altLabel "material geologico" xsd:string +property_value: IAO:0000112 "Examples are an amount of sandstone, an amount of petroleum, an amount of\nnatural gas." xsd:string +property_value: IAO:0000116 "Earth Materials are natural amounts of matter. Thus, they come into existence by nature, without any artificial aid. Since they are amounts, they don’t hold unity criteria, but they are ontologically rigid and provide an identity criteria. Earth Materials and BFO Objects are disjoint. They are either solid, fluid, or unconsolidated. We usually observe earth materials when constituting other objects, such as an amount of rock constituting a geological unity or an amount of sand constituting a dune." xsd:string + +[Term] +id: GEOCORE:0000007 +name: amount of mineral +def: "An amount of rock is an 'earth material' that is a naturally occuring, inorganic, solid, homogeneous chemical compound with a crystalline structure." [] +is_a: GEOCORE:0000006 ! earth material +disjoint_from: GEOCORE:0000008 ! amount of rock +disjoint_from: GEOCORE:0000008 ! amount of rock +property_value: altLabel "quantidade de mineral" xsd:string +property_value: IAO:0000112 "The amount of quarts that constitutes some grain, the amount of feldspar that is part of an amount of rock." xsd:string +property_value: IAO:0000116 "Amounts of mineral lack a unity criteria as every other 'earth material'. We usually observe them when they are constitution objects such as crystals or grains." xsd:string + +[Term] +id: GEOCORE:0000008 +name: amount of rock +def: "An amount of rock is a solid consolidated 'earth material' that is 'constituted by' an aggregate of particles made of mineral matter or material of biological origin." [] +is_a: GEOCORE:0000006 ! earth material +disjoint_from: GEOCORE:0000009 ! earth fluid +relationship: BFO:0000196 GEORES:0000024 ! bearer of lithology +property_value: altLabel "quantidade de rocha" xsd:string +property_value: IAO:0000112 "The amount of sandstone that constitutes a lithostratigraphic unit." xsd:string +property_value: IAO:0000116 "Geologists define rocks at a scale of observation where they consider them homogeneous, even though an aggregate of solid particles constitutes it. These particles are usually geological objects, such as grains or crystals, or the rest of dead animals or plants. \n\nAmounts of rock, like other earth materials, are independent rigid entities that do not hold any unity criteria. We can observe them in nature when they are constituting objects such as geological unities." xsd:string + +[Term] +id: GEOCORE:0000009 +name: earth fluid +def: "Earth fluid is an 'earth material' that is fluild." [] +is_a: GEOCORE:0000006 ! earth material +property_value: altLabel "fluido da terra" xsd:string +property_value: IAO:0000116 "Earth fluids can be water, oil, gas or a mixture of those fluids." xsd:string + +[Term] +id: GEOCORE:0000010 +name: unconsolidated earth material +def: "Unconsolidated earth material is an 'earth material' that is consituted by an aggregate of solid particles but is not consolidated into a 'rock' it self." [] +is_a: GEOCORE:0000006 ! earth material +property_value: altLabel "material geológico inconsolidado" xsd:string + +[Term] +id: GEOCORE:0000011 +name: geological boundary +def: "It is a fiat surface that is 'located in' the external surface of a 'geological object'." [] +is_a: BFO:0000146 ! fiat surface +property_value: altLabel "limite geológico" xsd:string +property_value: IAO:0000116 "The 'geological boundary' of a 'geological object' coincides with the complete physical discontinuity that delimits it." xsd:string + +[Term] +id: GEOCORE:0000012 +name: geological contact +def: "It is a 'relational quality' that 'inheres in' two distinct 'geological object' that are 'externally connected with'" [] +is_a: BFO:0000145 ! relational quality +relationship: BFO:0000197 GEOCORE:0000001 {cardinality="2"} ! inheres in geological object +property_value: altLabel "contato geológico" xsd:string +property_value: IAO:0000116 "A geological contact exists when two distinct geological objects are externally\nconnected with, i.e., their external boundaries are physically adjacent. Objects that are in contact do not have any kind of proper parthood relationship between them." xsd:string + +[Term] +id: GEORES:0000001 +name: body of rock +is_a: GEOCORE:0000001 ! geological object +intersection_of: GEOCORE:0000001 ! geological object +intersection_of: GEOCORE:0000017 GEOCORE:0000008 ! constituted by amount of rock +relationship: BFO:0000101 GEOCORE:0000004 ! is carrier of geological structure +relationship: BFO:0000129 GEORES:0000020 ! member part of depositional system +relationship: BFO:0000129 GEORES:0000021 ! member part of sedimentary environment +relationship: GEOCORE:0000017 GEOCORE:0000008 ! constituted by amount of rock +property_value: altLabel "corpo de rocha" xsd:string +property_value: definition "'body of rock' is a 'geological object' that is 'constituted by' some 'amount of rock'" xsd:string + +[Term] +id: GEORES:0000002 +name: stratigraphic unit +comment: Os diferentes elementos arquiteturais ocorrem dentro de uma unidade com uma idade definida que é a unidade estratigráfica.\n\nAinda não sabemos se poderia ser uma unidade litoestratigráfica. +is_a: GEORES:0000001 ! body of rock +property_value: altLabel "unidade estratigráfica" xsd:string + +[Term] +id: GEORES:0000003 +name: lithostratigraphic unit +is_a: GEORES:0000001 ! body of rock +property_value: altLabel "unidade litoestratigráfica" xsd:string + +[Term] +id: GEORES:0000004 +name: formation +is_a: GEORES:0000003 ! lithostratigraphic unit +relationship: BFO:0000129 GEORES:0000019 ! member part of group +property_value: altLabel "formação" xsd:string + +[Term] +id: GEORES:0000005 +name: member +is_a: GEORES:0000003 ! lithostratigraphic unit +relationship: BFO:0000176 GEORES:0000004 ! continuant part of formation +property_value: altLabel "membro" xsd:string + +[Term] +id: GEORES:0000006 +name: architectural element +comment: A restrição de partes de escala menores ainda não foi implementada. +comment: Luan: Elementos arquiteturais são os objetos básicos que os geólogos vão reconhecer e descrever. Eles podem ocorrer em diversas escalas.\nUm elemento pode ter outro elemento como parte, desde que de uma escala menor. +is_a: GEORES:0000001 ! body of rock +relationship: BFO:0000196 GEORES:0000023 ! bearer of geometry +property_value: altLabel "elemento arquitetural" xsd:string + +[Term] +id: GEORES:0000007 +name: build up unit +is_a: GEORES:0000006 ! architectural element +disjoint_from: GEORES:0000008 ! channel unit +property_value: altLabel "edifício" xsd:string + +[Term] +id: GEORES:0000008 +name: channel unit +def: "An elongated Depositional Unit having some Channel Surface as its boundary and constituted by some Sediment or Sedimentary Rock that fills it (McHargue et al., 2011)." [] +comment: In stratigraphic terms, a channel unit is constituted by the sediments or sedimentary rocks that fill a channel. It is important to notice that, in more general terms, a channel is a passageway for fluids or sediments, i.e., an immaterial entity. If one elaborates about the erosion and deposition processes that generate these units (McHargue et al., 2011), it is essential to have this disambiguation. +comment: In this work, we decided not to model the named hierarchical scales as entities (e.g., Channel Element, Channel Complex, Channel Complex Set - McHargue et al., 2011) because there exists a wide variety of hierarchical schemes in the literature, and they are not necessarily interoperable (Cullis et al., 2018). Instead, we focus on the fact that units can be fractally nested: a unit can be a Proper Spatial Part Of another unit, which can be a Proper Spatial Part Of another unit, and so forth. We consider that this approach solves the problem of implementing a solution for the repeatability of the geological objects in multiple scales. As so, a Channel Unit can be decomposed in other Channel Units many times as necessary, keeping the representation structure. In the future, we can study the integration of hierarchical schemes and try to infer scales from the spatial relations. +is_a: GEORES:0000006 ! architectural element +disjoint_from: GEORES:0000013 ! levee unit +property_value: altLabel "canal" xsd:string +property_value: GEORES:0000050 "R+ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000009 +name: dome unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "domo" xsd:string + +[Term] +id: GEORES:0000010 +name: dune unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "duna" xsd:string + +[Term] +id: GEORES:0000011 +name: intrusive dike +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "dique intrusivo" xsd:string + +[Term] +id: GEORES:0000012 +name: intrusive sill unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "soleira intrusiva" xsd:string + +[Term] +id: GEORES:0000013 +name: levee unit +def: "A Depositional Unit having Wedge Geometry and forming a bank or ridge geomorphology associated with some Channel Unit." [] +comment: This term is not consensual as some authors refer to these units as the wedge-shape embankments around channels, which is the definition that we adopt here, while other authors refer to them as not necessarily being these embankments and possibly having wing shapes, among other definitions. +comment: This term refers to the geomorphological association of some wegde-shaped unit with some channel unit, even if the channel does not exist at the moment of the observation by the geologist and the levee is probabilistically identified by tendencies (e.g., typical facies). In other words, the term "levee" ontologicallly denotes this relation even though it cannot be deterministically observed. +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "dique" xsd:string +property_value: GEORES:0000050 "R~ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000014 +name: lobe unit +def: "A Depositional Unit having some Lobe Geometry." [] +comment: For Lobe Unit hierarchical scales, we adopted the same approach as in Channel Unit. +comment: These depositional units are usually found at deep-water depositional system terminal regions, or at channel laterals as Overbank Units. +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "lobo" xsd:string +property_value: GEORES:0000050 "R+ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000015 +name: mound unit +def: "A Depositional Unit having Mound Geometry with an irregular top surface and internal chaotic facies." [] +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "monte" xsd:string +property_value: GEORES:0000050 "R+ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000016 +name: olistrostomes unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "olistrostomas" xsd:string +property_value: IAO:0000118 "megaclast" xsd:string +property_value: IAO:0000118 "megaclasto" xsd:string + +[Term] +id: GEORES:0000017 +name: sheet unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "lençol" xsd:string + +[Term] +id: GEORES:0000018 +name: fossil +is_a: GEOCORE:0000001 ! geological object +property_value: altLabel "fóssil" xsd:string + +[Term] +id: GEORES:0000019 +name: group +is_a: BFO:0000027 ! object aggregate +relationship: BFO:0000115 GEORES:0000004 {all_only="true"} ! has member part formation +property_value: altLabel "grupo" xsd:string + +[Term] +id: GEORES:0000020 +name: depositional system +def: "An Object Aggregate whose members are mereotopologically-linked Depositional Units." [] +is_a: BFO:0000027 ! object aggregate +property_value: altLabel "sistema deposicional" xsd:string +property_value: GEORES:0000050 "R+ I+ O+ U+ ED-" xsd:string + +[Term] +id: GEORES:0000021 +name: sedimentary environment +def: "The sedimentary environment is the specific depositional setting of a particular sedimentary rock and is unique in terms of physical, chemical, and biological characteristics." [] +is_a: BFO:0000027 ! object aggregate +property_value: altLabel "ambiente de sedimentação" xsd:string +property_value: IAO:0000119 "Britannica\nhttps://www.britannica.com/science/sedimentary-rock/Sedimentary-environments" xsd:string + +[Term] +id: GEORES:0000022 +name: dimension +def: "A Quality that inheres in an Independent Continuant by virtue of one of its one-dimensional extents. It is a category that includes at least the three dimensions defined in this ontology: Width, Length, and Thickness. All dimensions are expressed by a real number indicating its value and a literal string indicating its measurement unit." [] +is_a: BFO:0000019 ! quality + +[Term] +id: GEORES:0000023 +name: geometry +def: "A Quality that inheres in a Depositional Unit by virtue of its external three-dimensional shape. It does not reflect the exact mathematical specifications of a geometric shape but abstracts and simplifies these specifications (Rovetto, 2011)." [] +is_a: BFO:0000019 ! quality +relationship: GEORES:0000046 GEORES:0000042 {minCardinality="1"} ! has geometry type geometry type +property_value: altLabel "geometria" xsd:string + +[Term] +id: GEORES:0000024 +name: lithology +is_a: BFO:0000019 ! quality +property_value: altLabel "litologia" xsd:string + +[Term] +id: GEORES:0000025 +name: statigraphic contact +is_a: GEOCORE:0000012 ! geological contact +property_value: altLabel "contato estratigráfico" xsd:string + +[Term] +id: GEORES:0000026 +name: bed contact +is_a: GEOCORE:0000012 ! geological contact +relationship: GEORES:0000044 GEORES:0000041 {cardinality="1"} ! has contact position contact position +relationship: GEORES:0000045 GEORES:0000043 {cardinality="1"} ! has contact type contact type +property_value: altLabel "contato de camada" xsd:string + +[Term] +id: GEORES:0000027 +name: sinuosity +def: "A Quality that inheres in a Channel Unit by virtue of how wavy it is across its length. It is expressed by a real number given by its curved length divided by its length in a straight line." [] +is_a: BFO:0000019 ! quality +relationship: BFO:0000197 GEORES:0000008 {cardinality="1"} ! inheres in channel unit + +[Term] +id: GEORES:0000028 +name: facies +def: "A pattern of properties of Geological Objects." [] +comment: This entity is defined in the literature as a combination of features that differentiates a geological object from its adjacent geological objects (Walker and James, 1992). However, a Facies does not describe a single Geological Object’s features: it might repeat in several objects as a pattern. This particular aspect matches the definition of Generically Dependent Continuant in BFO. Another important aspect is that the features that compose facies vary depending on the research context, e.g., Sedimentary Facies, Petrofacies (De Ros and Goldberg, 2007), Lithofacies, Ichnofacies, and Biofacies (Nichols, 2009). +is_a: BFO:0000031 ! generically dependent continuant +relationship: BFO:0000084 GEORES:0000001 ! generically depends on body of rock +property_value: altLabel "fácies" xsd:string + +[Term] +id: GEORES:0000029 +name: sedimentary facies +def: "A Facies consisting of the sum of the sedimentological characteristics of Depositional Units (Middleton, 1973, Nichols, 2009, Carbonera et al., 2015)." [] +comment: As an example, if we would model Cross-bedded Sandstone (Nichols, 2009), it would be an entity subsumed by Sedimentary Facies having the following relations: (1) Generically Depends On some (Constituted By some Sandstone (a)); and (2) Has Part some Cross-bedding Structure (b). (a): Sandstone would be an entity subsumed by Sedimentary Rock. (b): Cross-bedding Structure would be an entity subsumed by Sedimentary Structure. +is_a: GEORES:0000028 ! facies +property_value: altLabel "fácies sedimentar" xsd:string + +[Term] +id: GEORES:0000030 +name: facies association +def: "A Generically Dependent Continuant that consists of an aggregate of Facies." [] +comment: It usually describes the Facies that are typically found in specific regions or sub-environments. For example, the Channel Axis Association (McHargue et al., 2011) describes Sedimentary Facies typically found at the center part of channels (in a cross-section point of view). +is_a: BFO:0000031 ! generically dependent continuant +relationship: BFO:0000178 GEORES:0000028 {minCardinality="2"} ! has continuant part facies +property_value: altLabel "associação de facies" xsd:string + +[Term] +id: GEORES:0000031 +name: sediment +def: "An Unconsolidated Earth Material constituted by some collection of sedimentary grains or particles (Garcia et al., 2019)." [] +is_a: GEOCORE:0000010 ! unconsolidated earth material +property_value: GEORES:0000050 "R+ I+ O- U- ED-" xsd:string + +[Term] +id: GEORES:0000032 +name: sedimentary rock +def: "'sedimentary rock' is an 'amount of rock' constituted by some collection of sedimentary grains or particles (Garcia et al., 2019)." [] +is_a: GEOCORE:0000008 ! amount of rock +disjoint_from: GEORES:0000033 ! igneous rock +property_value: altLabel "rocha sedimentar" xsd:string +property_value: GEORES:0000050 "R+ I+ O- U- ED-" xsd:string + +[Term] +id: GEORES:0000033 +name: igneous rock +is_a: GEOCORE:0000008 ! amount of rock +property_value: altLabel "rocha ígnea" xsd:string +property_value: definition "'igneous rock' is an 'amount of rock' generated by the cooling and solidification of molten 'earth material'." xsd:string +property_value: isDefinedBy "https://www.britannica.com/science/igneous-rock" xsd:string + +[Term] +id: GEORES:0000034 +name: metamorphic rock +is_a: GEOCORE:0000008 ! amount of rock +property_value: altLabel "rocha metamórfica" xsd:string +property_value: definition "'metamorphic rock' is an 'amount of rock' generated by the alteration of preexisting rocks in response to changing environmental conditions, such as variations in temperature, pressure, and mechanical stress, and the addition or subtraction of chemical components." xsd:string +property_value: isDefinedBy "Adapted from Brittanica.\nhttps://www.britannica.com/science/metamorphic-rock" xsd:string + +[Term] +id: GEORES:0000035 +name: complex architectural element +is_a: GEORES:0000001 ! body of rock +disjoint_from: GEORES:0000036 ! composite architectural element + +[Term] +id: GEORES:0000036 +name: composite architectural element +is_a: GEORES:0000001 ! body of rock + +[Term] +id: GEORES:0000037 +name: individual architectural element + +[Term] +id: GEORES:0000038 +name: channel surface +def: "A Geological Boundary that forms the basis of a Channel Unit, having a concave-up shape unless truncated by overlying depositional units." [] +is_a: GEOCORE:0000011 ! geological boundary +property_value: GEORES:0000050 "R+ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000039 +name: basin +is_a: BFO:0000029 ! site +property_value: altLabel "bacia" xsd:string + +[Term] +id: GEORES:0000040 +name: geological site +comment: Epistemologicamente não é possível determinar os limites deste site e, portanto, cada geólogo pode posicionar sua área de interesse em uma localização e limites distintos, o que torna muito difícil tratar computacionalmente a identidade do sítio geológico. Esse problema acontece com outras entidades do tipo site: Região da Serra Gaúcha, Litoral Norte, etc, cuja delimitação é problemática, mas existe uma identidade consensual. +is_a: BFO:0000029 ! site +property_value: altLabel "sítio geológico" xsd:string + +[Term] +id: GEORES:0000041 +name: contact position +property_value: altLabel "posição do contato" xsd:string + +[Term] +id: GEORES:0000042 +name: geometry type +comment: Luan: Talvez tipo de Geometria seja uma classe de segunda ordem, mas em primeiro momento não utilizaremos punning para representar isto. A classe geometry tem uma relação de 'has geometry type' com um 'geometry type' e as instâncias dessa classe é que definem o tipo de geometria de fato. Caso seja necessário criar alguma subclasse de um 'body of rock' que tenha um 'geometry type' específico é possível utilizar a primitiva do owl value para isto.\n\nNão sabemos ainda como classificar esta classe. Do que ela seria subclasse? +property_value: altLabel "tipo de geometria" xsd:string + +[Term] +id: GEORES:0000043 +name: contact type +property_value: altLabel "tipo de contato" xsd:string + +[Typedef] +id: BFO:0000084 +name: generically depends on +property_value: altLabel "g-depends on" xsd:string +property_value: definition "b generically depends on c =Def b is a generically dependent continuant & c is an independent continuant that is not a spatial region & at some time t there inheres in c a specifically dependent continuant which concretizes b at t" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "252-BFO" xsd:string +property_value: scopeNote "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: " xsd:string +domain: BFO:0000031 ! generically dependent continuant +inverse_of: BFO:0000101 ! is carrier of + +[Typedef] +id: BFO:0000101 +name: is carrier of +property_value: definition "b is carrier of c =Def there is some time t such that c generically depends on b at t" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "254-BFO" xsd:string +property_value: scopeNote "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: " xsd:string +range: BFO:0000031 ! generically dependent continuant + +[Typedef] +id: BFO:0000115 +name: has member part +property_value: definition "b has member part c =Def c member part of b" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "230-BFO" xsd:string +property_value: scopeNote "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: " xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: BFO:0000178 ! has continuant part +inverse_of: BFO:0000129 ! member part of + +[Typedef] +id: BFO:0000129 +name: member part of +property_value: definition "b member part of c =Def b is an object & c is a material entity & there is some time t such that b continuant part of c at t & there is a mutually exhaustive and pairwise disjoint partition of c into objects x1, ..., xn (for some n ≠ 1) with b = xi (for some 1 <= i <= n)" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "228-BFO" xsd:string +property_value: scopeNote "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: " xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: BFO:0000176 ! continuant part of + +[Typedef] +id: BFO:0000176 +name: continuant part of +property_value: definition "b continuant part of c =Def b and c are continuants & there is some time t such that b and c exist at t & b continuant part of c at t" xsd:string +property_value: example "Milk teeth continuant part of human; surgically removed tumour continuant part of organism" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "221-BFO" xsd:string +property_value: scopeNote "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: " xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +inverse_of: BFO:0000178 ! has continuant part + +[Typedef] +id: BFO:0000178 +name: has continuant part +property_value: definition "b has continuant part c =Def c continuant part of b" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "271-BFO" xsd:string +property_value: scopeNote "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: " xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant + +[Typedef] +id: BFO:0000194 +name: specifically depended on by +property_value: altLabel "s-depended on by" xsd:string +property_value: definition "b specifically depended on by c =Def c specifically depends on b" xsd:string +property_value: example "Coloured object specifically depended on by colour" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "260-BFO" xsd:string +range: BFO:0000020 ! specifically dependent continuant +inverse_of: BFO:0000195 ! specifically depends on + +[Typedef] +id: BFO:0000195 +name: specifically depends on +property_value: altLabel "s-depends on" xsd:string +property_value: definition "(Elucidation) specifically depends on is a relation between a specifically dependent continuant b and specifically dependent continuant or independent continuant that is not a spatial region c such that b and c share no parts in common & b is of a nature such that at all times t it cannot exist unless c exists & b is not a boundary of c" xsd:string +property_value: example "A shape specifically depends on the shaped object; hue, saturation and brightness of a colour sample specifically depends on each other" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "012-BFO" xsd:string +property_value: scopeNote "The analogue of specifically depends on for occurrents is has participant." xsd:string +domain: BFO:0000020 ! specifically dependent continuant + +[Typedef] +id: BFO:0000196 +name: bearer of +property_value: definition "b bearer of c =Def c inheres in b" xsd:string +property_value: example "A patch of ink is the bearer of a colour quality; an organism is the bearer of a temperature quality" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "053-BFO" xsd:string +range: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000194 ! specifically depended on by +inverse_of: BFO:0000197 ! inheres in + +[Typedef] +id: BFO:0000197 +name: inheres in +property_value: definition "b inheres in c =Def b is a specifically dependent continuant & c is an independent continuant that is not a spatial region & b specifically depends on c" xsd:string +property_value: example "A shape inheres in a shaped object; a mass inheres in a material entity" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "051-BFO" xsd:string +domain: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000195 ! specifically depends on + +[Typedef] +id: BFO:0000199 +name: occupies temporal region +property_value: definition "p occupies temporal region t =Def p is a process or process boundary & the spatiotemporal region occupied by p temporally projects onto t" xsd:string +property_value: example "The Second World War occupies the temporal region September 1, 1939 - September 2, 1945" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "132-BFO" xsd:string +range: BFO:0000008 ! temporal region +is_functional: true + +[Typedef] +id: GEOCORE:0000015 +name: has age +def: "The relation between a Geological Object and its Geological Age." [] +is_a: BFO:0000196 ! bearer of +inverse_of: GEOCORE:0000016 ! age of + +[Typedef] +id: GEOCORE:0000016 +name: age of +def: "The relation between a Geological Age and a Geological Object. Inverse of has age relation." [] +is_a: BFO:0000197 ! inheres in + +[Typedef] +id: GEOCORE:0000017 +name: constituted by +def: "The relation between some material entity and the material that it is made of." [] +property_value: IAO:0000116 "This is a material constitution relation intended to represent the relationship between material objects, such as geological objects and earth materials, or aggregates of them." xsd:string +property_value: IAO:0000119 "Evnine, S. J. (2011). Constitution and composition: Three approaches to their relation. ProtoSociology, 27, 212-235." xsd:string +is_asymmetric: true + +[Typedef] +id: GEORES:0000044 +name: has contact position +domain: GEORES:0000026 ! bed contact +range: GEORES:0000041 ! contact position + +[Typedef] +id: GEORES:0000045 +name: has contact type +domain: GEORES:0000026 ! bed contact +range: GEORES:0000043 ! contact type + +[Typedef] +id: GEORES:0000046 +name: has geometry type +comment: Luan: Geometry Type talvez seja uma classe de segunda ordem cuja as instâncias são os diferentes tipos de Geometria. Por exemplo, é errado dizer que Geometria Lenticular é subtipo da Quality Geometria. Lenticular é na realidade um subtipo de Tipo de Geometria e não de Geometria. +domain: GEORES:0000023 ! geometry +range: GEORES:0000042 ! geometry type + +[Typedef] +id: GEORES:0000047 +name: has base geometry +is_a: GEORES:0000046 ! has geometry type + +[Typedef] +id: GEORES:0000048 +name: has top geometry +is_a: GEORES:0000046 ! has geometry type + diff --git a/geores-full.owl b/geores-full.owl new file mode 100644 index 0000000..0aef0fe --- /dev/null +++ b/geores-full.owl @@ -0,0 +1,2130 @@ + + + + + Alcides Lopes + Fabrício Henrique Rodrigues + Fernando Cicconeto + Joel Luis Carbonera + Luan Fonseca Garcia + Lucas Valadares Vieira + Mara Abel + Renata dos Santos Alvarenga + Tiago Agne de Oliveira + Yuanwei Qu + GeoReservoir is an ontology to support the description of the geometry and the lithology of deep-marine deposits. The GeoReservoir ontology provides formal and clear definitions of deep-marine depositional system entities, creating an unambiguous terminology for geometrical and lithological properties of the deposits in the scale of outcrop and seismic sections. These definitions are independent of tasks, geological interpretations, and process inferences. We created this language to make it possible to formally and uniformly describe any deep-marine occurrence in the world with an adequate level of detail for sedimentological studies and computer processing. + https://creativecommons.org/licenses/by-nc/4.0/ + GeoReservoir Ontology + Cited references: + +1. Abel, M., Perrin, M., Carbonera, J.L.: Ontological analysis for information integration in geomodeling. Earth Science Informatics 8, 21–36 (2015) +2. Carbonera, J.L., Abel, M., Scherer, C.M.S.: Visual interpretation of events in petroleum exploration: An approach supported by well-founded ontologies. Expert Systems With Applications 42, 2749–2763 (2015) +3. Cullis, S., Colombera, L., Patacci, M., McCaffrey, W.D.: Hierarchical classifications of the sedimentary architecture of deep-marine depositional systems. Earth-Science Reviews 179, 38–71 (2018) +4. De Ros, L.F., Goldberg, K.: Reservoir petrofacies: A tool for quality characterization and prediction. In: AAPG Annual Conference and Exhibition. Long Beach (2007) +5. Garcia, L.F., Carbonera, J.L., Rodrigues, F.H., Antunes, C.R., Abel, M.: What rocks are made of: Towards an ontological pattern for material constitution in the geological domain. In: Laender, A.H.F., Pernici, B., Lim, E.P., Oliveira, J.P.M. (eds.) ER: 38th International Conference on Conceptual Modeling. pp. 275–286. Springer, Cham (2019) +6. Guarino, N., Welty, C.A.: An overview of ontoclean. In: Staab, S., Studer, R. (eds.) Handbook on Ontologies, pp. 151–171. Springer, Berlin, Heidelberg (2004) +7. McHargue, T., Pyrcz, M.J., Sullivan, M.D., Clark, J.D., Fildani, A., Romans, B.W., Covault, J.A., Levy, M., Posamentier, H.W., Drinkwater, N.J.: Architecture of turbidite channel systems on the continental slope: Patterns and predictions. Marine and Petroleum Geology 28, 728–743 (2011) +8. Middleton, G.V.: Johannes walther’s law of the correlation of facies. Bulletin of the Geological Society of America 84, 979–988 (1973) +9. Nichols, G.: Sedimentology and Stratigraphy. Wiley-Blackwell, Chichester, 2nd edn. (2009) +10. Rovetto, R.: The shape of shapes: An ontological exploration. In: Hastings, J., Kutz, O., Bhatt, M., Borgo, S. (eds.) Proceedings of the First Interdisciplinary Workshop on SHAPES. Karlsruhe (2011), http://ceur-ws.org/Vol-812/ +11. Walker, R.G., James, N.P.: Facies Models: Response to Sea Level Change. Geological Association of Canada, St. John’s (1992) + We acknowledge the Brazilian funding agencies CNPq and CAPES for financing this work and the Research Centre of Petrobras (CENPES) for collaborating on this project. + 2024-04-07 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + For metaproperties, we use the following notation (Guarino and Welty, 2004; Abel et al., 2015): + +– R+ / R- / R~: rigid / not rigid / anti-rigid; +– I+ / I-: carries / does not carry identity; +– O+ / O-: provides / does not provide identity; +– U+ / U-: carries / does not carry unity; +– ED+ / ED-: existentially dependent / independent. + metaproperties + + + + + + + + + + + + + + + + + + + + + + + + + 252-BFO + generically depends on + g-depends on + b generically depends on c =Def b is a generically dependent continuant & c is an independent continuant that is not a spatial region & at some time t there inheres in c a specifically dependent continuant which concretizes b at t + Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link> + + + + + + + + + + + + + + + + + + + 254-BFO + is carrier of + b is carrier of c =Def there is some time t such that c generically depends on b at t + Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link> + + + + + + + + + + + + 230-BFO + has member part + b has member part c =Def c member part of b + Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link> + + + + + + + + + + + 228-BFO + member part of + b member part of c =Def b is an object & c is a material entity & there is some time t such that b continuant part of c at t & there is a mutually exhaustive and pairwise disjoint partition of c into objects x1, ..., xn (for some n ≠ 1) with b = xi (for some 1 <= i <= n) + Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link> + + + + + + + + + + + 221-BFO + continuant part of + b continuant part of c =Def b and c are continuants & there is some time t such that b and c exist at t & b continuant part of c at t + Milk teeth continuant part of human; surgically removed tumour continuant part of organism + Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link> + + + + + + + + + + 271-BFO + has continuant part + b has continuant part c =Def c continuant part of b + Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link> + + + + + + + + + + + + + + + + + + + + + + + + + 260-BFO + specifically depended on by + s-depended on by + b specifically depended on by c =Def c specifically depends on b + Coloured object specifically depended on by colour + + + + + + + + + + + + + + + + + + + + + + + + 012-BFO + specifically depends on + s-depends on + (Elucidation) specifically depends on is a relation between a specifically dependent continuant b and specifically dependent continuant or independent continuant that is not a spatial region c such that b and c share no parts in common & b is of a nature such that at all times t it cannot exist unless c exists & b is not a boundary of c + A shape specifically depends on the shaped object; hue, saturation and brightness of a colour sample specifically depends on each other + The analogue of specifically depends on for occurrents is has participant. + + + + + + + + + + + + + + + + + + + + + 053-BFO + bearer of + b bearer of c =Def c inheres in b + A patch of ink is the bearer of a colour quality; an organism is the bearer of a temperature quality + + + + + + + + + + + + + + + + + + + + 051-BFO + inheres in + b inheres in c =Def b is a specifically dependent continuant & c is an independent continuant that is not a spatial region & b specifically depends on c + A shape inheres in a shaped object; a mass inheres in a material entity + + + + + + + + + + + + + + + + + + 132-BFO + occupies temporal region + p occupies temporal region t =Def p is a process or process boundary & the spatiotemporal region occupied by p temporally projects onto t + The Second World War occupies the temporal region September 1, 1939 - September 2, 1945 + + + + + + + + + + The relation between a Geological Object and its Geological Age. + has age + + + + + + + + + The relation between a Geological Age and a Geological Object. Inverse of has age relation. + age of + + + + + + + + + + The relation between some material entity and the material that it is made of. + This is a material constitution relation intended to represent the relationship between material objects, such as geological objects and earth materials, or aggregates of them. + Evnine, S. J. (2011). Constitution and composition: Three approaches to their relation. ProtoSociology, 27, 212-235. + constituted by + + + + + + + + + + + has contact position + + + + + + + + + + + has contact type + + + + + + + + + + Luan: Geometry Type talvez seja uma classe de segunda ordem cuja as instâncias são os diferentes tipos de Geometria. Por exemplo, é errado dizer que Geometria Lenticular é subtipo da Quality Geometria. Lenticular é na realidade um subtipo de Tipo de Geometria e não de Geometria. + has geometry type + + + + + + + + + has base geometry + + + + + + + + + has top geometry + + + + + + + + + + + + + + + A relation between a Quality and its values. + O objetivo desta data property é conectar em níveL de implementação uma qualidade com o valor em seu espaço de qualiades. Por exemplo, a qualidade dimensão tem um espaço de qualidade que é um valor real positivo para sua largura. + +A IAO possui uma propriedade has measurement datum cujo domínio é um measurement datum. Porém, o problema de usar tal propriedade é acrescentar a necessidade de criar uma instância de measurement datum. + has value + + + + + + + + + + has dimension value + + + + + + + + + + + has lenght value + + + + + + + + + + + A relation between a Quality and a literal string that represents its measurement unit. + has measurement unit + + + + + + + + + + + has thickness value + + + + + + + + + + + has width value + + + + + + + + + + + + + 001-BFO + entity + (Elucidation) An entity is anything that exists or has existed or will exist + Julius Caesar; the Second World War; your body mass index; Verdi's Requiem + + + + + + + + + + + + + + + + 008-BFO + continuant + (Elucidation) A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity + A human being; a tennis ball; a cave; a region of space; someone's temperature + + + + + + + + + 077-BFO + occurrent + (Elucidation) An occurrent is an entity that unfolds itself in time or it is the start or end of such an entity or it is a temporal or spatiotemporal region + As for process, history, process boundary, spatiotemporal region, zero-dimensional temporal region, one-dimensional temporal region, temporal interval, temporal instant. + + + + + + + + + + + + + + + 017-BFO + independent continuant + b is an independent continuant =Def b is a continuant & there is no c such that b specifically depends on c or b generically depends on c + An atom; a molecule; an organism; a heart; a chair; the bottom right portion of a human torso; a leg; the interior of your mouth; a spatial region; an orchestra + + + + + + + + + + + + + + + 035-BFO + spatial region + (Elucidation) A spatial region is a continuant entity that is a continuant part of the spatial projection of a portion of spacetime at a given time + As for zero-dimensional spatial region, one-dimensional spatial region, two-dimensional spatial region, three-dimensional spatial region + + + + + + + + + 100-BFO + temporal region + (Elucidation) A temporal region is an occurrent over which processes can unfold + As for zero-dimensional temporal region and one-dimensional temporal region + + + + + + + + + 095-BFO + spatiotemporal region + (Elucidation) A spatiotemporal region is an occurrent that is an occurrent part of spacetime + The spatiotemporal region occupied by the development of a cancer tumour; the spatiotemporal region occupied by an orbiting satellite + 'Spacetime' here refers to the maximal instance of the universal spatiotemporal region. + + + + + + + + + 083-BFO + process + event + (Elucidation) p is a process means p is an occurrent that has some temporal proper part and for some time t, p has some material entity as participant + An act of selling; the life of an organism; a process of sleeping; a process of cell-division; a beating of the heart; a process of meiosis; the taxiing of an aircraft; the programming of a computer + + + + + + + + + 055-BFO + quality + (Elucidation) A quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized + The colour of a tomato; the ambient temperature of this portion of air; the length of the circumference of your waist; the shape of your nose; the shape of your nostril; the mass of this piece of gold + + + + + + + + + 050-BFO + specifically dependent continuant + b is a specifically dependent continuant =Def b is a continuant & there is some independent continuant c which is not a spatial region & which is such that b specifically depends on c + (with multiple bearers) John's love for Mary; the ownership relation between John and this statue; the relation of authority between John and his subordinates + (with one bearer) The mass of this tomato; the pink colour of a medium rare piece of grilled filet mignon at its centre; the smell of this portion of mozzarella; the disposition of this fish to decay; the role of being a doctor; the function of this heart to pump blood; the shape of this hole + + + + + + + + + 025-BFO + object aggregate + (Elucidation) An object aggregate is a material entity consisting exactly of a plurality (≥1) of objects as member parts which together form a unit + The aggregate of the musicians in a symphony orchestra and their instruments; the aggregate of bearings in a constant velocity axle joint; the nitrogen atoms in the atmosphere; a collection of cells in a blood biobank + 'Exactly' means that there are no parts of the object aggregate other than its member parts. + The unit can, at certain times, consist of exactly one object, for example, when a wolf litter loses all but one of its pups, but it must at some time have a plurality of member parts. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 034-BFO + site + (Elucidation) A site is a three-dimensional immaterial entity whose boundaries either (partially or wholly) coincide with the boundaries of one or more material entities or have locations determined in relation to some material entity + A hole in a portion of cheese; a rabbit hole; the Grand Canyon; the Piazza San Marco; the kangaroo-joey-containing hole of a kangaroo pouch; your left nostril (a fiat part - the opening - of your left nasal cavity); the lumen of your gut; the hold of a ship; the interior of the trunk of your car; hole in an engineered floor joist + + + + + + + + + 024-BFO + object + (Elucidation) An object is a material entity which manifests causal unity & is of a type instances of which are maximal relative to the sort of causal unity manifested + An organism; a fish tank; a planet; a laptop; a valve; a block of marble; an ice cube + A description of three primary sorts of causal unity is provided in Basic Formal Ontology 2.0. Specification and User Guide + + + + + + + + + 074-BFO + generically dependent continuant + g-dependent continuant + (Elucidation) A generically dependent continuant is an entity that exists in virtue of the fact that there is at least one of what may be multiple copies which is the content or the pattern that multiple copies would share + The pdf file on your laptop; the pdf file that is a copy thereof on my laptop; the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule; the content that is shared by a string of dots and dashes written on a page and the transmitted Morse code signal; the content of a sentence; an engineering blueprint + + + + + + + + + 084-BFO + process boundary + p is a process boundary =Def p is a temporal part of a process & p has no proper temporal parts + The boundary between the 2nd and 3rd year of your life + + + + + + + + + 103-BFO + one-dimensional temporal region + (Elucidation) A one-dimensional temporal region is a temporal region that is a whole that has a temporal interval and zero or more temporal intervals and temporal instants as parts + The temporal region during which a process occurs + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 019-BFO + material entity + (Elucidation) A material entity is an independent continuant has some portion of matter as continuant part + A human being; the undetached arm of a human being; an aggregate of human beings + + + + + + + + + + + + + + + 029-BFO + continuant fiat boundary + (Elucidation) A continuant fiat boundary b is an immaterial entity that is of zero, one or two dimensions & such that there is no time t when b has a spatial region as continuant part & whose location is determined in relation to some material entity + As for fiat point, fiat line, fiat surface + + + + + + + + + 028-BFO + immaterial entity + b is an immaterial entity =Def b is an independent continuant which is such that there is no time t when it has a material entity as continuant part + As for fiat point, fiat line, fiat surface, site + + + + + + + + + 057-BFO + relational quality + b is a relational quality =Def b is a quality & there exists c and d such that c and d are not identical & b specifically depends on c & b specifically depends on d + A marriage bond; an instance of love; an obligation between one person and another + + + + + + + + + 033-BFO + fiat surface + (Elucidation) A fiat surface is a two-dimensional continuant fiat boundary that is self-connected + The surface of the Earth; the plane separating the smoking from the non-smoking zone in a restaurant + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An object that is 'generated by' some 'geological process' and has at least one part 'constituted by' some 'earth material' that is not an 'earth fluid'. + A geological object is a naturally occurring entity because a geological process +generates it, and some earth material constitutes it. Thus, we can differentiate geological objects from artificial objects, such as a well-core, because even though some earth material constitutes artificial objects, they are human-made rather than generated by some geological process. Furthermore, Geological Objects are specializations of BFO Objects, meaning they must necessarily have some unity criteria. The unity is what differentiates geological objects from Earth Materials. + geological object + objeto geológico + + + + + + + + + + + + + + + Examples are the process of deposition, the process of folding, a tectonic process, a sedimentary process. + It is a physical, or chemical, or biological, naturally occurring process that occurs on the Earth’s surface or subsurface and occupies some 'geological time interval' + Geological processes are macro processes that generate, transform, deform, transport, or destroy geological objects and earth materials. These processes are not necessarily atomic and may have other geological processes as parts. + geological process + processo geológico + + + + + + + + + It is a quality that 'inheres in' a 'geological object' or 'earth material' that corresponds to the 'geological time interval' in which the 'geological process' that it was 'generated by' occupied. + geological age + idade geológica + + + + + + + + + + + + + + + It is a 'generically dependent continuant' that is the pattern of a non-atomic 'geological object''s internal arrangement. + Geological structures are general material patterns repeated in many geological +objects. The pattern comprises the material configuration and the mutual relationships of the object’s different parts. Structures result from one or a series of geological processes that generated or transformed the geological object they generically depend on. Thus, there is some historical dependence relation between the structure and this geological process, but what concretizes the structure is some complex quality inhering in the object, not the process. + geological structure + estrutura geológica + + + + + + + + + It is a BFO temporal interval that corresponds to a time interval within the Geological Time Scale. + geological time interval + intervalo de tempo geológico + + + + + + + + + + + + + + + Examples are an amount of sandstone, an amount of petroleum, an amount of +natural gas. + It is a natural amount of matter 'generated by' some 'geological process'. + Earth Materials are natural amounts of matter. Thus, they come into existence by nature, without any artificial aid. Since they are amounts, they don’t hold unity criteria, but they are ontologically rigid and provide an identity criteria. Earth Materials and BFO Objects are disjoint. They are either solid, fluid, or unconsolidated. We usually observe earth materials when constituting other objects, such as an amount of rock constituting a geological unity or an amount of sand constituting a dune. + earth material + material geologico + + + + + + + + + The amount of quarts that constitutes some grain, the amount of feldspar that is part of an amount of rock. + An amount of rock is an 'earth material' that is a naturally occuring, inorganic, solid, homogeneous chemical compound with a crystalline structure. + Amounts of mineral lack a unity criteria as every other 'earth material'. We usually observe them when they are constitution objects such as crystals or grains. + amount of mineral + quantidade de mineral + + + + + + + + + + + + + + + + The amount of sandstone that constitutes a lithostratigraphic unit. + An amount of rock is a solid consolidated 'earth material' that is 'constituted by' an aggregate of particles made of mineral matter or material of biological origin. + Geologists define rocks at a scale of observation where they consider them homogeneous, even though an aggregate of solid particles constitutes it. These particles are usually geological objects, such as grains or crystals, or the rest of dead animals or plants. + +Amounts of rock, like other earth materials, are independent rigid entities that do not hold any unity criteria. We can observe them in nature when they are constituting objects such as geological unities. + amount of rock + quantidade de rocha + + + + + + + + + Earth fluid is an 'earth material' that is fluild. + Earth fluids can be water, oil, gas or a mixture of those fluids. + earth fluid + fluido da terra + + + + + + + + + Unconsolidated earth material is an 'earth material' that is consituted by an aggregate of solid particles but is not consolidated into a 'rock' it self. + unconsolidated earth material + material geológico inconsolidado + + + + + + + + + It is a fiat surface that is 'located in' the external surface of a 'geological object'. + The 'geological boundary' of a 'geological object' coincides with the complete physical discontinuity that delimits it. + geological boundary + limite geológico + + + + + + + + + + + + 2 + + + + It is a 'relational quality' that 'inheres in' two distinct 'geological object' that are 'externally connected with' + A geological contact exists when two distinct geological objects are externally +connected with, i.e., their external boundaries are physically adjacent. Objects that are in contact do not have any kind of proper parthood relationship between them. + geological contact + contato geológico + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + body of rock + corpo de rocha + 'body of rock' is a 'geological object' that is 'constituted by' some 'amount of rock' + + + + + + + + + Os diferentes elementos arquiteturais ocorrem dentro de uma unidade com uma idade definida que é a unidade estratigráfica. + +Ainda não sabemos se poderia ser uma unidade litoestratigráfica. + stratigraphic unit + unidade estratigráfica + + + + + + + + + lithostratigraphic unit + unidade litoestratigráfica + + + + + + + + + + + + + + + formation + formação + + + + + + + + + + + + + + + member + membro + + + + + + + + + + + + + + + A restrição de partes de escala menores ainda não foi implementada. + Luan: Elementos arquiteturais são os objetos básicos que os geólogos vão reconhecer e descrever. Eles podem ocorrer em diversas escalas. +Um elemento pode ter outro elemento como parte, desde que de uma escala menor. + architectural element + elemento arquitetural + + + + + + + + + build up unit + edifício + + + + + + + + + An elongated Depositional Unit having some Channel Surface as its boundary and constituted by some Sediment or Sedimentary Rock that fills it (McHargue et al., 2011). + In stratigraphic terms, a channel unit is constituted by the sediments or sedimentary rocks that fill a channel. It is important to notice that, in more general terms, a channel is a passageway for fluids or sediments, i.e., an immaterial entity. If one elaborates about the erosion and deposition processes that generate these units (McHargue et al., 2011), it is essential to have this disambiguation. + In this work, we decided not to model the named hierarchical scales as entities (e.g., Channel Element, Channel Complex, Channel Complex Set - McHargue et al., 2011) because there exists a wide variety of hierarchical schemes in the literature, and they are not necessarily interoperable (Cullis et al., 2018). Instead, we focus on the fact that units can be fractally nested: a unit can be a Proper Spatial Part Of another unit, which can be a Proper Spatial Part Of another unit, and so forth. We consider that this approach solves the problem of implementing a solution for the repeatability of the geological objects in multiple scales. As so, a Channel Unit can be decomposed in other Channel Units many times as necessary, keeping the representation structure. In the future, we can study the integration of hierarchical schemes and try to infer scales from the spatial relations. + channel unit + canal + R+ I+ O- U+ ED- + + + + + + + + + dome unit + domo + + + + + + + + + dune unit + duna + + + + + + + + + intrusive dike + dique intrusivo + + + + + + + + + intrusive sill unit + soleira intrusiva + + + + + + + + + A Depositional Unit having Wedge Geometry and forming a bank or ridge geomorphology associated with some Channel Unit. + This term is not consensual as some authors refer to these units as the wedge-shape embankments around channels, which is the definition that we adopt here, while other authors refer to them as not necessarily being these embankments and possibly having wing shapes, among other definitions. + This term refers to the geomorphological association of some wegde-shaped unit with some channel unit, even if the channel does not exist at the moment of the observation by the geologist and the levee is probabilistically identified by tendencies (e.g., typical facies). In other words, the term "levee" ontologicallly denotes this relation even though it cannot be deterministically observed. + levee unit + dique + R~ I+ O- U+ ED- + + + + + + + + + A Depositional Unit having some Lobe Geometry. + For Lobe Unit hierarchical scales, we adopted the same approach as in Channel Unit. + These depositional units are usually found at deep-water depositional system terminal regions, or at channel laterals as Overbank Units. + lobe unit + lobo + R+ I+ O- U+ ED- + + + + + + + + + A Depositional Unit having Mound Geometry with an irregular top surface and internal chaotic facies. + mound unit + monte + R+ I+ O- U+ ED- + + + + + + + + + megaclast + megaclasto + olistrostomes unit + olistrostomas + + + + + + + + + sheet unit + lençol + + + + + + + + + fossil + fóssil + + + + + + + + + + + + + + + group + grupo + + + + + + + + + An Object Aggregate whose members are mereotopologically-linked Depositional Units. + depositional system + sistema deposicional + R+ I+ O+ U+ ED- + + + + + + + + + The sedimentary environment is the specific depositional setting of a particular sedimentary rock and is unique in terms of physical, chemical, and biological characteristics. + Britannica +https://www.britannica.com/science/sedimentary-rock/Sedimentary-environments + sedimentary environment + ambiente de sedimentação + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A Quality that inheres in an Independent Continuant by virtue of one of its one-dimensional extents. It is a category that includes at least the three dimensions defined in this ontology: Width, Length, and Thickness. All dimensions are expressed by a real number indicating its value and a literal string indicating its measurement unit. + dimension + + + + + + + + + + + + 1 + + + + A Quality that inheres in a Depositional Unit by virtue of its external three-dimensional shape. It does not reflect the exact mathematical specifications of a geometric shape but abstracts and simplifies these specifications (Rovetto, 2011). + geometry + geometria + + + + + + + + + lithology + litologia + + + + + + + + + statigraphic contact + contato estratigráfico + + + + + + + + + + + + 1 + + + + + + + 1 + + + + bed contact + contato de camada + + + + + + + + + + + + 1 + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + 1 + + + + + + + A Quality that inheres in a Channel Unit by virtue of how wavy it is across its length. It is expressed by a real number given by its curved length divided by its length in a straight line. + sinuosity + + + + + + + + + + + + + + + A pattern of properties of Geological Objects. + This entity is defined in the literature as a combination of features that differentiates a geological object from its adjacent geological objects (Walker and James, 1992). However, a Facies does not describe a single Geological Object’s features: it might repeat in several objects as a pattern. This particular aspect matches the definition of Generically Dependent Continuant in BFO. Another important aspect is that the features that compose facies vary depending on the research context, e.g., Sedimentary Facies, Petrofacies (De Ros and Goldberg, 2007), Lithofacies, Ichnofacies, and Biofacies (Nichols, 2009). + facies + fácies + + + + + + + + + A Facies consisting of the sum of the sedimentological characteristics of Depositional Units (Middleton, 1973, Nichols, 2009, Carbonera et al., 2015). + As an example, if we would model Cross-bedded Sandstone (Nichols, 2009), it would be an entity subsumed by Sedimentary Facies having the following relations: (1) Generically Depends On some (Constituted By some Sandstone (a)); and (2) Has Part some Cross-bedding Structure (b). (a): Sandstone would be an entity subsumed by Sedimentary Rock. (b): Cross-bedding Structure would be an entity subsumed by Sedimentary Structure. + sedimentary facies + fácies sedimentar + + + + + + + + + + + + 2 + + + + A Generically Dependent Continuant that consists of an aggregate of Facies. + It usually describes the Facies that are typically found in specific regions or sub-environments. For example, the Channel Axis Association (McHargue et al., 2011) describes Sedimentary Facies typically found at the center part of channels (in a cross-section point of view). + facies association + associação de facies + + + + + + + + + An Unconsolidated Earth Material constituted by some collection of sedimentary grains or particles (Garcia et al., 2019). + sediment + R+ I+ O- U- ED- + + + + + + + + + 'sedimentary rock' is an 'amount of rock' constituted by some collection of sedimentary grains or particles (Garcia et al., 2019). + sedimentary rock + rocha sedimentar + R+ I+ O- U- ED- + + + + + + + + + https://www.britannica.com/science/igneous-rock + igneous rock + rocha ígnea + 'igneous rock' is an 'amount of rock' generated by the cooling and solidification of molten 'earth material'. + + + + + + + + + Adapted from Brittanica. +https://www.britannica.com/science/metamorphic-rock + metamorphic rock + rocha metamórfica + 'metamorphic rock' is an 'amount of rock' generated by the alteration of preexisting rocks in response to changing environmental conditions, such as variations in temperature, pressure, and mechanical stress, and the addition or subtraction of chemical components. + + + + + + + + + + + + + + + + + + + + + + + + + + + complex architectural element + + + + + + + + + + + + + + + + + + + + composite architectural element + + + + + + + + + + + + + + + + + + + + + + + individual architectural element + + + + + + + + + A Geological Boundary that forms the basis of a Channel Unit, having a concave-up shape unless truncated by overlying depositional units. + channel surface + R+ I+ O- U+ ED- + + + + + + + + + basin + bacia + + + + + + + + + Epistemologicamente não é possível determinar os limites deste site e, portanto, cada geólogo pode posicionar sua área de interesse em uma localização e limites distintos, o que torna muito difícil tratar computacionalmente a identidade do sítio geológico. Esse problema acontece com outras entidades do tipo site: Região da Serra Gaúcha, Litoral Norte, etc, cuja delimitação é problemática, mas existe uma identidade consensual. + geological site + sítio geológico + + + + + + + + + + + + + + + + + contact position + posição do contato + + + + + + + + + + + + + + + + + + + + + + Luan: Talvez tipo de Geometria seja uma classe de segunda ordem, mas em primeiro momento não utilizaremos punning para representar isto. A classe geometry tem uma relação de 'has geometry type' com um 'geometry type' e as instâncias dessa classe é que definem o tipo de geometria de fato. Caso seja necessário criar alguma subclasse de um 'body of rock' que tenha um 'geometry type' específico é possível utilizar a primitiva do owl value para isto. + +Não sabemos ainda como classificar esta classe. Do que ela seria subclasse? + geometry type + tipo de geometria + + + + + + + + + + + + + + + + + + + + + + contact type + tipo de contato + + + + + + + + + + + + + + amalgamated contact + contato amalgamado + + + + + + + + + base position contact + contato de base + + + + + + + + + cryptic/covered contact + contato críptico/encoberto + + + + + + + + + conformable contact + contato concordante + + + + + + + + + erosive contact + contato erosivo + + + + + + + + + faulted contact + contato de falha + + + + + + + + + gradational contact + contato gradacional + + + + + + + + + intrusive contact + contato intrusivo + + + + + + + + + sharp contact + contato abrupto + + + + + + + + + irregular geometry + geometria irregular + + + + + + + + + lenticular convex top flatbed geometry + geometria lenticular topo convexo base plana + + + + + + + + + lenticular concave convex geometry + geometria lenticular côncavo convexa + + + + + + + + + lateral position contact + contato lateral + + + + + + + + + lenticular flattop concave base geometry + geometria lenticular topo plano base convexa + + + + + + + + + sheet geometry + geometria lençoidal + + + + + + + + + sigmoidal geometry + geometria sigmoidal + + + + + + + + + tabular geometry + geometria tabular + + + + + + + + + top position contact + contato de topo + + + + + + + + + wedge shape geometry + geometria de cunha + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/geores-simple.obo b/geores-simple.obo new file mode 100644 index 0000000..0ee1fa0 --- /dev/null +++ b/geores-simple.obo @@ -0,0 +1,414 @@ +format-version: 1.2 +data-version: https://www.inf.ufrgs.br/bdi/ontologies/geores/releases/2024-04-07/geores-simple.owl +remark: Cited references:\n\n1. Abel, M., Perrin, M., Carbonera, J.L.: Ontological analysis for information integration in geomodeling. Earth Science Informatics 8, 21–36 (2015)\n2. Carbonera, J.L., Abel, M., Scherer, C.M.S.: Visual interpretation of events in petroleum exploration: An approach supported by well-founded ontologies. Expert Systems With Applications 42, 2749–2763 (2015)\n3. Cullis, S., Colombera, L., Patacci, M., McCaffrey, W.D.: Hierarchical classifications of the sedimentary architecture of deep-marine depositional systems. Earth-Science Reviews 179, 38–71 (2018)\n4. De Ros, L.F., Goldberg, K.: Reservoir petrofacies: A tool for quality characterization and prediction. In: AAPG Annual Conference and Exhibition. Long Beach (2007)\n5. Garcia, L.F., Carbonera, J.L., Rodrigues, F.H., Antunes, C.R., Abel, M.: What rocks are made of: Towards an ontological pattern for material constitution in the geological domain. In: Laender, A.H.F., Pernici, B., Lim, E.P., Oliveira, J.P.M. (eds.) ER: 38th International Conference on Conceptual Modeling. pp. 275–286. Springer, Cham (2019)\n6. Guarino, N., Welty, C.A.: An overview of ontoclean. In: Staab, S., Studer, R. (eds.) Handbook on Ontologies, pp. 151–171. Springer, Berlin, Heidelberg (2004)\n7. McHargue, T., Pyrcz, M.J., Sullivan, M.D., Clark, J.D., Fildani, A., Romans, B.W., Covault, J.A., Levy, M., Posamentier, H.W., Drinkwater, N.J.: Architecture of turbidite channel systems on the continental slope: Patterns and predictions. Marine and Petroleum Geology 28, 728–743 (2011)\n8. Middleton, G.V.: Johannes walther’s law of the correlation of facies. Bulletin of the Geological Society of America 84, 979–988 (1973)\n9. Nichols, G.: Sedimentology and Stratigraphy. Wiley-Blackwell, Chichester, 2nd edn. (2009)\n10. Rovetto, R.: The shape of shapes: An ontological exploration. In: Hastings, J., Kutz, O., Bhatt, M., Borgo, S. (eds.) Proceedings of the First Interdisciplinary Workshop on SHAPES. Karlsruhe (2011), http://ceur-ws.org/Vol-812/\n11. Walker, R.G., James, N.P.: Facies Models: Response to Sea Level Change. Geological Association of Canada, St. John’s (1992) +remark: We acknowledge the Brazilian funding agencies CNPq and CAPES for financing this work and the Research Centre of Petrobras (CENPES) for collaborating on this project. +ontology: https://www.inf.ufrgs.br/bdi/ontologies/geores/geores-simple.owl +property_value: http://purl.org/dc/elements/1.1/contributor "Alcides Lopes" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Fabrício Henrique Rodrigues" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Fernando Cicconeto" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Joel Luis Carbonera" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Luan Fonseca Garcia" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Lucas Valadares Vieira" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Mara Abel" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Renata dos Santos Alvarenga" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Tiago Agne de Oliveira" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Yuanwei Qu" xsd:string +property_value: http://purl.org/dc/terms/description "GeoReservoir is an ontology to support the description of the geometry and the lithology of deep-marine deposits. The GeoReservoir ontology provides formal and clear definitions of deep-marine depositional system entities, creating an unambiguous terminology for geometrical and lithological properties of the deposits in the scale of outcrop and seismic sections. These definitions are independent of tasks, geological interpretations, and process inferences. We created this language to make it possible to formally and uniformly describe any deep-marine occurrence in the world with an adequate level of detail for sedimentological studies and computer processing." xsd:string +property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by-nc/4.0/" xsd:string +property_value: http://purl.org/dc/terms/title "GeoReservoir Ontology" xsd:string +property_value: owl:versionInfo "2024-04-07" xsd:string + +[Term] +id: GEORES:0000001 +name: body of rock +relationship: BFO:0000129 GEORES:0000020 ! member part of depositional system +relationship: BFO:0000129 GEORES:0000021 ! member part of sedimentary environment +relationship: BFO:0000196 GEORES:0000022 ! bearer of dimension +property_value: altLabel "corpo de rocha" xsd:string +property_value: definition "'body of rock' is a 'geological object' that is 'constituted by' some 'amount of rock'" xsd:string + +[Term] +id: GEORES:0000002 +name: stratigraphic unit +comment: Os diferentes elementos arquiteturais ocorrem dentro de uma unidade com uma idade definida que é a unidade estratigráfica.\n\nAinda não sabemos se poderia ser uma unidade litoestratigráfica. +is_a: GEORES:0000001 ! body of rock +property_value: altLabel "unidade estratigráfica" xsd:string + +[Term] +id: GEORES:0000003 +name: lithostratigraphic unit +is_a: GEORES:0000001 ! body of rock +property_value: altLabel "unidade litoestratigráfica" xsd:string + +[Term] +id: GEORES:0000004 +name: formation +is_a: GEORES:0000003 ! lithostratigraphic unit +relationship: BFO:0000129 GEORES:0000019 ! member part of group +property_value: altLabel "formação" xsd:string + +[Term] +id: GEORES:0000005 +name: member +is_a: GEORES:0000003 ! lithostratigraphic unit +relationship: BFO:0000176 GEORES:0000004 ! continuant part of formation +property_value: altLabel "membro" xsd:string + +[Term] +id: GEORES:0000006 +name: architectural element +comment: A restrição de partes de escala menores ainda não foi implementada. +comment: Luan: Elementos arquiteturais são os objetos básicos que os geólogos vão reconhecer e descrever. Eles podem ocorrer em diversas escalas.\nUm elemento pode ter outro elemento como parte, desde que de uma escala menor. +is_a: GEORES:0000001 ! body of rock +relationship: BFO:0000196 GEORES:0000023 ! bearer of geometry +property_value: altLabel "elemento arquitetural" xsd:string + +[Term] +id: GEORES:0000007 +name: build up unit +is_a: GEORES:0000006 ! architectural element +disjoint_from: GEORES:0000008 ! channel unit +property_value: altLabel "edifício" xsd:string + +[Term] +id: GEORES:0000008 +name: channel unit +def: "An elongated Depositional Unit having some Channel Surface as its boundary and constituted by some Sediment or Sedimentary Rock that fills it (McHargue et al., 2011)." [] +comment: In stratigraphic terms, a channel unit is constituted by the sediments or sedimentary rocks that fill a channel. It is important to notice that, in more general terms, a channel is a passageway for fluids or sediments, i.e., an immaterial entity. If one elaborates about the erosion and deposition processes that generate these units (McHargue et al., 2011), it is essential to have this disambiguation. +comment: In this work, we decided not to model the named hierarchical scales as entities (e.g., Channel Element, Channel Complex, Channel Complex Set - McHargue et al., 2011) because there exists a wide variety of hierarchical schemes in the literature, and they are not necessarily interoperable (Cullis et al., 2018). Instead, we focus on the fact that units can be fractally nested: a unit can be a Proper Spatial Part Of another unit, which can be a Proper Spatial Part Of another unit, and so forth. We consider that this approach solves the problem of implementing a solution for the repeatability of the geological objects in multiple scales. As so, a Channel Unit can be decomposed in other Channel Units many times as necessary, keeping the representation structure. In the future, we can study the integration of hierarchical schemes and try to infer scales from the spatial relations. +is_a: GEORES:0000006 ! architectural element +disjoint_from: GEORES:0000013 ! levee unit +property_value: altLabel "canal" xsd:string +property_value: GEORES:0000050 "R+ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000009 +name: dome unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "domo" xsd:string + +[Term] +id: GEORES:0000010 +name: dune unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "duna" xsd:string + +[Term] +id: GEORES:0000011 +name: intrusive dike +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "dique intrusivo" xsd:string + +[Term] +id: GEORES:0000012 +name: intrusive sill unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "soleira intrusiva" xsd:string + +[Term] +id: GEORES:0000013 +name: levee unit +def: "A Depositional Unit having Wedge Geometry and forming a bank or ridge geomorphology associated with some Channel Unit." [] +comment: This term is not consensual as some authors refer to these units as the wedge-shape embankments around channels, which is the definition that we adopt here, while other authors refer to them as not necessarily being these embankments and possibly having wing shapes, among other definitions. +comment: This term refers to the geomorphological association of some wegde-shaped unit with some channel unit, even if the channel does not exist at the moment of the observation by the geologist and the levee is probabilistically identified by tendencies (e.g., typical facies). In other words, the term "levee" ontologicallly denotes this relation even though it cannot be deterministically observed. +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "dique" xsd:string +property_value: GEORES:0000050 "R~ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000014 +name: lobe unit +def: "A Depositional Unit having some Lobe Geometry." [] +comment: For Lobe Unit hierarchical scales, we adopted the same approach as in Channel Unit. +comment: These depositional units are usually found at deep-water depositional system terminal regions, or at channel laterals as Overbank Units. +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "lobo" xsd:string +property_value: GEORES:0000050 "R+ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000015 +name: mound unit +def: "A Depositional Unit having Mound Geometry with an irregular top surface and internal chaotic facies." [] +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "monte" xsd:string +property_value: GEORES:0000050 "R+ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000016 +name: olistrostomes unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "olistrostomas" xsd:string +property_value: IAO:0000118 "megaclast" xsd:string +property_value: IAO:0000118 "megaclasto" xsd:string + +[Term] +id: GEORES:0000017 +name: sheet unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "lençol" xsd:string + +[Term] +id: GEORES:0000018 +name: fossil +relationship: BFO:0000196 GEORES:0000022 ! bearer of dimension +property_value: altLabel "fóssil" xsd:string + +[Term] +id: GEORES:0000019 +name: group +relationship: BFO:0000115 GEORES:0000004 {all_only="true"} ! has member part formation +property_value: altLabel "grupo" xsd:string + +[Term] +id: GEORES:0000020 +name: depositional system +def: "An Object Aggregate whose members are mereotopologically-linked Depositional Units." [] +property_value: altLabel "sistema deposicional" xsd:string +property_value: GEORES:0000050 "R+ I+ O+ U+ ED-" xsd:string + +[Term] +id: GEORES:0000021 +name: sedimentary environment +def: "The sedimentary environment is the specific depositional setting of a particular sedimentary rock and is unique in terms of physical, chemical, and biological characteristics." [] +property_value: altLabel "ambiente de sedimentação" xsd:string +property_value: IAO:0000119 "Britannica\nhttps://www.britannica.com/science/sedimentary-rock/Sedimentary-environments" xsd:string + +[Term] +id: GEORES:0000022 +name: dimension +def: "A Quality that inheres in an Independent Continuant by virtue of one of its one-dimensional extents. It is a category that includes at least the three dimensions defined in this ontology: Width, Length, and Thickness. All dimensions are expressed by a real number indicating its value and a literal string indicating its measurement unit." [] + +[Term] +id: GEORES:0000023 +name: geometry +def: "A Quality that inheres in a Depositional Unit by virtue of its external three-dimensional shape. It does not reflect the exact mathematical specifications of a geometric shape but abstracts and simplifies these specifications (Rovetto, 2011)." [] +relationship: GEORES:0000046 GEORES:0000042 {minCardinality="1"} ! has geometry type geometry type +property_value: altLabel "geometria" xsd:string + +[Term] +id: GEORES:0000024 +name: lithology +property_value: altLabel "litologia" xsd:string + +[Term] +id: GEORES:0000025 +name: statigraphic contact +property_value: altLabel "contato estratigráfico" xsd:string + +[Term] +id: GEORES:0000026 +name: bed contact +relationship: GEORES:0000044 GEORES:0000041 {cardinality="1"} ! has contact position contact position +relationship: GEORES:0000045 GEORES:0000043 {cardinality="1"} ! has contact type contact type +property_value: altLabel "contato de camada" xsd:string + +[Term] +id: GEORES:0000027 +name: sinuosity +def: "A Quality that inheres in a Channel Unit by virtue of how wavy it is across its length. It is expressed by a real number given by its curved length divided by its length in a straight line." [] +relationship: BFO:0000197 GEORES:0000008 {cardinality="1"} ! inheres in channel unit + +[Term] +id: GEORES:0000028 +name: facies +def: "A pattern of properties of Geological Objects." [] +comment: This entity is defined in the literature as a combination of features that differentiates a geological object from its adjacent geological objects (Walker and James, 1992). However, a Facies does not describe a single Geological Object’s features: it might repeat in several objects as a pattern. This particular aspect matches the definition of Generically Dependent Continuant in BFO. Another important aspect is that the features that compose facies vary depending on the research context, e.g., Sedimentary Facies, Petrofacies (De Ros and Goldberg, 2007), Lithofacies, Ichnofacies, and Biofacies (Nichols, 2009). +relationship: BFO:0000084 GEORES:0000001 ! generically depends on body of rock +property_value: altLabel "fácies" xsd:string + +[Term] +id: GEORES:0000029 +name: sedimentary facies +def: "A Facies consisting of the sum of the sedimentological characteristics of Depositional Units (Middleton, 1973, Nichols, 2009, Carbonera et al., 2015)." [] +comment: As an example, if we would model Cross-bedded Sandstone (Nichols, 2009), it would be an entity subsumed by Sedimentary Facies having the following relations: (1) Generically Depends On some (Constituted By some Sandstone (a)); and (2) Has Part some Cross-bedding Structure (b). (a): Sandstone would be an entity subsumed by Sedimentary Rock. (b): Cross-bedding Structure would be an entity subsumed by Sedimentary Structure. +is_a: GEORES:0000028 ! facies +property_value: altLabel "fácies sedimentar" xsd:string + +[Term] +id: GEORES:0000030 +name: facies association +def: "A Generically Dependent Continuant that consists of an aggregate of Facies." [] +comment: It usually describes the Facies that are typically found in specific regions or sub-environments. For example, the Channel Axis Association (McHargue et al., 2011) describes Sedimentary Facies typically found at the center part of channels (in a cross-section point of view). +relationship: BFO:0000178 GEORES:0000028 {minCardinality="2"} ! has continuant part facies +property_value: altLabel "associação de facies" xsd:string + +[Term] +id: GEORES:0000031 +name: sediment +def: "An Unconsolidated Earth Material constituted by some collection of sedimentary grains or particles (Garcia et al., 2019)." [] +property_value: GEORES:0000050 "R+ I+ O- U- ED-" xsd:string + +[Term] +id: GEORES:0000032 +name: sedimentary rock +def: "'sedimentary rock' is an 'amount of rock' constituted by some collection of sedimentary grains or particles (Garcia et al., 2019)." [] +disjoint_from: GEORES:0000033 ! igneous rock +relationship: BFO:0000196 GEORES:0000024 ! bearer of lithology +property_value: altLabel "rocha sedimentar" xsd:string +property_value: GEORES:0000050 "R+ I+ O- U- ED-" xsd:string + +[Term] +id: GEORES:0000033 +name: igneous rock +relationship: BFO:0000196 GEORES:0000024 ! bearer of lithology +property_value: altLabel "rocha ígnea" xsd:string +property_value: definition "'igneous rock' is an 'amount of rock' generated by the cooling and solidification of molten 'earth material'." xsd:string +property_value: isDefinedBy "https://www.britannica.com/science/igneous-rock" xsd:string + +[Term] +id: GEORES:0000034 +name: metamorphic rock +relationship: BFO:0000196 GEORES:0000024 ! bearer of lithology +property_value: altLabel "rocha metamórfica" xsd:string +property_value: definition "'metamorphic rock' is an 'amount of rock' generated by the alteration of preexisting rocks in response to changing environmental conditions, such as variations in temperature, pressure, and mechanical stress, and the addition or subtraction of chemical components." xsd:string +property_value: isDefinedBy "Adapted from Brittanica.\nhttps://www.britannica.com/science/metamorphic-rock" xsd:string + +[Term] +id: GEORES:0000035 +name: complex architectural element +is_a: GEORES:0000001 ! body of rock +disjoint_from: GEORES:0000036 ! composite architectural element + +[Term] +id: GEORES:0000036 +name: composite architectural element +is_a: GEORES:0000001 ! body of rock + +[Term] +id: GEORES:0000037 +name: individual architectural element + +[Term] +id: GEORES:0000038 +name: channel surface +def: "A Geological Boundary that forms the basis of a Channel Unit, having a concave-up shape unless truncated by overlying depositional units." [] +property_value: GEORES:0000050 "R+ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000039 +name: basin +property_value: altLabel "bacia" xsd:string + +[Term] +id: GEORES:0000040 +name: geological site +comment: Epistemologicamente não é possível determinar os limites deste site e, portanto, cada geólogo pode posicionar sua área de interesse em uma localização e limites distintos, o que torna muito difícil tratar computacionalmente a identidade do sítio geológico. Esse problema acontece com outras entidades do tipo site: Região da Serra Gaúcha, Litoral Norte, etc, cuja delimitação é problemática, mas existe uma identidade consensual. +property_value: altLabel "sítio geológico" xsd:string + +[Term] +id: GEORES:0000041 +name: contact position +property_value: altLabel "posição do contato" xsd:string + +[Term] +id: GEORES:0000042 +name: geometry type +comment: Luan: Talvez tipo de Geometria seja uma classe de segunda ordem, mas em primeiro momento não utilizaremos punning para representar isto. A classe geometry tem uma relação de 'has geometry type' com um 'geometry type' e as instâncias dessa classe é que definem o tipo de geometria de fato. Caso seja necessário criar alguma subclasse de um 'body of rock' que tenha um 'geometry type' específico é possível utilizar a primitiva do owl value para isto.\n\nNão sabemos ainda como classificar esta classe. Do que ela seria subclasse? +property_value: altLabel "tipo de geometria" xsd:string + +[Term] +id: GEORES:0000043 +name: contact type +property_value: altLabel "tipo de contato" xsd:string + +[Typedef] +id: BFO:0000084 +name: generically depends on +property_value: altLabel "g-depends on" xsd:string +property_value: definition "b generically depends on c =Def b is a generically dependent continuant & c is an independent continuant that is not a spatial region & at some time t there inheres in c a specifically dependent continuant which concretizes b at t" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "252-BFO" xsd:string +property_value: scopeNote "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: " xsd:string +inverse_of: BFO:0000101 ! is carrier of + +[Typedef] +id: BFO:0000101 +name: is carrier of +property_value: definition "b is carrier of c =Def there is some time t such that c generically depends on b at t" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "254-BFO" xsd:string +property_value: scopeNote "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: " xsd:string + +[Typedef] +id: BFO:0000115 +name: has member part +property_value: definition "b has member part c =Def c member part of b" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "230-BFO" xsd:string +property_value: scopeNote "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: " xsd:string +is_a: BFO:0000178 ! has continuant part +inverse_of: BFO:0000129 ! member part of + +[Typedef] +id: BFO:0000129 +name: member part of +property_value: definition "b member part of c =Def b is an object & c is a material entity & there is some time t such that b continuant part of c at t & there is a mutually exhaustive and pairwise disjoint partition of c into objects x1, ..., xn (for some n ≠ 1) with b = xi (for some 1 <= i <= n)" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "228-BFO" xsd:string +property_value: scopeNote "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: " xsd:string +is_a: BFO:0000176 ! continuant part of + +[Typedef] +id: BFO:0000176 +name: continuant part of +property_value: definition "b continuant part of c =Def b and c are continuants & there is some time t such that b and c exist at t & b continuant part of c at t" xsd:string +property_value: example "Milk teeth continuant part of human; surgically removed tumour continuant part of organism" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "221-BFO" xsd:string +property_value: scopeNote "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: " xsd:string +inverse_of: BFO:0000178 ! has continuant part + +[Typedef] +id: BFO:0000178 +name: has continuant part +property_value: definition "b has continuant part c =Def c continuant part of b" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "271-BFO" xsd:string +property_value: scopeNote "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: " xsd:string + +[Typedef] +id: BFO:0000196 +name: bearer of +property_value: definition "b bearer of c =Def c inheres in b" xsd:string +property_value: example "A patch of ink is the bearer of a colour quality; an organism is the bearer of a temperature quality" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "053-BFO" xsd:string +inverse_of: BFO:0000197 ! inheres in + +[Typedef] +id: BFO:0000197 +name: inheres in +property_value: definition "b inheres in c =Def b is a specifically dependent continuant & c is an independent continuant that is not a spatial region & b specifically depends on c" xsd:string +property_value: example "A shape inheres in a shaped object; a mass inheres in a material entity" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "051-BFO" xsd:string + +[Typedef] +id: GEOCORE:0000017 +name: constituted by +def: "The relation between some material entity and the material that it is made of." [] +property_value: IAO:0000116 "This is a material constitution relation intended to represent the relationship between material objects, such as geological objects and earth materials, or aggregates of them." xsd:string +property_value: IAO:0000119 "Evnine, S. J. (2011). Constitution and composition: Three approaches to their relation. ProtoSociology, 27, 212-235." xsd:string +is_asymmetric: true + +[Typedef] +id: GEORES:0000044 +name: has contact position +domain: GEORES:0000026 ! bed contact +range: GEORES:0000041 ! contact position + +[Typedef] +id: GEORES:0000045 +name: has contact type +domain: GEORES:0000026 ! bed contact +range: GEORES:0000043 ! contact type + +[Typedef] +id: GEORES:0000046 +name: has geometry type +comment: Luan: Geometry Type talvez seja uma classe de segunda ordem cuja as instâncias são os diferentes tipos de Geometria. Por exemplo, é errado dizer que Geometria Lenticular é subtipo da Quality Geometria. Lenticular é na realidade um subtipo de Tipo de Geometria e não de Geometria. +domain: GEORES:0000023 ! geometry +range: GEORES:0000042 ! geometry type + +[Typedef] +id: GEORES:0000047 +name: has base geometry +is_a: GEORES:0000046 ! has geometry type + +[Typedef] +id: GEORES:0000048 +name: has top geometry +is_a: GEORES:0000046 ! has geometry type + diff --git a/geores-simple.owl b/geores-simple.owl new file mode 100644 index 0000000..2af9248 --- /dev/null +++ b/geores-simple.owl @@ -0,0 +1,1268 @@ + + + + + Alcides Lopes + Fabrício Henrique Rodrigues + Fernando Cicconeto + Joel Luis Carbonera + Luan Fonseca Garcia + Lucas Valadares Vieira + Mara Abel + Renata dos Santos Alvarenga + Tiago Agne de Oliveira + Yuanwei Qu + GeoReservoir is an ontology to support the description of the geometry and the lithology of deep-marine deposits. The GeoReservoir ontology provides formal and clear definitions of deep-marine depositional system entities, creating an unambiguous terminology for geometrical and lithological properties of the deposits in the scale of outcrop and seismic sections. These definitions are independent of tasks, geological interpretations, and process inferences. We created this language to make it possible to formally and uniformly describe any deep-marine occurrence in the world with an adequate level of detail for sedimentological studies and computer processing. + https://creativecommons.org/licenses/by-nc/4.0/ + GeoReservoir Ontology + Cited references: + +1. Abel, M., Perrin, M., Carbonera, J.L.: Ontological analysis for information integration in geomodeling. Earth Science Informatics 8, 21–36 (2015) +2. Carbonera, J.L., Abel, M., Scherer, C.M.S.: Visual interpretation of events in petroleum exploration: An approach supported by well-founded ontologies. Expert Systems With Applications 42, 2749–2763 (2015) +3. Cullis, S., Colombera, L., Patacci, M., McCaffrey, W.D.: Hierarchical classifications of the sedimentary architecture of deep-marine depositional systems. Earth-Science Reviews 179, 38–71 (2018) +4. De Ros, L.F., Goldberg, K.: Reservoir petrofacies: A tool for quality characterization and prediction. In: AAPG Annual Conference and Exhibition. Long Beach (2007) +5. Garcia, L.F., Carbonera, J.L., Rodrigues, F.H., Antunes, C.R., Abel, M.: What rocks are made of: Towards an ontological pattern for material constitution in the geological domain. In: Laender, A.H.F., Pernici, B., Lim, E.P., Oliveira, J.P.M. (eds.) ER: 38th International Conference on Conceptual Modeling. pp. 275–286. Springer, Cham (2019) +6. Guarino, N., Welty, C.A.: An overview of ontoclean. In: Staab, S., Studer, R. (eds.) Handbook on Ontologies, pp. 151–171. Springer, Berlin, Heidelberg (2004) +7. McHargue, T., Pyrcz, M.J., Sullivan, M.D., Clark, J.D., Fildani, A., Romans, B.W., Covault, J.A., Levy, M., Posamentier, H.W., Drinkwater, N.J.: Architecture of turbidite channel systems on the continental slope: Patterns and predictions. Marine and Petroleum Geology 28, 728–743 (2011) +8. Middleton, G.V.: Johannes walther’s law of the correlation of facies. Bulletin of the Geological Society of America 84, 979–988 (1973) +9. Nichols, G.: Sedimentology and Stratigraphy. Wiley-Blackwell, Chichester, 2nd edn. (2009) +10. Rovetto, R.: The shape of shapes: An ontological exploration. In: Hastings, J., Kutz, O., Bhatt, M., Borgo, S. (eds.) Proceedings of the First Interdisciplinary Workshop on SHAPES. Karlsruhe (2011), http://ceur-ws.org/Vol-812/ +11. Walker, R.G., James, N.P.: Facies Models: Response to Sea Level Change. Geological Association of Canada, St. John’s (1992) + We acknowledge the Brazilian funding agencies CNPq and CAPES for financing this work and the Research Centre of Petrobras (CENPES) for collaborating on this project. + 2024-04-07 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + For metaproperties, we use the following notation (Guarino and Welty, 2004; Abel et al., 2015): + +– R+ / R- / R~: rigid / not rigid / anti-rigid; +– I+ / I-: carries / does not carry identity; +– O+ / O-: provides / does not provide identity; +– U+ / U-: carries / does not carry unity; +– ED+ / ED-: existentially dependent / independent. + metaproperties + + + + + + + + + + + + + + 252-BFO + generically depends on + g-depends on + b generically depends on c =Def b is a generically dependent continuant & c is an independent continuant that is not a spatial region & at some time t there inheres in c a specifically dependent continuant which concretizes b at t + Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link> + + + + + + + + 254-BFO + is carrier of + b is carrier of c =Def there is some time t such that c generically depends on b at t + Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link> + + + + + + + + + + 230-BFO + has member part + b has member part c =Def c member part of b + Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link> + + + + + + + + + 228-BFO + member part of + b member part of c =Def b is an object & c is a material entity & there is some time t such that b continuant part of c at t & there is a mutually exhaustive and pairwise disjoint partition of c into objects x1, ..., xn (for some n ≠ 1) with b = xi (for some 1 <= i <= n) + Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link> + + + + + + + + + 221-BFO + continuant part of + b continuant part of c =Def b and c are continuants & there is some time t such that b and c exist at t & b continuant part of c at t + Milk teeth continuant part of human; surgically removed tumour continuant part of organism + Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link> + + + + + + + + 271-BFO + has continuant part + b has continuant part c =Def c continuant part of b + Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link> + + + + + + + + + 053-BFO + bearer of + b bearer of c =Def c inheres in b + A patch of ink is the bearer of a colour quality; an organism is the bearer of a temperature quality + + + + + + + + 051-BFO + inheres in + b inheres in c =Def b is a specifically dependent continuant & c is an independent continuant that is not a spatial region & b specifically depends on c + A shape inheres in a shaped object; a mass inheres in a material entity + + + + + + + + + + The relation between some material entity and the material that it is made of. + This is a material constitution relation intended to represent the relationship between material objects, such as geological objects and earth materials, or aggregates of them. + Evnine, S. J. (2011). Constitution and composition: Three approaches to their relation. ProtoSociology, 27, 212-235. + constituted by + + + + + + + + + + has contact position + + + + + + + + + + has contact type + + + + + + + + + + Luan: Geometry Type talvez seja uma classe de segunda ordem cuja as instâncias são os diferentes tipos de Geometria. Por exemplo, é errado dizer que Geometria Lenticular é subtipo da Quality Geometria. Lenticular é na realidade um subtipo de Tipo de Geometria e não de Geometria. + has geometry type + + + + + + + + + has base geometry + + + + + + + + + has top geometry + + + + + + + + + + + + + A relation between a Quality and its values. + O objetivo desta data property é conectar em níveL de implementação uma qualidade com o valor em seu espaço de qualiades. Por exemplo, a qualidade dimensão tem um espaço de qualidade que é um valor real positivo para sua largura. + +A IAO possui uma propriedade has measurement datum cujo domínio é um measurement datum. Porém, o problema de usar tal propriedade é acrescentar a necessidade de criar uma instância de measurement datum. + has value + + + + + + + + + + has dimension value + + + + + + + + + + has lenght value + + + + + + + + + A relation between a Quality and a literal string that represents its measurement unit. + has measurement unit + + + + + + + + + + has thickness value + + + + + + + + + + has width value + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + body of rock + corpo de rocha + 'body of rock' is a 'geological object' that is 'constituted by' some 'amount of rock' + + + + + + + + + Os diferentes elementos arquiteturais ocorrem dentro de uma unidade com uma idade definida que é a unidade estratigráfica. + +Ainda não sabemos se poderia ser uma unidade litoestratigráfica. + stratigraphic unit + unidade estratigráfica + + + + + + + + + lithostratigraphic unit + unidade litoestratigráfica + + + + + + + + + + + + + + + formation + formação + + + + + + + + + + + + + + + member + membro + + + + + + + + + + + + + + + A restrição de partes de escala menores ainda não foi implementada. + Luan: Elementos arquiteturais são os objetos básicos que os geólogos vão reconhecer e descrever. Eles podem ocorrer em diversas escalas. +Um elemento pode ter outro elemento como parte, desde que de uma escala menor. + architectural element + elemento arquitetural + + + + + + + + + build up unit + edifício + + + + + + + + + An elongated Depositional Unit having some Channel Surface as its boundary and constituted by some Sediment or Sedimentary Rock that fills it (McHargue et al., 2011). + In stratigraphic terms, a channel unit is constituted by the sediments or sedimentary rocks that fill a channel. It is important to notice that, in more general terms, a channel is a passageway for fluids or sediments, i.e., an immaterial entity. If one elaborates about the erosion and deposition processes that generate these units (McHargue et al., 2011), it is essential to have this disambiguation. + In this work, we decided not to model the named hierarchical scales as entities (e.g., Channel Element, Channel Complex, Channel Complex Set - McHargue et al., 2011) because there exists a wide variety of hierarchical schemes in the literature, and they are not necessarily interoperable (Cullis et al., 2018). Instead, we focus on the fact that units can be fractally nested: a unit can be a Proper Spatial Part Of another unit, which can be a Proper Spatial Part Of another unit, and so forth. We consider that this approach solves the problem of implementing a solution for the repeatability of the geological objects in multiple scales. As so, a Channel Unit can be decomposed in other Channel Units many times as necessary, keeping the representation structure. In the future, we can study the integration of hierarchical schemes and try to infer scales from the spatial relations. + channel unit + canal + R+ I+ O- U+ ED- + + + + + + + + + dome unit + domo + + + + + + + + + dune unit + duna + + + + + + + + + intrusive dike + dique intrusivo + + + + + + + + + intrusive sill unit + soleira intrusiva + + + + + + + + + A Depositional Unit having Wedge Geometry and forming a bank or ridge geomorphology associated with some Channel Unit. + This term is not consensual as some authors refer to these units as the wedge-shape embankments around channels, which is the definition that we adopt here, while other authors refer to them as not necessarily being these embankments and possibly having wing shapes, among other definitions. + This term refers to the geomorphological association of some wegde-shaped unit with some channel unit, even if the channel does not exist at the moment of the observation by the geologist and the levee is probabilistically identified by tendencies (e.g., typical facies). In other words, the term "levee" ontologicallly denotes this relation even though it cannot be deterministically observed. + levee unit + dique + R~ I+ O- U+ ED- + + + + + + + + + A Depositional Unit having some Lobe Geometry. + For Lobe Unit hierarchical scales, we adopted the same approach as in Channel Unit. + These depositional units are usually found at deep-water depositional system terminal regions, or at channel laterals as Overbank Units. + lobe unit + lobo + R+ I+ O- U+ ED- + + + + + + + + + A Depositional Unit having Mound Geometry with an irregular top surface and internal chaotic facies. + mound unit + monte + R+ I+ O- U+ ED- + + + + + + + + + megaclast + megaclasto + olistrostomes unit + olistrostomas + + + + + + + + + sheet unit + lençol + + + + + + + + + + + + + + fossil + fóssil + + + + + + + + + + + + + + group + grupo + + + + + + + + An Object Aggregate whose members are mereotopologically-linked Depositional Units. + depositional system + sistema deposicional + R+ I+ O+ U+ ED- + + + + + + + + The sedimentary environment is the specific depositional setting of a particular sedimentary rock and is unique in terms of physical, chemical, and biological characteristics. + Britannica +https://www.britannica.com/science/sedimentary-rock/Sedimentary-environments + sedimentary environment + ambiente de sedimentação + + + + + + + + A Quality that inheres in an Independent Continuant by virtue of one of its one-dimensional extents. It is a category that includes at least the three dimensions defined in this ontology: Width, Length, and Thickness. All dimensions are expressed by a real number indicating its value and a literal string indicating its measurement unit. + dimension + + + + + + + + + + + 1 + + + + A Quality that inheres in a Depositional Unit by virtue of its external three-dimensional shape. It does not reflect the exact mathematical specifications of a geometric shape but abstracts and simplifies these specifications (Rovetto, 2011). + geometry + geometria + + + + + + + + lithology + litologia + + + + + + + + statigraphic contact + contato estratigráfico + + + + + + + + + + + 1 + + + + + + + 1 + + + + bed contact + contato de camada + + + + + + + + + + + 1 + + + + A Quality that inheres in a Channel Unit by virtue of how wavy it is across its length. It is expressed by a real number given by its curved length divided by its length in a straight line. + sinuosity + + + + + + + + + + + + + + A pattern of properties of Geological Objects. + This entity is defined in the literature as a combination of features that differentiates a geological object from its adjacent geological objects (Walker and James, 1992). However, a Facies does not describe a single Geological Object’s features: it might repeat in several objects as a pattern. This particular aspect matches the definition of Generically Dependent Continuant in BFO. Another important aspect is that the features that compose facies vary depending on the research context, e.g., Sedimentary Facies, Petrofacies (De Ros and Goldberg, 2007), Lithofacies, Ichnofacies, and Biofacies (Nichols, 2009). + facies + fácies + + + + + + + + + A Facies consisting of the sum of the sedimentological characteristics of Depositional Units (Middleton, 1973, Nichols, 2009, Carbonera et al., 2015). + As an example, if we would model Cross-bedded Sandstone (Nichols, 2009), it would be an entity subsumed by Sedimentary Facies having the following relations: (1) Generically Depends On some (Constituted By some Sandstone (a)); and (2) Has Part some Cross-bedding Structure (b). (a): Sandstone would be an entity subsumed by Sedimentary Rock. (b): Cross-bedding Structure would be an entity subsumed by Sedimentary Structure. + sedimentary facies + fácies sedimentar + + + + + + + + + + + 2 + + + + A Generically Dependent Continuant that consists of an aggregate of Facies. + It usually describes the Facies that are typically found in specific regions or sub-environments. For example, the Channel Axis Association (McHargue et al., 2011) describes Sedimentary Facies typically found at the center part of channels (in a cross-section point of view). + facies association + associação de facies + + + + + + + + An Unconsolidated Earth Material constituted by some collection of sedimentary grains or particles (Garcia et al., 2019). + sediment + R+ I+ O- U- ED- + + + + + + + + + + + + + + 'sedimentary rock' is an 'amount of rock' constituted by some collection of sedimentary grains or particles (Garcia et al., 2019). + sedimentary rock + rocha sedimentar + R+ I+ O- U- ED- + + + + + + + + + + + + + + https://www.britannica.com/science/igneous-rock + igneous rock + rocha ígnea + 'igneous rock' is an 'amount of rock' generated by the cooling and solidification of molten 'earth material'. + + + + + + + + + + + + + + Adapted from Brittanica. +https://www.britannica.com/science/metamorphic-rock + metamorphic rock + rocha metamórfica + 'metamorphic rock' is an 'amount of rock' generated by the alteration of preexisting rocks in response to changing environmental conditions, such as variations in temperature, pressure, and mechanical stress, and the addition or subtraction of chemical components. + + + + + + + + + + + + + + + + + + + + + + + + + + + complex architectural element + + + + + + + + + + + + + + + + + + + + composite architectural element + + + + + + + + + + + + + + + + + + + + + + + individual architectural element + + + + + + + + A Geological Boundary that forms the basis of a Channel Unit, having a concave-up shape unless truncated by overlying depositional units. + channel surface + R+ I+ O- U+ ED- + + + + + + + + basin + bacia + + + + + + + + Epistemologicamente não é possível determinar os limites deste site e, portanto, cada geólogo pode posicionar sua área de interesse em uma localização e limites distintos, o que torna muito difícil tratar computacionalmente a identidade do sítio geológico. Esse problema acontece com outras entidades do tipo site: Região da Serra Gaúcha, Litoral Norte, etc, cuja delimitação é problemática, mas existe uma identidade consensual. + geological site + sítio geológico + + + + + + + + contact position + posição do contato + + + + + + + + Luan: Talvez tipo de Geometria seja uma classe de segunda ordem, mas em primeiro momento não utilizaremos punning para representar isto. A classe geometry tem uma relação de 'has geometry type' com um 'geometry type' e as instâncias dessa classe é que definem o tipo de geometria de fato. Caso seja necessário criar alguma subclasse de um 'body of rock' que tenha um 'geometry type' específico é possível utilizar a primitiva do owl value para isto. + +Não sabemos ainda como classificar esta classe. Do que ela seria subclasse? + geometry type + tipo de geometria + + + + + + + + contact type + tipo de contato + + + + + + + + + + + + + + amalgamated contact + contato amalgamado + + + + + + + + + base position contact + contato de base + + + + + + + + + cryptic/covered contact + contato críptico/encoberto + + + + + + + + + conformable contact + contato concordante + + + + + + + + + erosive contact + contato erosivo + + + + + + + + + faulted contact + contato de falha + + + + + + + + + gradational contact + contato gradacional + + + + + + + + + intrusive contact + contato intrusivo + + + + + + + + + sharp contact + contato abrupto + + + + + + + + + irregular geometry + geometria irregular + + + + + + + + + lenticular convex top flatbed geometry + geometria lenticular topo convexo base plana + + + + + + + + + lenticular concave convex geometry + geometria lenticular côncavo convexa + + + + + + + + + lateral position contact + contato lateral + + + + + + + + + lenticular flattop concave base geometry + geometria lenticular topo plano base convexa + + + + + + + + + sheet geometry + geometria lençoidal + + + + + + + + + sigmoidal geometry + geometria sigmoidal + + + + + + + + + tabular geometry + geometria tabular + + + + + + + + + top position contact + contato de topo + + + + + + + + + wedge shape geometry + geometria de cunha + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/geores.obo b/geores.obo new file mode 100644 index 0000000..a582b76 --- /dev/null +++ b/geores.obo @@ -0,0 +1,781 @@ +format-version: 1.2 +data-version: https://www.inf.ufrgs.br/bdi/ontologies/geores/releases/2024-04-07/geores.owl +remark: Cited references:\n\n1. Abel, M., Perrin, M., Carbonera, J.L.: Ontological analysis for information integration in geomodeling. Earth Science Informatics 8, 21–36 (2015)\n2. Carbonera, J.L., Abel, M., Scherer, C.M.S.: Visual interpretation of events in petroleum exploration: An approach supported by well-founded ontologies. Expert Systems With Applications 42, 2749–2763 (2015)\n3. Cullis, S., Colombera, L., Patacci, M., McCaffrey, W.D.: Hierarchical classifications of the sedimentary architecture of deep-marine depositional systems. Earth-Science Reviews 179, 38–71 (2018)\n4. De Ros, L.F., Goldberg, K.: Reservoir petrofacies: A tool for quality characterization and prediction. In: AAPG Annual Conference and Exhibition. Long Beach (2007)\n5. Garcia, L.F., Carbonera, J.L., Rodrigues, F.H., Antunes, C.R., Abel, M.: What rocks are made of: Towards an ontological pattern for material constitution in the geological domain. In: Laender, A.H.F., Pernici, B., Lim, E.P., Oliveira, J.P.M. (eds.) ER: 38th International Conference on Conceptual Modeling. pp. 275–286. Springer, Cham (2019)\n6. Guarino, N., Welty, C.A.: An overview of ontoclean. In: Staab, S., Studer, R. (eds.) Handbook on Ontologies, pp. 151–171. Springer, Berlin, Heidelberg (2004)\n7. McHargue, T., Pyrcz, M.J., Sullivan, M.D., Clark, J.D., Fildani, A., Romans, B.W., Covault, J.A., Levy, M., Posamentier, H.W., Drinkwater, N.J.: Architecture of turbidite channel systems on the continental slope: Patterns and predictions. Marine and Petroleum Geology 28, 728–743 (2011)\n8. Middleton, G.V.: Johannes walther’s law of the correlation of facies. Bulletin of the Geological Society of America 84, 979–988 (1973)\n9. Nichols, G.: Sedimentology and Stratigraphy. Wiley-Blackwell, Chichester, 2nd edn. (2009)\n10. Rovetto, R.: The shape of shapes: An ontological exploration. In: Hastings, J., Kutz, O., Bhatt, M., Borgo, S. (eds.) Proceedings of the First Interdisciplinary Workshop on SHAPES. Karlsruhe (2011), http://ceur-ws.org/Vol-812/\n11. Walker, R.G., James, N.P.: Facies Models: Response to Sea Level Change. Geological Association of Canada, St. John’s (1992) +remark: We acknowledge the Brazilian funding agencies CNPq and CAPES for financing this work and the Research Centre of Petrobras (CENPES) for collaborating on this project. +ontology: https://www.inf.ufrgs.br/bdi/ontologies/geores.owl +property_value: http://purl.org/dc/elements/1.1/contributor "Alcides Lopes" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Fabrício Henrique Rodrigues" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Fernando Cicconeto" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Joel Luis Carbonera" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Luan Fonseca Garcia" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Lucas Valadares Vieira" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Mara Abel" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Renata dos Santos Alvarenga" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Tiago Agne de Oliveira" xsd:string +property_value: http://purl.org/dc/elements/1.1/contributor "Yuanwei Qu" xsd:string +property_value: http://purl.org/dc/terms/description "GeoReservoir is an ontology to support the description of the geometry and the lithology of deep-marine deposits. The GeoReservoir ontology provides formal and clear definitions of deep-marine depositional system entities, creating an unambiguous terminology for geometrical and lithological properties of the deposits in the scale of outcrop and seismic sections. These definitions are independent of tasks, geological interpretations, and process inferences. We created this language to make it possible to formally and uniformly describe any deep-marine occurrence in the world with an adequate level of detail for sedimentological studies and computer processing." xsd:string +property_value: http://purl.org/dc/terms/license "https://creativecommons.org/licenses/by-nc/4.0/" xsd:string +property_value: http://purl.org/dc/terms/title "GeoReservoir Ontology" xsd:string +property_value: owl:versionInfo "2024-04-07" xsd:string + +[Term] +id: BFO:0000001 +name: entity +property_value: definition "(Elucidation) An entity is anything that exists or has existed or will exist" xsd:string +property_value: example "Julius Caesar; the Second World War; your body mass index; Verdi's Requiem" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "001-BFO" xsd:string + +[Term] +id: BFO:0000002 +name: continuant +is_a: BFO:0000001 ! entity +disjoint_from: BFO:0000003 ! occurrent +relationship: BFO:0000176 BFO:0000002 {all_only="true"} ! continuant part of continuant +property_value: definition "(Elucidation) A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity" xsd:string +property_value: example "A human being; a tennis ball; a cave; a region of space; someone's temperature" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "008-BFO" xsd:string + +[Term] +id: BFO:0000003 +name: occurrent +is_a: BFO:0000001 ! entity +property_value: definition "(Elucidation) An occurrent is an entity that unfolds itself in time or it is the start or end of such an entity or it is a temporal or spatiotemporal region" xsd:string +property_value: example "As for process, history, process boundary, spatiotemporal region, zero-dimensional temporal region, one-dimensional temporal region, temporal interval, temporal instant." xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "077-BFO" xsd:string + +[Term] +id: BFO:0000004 +name: independent continuant +is_a: BFO:0000002 ! continuant +disjoint_from: BFO:0000020 ! specifically dependent continuant +relationship: BFO:0000176 BFO:0000004 {all_only="true"} ! continuant part of independent continuant +property_value: definition "b is an independent continuant =Def b is a continuant & there is no c such that b specifically depends on c or b generically depends on c" xsd:string +property_value: example "An atom; a molecule; an organism; a heart; a chair; the bottom right portion of a human torso; a leg; the interior of your mouth; a spatial region; an orchestra" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "017-BFO" xsd:string + +[Term] +id: BFO:0000006 +name: spatial region +is_a: BFO:0000141 ! immaterial entity +disjoint_from: BFO:0000029 ! site +relationship: BFO:0000176 BFO:0000006 {all_only="true"} ! continuant part of spatial region +property_value: definition "(Elucidation) A spatial region is a continuant entity that is a continuant part of the spatial projection of a portion of spacetime at a given time" xsd:string +property_value: example "As for zero-dimensional spatial region, one-dimensional spatial region, two-dimensional spatial region, three-dimensional spatial region" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "035-BFO" xsd:string + +[Term] +id: BFO:0000008 +name: temporal region +is_a: BFO:0000003 ! occurrent +disjoint_from: BFO:0000011 ! spatiotemporal region +property_value: definition "(Elucidation) A temporal region is an occurrent over which processes can unfold" xsd:string +property_value: example "As for zero-dimensional temporal region and one-dimensional temporal region" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "100-BFO" xsd:string + +[Term] +id: BFO:0000011 +name: spatiotemporal region +is_a: BFO:0000003 ! occurrent +property_value: definition "(Elucidation) A spatiotemporal region is an occurrent that is an occurrent part of spacetime" xsd:string +property_value: example "The spatiotemporal region occupied by the development of a cancer tumour; the spatiotemporal region occupied by an orbiting satellite" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "095-BFO" xsd:string +property_value: scopeNote "'Spacetime' here refers to the maximal instance of the universal spatiotemporal region." xsd:string + +[Term] +id: BFO:0000015 +name: process +is_a: BFO:0000003 ! occurrent +property_value: altLabel "event" xsd:string +property_value: definition "(Elucidation) p is a process means p is an occurrent that has some temporal proper part and for some time t, p has some material entity as participant" xsd:string +property_value: example "An act of selling; the life of an organism; a process of sleeping; a process of cell-division; a beating of the heart; a process of meiosis; the taxiing of an aircraft; the programming of a computer" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "083-BFO" xsd:string + +[Term] +id: BFO:0000019 +name: quality +is_a: BFO:0000020 ! specifically dependent continuant +property_value: definition "(Elucidation) A quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized" xsd:string +property_value: example "The colour of a tomato; the ambient temperature of this portion of air; the length of the circumference of your waist; the shape of your nose; the shape of your nostril; the mass of this piece of gold" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "055-BFO" xsd:string + +[Term] +id: BFO:0000020 +name: specifically dependent continuant +is_a: BFO:0000002 ! continuant +property_value: definition "b is a specifically dependent continuant =Def b is a continuant & there is some independent continuant c which is not a spatial region & which is such that b specifically depends on c" xsd:string +property_value: example "(with multiple bearers) John's love for Mary; the ownership relation between John and this statue; the relation of authority between John and his subordinates" xsd:string +property_value: example "(with one bearer) The mass of this tomato; the pink colour of a medium rare piece of grilled filet mignon at its centre; the smell of this portion of mozzarella; the disposition of this fish to decay; the role of being a doctor; the function of this heart to pump blood; the shape of this hole" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "050-BFO" xsd:string + +[Term] +id: BFO:0000027 +name: object aggregate +is_a: BFO:0000040 ! material entity +property_value: definition "(Elucidation) An object aggregate is a material entity consisting exactly of a plurality (≥1) of objects as member parts which together form a unit" xsd:string +property_value: example "The aggregate of the musicians in a symphony orchestra and their instruments; the aggregate of bearings in a constant velocity axle joint; the nitrogen atoms in the atmosphere; a collection of cells in a blood biobank" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "025-BFO" xsd:string +property_value: scopeNote "'Exactly' means that there are no parts of the object aggregate other than its member parts." xsd:string +property_value: scopeNote "The unit can, at certain times, consist of exactly one object, for example, when a wolf litter loses all but one of its pups, but it must at some time have a plurality of member parts." xsd:string + +[Term] +id: BFO:0000029 +name: site +is_a: BFO:0000141 ! immaterial entity +property_value: definition "(Elucidation) A site is a three-dimensional immaterial entity whose boundaries either (partially or wholly) coincide with the boundaries of one or more material entities or have locations determined in relation to some material entity" xsd:string +property_value: example "A hole in a portion of cheese; a rabbit hole; the Grand Canyon; the Piazza San Marco; the kangaroo-joey-containing hole of a kangaroo pouch; your left nostril (a fiat part - the opening - of your left nasal cavity); the lumen of your gut; the hold of a ship; the interior of the trunk of your car; hole in an engineered floor joist" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "034-BFO" xsd:string + +[Term] +id: BFO:0000030 +name: object +is_a: BFO:0000040 ! material entity +property_value: definition "(Elucidation) An object is a material entity which manifests causal unity & is of a type instances of which are maximal relative to the sort of causal unity manifested" xsd:string +property_value: example "An organism; a fish tank; a planet; a laptop; a valve; a block of marble; an ice cube" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "024-BFO" xsd:string +property_value: scopeNote "A description of three primary sorts of causal unity is provided in Basic Formal Ontology 2.0. Specification and User Guide" xsd:string + +[Term] +id: BFO:0000031 +name: generically dependent continuant +is_a: BFO:0000002 ! continuant +property_value: altLabel "g-dependent continuant" xsd:string +property_value: definition "(Elucidation) A generically dependent continuant is an entity that exists in virtue of the fact that there is at least one of what may be multiple copies which is the content or the pattern that multiple copies would share" xsd:string +property_value: example "The pdf file on your laptop; the pdf file that is a copy thereof on my laptop; the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule; the content that is shared by a string of dots and dashes written on a page and the transmitted Morse code signal; the content of a sentence; an engineering blueprint" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "074-BFO" xsd:string + +[Term] +id: BFO:0000035 +name: process boundary +is_a: BFO:0000003 ! occurrent +property_value: definition "p is a process boundary =Def p is a temporal part of a process & p has no proper temporal parts" xsd:string +property_value: example "The boundary between the 2nd and 3rd year of your life" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "084-BFO" xsd:string + +[Term] +id: BFO:0000038 +name: one-dimensional temporal region +is_a: BFO:0000008 ! temporal region +property_value: definition "(Elucidation) A one-dimensional temporal region is a temporal region that is a whole that has a temporal interval and zero or more temporal intervals and temporal instants as parts" xsd:string +property_value: example "The temporal region during which a process occurs" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "103-BFO" xsd:string + +[Term] +id: BFO:0000040 +name: material entity +is_a: BFO:0000004 ! independent continuant +disjoint_from: BFO:0000141 ! immaterial entity +relationship: BFO:0000176 BFO:0000040 {all_only="true"} ! continuant part of material entity +property_value: definition "(Elucidation) A material entity is an independent continuant has some portion of matter as continuant part" xsd:string +property_value: example "A human being; the undetached arm of a human being; an aggregate of human beings" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "019-BFO" xsd:string + +[Term] +id: BFO:0000140 +name: continuant fiat boundary +is_a: BFO:0000141 ! immaterial entity +relationship: BFO:0000178 BFO:0000140 {all_only="true"} ! has continuant part continuant fiat boundary +property_value: definition "(Elucidation) A continuant fiat boundary b is an immaterial entity that is of zero, one or two dimensions & such that there is no time t when b has a spatial region as continuant part & whose location is determined in relation to some material entity" xsd:string +property_value: example "As for fiat point, fiat line, fiat surface" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "029-BFO" xsd:string + +[Term] +id: BFO:0000141 +name: immaterial entity +is_a: BFO:0000004 ! independent continuant +property_value: definition "b is an immaterial entity =Def b is an independent continuant which is such that there is no time t when it has a material entity as continuant part" xsd:string +property_value: example "As for fiat point, fiat line, fiat surface, site" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "028-BFO" xsd:string + +[Term] +id: BFO:0000145 +name: relational quality +is_a: BFO:0000019 ! quality +property_value: definition "b is a relational quality =Def b is a quality & there exists c and d such that c and d are not identical & b specifically depends on c & b specifically depends on d" xsd:string +property_value: example "A marriage bond; an instance of love; an obligation between one person and another" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "057-BFO" xsd:string + +[Term] +id: BFO:0000146 +name: fiat surface +is_a: BFO:0000140 ! continuant fiat boundary +property_value: definition "(Elucidation) A fiat surface is a two-dimensional continuant fiat boundary that is self-connected" xsd:string +property_value: example "The surface of the Earth; the plane separating the smoking from the non-smoking zone in a restaurant" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "033-BFO" xsd:string + +[Term] +id: GEOCORE:0000001 +name: geological object +def: "An object that is 'generated by' some 'geological process' and has at least one part 'constituted by' some 'earth material' that is not an 'earth fluid'." [] +is_a: BFO:0000030 ! object +disjoint_from: GEOCORE:0000006 ! earth material +relationship: BFO:0000196 GEORES:0000022 ! bearer of dimension +relationship: GEOCORE:0000015 GEOCORE:0000003 ! has age geological age +property_value: altLabel "objeto geológico" xsd:string +property_value: IAO:0000116 "A geological object is a naturally occurring entity because a geological process\ngenerates it, and some earth material constitutes it. Thus, we can differentiate geological objects from artificial objects, such as a well-core, because even though some earth material constitutes artificial objects, they are human-made rather than generated by some geological process. Furthermore, Geological Objects are specializations of BFO Objects, meaning they must necessarily have some unity criteria. The unity is what differentiates geological objects from Earth Materials." xsd:string + +[Term] +id: GEOCORE:0000002 +name: geological process +def: "It is a physical, or chemical, or biological, naturally occurring process that occurs on the Earth’s surface or subsurface and occupies some 'geological time interval'" [] +is_a: BFO:0000015 ! process +relationship: BFO:0000199 GEOCORE:0000005 ! occupies temporal region geological time interval +property_value: altLabel "processo geológico" xsd:string +property_value: IAO:0000112 "Examples are the process of deposition, the process of folding, a tectonic process, a sedimentary process." xsd:string +property_value: IAO:0000116 "Geological processes are macro processes that generate, transform, deform, transport, or destroy geological objects and earth materials. These processes are not necessarily atomic and may have other geological processes as parts." xsd:string + +[Term] +id: GEOCORE:0000003 +name: geological age +def: "It is a quality that 'inheres in' a 'geological object' or 'earth material' that corresponds to the 'geological time interval' in which the 'geological process' that it was 'generated by' occupied." [] +is_a: BFO:0000019 ! quality +property_value: altLabel "idade geológica" xsd:string + +[Term] +id: GEOCORE:0000004 +name: geological structure +def: "It is a 'generically dependent continuant' that is the pattern of a non-atomic 'geological object''s internal arrangement." [] +is_a: BFO:0000031 ! generically dependent continuant +relationship: BFO:0000084 GEOCORE:0000001 ! generically depends on geological object +property_value: altLabel "estrutura geológica" xsd:string +property_value: IAO:0000116 "Geological structures are general material patterns repeated in many geological\nobjects. The pattern comprises the material configuration and the mutual relationships of the object’s different parts. Structures result from one or a series of geological processes that generated or transformed the geological object they generically depend on. Thus, there is some historical dependence relation between the structure and this geological process, but what concretizes the structure is some complex quality inhering in the object, not the process." xsd:string + +[Term] +id: GEOCORE:0000005 +name: geological time interval +def: "It is a BFO temporal interval that corresponds to a time interval within the Geological Time Scale." [] +is_a: BFO:0000038 ! one-dimensional temporal region +property_value: altLabel "intervalo de tempo geológico" xsd:string + +[Term] +id: GEOCORE:0000006 +name: earth material +def: "It is a natural amount of matter 'generated by' some 'geological process'." [] +is_a: BFO:0000040 ! material entity +relationship: GEOCORE:0000015 GEOCORE:0000003 ! has age geological age +property_value: altLabel "material geologico" xsd:string +property_value: IAO:0000112 "Examples are an amount of sandstone, an amount of petroleum, an amount of\nnatural gas." xsd:string +property_value: IAO:0000116 "Earth Materials are natural amounts of matter. Thus, they come into existence by nature, without any artificial aid. Since they are amounts, they don’t hold unity criteria, but they are ontologically rigid and provide an identity criteria. Earth Materials and BFO Objects are disjoint. They are either solid, fluid, or unconsolidated. We usually observe earth materials when constituting other objects, such as an amount of rock constituting a geological unity or an amount of sand constituting a dune." xsd:string + +[Term] +id: GEOCORE:0000007 +name: amount of mineral +def: "An amount of rock is an 'earth material' that is a naturally occuring, inorganic, solid, homogeneous chemical compound with a crystalline structure." [] +is_a: GEOCORE:0000006 ! earth material +disjoint_from: GEOCORE:0000008 ! amount of rock +disjoint_from: GEOCORE:0000008 ! amount of rock +property_value: altLabel "quantidade de mineral" xsd:string +property_value: IAO:0000112 "The amount of quarts that constitutes some grain, the amount of feldspar that is part of an amount of rock." xsd:string +property_value: IAO:0000116 "Amounts of mineral lack a unity criteria as every other 'earth material'. We usually observe them when they are constitution objects such as crystals or grains." xsd:string + +[Term] +id: GEOCORE:0000008 +name: amount of rock +def: "An amount of rock is a solid consolidated 'earth material' that is 'constituted by' an aggregate of particles made of mineral matter or material of biological origin." [] +is_a: GEOCORE:0000006 ! earth material +disjoint_from: GEOCORE:0000009 ! earth fluid +relationship: BFO:0000196 GEORES:0000024 ! bearer of lithology +property_value: altLabel "quantidade de rocha" xsd:string +property_value: IAO:0000112 "The amount of sandstone that constitutes a lithostratigraphic unit." xsd:string +property_value: IAO:0000116 "Geologists define rocks at a scale of observation where they consider them homogeneous, even though an aggregate of solid particles constitutes it. These particles are usually geological objects, such as grains or crystals, or the rest of dead animals or plants. \n\nAmounts of rock, like other earth materials, are independent rigid entities that do not hold any unity criteria. We can observe them in nature when they are constituting objects such as geological unities." xsd:string + +[Term] +id: GEOCORE:0000009 +name: earth fluid +def: "Earth fluid is an 'earth material' that is fluild." [] +is_a: GEOCORE:0000006 ! earth material +property_value: altLabel "fluido da terra" xsd:string +property_value: IAO:0000116 "Earth fluids can be water, oil, gas or a mixture of those fluids." xsd:string + +[Term] +id: GEOCORE:0000010 +name: unconsolidated earth material +def: "Unconsolidated earth material is an 'earth material' that is consituted by an aggregate of solid particles but is not consolidated into a 'rock' it self." [] +is_a: GEOCORE:0000006 ! earth material +property_value: altLabel "material geológico inconsolidado" xsd:string + +[Term] +id: GEOCORE:0000011 +name: geological boundary +def: "It is a fiat surface that is 'located in' the external surface of a 'geological object'." [] +is_a: BFO:0000146 ! fiat surface +property_value: altLabel "limite geológico" xsd:string +property_value: IAO:0000116 "The 'geological boundary' of a 'geological object' coincides with the complete physical discontinuity that delimits it." xsd:string + +[Term] +id: GEOCORE:0000012 +name: geological contact +def: "It is a 'relational quality' that 'inheres in' two distinct 'geological object' that are 'externally connected with'" [] +is_a: BFO:0000145 ! relational quality +relationship: BFO:0000197 GEOCORE:0000001 {cardinality="2"} ! inheres in geological object +property_value: altLabel "contato geológico" xsd:string +property_value: IAO:0000116 "A geological contact exists when two distinct geological objects are externally\nconnected with, i.e., their external boundaries are physically adjacent. Objects that are in contact do not have any kind of proper parthood relationship between them." xsd:string + +[Term] +id: GEORES:0000001 +name: body of rock +is_a: GEOCORE:0000001 ! geological object +intersection_of: GEOCORE:0000001 ! geological object +intersection_of: GEOCORE:0000017 GEOCORE:0000008 ! constituted by amount of rock +relationship: BFO:0000101 GEOCORE:0000004 ! is carrier of geological structure +relationship: BFO:0000129 GEORES:0000020 ! member part of depositional system +relationship: BFO:0000129 GEORES:0000021 ! member part of sedimentary environment +relationship: GEOCORE:0000017 GEOCORE:0000008 ! constituted by amount of rock +property_value: altLabel "corpo de rocha" xsd:string +property_value: definition "'body of rock' is a 'geological object' that is 'constituted by' some 'amount of rock'" xsd:string + +[Term] +id: GEORES:0000002 +name: stratigraphic unit +comment: Os diferentes elementos arquiteturais ocorrem dentro de uma unidade com uma idade definida que é a unidade estratigráfica.\n\nAinda não sabemos se poderia ser uma unidade litoestratigráfica. +is_a: GEORES:0000001 ! body of rock +property_value: altLabel "unidade estratigráfica" xsd:string + +[Term] +id: GEORES:0000003 +name: lithostratigraphic unit +is_a: GEORES:0000001 ! body of rock +property_value: altLabel "unidade litoestratigráfica" xsd:string + +[Term] +id: GEORES:0000004 +name: formation +is_a: GEORES:0000003 ! lithostratigraphic unit +relationship: BFO:0000129 GEORES:0000019 ! member part of group +property_value: altLabel "formação" xsd:string + +[Term] +id: GEORES:0000005 +name: member +is_a: GEORES:0000003 ! lithostratigraphic unit +relationship: BFO:0000176 GEORES:0000004 ! continuant part of formation +property_value: altLabel "membro" xsd:string + +[Term] +id: GEORES:0000006 +name: architectural element +comment: A restrição de partes de escala menores ainda não foi implementada. +comment: Luan: Elementos arquiteturais são os objetos básicos que os geólogos vão reconhecer e descrever. Eles podem ocorrer em diversas escalas.\nUm elemento pode ter outro elemento como parte, desde que de uma escala menor. +is_a: GEORES:0000001 ! body of rock +relationship: BFO:0000196 GEORES:0000023 ! bearer of geometry +property_value: altLabel "elemento arquitetural" xsd:string + +[Term] +id: GEORES:0000007 +name: build up unit +is_a: GEORES:0000006 ! architectural element +disjoint_from: GEORES:0000008 ! channel unit +property_value: altLabel "edifício" xsd:string + +[Term] +id: GEORES:0000008 +name: channel unit +def: "An elongated Depositional Unit having some Channel Surface as its boundary and constituted by some Sediment or Sedimentary Rock that fills it (McHargue et al., 2011)." [] +comment: In stratigraphic terms, a channel unit is constituted by the sediments or sedimentary rocks that fill a channel. It is important to notice that, in more general terms, a channel is a passageway for fluids or sediments, i.e., an immaterial entity. If one elaborates about the erosion and deposition processes that generate these units (McHargue et al., 2011), it is essential to have this disambiguation. +comment: In this work, we decided not to model the named hierarchical scales as entities (e.g., Channel Element, Channel Complex, Channel Complex Set - McHargue et al., 2011) because there exists a wide variety of hierarchical schemes in the literature, and they are not necessarily interoperable (Cullis et al., 2018). Instead, we focus on the fact that units can be fractally nested: a unit can be a Proper Spatial Part Of another unit, which can be a Proper Spatial Part Of another unit, and so forth. We consider that this approach solves the problem of implementing a solution for the repeatability of the geological objects in multiple scales. As so, a Channel Unit can be decomposed in other Channel Units many times as necessary, keeping the representation structure. In the future, we can study the integration of hierarchical schemes and try to infer scales from the spatial relations. +is_a: GEORES:0000006 ! architectural element +disjoint_from: GEORES:0000013 ! levee unit +property_value: altLabel "canal" xsd:string +property_value: GEORES:0000050 "R+ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000009 +name: dome unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "domo" xsd:string + +[Term] +id: GEORES:0000010 +name: dune unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "duna" xsd:string + +[Term] +id: GEORES:0000011 +name: intrusive dike +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "dique intrusivo" xsd:string + +[Term] +id: GEORES:0000012 +name: intrusive sill unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "soleira intrusiva" xsd:string + +[Term] +id: GEORES:0000013 +name: levee unit +def: "A Depositional Unit having Wedge Geometry and forming a bank or ridge geomorphology associated with some Channel Unit." [] +comment: This term is not consensual as some authors refer to these units as the wedge-shape embankments around channels, which is the definition that we adopt here, while other authors refer to them as not necessarily being these embankments and possibly having wing shapes, among other definitions. +comment: This term refers to the geomorphological association of some wegde-shaped unit with some channel unit, even if the channel does not exist at the moment of the observation by the geologist and the levee is probabilistically identified by tendencies (e.g., typical facies). In other words, the term "levee" ontologicallly denotes this relation even though it cannot be deterministically observed. +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "dique" xsd:string +property_value: GEORES:0000050 "R~ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000014 +name: lobe unit +def: "A Depositional Unit having some Lobe Geometry." [] +comment: For Lobe Unit hierarchical scales, we adopted the same approach as in Channel Unit. +comment: These depositional units are usually found at deep-water depositional system terminal regions, or at channel laterals as Overbank Units. +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "lobo" xsd:string +property_value: GEORES:0000050 "R+ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000015 +name: mound unit +def: "A Depositional Unit having Mound Geometry with an irregular top surface and internal chaotic facies." [] +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "monte" xsd:string +property_value: GEORES:0000050 "R+ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000016 +name: olistrostomes unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "olistrostomas" xsd:string +property_value: IAO:0000118 "megaclast" xsd:string +property_value: IAO:0000118 "megaclasto" xsd:string + +[Term] +id: GEORES:0000017 +name: sheet unit +is_a: GEORES:0000006 ! architectural element +property_value: altLabel "lençol" xsd:string + +[Term] +id: GEORES:0000018 +name: fossil +is_a: GEOCORE:0000001 ! geological object +property_value: altLabel "fóssil" xsd:string + +[Term] +id: GEORES:0000019 +name: group +is_a: BFO:0000027 ! object aggregate +relationship: BFO:0000115 GEORES:0000004 {all_only="true"} ! has member part formation +property_value: altLabel "grupo" xsd:string + +[Term] +id: GEORES:0000020 +name: depositional system +def: "An Object Aggregate whose members are mereotopologically-linked Depositional Units." [] +is_a: BFO:0000027 ! object aggregate +property_value: altLabel "sistema deposicional" xsd:string +property_value: GEORES:0000050 "R+ I+ O+ U+ ED-" xsd:string + +[Term] +id: GEORES:0000021 +name: sedimentary environment +def: "The sedimentary environment is the specific depositional setting of a particular sedimentary rock and is unique in terms of physical, chemical, and biological characteristics." [] +is_a: BFO:0000027 ! object aggregate +property_value: altLabel "ambiente de sedimentação" xsd:string +property_value: IAO:0000119 "Britannica\nhttps://www.britannica.com/science/sedimentary-rock/Sedimentary-environments" xsd:string + +[Term] +id: GEORES:0000022 +name: dimension +def: "A Quality that inheres in an Independent Continuant by virtue of one of its one-dimensional extents. It is a category that includes at least the three dimensions defined in this ontology: Width, Length, and Thickness. All dimensions are expressed by a real number indicating its value and a literal string indicating its measurement unit." [] +is_a: BFO:0000019 ! quality + +[Term] +id: GEORES:0000023 +name: geometry +def: "A Quality that inheres in a Depositional Unit by virtue of its external three-dimensional shape. It does not reflect the exact mathematical specifications of a geometric shape but abstracts and simplifies these specifications (Rovetto, 2011)." [] +is_a: BFO:0000019 ! quality +relationship: GEORES:0000046 GEORES:0000042 {minCardinality="1"} ! has geometry type geometry type +property_value: altLabel "geometria" xsd:string + +[Term] +id: GEORES:0000024 +name: lithology +is_a: BFO:0000019 ! quality +property_value: altLabel "litologia" xsd:string + +[Term] +id: GEORES:0000025 +name: statigraphic contact +is_a: GEOCORE:0000012 ! geological contact +property_value: altLabel "contato estratigráfico" xsd:string + +[Term] +id: GEORES:0000026 +name: bed contact +is_a: GEOCORE:0000012 ! geological contact +relationship: GEORES:0000044 GEORES:0000041 {cardinality="1"} ! has contact position contact position +relationship: GEORES:0000045 GEORES:0000043 {cardinality="1"} ! has contact type contact type +property_value: altLabel "contato de camada" xsd:string + +[Term] +id: GEORES:0000027 +name: sinuosity +def: "A Quality that inheres in a Channel Unit by virtue of how wavy it is across its length. It is expressed by a real number given by its curved length divided by its length in a straight line." [] +is_a: BFO:0000019 ! quality +relationship: BFO:0000197 GEORES:0000008 {cardinality="1"} ! inheres in channel unit + +[Term] +id: GEORES:0000028 +name: facies +def: "A pattern of properties of Geological Objects." [] +comment: This entity is defined in the literature as a combination of features that differentiates a geological object from its adjacent geological objects (Walker and James, 1992). However, a Facies does not describe a single Geological Object’s features: it might repeat in several objects as a pattern. This particular aspect matches the definition of Generically Dependent Continuant in BFO. Another important aspect is that the features that compose facies vary depending on the research context, e.g., Sedimentary Facies, Petrofacies (De Ros and Goldberg, 2007), Lithofacies, Ichnofacies, and Biofacies (Nichols, 2009). +is_a: BFO:0000031 ! generically dependent continuant +relationship: BFO:0000084 GEORES:0000001 ! generically depends on body of rock +property_value: altLabel "fácies" xsd:string + +[Term] +id: GEORES:0000029 +name: sedimentary facies +def: "A Facies consisting of the sum of the sedimentological characteristics of Depositional Units (Middleton, 1973, Nichols, 2009, Carbonera et al., 2015)." [] +comment: As an example, if we would model Cross-bedded Sandstone (Nichols, 2009), it would be an entity subsumed by Sedimentary Facies having the following relations: (1) Generically Depends On some (Constituted By some Sandstone (a)); and (2) Has Part some Cross-bedding Structure (b). (a): Sandstone would be an entity subsumed by Sedimentary Rock. (b): Cross-bedding Structure would be an entity subsumed by Sedimentary Structure. +is_a: GEORES:0000028 ! facies +property_value: altLabel "fácies sedimentar" xsd:string + +[Term] +id: GEORES:0000030 +name: facies association +def: "A Generically Dependent Continuant that consists of an aggregate of Facies." [] +comment: It usually describes the Facies that are typically found in specific regions or sub-environments. For example, the Channel Axis Association (McHargue et al., 2011) describes Sedimentary Facies typically found at the center part of channels (in a cross-section point of view). +is_a: BFO:0000031 ! generically dependent continuant +relationship: BFO:0000178 GEORES:0000028 {minCardinality="2"} ! has continuant part facies +property_value: altLabel "associação de facies" xsd:string + +[Term] +id: GEORES:0000031 +name: sediment +def: "An Unconsolidated Earth Material constituted by some collection of sedimentary grains or particles (Garcia et al., 2019)." [] +is_a: GEOCORE:0000010 ! unconsolidated earth material +property_value: GEORES:0000050 "R+ I+ O- U- ED-" xsd:string + +[Term] +id: GEORES:0000032 +name: sedimentary rock +def: "'sedimentary rock' is an 'amount of rock' constituted by some collection of sedimentary grains or particles (Garcia et al., 2019)." [] +is_a: GEOCORE:0000008 ! amount of rock +disjoint_from: GEORES:0000033 ! igneous rock +property_value: altLabel "rocha sedimentar" xsd:string +property_value: GEORES:0000050 "R+ I+ O- U- ED-" xsd:string + +[Term] +id: GEORES:0000033 +name: igneous rock +is_a: GEOCORE:0000008 ! amount of rock +property_value: altLabel "rocha ígnea" xsd:string +property_value: definition "'igneous rock' is an 'amount of rock' generated by the cooling and solidification of molten 'earth material'." xsd:string +property_value: isDefinedBy "https://www.britannica.com/science/igneous-rock" xsd:string + +[Term] +id: GEORES:0000034 +name: metamorphic rock +is_a: GEOCORE:0000008 ! amount of rock +property_value: altLabel "rocha metamórfica" xsd:string +property_value: definition "'metamorphic rock' is an 'amount of rock' generated by the alteration of preexisting rocks in response to changing environmental conditions, such as variations in temperature, pressure, and mechanical stress, and the addition or subtraction of chemical components." xsd:string +property_value: isDefinedBy "Adapted from Brittanica.\nhttps://www.britannica.com/science/metamorphic-rock" xsd:string + +[Term] +id: GEORES:0000035 +name: complex architectural element +is_a: GEORES:0000001 ! body of rock +disjoint_from: GEORES:0000036 ! composite architectural element + +[Term] +id: GEORES:0000036 +name: composite architectural element +is_a: GEORES:0000001 ! body of rock + +[Term] +id: GEORES:0000037 +name: individual architectural element + +[Term] +id: GEORES:0000038 +name: channel surface +def: "A Geological Boundary that forms the basis of a Channel Unit, having a concave-up shape unless truncated by overlying depositional units." [] +is_a: GEOCORE:0000011 ! geological boundary +property_value: GEORES:0000050 "R+ I+ O- U+ ED-" xsd:string + +[Term] +id: GEORES:0000039 +name: basin +is_a: BFO:0000029 ! site +property_value: altLabel "bacia" xsd:string + +[Term] +id: GEORES:0000040 +name: geological site +comment: Epistemologicamente não é possível determinar os limites deste site e, portanto, cada geólogo pode posicionar sua área de interesse em uma localização e limites distintos, o que torna muito difícil tratar computacionalmente a identidade do sítio geológico. Esse problema acontece com outras entidades do tipo site: Região da Serra Gaúcha, Litoral Norte, etc, cuja delimitação é problemática, mas existe uma identidade consensual. +is_a: BFO:0000029 ! site +property_value: altLabel "sítio geológico" xsd:string + +[Term] +id: GEORES:0000041 +name: contact position +property_value: altLabel "posição do contato" xsd:string + +[Term] +id: GEORES:0000042 +name: geometry type +comment: Luan: Talvez tipo de Geometria seja uma classe de segunda ordem, mas em primeiro momento não utilizaremos punning para representar isto. A classe geometry tem uma relação de 'has geometry type' com um 'geometry type' e as instâncias dessa classe é que definem o tipo de geometria de fato. Caso seja necessário criar alguma subclasse de um 'body of rock' que tenha um 'geometry type' específico é possível utilizar a primitiva do owl value para isto.\n\nNão sabemos ainda como classificar esta classe. Do que ela seria subclasse? +property_value: altLabel "tipo de geometria" xsd:string + +[Term] +id: GEORES:0000043 +name: contact type +property_value: altLabel "tipo de contato" xsd:string + +[Typedef] +id: BFO:0000084 +name: generically depends on +property_value: altLabel "g-depends on" xsd:string +property_value: definition "b generically depends on c =Def b is a generically dependent continuant & c is an independent continuant that is not a spatial region & at some time t there inheres in c a specifically dependent continuant which concretizes b at t" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "252-BFO" xsd:string +property_value: scopeNote "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: " xsd:string +domain: BFO:0000031 ! generically dependent continuant +inverse_of: BFO:0000101 ! is carrier of + +[Typedef] +id: BFO:0000101 +name: is carrier of +property_value: definition "b is carrier of c =Def there is some time t such that c generically depends on b at t" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "254-BFO" xsd:string +property_value: scopeNote "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: " xsd:string +range: BFO:0000031 ! generically dependent continuant + +[Typedef] +id: BFO:0000115 +name: has member part +property_value: definition "b has member part c =Def c member part of b" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "230-BFO" xsd:string +property_value: scopeNote "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: " xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: BFO:0000178 ! has continuant part +inverse_of: BFO:0000129 ! member part of + +[Typedef] +id: BFO:0000129 +name: member part of +property_value: definition "b member part of c =Def b is an object & c is a material entity & there is some time t such that b continuant part of c at t & there is a mutually exhaustive and pairwise disjoint partition of c into objects x1, ..., xn (for some n ≠ 1) with b = xi (for some 1 <= i <= n)" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "228-BFO" xsd:string +property_value: scopeNote "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: " xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: BFO:0000176 ! continuant part of + +[Typedef] +id: BFO:0000176 +name: continuant part of +property_value: definition "b continuant part of c =Def b and c are continuants & there is some time t such that b and c exist at t & b continuant part of c at t" xsd:string +property_value: example "Milk teeth continuant part of human; surgically removed tumour continuant part of organism" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "221-BFO" xsd:string +property_value: scopeNote "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: " xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant +inverse_of: BFO:0000178 ! has continuant part + +[Typedef] +id: BFO:0000178 +name: has continuant part +property_value: definition "b has continuant part c =Def c continuant part of b" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "271-BFO" xsd:string +property_value: scopeNote "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: " xsd:string +domain: BFO:0000002 ! continuant +range: BFO:0000002 ! continuant + +[Typedef] +id: BFO:0000194 +name: specifically depended on by +property_value: altLabel "s-depended on by" xsd:string +property_value: definition "b specifically depended on by c =Def c specifically depends on b" xsd:string +property_value: example "Coloured object specifically depended on by colour" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "260-BFO" xsd:string +range: BFO:0000020 ! specifically dependent continuant +inverse_of: BFO:0000195 ! specifically depends on + +[Typedef] +id: BFO:0000195 +name: specifically depends on +property_value: altLabel "s-depends on" xsd:string +property_value: definition "(Elucidation) specifically depends on is a relation between a specifically dependent continuant b and specifically dependent continuant or independent continuant that is not a spatial region c such that b and c share no parts in common & b is of a nature such that at all times t it cannot exist unless c exists & b is not a boundary of c" xsd:string +property_value: example "A shape specifically depends on the shaped object; hue, saturation and brightness of a colour sample specifically depends on each other" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "012-BFO" xsd:string +property_value: scopeNote "The analogue of specifically depends on for occurrents is has participant." xsd:string +domain: BFO:0000020 ! specifically dependent continuant + +[Typedef] +id: BFO:0000196 +name: bearer of +property_value: definition "b bearer of c =Def c inheres in b" xsd:string +property_value: example "A patch of ink is the bearer of a colour quality; an organism is the bearer of a temperature quality" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "053-BFO" xsd:string +range: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000194 ! specifically depended on by +inverse_of: BFO:0000197 ! inheres in + +[Typedef] +id: BFO:0000197 +name: inheres in +property_value: definition "b inheres in c =Def b is a specifically dependent continuant & c is an independent continuant that is not a spatial region & b specifically depends on c" xsd:string +property_value: example "A shape inheres in a shaped object; a mass inheres in a material entity" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "051-BFO" xsd:string +domain: BFO:0000020 ! specifically dependent continuant +is_a: BFO:0000195 ! specifically depends on + +[Typedef] +id: BFO:0000199 +name: occupies temporal region +property_value: definition "p occupies temporal region t =Def p is a process or process boundary & the spatiotemporal region occupied by p temporally projects onto t" xsd:string +property_value: example "The Second World War occupies the temporal region September 1, 1939 - September 2, 1945" xsd:string +property_value: http://purl.org/dc/elements/1.1/identifier "132-BFO" xsd:string +range: BFO:0000008 ! temporal region +is_functional: true + +[Typedef] +id: GEOCORE:0000015 +name: has age +def: "The relation between a Geological Object and its Geological Age." [] +is_a: BFO:0000196 ! bearer of +inverse_of: GEOCORE:0000016 ! age of + +[Typedef] +id: GEOCORE:0000016 +name: age of +def: "The relation between a Geological Age and a Geological Object. Inverse of has age relation." [] +is_a: BFO:0000197 ! inheres in + +[Typedef] +id: GEOCORE:0000017 +name: constituted by +def: "The relation between some material entity and the material that it is made of." [] +property_value: IAO:0000116 "This is a material constitution relation intended to represent the relationship between material objects, such as geological objects and earth materials, or aggregates of them." xsd:string +property_value: IAO:0000119 "Evnine, S. J. (2011). Constitution and composition: Three approaches to their relation. ProtoSociology, 27, 212-235." xsd:string +is_asymmetric: true + +[Typedef] +id: GEORES:0000044 +name: has contact position +domain: GEORES:0000026 ! bed contact +range: GEORES:0000041 ! contact position + +[Typedef] +id: GEORES:0000045 +name: has contact type +domain: GEORES:0000026 ! bed contact +range: GEORES:0000043 ! contact type + +[Typedef] +id: GEORES:0000046 +name: has geometry type +comment: Luan: Geometry Type talvez seja uma classe de segunda ordem cuja as instâncias são os diferentes tipos de Geometria. Por exemplo, é errado dizer que Geometria Lenticular é subtipo da Quality Geometria. Lenticular é na realidade um subtipo de Tipo de Geometria e não de Geometria. +domain: GEORES:0000023 ! geometry +range: GEORES:0000042 ! geometry type + +[Typedef] +id: GEORES:0000047 +name: has base geometry +is_a: GEORES:0000046 ! has geometry type + +[Typedef] +id: GEORES:0000048 +name: has top geometry +is_a: GEORES:0000046 ! has geometry type + diff --git a/geores.owl b/geores.owl new file mode 100644 index 0000000..3b6bfb5 --- /dev/null +++ b/geores.owl @@ -0,0 +1,2130 @@ + + + + + Alcides Lopes + Fabrício Henrique Rodrigues + Fernando Cicconeto + Joel Luis Carbonera + Luan Fonseca Garcia + Lucas Valadares Vieira + Mara Abel + Renata dos Santos Alvarenga + Tiago Agne de Oliveira + Yuanwei Qu + GeoReservoir is an ontology to support the description of the geometry and the lithology of deep-marine deposits. The GeoReservoir ontology provides formal and clear definitions of deep-marine depositional system entities, creating an unambiguous terminology for geometrical and lithological properties of the deposits in the scale of outcrop and seismic sections. These definitions are independent of tasks, geological interpretations, and process inferences. We created this language to make it possible to formally and uniformly describe any deep-marine occurrence in the world with an adequate level of detail for sedimentological studies and computer processing. + https://creativecommons.org/licenses/by-nc/4.0/ + GeoReservoir Ontology + Cited references: + +1. Abel, M., Perrin, M., Carbonera, J.L.: Ontological analysis for information integration in geomodeling. Earth Science Informatics 8, 21–36 (2015) +2. Carbonera, J.L., Abel, M., Scherer, C.M.S.: Visual interpretation of events in petroleum exploration: An approach supported by well-founded ontologies. Expert Systems With Applications 42, 2749–2763 (2015) +3. Cullis, S., Colombera, L., Patacci, M., McCaffrey, W.D.: Hierarchical classifications of the sedimentary architecture of deep-marine depositional systems. Earth-Science Reviews 179, 38–71 (2018) +4. De Ros, L.F., Goldberg, K.: Reservoir petrofacies: A tool for quality characterization and prediction. In: AAPG Annual Conference and Exhibition. Long Beach (2007) +5. Garcia, L.F., Carbonera, J.L., Rodrigues, F.H., Antunes, C.R., Abel, M.: What rocks are made of: Towards an ontological pattern for material constitution in the geological domain. In: Laender, A.H.F., Pernici, B., Lim, E.P., Oliveira, J.P.M. (eds.) ER: 38th International Conference on Conceptual Modeling. pp. 275–286. Springer, Cham (2019) +6. Guarino, N., Welty, C.A.: An overview of ontoclean. In: Staab, S., Studer, R. (eds.) Handbook on Ontologies, pp. 151–171. Springer, Berlin, Heidelberg (2004) +7. McHargue, T., Pyrcz, M.J., Sullivan, M.D., Clark, J.D., Fildani, A., Romans, B.W., Covault, J.A., Levy, M., Posamentier, H.W., Drinkwater, N.J.: Architecture of turbidite channel systems on the continental slope: Patterns and predictions. Marine and Petroleum Geology 28, 728–743 (2011) +8. Middleton, G.V.: Johannes walther’s law of the correlation of facies. Bulletin of the Geological Society of America 84, 979–988 (1973) +9. Nichols, G.: Sedimentology and Stratigraphy. Wiley-Blackwell, Chichester, 2nd edn. (2009) +10. Rovetto, R.: The shape of shapes: An ontological exploration. In: Hastings, J., Kutz, O., Bhatt, M., Borgo, S. (eds.) Proceedings of the First Interdisciplinary Workshop on SHAPES. Karlsruhe (2011), http://ceur-ws.org/Vol-812/ +11. Walker, R.G., James, N.P.: Facies Models: Response to Sea Level Change. Geological Association of Canada, St. John’s (1992) + We acknowledge the Brazilian funding agencies CNPq and CAPES for financing this work and the Research Centre of Petrobras (CENPES) for collaborating on this project. + 2024-04-07 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + For metaproperties, we use the following notation (Guarino and Welty, 2004; Abel et al., 2015): + +– R+ / R- / R~: rigid / not rigid / anti-rigid; +– I+ / I-: carries / does not carry identity; +– O+ / O-: provides / does not provide identity; +– U+ / U-: carries / does not carry unity; +– ED+ / ED-: existentially dependent / independent. + metaproperties + + + + + + + + + + + + + + + + + + + + + + + + + 252-BFO + generically depends on + g-depends on + b generically depends on c =Def b is a generically dependent continuant & c is an independent continuant that is not a spatial region & at some time t there inheres in c a specifically dependent continuant which concretizes b at t + Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link> + + + + + + + + + + + + + + + + + + + 254-BFO + is carrier of + b is carrier of c =Def there is some time t such that c generically depends on b at t + Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link> + + + + + + + + + + + + 230-BFO + has member part + b has member part c =Def c member part of b + Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link> + + + + + + + + + + + 228-BFO + member part of + b member part of c =Def b is an object & c is a material entity & there is some time t such that b continuant part of c at t & there is a mutually exhaustive and pairwise disjoint partition of c into objects x1, ..., xn (for some n ≠ 1) with b = xi (for some 1 <= i <= n) + Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link> + + + + + + + + + + + 221-BFO + continuant part of + b continuant part of c =Def b and c are continuants & there is some time t such that b and c exist at t & b continuant part of c at t + Milk teeth continuant part of human; surgically removed tumour continuant part of organism + Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link> + + + + + + + + + + 271-BFO + has continuant part + b has continuant part c =Def c continuant part of b + Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: <Link> + + + + + + + + + + + + + + + + + + + + + + + + + 260-BFO + specifically depended on by + s-depended on by + b specifically depended on by c =Def c specifically depends on b + Coloured object specifically depended on by colour + + + + + + + + + + + + + + + + + + + + + + + + 012-BFO + specifically depends on + s-depends on + (Elucidation) specifically depends on is a relation between a specifically dependent continuant b and specifically dependent continuant or independent continuant that is not a spatial region c such that b and c share no parts in common & b is of a nature such that at all times t it cannot exist unless c exists & b is not a boundary of c + A shape specifically depends on the shaped object; hue, saturation and brightness of a colour sample specifically depends on each other + The analogue of specifically depends on for occurrents is has participant. + + + + + + + + + + + + + + + + + + + + + 053-BFO + bearer of + b bearer of c =Def c inheres in b + A patch of ink is the bearer of a colour quality; an organism is the bearer of a temperature quality + + + + + + + + + + + + + + + + + + + + 051-BFO + inheres in + b inheres in c =Def b is a specifically dependent continuant & c is an independent continuant that is not a spatial region & b specifically depends on c + A shape inheres in a shaped object; a mass inheres in a material entity + + + + + + + + + + + + + + + + + + 132-BFO + occupies temporal region + p occupies temporal region t =Def p is a process or process boundary & the spatiotemporal region occupied by p temporally projects onto t + The Second World War occupies the temporal region September 1, 1939 - September 2, 1945 + + + + + + + + + + The relation between a Geological Object and its Geological Age. + has age + + + + + + + + + The relation between a Geological Age and a Geological Object. Inverse of has age relation. + age of + + + + + + + + + + The relation between some material entity and the material that it is made of. + This is a material constitution relation intended to represent the relationship between material objects, such as geological objects and earth materials, or aggregates of them. + Evnine, S. J. (2011). Constitution and composition: Three approaches to their relation. ProtoSociology, 27, 212-235. + constituted by + + + + + + + + + + + has contact position + + + + + + + + + + + has contact type + + + + + + + + + + Luan: Geometry Type talvez seja uma classe de segunda ordem cuja as instâncias são os diferentes tipos de Geometria. Por exemplo, é errado dizer que Geometria Lenticular é subtipo da Quality Geometria. Lenticular é na realidade um subtipo de Tipo de Geometria e não de Geometria. + has geometry type + + + + + + + + + has base geometry + + + + + + + + + has top geometry + + + + + + + + + + + + + + + A relation between a Quality and its values. + O objetivo desta data property é conectar em níveL de implementação uma qualidade com o valor em seu espaço de qualiades. Por exemplo, a qualidade dimensão tem um espaço de qualidade que é um valor real positivo para sua largura. + +A IAO possui uma propriedade has measurement datum cujo domínio é um measurement datum. Porém, o problema de usar tal propriedade é acrescentar a necessidade de criar uma instância de measurement datum. + has value + + + + + + + + + + has dimension value + + + + + + + + + + + has lenght value + + + + + + + + + + + A relation between a Quality and a literal string that represents its measurement unit. + has measurement unit + + + + + + + + + + + has thickness value + + + + + + + + + + + has width value + + + + + + + + + + + + + 001-BFO + entity + (Elucidation) An entity is anything that exists or has existed or will exist + Julius Caesar; the Second World War; your body mass index; Verdi's Requiem + + + + + + + + + + + + + + + + 008-BFO + continuant + (Elucidation) A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity + A human being; a tennis ball; a cave; a region of space; someone's temperature + + + + + + + + + 077-BFO + occurrent + (Elucidation) An occurrent is an entity that unfolds itself in time or it is the start or end of such an entity or it is a temporal or spatiotemporal region + As for process, history, process boundary, spatiotemporal region, zero-dimensional temporal region, one-dimensional temporal region, temporal interval, temporal instant. + + + + + + + + + + + + + + + 017-BFO + independent continuant + b is an independent continuant =Def b is a continuant & there is no c such that b specifically depends on c or b generically depends on c + An atom; a molecule; an organism; a heart; a chair; the bottom right portion of a human torso; a leg; the interior of your mouth; a spatial region; an orchestra + + + + + + + + + + + + + + + 035-BFO + spatial region + (Elucidation) A spatial region is a continuant entity that is a continuant part of the spatial projection of a portion of spacetime at a given time + As for zero-dimensional spatial region, one-dimensional spatial region, two-dimensional spatial region, three-dimensional spatial region + + + + + + + + + 100-BFO + temporal region + (Elucidation) A temporal region is an occurrent over which processes can unfold + As for zero-dimensional temporal region and one-dimensional temporal region + + + + + + + + + 095-BFO + spatiotemporal region + (Elucidation) A spatiotemporal region is an occurrent that is an occurrent part of spacetime + The spatiotemporal region occupied by the development of a cancer tumour; the spatiotemporal region occupied by an orbiting satellite + 'Spacetime' here refers to the maximal instance of the universal spatiotemporal region. + + + + + + + + + 083-BFO + process + event + (Elucidation) p is a process means p is an occurrent that has some temporal proper part and for some time t, p has some material entity as participant + An act of selling; the life of an organism; a process of sleeping; a process of cell-division; a beating of the heart; a process of meiosis; the taxiing of an aircraft; the programming of a computer + + + + + + + + + 055-BFO + quality + (Elucidation) A quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized + The colour of a tomato; the ambient temperature of this portion of air; the length of the circumference of your waist; the shape of your nose; the shape of your nostril; the mass of this piece of gold + + + + + + + + + 050-BFO + specifically dependent continuant + b is a specifically dependent continuant =Def b is a continuant & there is some independent continuant c which is not a spatial region & which is such that b specifically depends on c + (with multiple bearers) John's love for Mary; the ownership relation between John and this statue; the relation of authority between John and his subordinates + (with one bearer) The mass of this tomato; the pink colour of a medium rare piece of grilled filet mignon at its centre; the smell of this portion of mozzarella; the disposition of this fish to decay; the role of being a doctor; the function of this heart to pump blood; the shape of this hole + + + + + + + + + 025-BFO + object aggregate + (Elucidation) An object aggregate is a material entity consisting exactly of a plurality (≥1) of objects as member parts which together form a unit + The aggregate of the musicians in a symphony orchestra and their instruments; the aggregate of bearings in a constant velocity axle joint; the nitrogen atoms in the atmosphere; a collection of cells in a blood biobank + 'Exactly' means that there are no parts of the object aggregate other than its member parts. + The unit can, at certain times, consist of exactly one object, for example, when a wolf litter loses all but one of its pups, but it must at some time have a plurality of member parts. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 034-BFO + site + (Elucidation) A site is a three-dimensional immaterial entity whose boundaries either (partially or wholly) coincide with the boundaries of one or more material entities or have locations determined in relation to some material entity + A hole in a portion of cheese; a rabbit hole; the Grand Canyon; the Piazza San Marco; the kangaroo-joey-containing hole of a kangaroo pouch; your left nostril (a fiat part - the opening - of your left nasal cavity); the lumen of your gut; the hold of a ship; the interior of the trunk of your car; hole in an engineered floor joist + + + + + + + + + 024-BFO + object + (Elucidation) An object is a material entity which manifests causal unity & is of a type instances of which are maximal relative to the sort of causal unity manifested + An organism; a fish tank; a planet; a laptop; a valve; a block of marble; an ice cube + A description of three primary sorts of causal unity is provided in Basic Formal Ontology 2.0. Specification and User Guide + + + + + + + + + 074-BFO + generically dependent continuant + g-dependent continuant + (Elucidation) A generically dependent continuant is an entity that exists in virtue of the fact that there is at least one of what may be multiple copies which is the content or the pattern that multiple copies would share + The pdf file on your laptop; the pdf file that is a copy thereof on my laptop; the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule; the content that is shared by a string of dots and dashes written on a page and the transmitted Morse code signal; the content of a sentence; an engineering blueprint + + + + + + + + + 084-BFO + process boundary + p is a process boundary =Def p is a temporal part of a process & p has no proper temporal parts + The boundary between the 2nd and 3rd year of your life + + + + + + + + + 103-BFO + one-dimensional temporal region + (Elucidation) A one-dimensional temporal region is a temporal region that is a whole that has a temporal interval and zero or more temporal intervals and temporal instants as parts + The temporal region during which a process occurs + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 019-BFO + material entity + (Elucidation) A material entity is an independent continuant has some portion of matter as continuant part + A human being; the undetached arm of a human being; an aggregate of human beings + + + + + + + + + + + + + + + 029-BFO + continuant fiat boundary + (Elucidation) A continuant fiat boundary b is an immaterial entity that is of zero, one or two dimensions & such that there is no time t when b has a spatial region as continuant part & whose location is determined in relation to some material entity + As for fiat point, fiat line, fiat surface + + + + + + + + + 028-BFO + immaterial entity + b is an immaterial entity =Def b is an independent continuant which is such that there is no time t when it has a material entity as continuant part + As for fiat point, fiat line, fiat surface, site + + + + + + + + + 057-BFO + relational quality + b is a relational quality =Def b is a quality & there exists c and d such that c and d are not identical & b specifically depends on c & b specifically depends on d + A marriage bond; an instance of love; an obligation between one person and another + + + + + + + + + 033-BFO + fiat surface + (Elucidation) A fiat surface is a two-dimensional continuant fiat boundary that is self-connected + The surface of the Earth; the plane separating the smoking from the non-smoking zone in a restaurant + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An object that is 'generated by' some 'geological process' and has at least one part 'constituted by' some 'earth material' that is not an 'earth fluid'. + A geological object is a naturally occurring entity because a geological process +generates it, and some earth material constitutes it. Thus, we can differentiate geological objects from artificial objects, such as a well-core, because even though some earth material constitutes artificial objects, they are human-made rather than generated by some geological process. Furthermore, Geological Objects are specializations of BFO Objects, meaning they must necessarily have some unity criteria. The unity is what differentiates geological objects from Earth Materials. + geological object + objeto geológico + + + + + + + + + + + + + + + Examples are the process of deposition, the process of folding, a tectonic process, a sedimentary process. + It is a physical, or chemical, or biological, naturally occurring process that occurs on the Earth’s surface or subsurface and occupies some 'geological time interval' + Geological processes are macro processes that generate, transform, deform, transport, or destroy geological objects and earth materials. These processes are not necessarily atomic and may have other geological processes as parts. + geological process + processo geológico + + + + + + + + + It is a quality that 'inheres in' a 'geological object' or 'earth material' that corresponds to the 'geological time interval' in which the 'geological process' that it was 'generated by' occupied. + geological age + idade geológica + + + + + + + + + + + + + + + It is a 'generically dependent continuant' that is the pattern of a non-atomic 'geological object''s internal arrangement. + Geological structures are general material patterns repeated in many geological +objects. The pattern comprises the material configuration and the mutual relationships of the object’s different parts. Structures result from one or a series of geological processes that generated or transformed the geological object they generically depend on. Thus, there is some historical dependence relation between the structure and this geological process, but what concretizes the structure is some complex quality inhering in the object, not the process. + geological structure + estrutura geológica + + + + + + + + + It is a BFO temporal interval that corresponds to a time interval within the Geological Time Scale. + geological time interval + intervalo de tempo geológico + + + + + + + + + + + + + + + Examples are an amount of sandstone, an amount of petroleum, an amount of +natural gas. + It is a natural amount of matter 'generated by' some 'geological process'. + Earth Materials are natural amounts of matter. Thus, they come into existence by nature, without any artificial aid. Since they are amounts, they don’t hold unity criteria, but they are ontologically rigid and provide an identity criteria. Earth Materials and BFO Objects are disjoint. They are either solid, fluid, or unconsolidated. We usually observe earth materials when constituting other objects, such as an amount of rock constituting a geological unity or an amount of sand constituting a dune. + earth material + material geologico + + + + + + + + + The amount of quarts that constitutes some grain, the amount of feldspar that is part of an amount of rock. + An amount of rock is an 'earth material' that is a naturally occuring, inorganic, solid, homogeneous chemical compound with a crystalline structure. + Amounts of mineral lack a unity criteria as every other 'earth material'. We usually observe them when they are constitution objects such as crystals or grains. + amount of mineral + quantidade de mineral + + + + + + + + + + + + + + + + The amount of sandstone that constitutes a lithostratigraphic unit. + An amount of rock is a solid consolidated 'earth material' that is 'constituted by' an aggregate of particles made of mineral matter or material of biological origin. + Geologists define rocks at a scale of observation where they consider them homogeneous, even though an aggregate of solid particles constitutes it. These particles are usually geological objects, such as grains or crystals, or the rest of dead animals or plants. + +Amounts of rock, like other earth materials, are independent rigid entities that do not hold any unity criteria. We can observe them in nature when they are constituting objects such as geological unities. + amount of rock + quantidade de rocha + + + + + + + + + Earth fluid is an 'earth material' that is fluild. + Earth fluids can be water, oil, gas or a mixture of those fluids. + earth fluid + fluido da terra + + + + + + + + + Unconsolidated earth material is an 'earth material' that is consituted by an aggregate of solid particles but is not consolidated into a 'rock' it self. + unconsolidated earth material + material geológico inconsolidado + + + + + + + + + It is a fiat surface that is 'located in' the external surface of a 'geological object'. + The 'geological boundary' of a 'geological object' coincides with the complete physical discontinuity that delimits it. + geological boundary + limite geológico + + + + + + + + + + + + 2 + + + + It is a 'relational quality' that 'inheres in' two distinct 'geological object' that are 'externally connected with' + A geological contact exists when two distinct geological objects are externally +connected with, i.e., their external boundaries are physically adjacent. Objects that are in contact do not have any kind of proper parthood relationship between them. + geological contact + contato geológico + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + body of rock + corpo de rocha + 'body of rock' is a 'geological object' that is 'constituted by' some 'amount of rock' + + + + + + + + + Os diferentes elementos arquiteturais ocorrem dentro de uma unidade com uma idade definida que é a unidade estratigráfica. + +Ainda não sabemos se poderia ser uma unidade litoestratigráfica. + stratigraphic unit + unidade estratigráfica + + + + + + + + + lithostratigraphic unit + unidade litoestratigráfica + + + + + + + + + + + + + + + formation + formação + + + + + + + + + + + + + + + member + membro + + + + + + + + + + + + + + + A restrição de partes de escala menores ainda não foi implementada. + Luan: Elementos arquiteturais são os objetos básicos que os geólogos vão reconhecer e descrever. Eles podem ocorrer em diversas escalas. +Um elemento pode ter outro elemento como parte, desde que de uma escala menor. + architectural element + elemento arquitetural + + + + + + + + + build up unit + edifício + + + + + + + + + An elongated Depositional Unit having some Channel Surface as its boundary and constituted by some Sediment or Sedimentary Rock that fills it (McHargue et al., 2011). + In stratigraphic terms, a channel unit is constituted by the sediments or sedimentary rocks that fill a channel. It is important to notice that, in more general terms, a channel is a passageway for fluids or sediments, i.e., an immaterial entity. If one elaborates about the erosion and deposition processes that generate these units (McHargue et al., 2011), it is essential to have this disambiguation. + In this work, we decided not to model the named hierarchical scales as entities (e.g., Channel Element, Channel Complex, Channel Complex Set - McHargue et al., 2011) because there exists a wide variety of hierarchical schemes in the literature, and they are not necessarily interoperable (Cullis et al., 2018). Instead, we focus on the fact that units can be fractally nested: a unit can be a Proper Spatial Part Of another unit, which can be a Proper Spatial Part Of another unit, and so forth. We consider that this approach solves the problem of implementing a solution for the repeatability of the geological objects in multiple scales. As so, a Channel Unit can be decomposed in other Channel Units many times as necessary, keeping the representation structure. In the future, we can study the integration of hierarchical schemes and try to infer scales from the spatial relations. + channel unit + canal + R+ I+ O- U+ ED- + + + + + + + + + dome unit + domo + + + + + + + + + dune unit + duna + + + + + + + + + intrusive dike + dique intrusivo + + + + + + + + + intrusive sill unit + soleira intrusiva + + + + + + + + + A Depositional Unit having Wedge Geometry and forming a bank or ridge geomorphology associated with some Channel Unit. + This term is not consensual as some authors refer to these units as the wedge-shape embankments around channels, which is the definition that we adopt here, while other authors refer to them as not necessarily being these embankments and possibly having wing shapes, among other definitions. + This term refers to the geomorphological association of some wegde-shaped unit with some channel unit, even if the channel does not exist at the moment of the observation by the geologist and the levee is probabilistically identified by tendencies (e.g., typical facies). In other words, the term "levee" ontologicallly denotes this relation even though it cannot be deterministically observed. + levee unit + dique + R~ I+ O- U+ ED- + + + + + + + + + A Depositional Unit having some Lobe Geometry. + For Lobe Unit hierarchical scales, we adopted the same approach as in Channel Unit. + These depositional units are usually found at deep-water depositional system terminal regions, or at channel laterals as Overbank Units. + lobe unit + lobo + R+ I+ O- U+ ED- + + + + + + + + + A Depositional Unit having Mound Geometry with an irregular top surface and internal chaotic facies. + mound unit + monte + R+ I+ O- U+ ED- + + + + + + + + + megaclast + megaclasto + olistrostomes unit + olistrostomas + + + + + + + + + sheet unit + lençol + + + + + + + + + fossil + fóssil + + + + + + + + + + + + + + + group + grupo + + + + + + + + + An Object Aggregate whose members are mereotopologically-linked Depositional Units. + depositional system + sistema deposicional + R+ I+ O+ U+ ED- + + + + + + + + + The sedimentary environment is the specific depositional setting of a particular sedimentary rock and is unique in terms of physical, chemical, and biological characteristics. + Britannica +https://www.britannica.com/science/sedimentary-rock/Sedimentary-environments + sedimentary environment + ambiente de sedimentação + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A Quality that inheres in an Independent Continuant by virtue of one of its one-dimensional extents. It is a category that includes at least the three dimensions defined in this ontology: Width, Length, and Thickness. All dimensions are expressed by a real number indicating its value and a literal string indicating its measurement unit. + dimension + + + + + + + + + + + + 1 + + + + A Quality that inheres in a Depositional Unit by virtue of its external three-dimensional shape. It does not reflect the exact mathematical specifications of a geometric shape but abstracts and simplifies these specifications (Rovetto, 2011). + geometry + geometria + + + + + + + + + lithology + litologia + + + + + + + + + statigraphic contact + contato estratigráfico + + + + + + + + + + + + 1 + + + + + + + 1 + + + + bed contact + contato de camada + + + + + + + + + + + + 1 + + + + + + + + + + + + 1 + + + + + + + + + + + + + + + 1 + + + + + + + A Quality that inheres in a Channel Unit by virtue of how wavy it is across its length. It is expressed by a real number given by its curved length divided by its length in a straight line. + sinuosity + + + + + + + + + + + + + + + A pattern of properties of Geological Objects. + This entity is defined in the literature as a combination of features that differentiates a geological object from its adjacent geological objects (Walker and James, 1992). However, a Facies does not describe a single Geological Object’s features: it might repeat in several objects as a pattern. This particular aspect matches the definition of Generically Dependent Continuant in BFO. Another important aspect is that the features that compose facies vary depending on the research context, e.g., Sedimentary Facies, Petrofacies (De Ros and Goldberg, 2007), Lithofacies, Ichnofacies, and Biofacies (Nichols, 2009). + facies + fácies + + + + + + + + + A Facies consisting of the sum of the sedimentological characteristics of Depositional Units (Middleton, 1973, Nichols, 2009, Carbonera et al., 2015). + As an example, if we would model Cross-bedded Sandstone (Nichols, 2009), it would be an entity subsumed by Sedimentary Facies having the following relations: (1) Generically Depends On some (Constituted By some Sandstone (a)); and (2) Has Part some Cross-bedding Structure (b). (a): Sandstone would be an entity subsumed by Sedimentary Rock. (b): Cross-bedding Structure would be an entity subsumed by Sedimentary Structure. + sedimentary facies + fácies sedimentar + + + + + + + + + + + + 2 + + + + A Generically Dependent Continuant that consists of an aggregate of Facies. + It usually describes the Facies that are typically found in specific regions or sub-environments. For example, the Channel Axis Association (McHargue et al., 2011) describes Sedimentary Facies typically found at the center part of channels (in a cross-section point of view). + facies association + associação de facies + + + + + + + + + An Unconsolidated Earth Material constituted by some collection of sedimentary grains or particles (Garcia et al., 2019). + sediment + R+ I+ O- U- ED- + + + + + + + + + 'sedimentary rock' is an 'amount of rock' constituted by some collection of sedimentary grains or particles (Garcia et al., 2019). + sedimentary rock + rocha sedimentar + R+ I+ O- U- ED- + + + + + + + + + https://www.britannica.com/science/igneous-rock + igneous rock + rocha ígnea + 'igneous rock' is an 'amount of rock' generated by the cooling and solidification of molten 'earth material'. + + + + + + + + + Adapted from Brittanica. +https://www.britannica.com/science/metamorphic-rock + metamorphic rock + rocha metamórfica + 'metamorphic rock' is an 'amount of rock' generated by the alteration of preexisting rocks in response to changing environmental conditions, such as variations in temperature, pressure, and mechanical stress, and the addition or subtraction of chemical components. + + + + + + + + + + + + + + + + + + + + + + + + + + + complex architectural element + + + + + + + + + + + + + + + + + + + + composite architectural element + + + + + + + + + + + + + + + + + + + + + + + individual architectural element + + + + + + + + + A Geological Boundary that forms the basis of a Channel Unit, having a concave-up shape unless truncated by overlying depositional units. + channel surface + R+ I+ O- U+ ED- + + + + + + + + + basin + bacia + + + + + + + + + Epistemologicamente não é possível determinar os limites deste site e, portanto, cada geólogo pode posicionar sua área de interesse em uma localização e limites distintos, o que torna muito difícil tratar computacionalmente a identidade do sítio geológico. Esse problema acontece com outras entidades do tipo site: Região da Serra Gaúcha, Litoral Norte, etc, cuja delimitação é problemática, mas existe uma identidade consensual. + geological site + sítio geológico + + + + + + + + + + + + + + + + + contact position + posição do contato + + + + + + + + + + + + + + + + + + + + + + Luan: Talvez tipo de Geometria seja uma classe de segunda ordem, mas em primeiro momento não utilizaremos punning para representar isto. A classe geometry tem uma relação de 'has geometry type' com um 'geometry type' e as instâncias dessa classe é que definem o tipo de geometria de fato. Caso seja necessário criar alguma subclasse de um 'body of rock' que tenha um 'geometry type' específico é possível utilizar a primitiva do owl value para isto. + +Não sabemos ainda como classificar esta classe. Do que ela seria subclasse? + geometry type + tipo de geometria + + + + + + + + + + + + + + + + + + + + + + contact type + tipo de contato + + + + + + + + + + + + + + amalgamated contact + contato amalgamado + + + + + + + + + base position contact + contato de base + + + + + + + + + cryptic/covered contact + contato críptico/encoberto + + + + + + + + + conformable contact + contato concordante + + + + + + + + + erosive contact + contato erosivo + + + + + + + + + faulted contact + contato de falha + + + + + + + + + gradational contact + contato gradacional + + + + + + + + + intrusive contact + contato intrusivo + + + + + + + + + sharp contact + contato abrupto + + + + + + + + + irregular geometry + geometria irregular + + + + + + + + + lenticular convex top flatbed geometry + geometria lenticular topo convexo base plana + + + + + + + + + lenticular concave convex geometry + geometria lenticular côncavo convexa + + + + + + + + + lateral position contact + contato lateral + + + + + + + + + lenticular flattop concave base geometry + geometria lenticular topo plano base convexa + + + + + + + + + sheet geometry + geometria lençoidal + + + + + + + + + sigmoidal geometry + geometria sigmoidal + + + + + + + + + tabular geometry + geometria tabular + + + + + + + + + top position contact + contato de topo + + + + + + + + + wedge shape geometry + geometria de cunha + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/imports/GeoCoreOntology.owl b/imports/GeoCoreOntology.owl deleted file mode 100644 index f05f328..0000000 --- a/imports/GeoCoreOntology.owl +++ /dev/null @@ -1,469 +0,0 @@ - - - - - - - - - http://purl.obolibrary.org/obo/ro/core.owl - http://purl.obolibrary.org/obo/bfo/2.0/bfo.owl - - - Luan Fonseca Garcia - - - - Michel Perrin - - - - Mara Abel - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #UFRGS:GeoCoreOntology_age_of - The relation between a Geological Age and a Geological Object. Inverse of has age relation. - - - - #UFRGS:GeoCoreOntology_age_of - age of - - - - #UFRGS:GeoCoreOntology_constituted_by - The relation between some material entity and the material that it is made of. - - - - #UFRGS:GeoCoreOntology_constituted_by - Evnine, S. J. (2011). Constitution and composition: Three approaches to their relation. ProtoSociology, 27, 212-235. - - - - #UFRGS:GeoCoreOntology_constituted_by - constituted by - - - - #UFRGS:GeoCoreOntology_earth_fluid - Earth fluid is an 'earth material' that is fluild. - -They can be water, oil, gas or a mixture of those fluids. - - - - #UFRGS:GeoCoreOntology_earth_fluid - earth fluid - - - - #UFRGS:GeoCoreOntology_earth_fluid - fluido da terra - - - - #UFRGS:GeoCoreOntology_earth_material - Earth material is a 'material entity' that is a natural amount of matter, which is solid, fluid or unconsolidated. Earth materials are generated by some 'geological process'. - -They are rigid entities with a definite identity criteria, but no unifying relation. - - - - #UFRGS:GeoCoreOntology_earth_material - earth material - - - - #UFRGS:GeoCoreOntology_earth_material - material geologico - - - - #UFRGS:GeoCoreOntology_generated_by - A relation between a continuant and a process, in which the continuant was generated by the process - - - - #UFRGS:GeoCoreOntology_generated_by - generated by - - - - #UFRGS:GeoCoreOntology_generated_in - The Geological Time Interval in which the object was generated. - - - - #UFRGS:GeoCoreOntology_generated_in - generated in - - - - #UFRGS:GeoCoreOntology_geological_age - It is a Quality of Geological Object related to a Geological Time Interval during which some Geological Process operated. The age of a Geological Object is the age of the process that generated this object. - - - - #UFRGS:GeoCoreOntology_geological_age - geological age - - - - #UFRGS:GeoCoreOntology_geological_age - idade geológica - - - - #UFRGS:GeoCoreOntology_geological_boundary - A Geological Boundary is a Continuant Fiat Boundary corresponding to a physical discontinuity of any nature, located on the external surface of a Geological Object. - - - - #UFRGS:GeoCoreOntology_geological_boundary - geological boundary - - - - #UFRGS:GeoCoreOntology_geological_boundary - limite geológico - - - - #UFRGS:GeoCoreOntology_geological_contact - It is a Relational Quality which relates two Geologic Objects having the same dimension (1D, 2D, or 3D), whose external boundaries are adjacent to each other. - - - - #UFRGS:GeoCoreOntology_geological_contact - contato geológico - - - - #UFRGS:GeoCoreOntology_geological_contact - geological contact - - - - #UFRGS:GeoCoreOntology_geological_object - A Geological Object is a rigid entity that provides its own identity and holds a unity criteria. A Geological Object is constituted by Earth Material and is generated by some Geological Process. - - - - #UFRGS:GeoCoreOntology_geological_object - geological object - - - - #UFRGS:GeoCoreOntology_geological_object - objeto geológico - - - - #UFRGS:GeoCoreOntology_geological_process - It is a physical, chemical or biological process or series of processes that generate, destroy or modify the shape, the internal arrangement or the composition of at least one Geological Object. - - - - #UFRGS:GeoCoreOntology_geological_process - geological process - - - - #UFRGS:GeoCoreOntology_geological_process - processo geológico - - - - #UFRGS:GeoCoreOntology_geological_structure - It is a Generically Dependent Continuant which describes the internal arrangement of a Geological Object, i.e., the configuration and the mutual relationships of its different parts. - - - - #UFRGS:GeoCoreOntology_geological_structure - estrutura geológica - - - - #UFRGS:GeoCoreOntology_geological_structure - geological structure - - - - #UFRGS:GeoCoreOntology_geological_time_interval - It is a Temporal Region of one dimension within the Global Geological Time. A Geological Time Interval may be occupied by one or several Geological Processes. - - - - #UFRGS:GeoCoreOntology_geological_time_interval - geological time interval - - - - #UFRGS:GeoCoreOntology_geological_time_interval - intervalo de tempo geológico - - - - #UFRGS:GeoCoreOntology_has_age - The relation between a Geological Object and its Geological Age. - - - - #UFRGS:GeoCoreOntology_has_age - has age - - - - #UFRGS:GeoCoreOntology_mineral - Mineral is an 'earth material' that is an inorganic, solid, and homogenous chemical compound with crystalline structure. - - - - #UFRGS:GeoCoreOntology_mineral - mineral - - - - #UFRGS:GeoCoreOntology_mineral - mineral - - - - #UFRGS:GeoCoreOntology_rock - Rock is a solid consolidated 'earth material' that is made of mineral matter, or material of mineral origin. - - - - #UFRGS:GeoCoreOntology_rock - Geologists define rock at a scale of observation where they consider it a homogeneous mass. - - - - #UFRGS:GeoCoreOntology_rock - rocha - - - - #UFRGS:GeoCoreOntology_rock - rock - - - - #UFRGS:GeoCoreOntology_unconsolidated_earth_material - Unconsolidated earth material is an 'earth material' that is consituted by an aggregate of solid particles but is not consolidated into a 'rock' it self. - - - - #UFRGS:GeoCoreOntology_unconsolidated_earth_material - material geológico inconsolidado - - - - #UFRGS:GeoCoreOntology_unconsolidated_earth_material - unconsolidated earth material - - - - - - - diff --git a/imports/GeologicalSpatialRelationsOntology.owl b/imports/GeologicalSpatialRelationsOntology.owl deleted file mode 100644 index 5f5aede..0000000 --- a/imports/GeologicalSpatialRelationsOntology.owl +++ /dev/null @@ -1,527 +0,0 @@ - - - - - - - - - https://www.inf.ufrgs.br/bdi/ontologies/geocoreontology/1.0 - - - Fernando Cicconeto - - - - Joel Luis Carbonera - - - - Lucas Valadares Vieira - - - - Mara Abel - - - - Renata dos Santos Alvarenga - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - #UFRGS:GeologicalSpatialRelationsOntology_above - A spatial relation between two Independent Continuants (BFO), x and y, in which x has a location greater than the location of y in the vertical axis corresponding to the same frame of reference. It is the inverse relation of Below. - - - - #UFRGS:GeologicalSpatialRelationsOntology_above - above - - - - #UFRGS:GeologicalSpatialRelationsOntology_behind - A spatial relation between two Independent Continuants(BFO), x and y, in which y has a location that makes it nearer than x in the longitudinal axis corresponding to the same frame of reference. It is the inverse relation of In Front Of. - - - - #UFRGS:GeologicalSpatialRelationsOntology_behind - behind - - - - #UFRGS:GeologicalSpatialRelationsOntology_below - A spatial relation between two Independent Continuants (BFO), x and y, in which x has a location lower than the location of y in the vertical axis corresponding to the same frame of reference. It is the inverse relation of Above. - - - - #UFRGS:GeologicalSpatialRelationsOntology_below - below - - - - #UFRGS:GeologicalSpatialRelationsOntology_externally_connected_with - A symmetric subrelation of Spatially Discrete From between two Independent Continuants (BFO) whose external boundaries are adjacent. - - - - #UFRGS:GeologicalSpatialRelationsOntology_externally_connected_with - externally connected with - - - - #UFRGS:GeologicalSpatialRelationsOntology_has_non_tangential_proper_spatial_part - A subrelation of Has Proper Spatial Part between two Independent Continuants (BFO) whose external boundaries are not adjacent. It is the inverse relation of Non-tangential Proper Spatial Part Of. - - - - #UFRGS:GeologicalSpatialRelationsOntology_has_non_tangential_proper_spatial_part - has non-tangential proper spatial part - - - - #UFRGS:GeologicalSpatialRelationsOntology_has_proper_spatial_part - A transitive subrelation of Location Of (BFO) between two Independent Continuants (BFO), x and y, in which the spatial region that y occupies is entirely inside the spatial region that x occupies. It is the inverse relation of Proper Spatial Part Of. - - - - #UFRGS:GeologicalSpatialRelationsOntology_has_proper_spatial_part - has proper spatial part - - - - #UFRGS:GeologicalSpatialRelationsOntology_has_tangential_proper_spatial_part - A subrelation of Has Proper Spatial Part between two Independent Continuants (BFO) whose external boundaries are adjacent. It is the inverse relation of Tangential Proper Spatial Part Of. - - - - #UFRGS:GeologicalSpatialRelationsOntology_has_tangential_proper_spatial_part - has tangential proper spatial part - - - - #UFRGS:GeologicalSpatialRelationsOntology_in_front_of - A spatial relation between two Independent Continuants (BFO), x and y, in which x has a location that makes it nearer than y in the longitudinal axis corresponding to the same frame of reference. It is the inverse relation of Behind. - - - - #UFRGS:GeologicalSpatialRelationsOntology_in_front_of - in front of - - - - #UFRGS:GeologicalSpatialRelationsOntology_left_of - A spatial relation between two Independent Continuants(BFO), x and y, in which x has a location to the east of the location of y in the horizontal axis corresponding to the same frame of reference. It is the inverse relation of Right Of. - - - - #UFRGS:GeologicalSpatialRelationsOntology_left_of - left of - - - - #UFRGS:GeologicalSpatialRelationsOntology_non_tangential_proper_spatial_part_of - A subrelation of Proper Spatial Part Of between two Independent Continuants (BFO) whose external boundaries are not adjacent. It is the inverse relation of Has Non-tangential Proper Spatial Part. - - - - #UFRGS:GeologicalSpatialRelationsOntology_non_tangential_proper_spatial_part_of - non-tangential proper spatial part of - - - - #UFRGS:GeologicalSpatialRelationsOntology_proper_spatial_part_of - A transitive subrelation of Located In (BFO) between two Independent Continuants (BFO), x and y, in which the spatial region that x occupies is entirely inside the spatial region that y occupies. It is the inverse relation of Has Proper Spatial Part. - - - - #UFRGS:GeologicalSpatialRelationsOntology_proper_spatial_part_of - proper spatial part of - - - - #UFRGS:GeologicalSpatialRelationsOntology_right_of - A spatial relation between two Independent Continuants (BFO), x and y, in which x has a location to the west of the location of y in the horizontal axis corresponding to the same frame of reference. It is the inverse relation of Left Of. - - - - #UFRGS:GeologicalSpatialRelationsOntology_right_of - right of - - - - #UFRGS:GeologicalSpatialRelationsOntology_spatially_disconnected_from - A symmetric subrelation of Spatially Discrete From between two Independent Continuants (BFO) whose external boundaries are not adjacent. - - - - #UFRGS:GeologicalSpatialRelationsOntology_spatially_disconnected_from - spatially disconnected from - - - - #UFRGS:GeologicalSpatialRelationsOntology_spatially_discrete_from - A symmetric spatial relation between two Independent Continuants (BFO) in which both do not share the same spatial region, either wholly or partially. - - - - #UFRGS:GeologicalSpatialRelationsOntology_spatially_discrete_from - spatially discrete from - - - - #UFRGS:GeologicalSpatialRelationsOntology_spatially_identical_to - A symmetric spatial relation between two Independent Continuants (BFO) in which both occupy precisely the same spatial region. - - - - #UFRGS:GeologicalSpatialRelationsOntology_spatially_identical_to - spatially identical to - - - - #UFRGS:GeologicalSpatialRelationsOntology_spatially_partially_overlaps - A symmetric spatial relation between two Independent Continuants (BFO) in which both share a part of the spatial regions they occupy. - - - - #UFRGS:GeologicalSpatialRelationsOntology_spatially_partially_overlaps - spatially partially overlaps - - - - #UFRGS:GeologicalSpatialRelationsOntology_tangential_proper_spatial_part_of - A subrelation of Proper Spatial Part Of between two Independent Continuants (BFO) whose external boundaries are adjacent. It is the inverse relation of Has Tangential Proper Spatial Part. - - - - #UFRGS:GeologicalSpatialRelationsOntology_tangential_proper_spatial_part_of - tangential proper spatial part of - - - - - - - diff --git a/issue_template.md b/issue_template.md new file mode 100644 index 0000000..173093d --- /dev/null +++ b/issue_template.md @@ -0,0 +1,21 @@ +For new term requests, please provide the following information: + +## Preferred term label + +(e.g., Asplenia) + +## Synonyms + +(e.g., Absent spleen) + +## Textual definition + +the definition should be understandable even for non-specialists. Include a PubMed ID to refer to any relevant article that provides additional information about the suggested term. + +## Suggested parent term + +Please look in the hierarchy in a browser such as [OLS](http://www.ebi.ac.uk/ols/ontologies/geores) + +## Attribution + +If you would like a nanoattribution, please indicate your ORCID id \ No newline at end of file diff --git a/src/metadata/README.md b/src/metadata/README.md new file mode 100644 index 0000000..35fa313 --- /dev/null +++ b/src/metadata/README.md @@ -0,0 +1,24 @@ +Metadata files for the OBO Library + + * [geores.yml](geores.yml) + * Determines how your purl.obolibrary.org/obo/geores/ redirects will be handled + * Go here: https://github.com/OBOFoundry/purl.obolibrary.org/tree/master/config + * Click [New File](https://github.com/OBOFoundry/purl.obolibrary.org/new/master/config) + * Paste in the contents of [geores.yml](geores.yml) + * Click "Commit new file" + * IMPORTANT: remember to make a pull request + * An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library* + * [geores.md](geores.md) + * Determines how your metadata is shown on OBO Library, OLS and AberOWL + * Go here: https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/ontology + * Click [New File](https://github.com/OBOFoundry/OBOFoundry.github.io/new/master/ontology) + * Paste in the contents of [geores.md](geores.md) + * Click "Commit new file" + * IMPORTANT: remember to make a pull request + * An OBO admin will merge your Pull Request *providing it meets the requirements of the OBO library* + +For more background see: + + * http://obofoundry.org/ + * http://obofoundry.org/faq/how-do-i-edit-metadata.html + diff --git a/src/metadata/geores.md b/src/metadata/geores.md new file mode 100644 index 0000000..a025ed2 --- /dev/null +++ b/src/metadata/geores.md @@ -0,0 +1,45 @@ +--- +layout: ontology_detail +id: geores +title: GeoReservoir Ontology +jobs: + - id: https://travis-ci.org/BDI-UFRGS/GeoReservoirOntology + type: travis-ci +build: + checkout: git clone https://github.com/BDI-UFRGS/GeoReservoirOntology.git + system: git + path: "." +contact: + email: + label: + github: +description: GeoReservoir Ontology is an ontology... +domain: stuff +homepage: https://github.com/BDI-UFRGS/GeoReservoirOntology +products: + - id: geores.owl + name: "GeoReservoir Ontology main release in OWL format" + - id: geores.obo + name: "GeoReservoir Ontology additional release in OBO format" + - id: geores.json + name: "GeoReservoir Ontology additional release in OBOJSon format" + - id: geores/geores-base.owl + name: "GeoReservoir Ontology main release in OWL format" + - id: geores/geores-base.obo + name: "GeoReservoir Ontology additional release in OBO format" + - id: geores/geores-base.json + name: "GeoReservoir Ontology additional release in OBOJSon format" +dependencies: +- id: bfo2020 +- id: geocore + +tracker: https://github.com/BDI-UFRGS/GeoReservoirOntology/issues +license: + url: http://creativecommons.org/licenses/by/3.0/ + label: CC-BY +activity_status: active +--- + +Enter a detailed description of your ontology here. You can use arbitrary markdown and HTML. +You can also embed images too. + diff --git a/src/metadata/geores.yml b/src/metadata/geores.yml new file mode 100644 index 0000000..5b7113d --- /dev/null +++ b/src/metadata/geores.yml @@ -0,0 +1,28 @@ +# PURL configuration for http://purl.obolibrary.org/obo/geores + +idspace: GEORES +base_url: /obo/geores + +products: +- geores.owl: https://raw.githubusercontent.com/BDI-UFRGS/GeoReservoirOntology/master/geores.owl +- geores.obo: https://raw.githubusercontent.com/BDI-UFRGS/GeoReservoirOntology/master/geores.obo + +term_browser: ontobee +example_terms: +- GEORES_0000000 + +entries: + +- prefix: /releases/ + replacement: https://raw.githubusercontent.com/BDI-UFRGS/GeoReservoirOntology/v + +- prefix: /tracker/ + replacement: https://github.com/BDI-UFRGS/GeoReservoirOntology/issues + +- prefix: /about/ + replacement: http://www.ontobee.org/ontology/GEORES?iri=http://purl.obolibrary.org/obo/ + +## generic fall-through, serve direct from github by default +- prefix: / + replacement: https://raw.githubusercontent.com/BDI-UFRGS/GeoReservoirOntology/master/ + diff --git a/src/ontology/Makefile b/src/ontology/Makefile new file mode 100644 index 0000000..a0ca851 --- /dev/null +++ b/src/ontology/Makefile @@ -0,0 +1,660 @@ +# ---------------------------------------- +# Makefile for geores +# Generated using ontology-development-kit +# ODK Version: v1.5 +# ---------------------------------------- +# IMPORTANT: DO NOT EDIT THIS FILE. To override default make goals, use geores.Makefile instead + + +# ---------------------------------------- +# More information: https://github.com/INCATools/ontology-development-kit/ + +# Fingerprint of the configuration file when this Makefile was last generated +CONFIG_HASH= 4386e2dd96eb76db6ea9a0bd919780cfc2b324ad182d857aaceaa9d03f9ad8a6 + + +# ---------------------------------------- +# Standard Constants +# ---------------------------------------- +# these can be overwritten on the command line + +OBOBASE= http://purl.obolibrary.org/obo +URIBASE= https://www.inf.ufrgs.br/bdi/ontologies +ONT= geores +ONTBASE= https://www.inf.ufrgs.br/bdi/ontologies/geores +EDIT_FORMAT= owl +SRC = $(ONT)-edit.$(EDIT_FORMAT) +MAKE_FAST= $(MAKE) IMP=false PAT=false COMP=false MIR=false +CATALOG= catalog-v001.xml +ROBOT= robot --catalog $(CATALOG) + +OWLTOOLS= owltools --use-catalog +RELEASEDIR= ../.. +REPORTDIR= reports +TEMPLATEDIR= ../templates +TMPDIR= tmp +MIRRORDIR= mirror +IMPORTDIR= imports +SUBSETDIR= subsets +SCRIPTSDIR= ../scripts +UPDATEREPODIR= target +SPARQLDIR = ../sparql +COMPONENTSDIR = components +REPORT_FAIL_ON = None +REPORT_LABEL = -l true +REPORT_PROFILE_OPTS = +OBO_FORMAT_OPTIONS = +SPARQL_VALIDATION_CHECKS = owldef-self-reference iri-range label-with-iri multiple-replaced_by dc-properties +SPARQL_EXPORTS = basic-report edges xrefs obsoletes synonyms +ODK_VERSION_MAKEFILE = v1.5 + +TODAY ?= $(shell date +%Y-%m-%d) +OBODATE ?= $(shell date +'%d:%m:%Y %H:%M') +VERSION= $(TODAY) +ANNOTATE_ONTOLOGY_VERSION = annotate -V $(ONTBASE)/releases/$(VERSION)/$@ --annotation owl:versionInfo $(VERSION) +ANNOTATE_CONVERT_FILE = annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) convert -f ofn --output $@.tmp.owl && mv $@.tmp.owl $@ +OTHER_SRC = +ONTOLOGYTERMS = $(TMPDIR)/ontologyterms.txt +EDIT_PREPROCESSED = $(TMPDIR)/$(ONT)-preprocess.owl + +FORMATS = $(sort owl obo owl) +FORMATS_INCL_TSV = $(sort $(FORMATS) tsv) +RELEASE_ARTEFACTS = $(sort $(ONT)-base $(ONT)-full $(ONT)-simple ) + +ifeq ($(ODK_DEBUG),yes) +ODK_DEBUG_FILE = debug.log +SHELL = $(SCRIPTSDIR)/run-command.sh +endif + +# ---------------------------------------- +# Top-level targets +# ---------------------------------------- + +.PHONY: .FORCE + +.PHONY: all +all: all_odk + +.PHONY: all_odk +all_odk: odkversion config_check test custom_reports all_assets + +.PHONY: test +test: odkversion reason_test sparql_test robot_reports $(REPORTDIR)/validate_profile_owl2dl_$(ONT).owl.txt + echo "Finished running all tests successfully." + +.PHONY: test +test_fast: + $(MAKE_FAST) test + +.PHONY: release_diff +release_diff: $(REPORTDIR)/release-diff.md + +.PHONY: reason_test +reason_test: $(EDIT_PREPROCESSED) + $(ROBOT) reason --input $< --reasoner ELK --equivalent-classes-allowed asserted-only \ + --exclude-tautologies structural --output test.owl && rm test.owl + +.PHONY: odkversion +odkversion: + @echo "ODK Makefile $(ODK_VERSION_MAKEFILE)" + @odk-info --tools +.PHONY: config_check +config_check: + @if [ "$$(sha256sum $(ONT)-odk.yaml | cut -c1-64)" = "$(CONFIG_HASH)" ]; then \ + echo "Repository is up-to-date." ; else \ + echo "Your ODK configuration has changed since this Makefile was generated. You may need to run 'make update_repo'." ; fi + + +$(TMPDIR) $(REPORTDIR) $(MIRRORDIR) $(IMPORTDIR) $(COMPONENTSDIR) $(SUBSETDIR): + mkdir -p $@ + +# ---------------------------------------- +# ODK-managed ROBOT plugins +# ---------------------------------------- + +# Make sure ROBOT knows where to find plugins +export ROBOT_PLUGINS_DIRECTORY=$(TMPDIR)/plugins + +# Override this rule in geores.Makefile to install custom plugins +.PHONY: custom_robot_plugins +custom_robot_plugins: + + +.PHONY: extra_robot_plugins +extra_robot_plugins: + + +# Install all ROBOT plugins to the runtime plugins directory +.PHONY: all_robot_plugins +all_robot_plugins: $(foreach plugin,$(notdir $(wildcard /tools/robot-plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \ + $(foreach plugin,$(notdir $(wildcard ../../plugins/*.jar)),$(ROBOT_PLUGINS_DIRECTORY)/$(plugin)) \ + custom_robot_plugins extra_robot_plugins \ + +# Default rule to install plugins +$(ROBOT_PLUGINS_DIRECTORY)/%.jar: + @mkdir -p $(ROBOT_PLUGINS_DIRECTORY) + @if [ -f ../../plugins/$*.jar ]; then \ + ln ../../plugins/$*.jar $@ ; \ + elif [ -f /tools/robot-plugins/$*.jar ]; then \ + cp /tools/robot-plugins/$*.jar $@ ; \ + fi + +# Specific rules for supplementary plugins defined in configuration + + +# ---------------------------------------- +# Release assets +# ---------------------------------------- + +MAIN_PRODUCTS = $(sort $(foreach r,$(RELEASE_ARTEFACTS), $(r)) $(ONT)) +MAIN_GZIPPED = +MAIN_FILES = $(foreach n,$(MAIN_PRODUCTS), $(foreach f,$(FORMATS), $(n).$(f))) $(MAIN_GZIPPED) +SRCMERGED = $(TMPDIR)/merged-$(SRC) + +.PHONY: all_main +all_main: $(MAIN_FILES) + +# ---------------------------------------- +# Import assets +# ---------------------------------------- + + +IMPORTS = bfo2020 geocore + +IMPORT_ROOTS = $(patsubst %, $(IMPORTDIR)/%_import, $(IMPORTS)) +IMPORT_OWL_FILES = $(foreach n,$(IMPORT_ROOTS), $(n).owl) +IMPORT_FILES = $(IMPORT_OWL_FILES) + + +.PHONY: all_imports +all_imports: $(IMPORT_FILES) + +# ---------------------------------------- +# Subset assets +# ---------------------------------------- + + +SUBSETS = + +SUBSET_ROOTS = $(patsubst %, $(SUBSETDIR)/%, $(SUBSETS)) +SUBSET_FILES = $(foreach n,$(SUBSET_ROOTS), $(foreach f,$(FORMATS_INCL_TSV), $(n).$(f))) + +.PHONY: all_subsets +all_subsets: $(SUBSET_FILES) + +# ---------------------------------------- +# Mapping assets +# ---------------------------------------- + + +MAPPINGS = + +MAPPING_FILES = $(patsubst %, $(MAPPINGDIR)/%.sssom.tsv, $(MAPPINGS)) + +.PHONY: all_mappings +all_mappings: $(MAPPING_FILES) + + +# ---------------------------------------- +# QC Reports & Utilities +# ---------------------------------------- + +OBO_REPORT = $(SRC)-obo-report +REPORTS = $(OBO_REPORT) +REPORT_FILES = $(patsubst %, $(REPORTDIR)/%.tsv, $(REPORTS)) + +.PHONY: robot_reports +robot_reports: $(REPORT_FILES) + +.PHONY: all_reports +all_reports: custom_reports robot_reports + +# ---------------------------------------- +# ROBOT OWL Profile checking +# ---------------------------------------- + +# The merge step is necessary to avoid undeclared entity violations. +$(REPORTDIR)/validate_profile_owl2dl_%.txt: % | $(REPORTDIR) $(TMPDIR) + $(ROBOT) merge -i $< convert -f ofn -o $(TMPDIR)/validate.ofn + $(ROBOT) validate-profile --profile DL -i $(TMPDIR)/validate.ofn -o $@ || { cat $@ && exit 1; } +.PRECIOUS: $(REPORTDIR)/validate_profile_owl2dl_%.txt + +validate_profile_%: $(REPORTDIR)/validate_profile_owl2dl_%.txt + echo "$* profile validation completed." + +# ---------------------------------------- +# Sparql queries: Q/C +# ---------------------------------------- + +# these live in the ../sparql directory, and have suffix -violation.sparql +# adding the name here will make the violation check live. + +SPARQL_VALIDATION_QUERIES = $(foreach V,$(SPARQL_VALIDATION_CHECKS),$(SPARQLDIR)/$(V)-violation.sparql) + +sparql_test: $(EDIT_PREPROCESSED) | $(REPORTDIR) +ifneq ($(SPARQL_VALIDATION_QUERIES),) + + $(ROBOT) verify -i $(EDIT_PREPROCESSED) --queries $(SPARQL_VALIDATION_QUERIES) -O $(REPORTDIR) +endif + +# ---------------------------------------- +# ROBOT report +# ---------------------------------------- + +$(REPORTDIR)/$(SRC)-obo-report.tsv: $(SRCMERGED) | $(REPORTDIR) + $(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --base-iri $(URIBASE)/GEORES_ --base-iri $(URIBASE)/geores --print 5 -o $@ + +$(REPORTDIR)/%-obo-report.tsv: % | $(REPORTDIR) + $(ROBOT) report -i $< $(REPORT_LABEL) $(REPORT_PROFILE_OPTS) --fail-on $(REPORT_FAIL_ON) --base-iri $(URIBASE)/GEORES_ --base-iri $(URIBASE)/geores --print 5 -o $@ + +check_for_robot_updates: + echo "You are not using a custom profile, so you are getting the joy of the latest ROBOT report!" + + +# ---------------------------------------- +# Release assets +# ---------------------------------------- + +ASSETS = \ + $(IMPORT_FILES) \ + $(MAIN_FILES) \ + $(REPORT_FILES) \ + $(SUBSET_FILES) \ + $(MAPPING_FILES) + +RELEASE_ASSETS = \ + $(MAIN_FILES) \ + $(SUBSET_FILES) + +.PHONY: all_assets +all_assets: $(ASSETS) check_rdfxml_assets + +.PHONY: show_assets +show_assets: + echo $(ASSETS) + du -sh $(ASSETS) + +check_rdfxml_%: % + @check-rdfxml $< + +.PHONY: check_rdfxml_assets +check_rdfxml_assets: $(foreach product,$(MAIN_PRODUCTS),check_rdfxml_$(product).owl) + +# ---------------------------------------- +# Release Management +# ---------------------------------------- + +CLEANFILES=$(MAIN_FILES) $(SRCMERGED) $(EDIT_PREPROCESSED) +# This should be executed by the release manager whenever time comes to make a release. +# It will ensure that all assets/files are fresh, and will copy to release folder + +.PHONY: prepare_release +prepare_release: all_odk + rsync -R $(RELEASE_ASSETS) $(RELEASEDIR) &&\ + rm -f $(CLEANFILES) &&\ + echo "Release files are now in $(RELEASEDIR) - now you should commit, push and make a release \ + on your git hosting site such as GitHub or GitLab" + +.PHONY: prepare_initial_release +prepare_initial_release: all_assets + rsync -R $(RELEASE_ASSETS) $(RELEASEDIR) &&\ + rm -f $(patsubst %, ./%, $(CLEANFILES)) &&\ + cd $(RELEASEDIR) && git add $(RELEASE_ASSETS) + +.PHONY: prepare_release_fast +prepare_release_fast: + $(MAKE) prepare_release IMP=false PAT=false MIR=false COMP=false + +CURRENT_RELEASE=$(ONTBASE).owl + +$(TMPDIR)/current-release.owl: + wget $(CURRENT_RELEASE) -O $@ + +$(REPORTDIR)/release-diff.md: $(ONT).owl $(TMPDIR)/current-release.owl + $(ROBOT) diff --labels true --left $(TMPDIR)/current-release.owl --right $(ONT).owl -f markdown -o $@ + +# ------------------------ +# Imports: Seeding system +# ------------------------ + +# seed.txt contains all referenced entities +IMPORTSEED=$(TMPDIR)/seed.txt +PRESEED=$(TMPDIR)/pre_seed.txt + +$(SRCMERGED): $(EDIT_PREPROCESSED) $(OTHER_SRC) + $(ROBOT) remove --input $< --select imports --trim false \ + merge $(patsubst %, -i %, $(OTHER_SRC)) -o $@ + +$(EDIT_PREPROCESSED): $(SRC) + $(ROBOT) convert --input $< --format ofn --output $@ + +$(PRESEED): $(SRCMERGED) + $(ROBOT) query -f csv -i $< --query ../sparql/terms.sparql $@.tmp &&\ + cat $@.tmp | sort | uniq > $@ + +SIMPLESEED=$(TMPDIR)/simple_seed.txt + +$(SIMPLESEED): $(SRCMERGED) $(ONTOLOGYTERMS) + $(ROBOT) query -f csv -i $< --query ../sparql/simple-seed.sparql $@.tmp &&\ + cat $@.tmp $(ONTOLOGYTERMS) | sort | uniq > $@ &&\ + echo "http://www.geneontology.org/formats/oboInOwl#SubsetProperty" >> $@ &&\ + echo "http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty" >> $@ + + +ALLSEED = $(PRESEED) \ + + +$(IMPORTSEED): $(ALLSEED) | $(TMPDIR) + if [ $(IMP) = true ]; then cat $(ALLSEED) | sort | uniq > $@; fi + +ANNOTATION_PROPERTIES=rdfs:label IAO:0000115 + +# ---------------------------------------- +# Import modules +# ---------------------------------------- +# Most ontologies are modularly constructed using portions of other ontologies +# These live in the imports/ folder +# This pattern uses ROBOT to generate an import module + +# Should be able to drop this if robot can just take a big messy list of terms as input. +$(IMPORTDIR)/%_terms_combined.txt: $(IMPORTSEED) $(IMPORTDIR)/%_terms.txt + if [ $(IMP) = true ]; then cat $^ | grep -v ^# | sort | uniq > $@; fi + + + + +$(IMPORTDIR)/%_import.owl: $(MIRRORDIR)/%.owl $(IMPORTDIR)/%_terms_combined.txt + if [ $(IMP) = true ]; then $(ROBOT) query -i $< --update ../sparql/preprocess-module.ru \ + extract -T $(IMPORTDIR)/$*_terms_combined.txt --force true --copy-ontology-annotations true --individuals include --method BOT \ + query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru --update ../sparql/postprocess-module.ru \ + $(ANNOTATE_CONVERT_FILE); fi + +.PRECIOUS: $(IMPORTDIR)/%_import.owl + +## Module for ontology: geocore + + +.PHONY: refresh-imports +refresh-imports: + $(MAKE) IMP=true MIR=true PAT=false IMP_LARGE=true all_imports -B + +.PHONY: no-mirror-refresh-imports +no-mirror-refresh-imports: + $(MAKE) IMP=true MIR=false PAT=false IMP_LARGE=true all_imports -B + +.PHONY: refresh-imports-excluding-large +refresh-imports-excluding-large: + $(MAKE) IMP=true MIR=true PAT=false IMP_LARGE=false all_imports -B + +.PHONY: refresh-% +refresh-%: + $(MAKE) IMP=true IMP_LARGE=true MIR=true PAT=false $(IMPORTDIR)/$*_import.owl -B + +.PHONY: no-mirror-refresh-% +no-mirror-refresh-%: + $(MAKE) IMP=true IMP_LARGE=true MIR=false PAT=false $(IMPORTDIR)/$*_import.owl -B + +# ---------------------------------------- +# Mirroring upstream ontologies +# ---------------------------------------- + +IMP=true # Global parameter to bypass import generation +MIR=true # Global parameter to bypass mirror generation +IMP_LARGE=true # Global parameter to bypass handling of large imports + +ifeq ($(strip $(MIR)),true) + + +## ONTOLOGY: bfo2020 +.PHONY: mirror-bfo2020 +.PRECIOUS: $(MIRRORDIR)/bfo2020.owl +mirror-bfo2020: | $(TMPDIR) + $(ROBOT) convert -I http://purl.obolibrary.org/obo/bfo/2020/bfo-core.owl -o $(TMPDIR)/$@.owl + + +## ONTOLOGY: geocore +.PHONY: mirror-geocore +.PRECIOUS: $(MIRRORDIR)/geocore.owl +mirror-geocore: | $(TMPDIR) + $(ROBOT) convert -I https://www.inf.ufrgs.br/bdi/ontologies/geocore/releases/2024-04-06/geocore.owl -o $(TMPDIR)/$@.owl + + +$(MIRRORDIR)/%.owl: mirror-% | $(MIRRORDIR) + if [ -f $(TMPDIR)/mirror-$*.owl ]; then if cmp -s $(TMPDIR)/mirror-$*.owl $@ ; then echo "Mirror identical, ignoring."; else echo "Mirrors different, updating." &&\ + cp $(TMPDIR)/mirror-$*.owl $@; fi; fi + +else # MIR=false +$(MIRRORDIR)/%.owl: + @echo "Not refreshing $@ because the mirrorring pipeline is disabled (MIR=$(MIR))." +endif + + + +# ---------------------------------------- +# Subsets +# ---------------------------------------- +$(SUBSETDIR)/%.tsv: $(SUBSETDIR)/%.owl + $(ROBOT) query -f tsv -i $< -s ../sparql/labels.sparql $@ +.PRECIOUS: $(SUBSETDIR)/%.tsv + +$(SUBSETDIR)/%.owl: $(ONT).owl | $(SUBSETDIR) + $(OWLTOOLS) $< --extract-ontology-subset --fill-gaps --subset $* -o $@.tmp.owl && mv $@.tmp.owl $@ &&\ + $(ROBOT) annotate --input $@ --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) -o $@.tmp.owl && mv $@.tmp.owl $@ +.PRECIOUS: $(SUBSETDIR)/%.owl + + +$(SUBSETDIR)/%.obo: $(SUBSETDIR)/%.owl + $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo + + +# --------------------------------------------- +# Sparql queries: Table exports / Query Reports +# --------------------------------------------- + +SPARQL_EXPORTS_ARGS = $(foreach V,$(SPARQL_EXPORTS),-s $(SPARQLDIR)/$(V).sparql $(REPORTDIR)/$(V).tsv) +# This combines all into one single command + +.PHONY: custom_reports +custom_reports: $(EDIT_PREPROCESSED) | $(REPORTDIR) +ifneq ($(SPARQL_EXPORTS_ARGS),) + $(ROBOT) query -f tsv --use-graphs true -i $< $(SPARQL_EXPORTS_ARGS) +endif + +# ---------------------------------------- +# Release artefacts: export formats +# ---------------------------------------- + + +$(ONT)-base.obo: $(ONT)-base.owl + $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo +$(ONT)-full.obo: $(ONT)-full.owl + $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo +$(ONT)-simple.obo: $(ONT)-simple.owl + $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo +# ---------------------------------------- +# Release artefacts: main release artefacts +# ---------------------------------------- + +$(ONT).owl: $(ONT)-full.owl + $(ROBOT) annotate --input $< --ontology-iri $(URIBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ + convert -o $@.tmp.owl && mv $@.tmp.owl $@ + +$(ONT).obo: $(ONT).owl + $(ROBOT) convert --input $< --check false -f obo $(OBO_FORMAT_OPTIONS) -o $@.tmp.obo && grep -v ^owl-axioms $@.tmp.obo > $@ && rm $@.tmp.obo +# ----------------------------------------------------- +# Release artefacts: variants (base, full, simple, etc) +# ----------------------------------------------------- +SHARED_ROBOT_COMMANDS = + +$(ONTOLOGYTERMS): $(SRCMERGED) + $(ROBOT) query -f csv -i $< --query ../sparql/geores_terms.sparql $@ + +# ROBOT pipeline that merges imports, including components. +ROBOT_RELEASE_IMPORT_MODE=$(ROBOT) merge --input $< + +# ROBOT pipeline that removes imports, then merges components. This is for release artefacts that start from "base" +ROBOT_RELEASE_IMPORT_MODE_BASE=$(ROBOT) remove --input $< --select imports --trim false merge $(patsubst %, -i %, $(OTHER_SRC)) + +# base: A version of the ontology that does not include any externally imported axioms. +$(ONT)-base.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) + $(ROBOT_RELEASE_IMPORT_MODE) \ + reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural --annotate-inferred-axioms False \ + relax \ + reduce -r ELK \ + remove --base-iri $(URIBASE)/GEORES --axioms external --preserve-structure false --trim false \ + $(SHARED_ROBOT_COMMANDS) \ + annotate --link-annotation http://purl.org/dc/elements/1.1/type http://purl.obolibrary.org/obo/IAO_8000001 \ + --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) \ + --output $@.tmp.owl && mv $@.tmp.owl $@ +# Full: The full artefacts with imports merged, reasoned. +$(ONT)-full.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(IMPORT_FILES) + $(ROBOT_RELEASE_IMPORT_MODE) \ + reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural \ + relax \ + reduce -r ELK \ + $(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@ +# foo-simple: (edit->reason,relax,reduce,drop imports, drop every axiom which contains an entity outside the "namespaces of interest") +# drop every axiom: filter --term-file keep_terms.txt --trim true +# remove --select imports --trim false +$(ONT)-simple.owl: $(EDIT_PREPROCESSED) $(OTHER_SRC) $(SIMPLESEED) $(IMPORT_FILES) + $(ROBOT_RELEASE_IMPORT_MODE) \ + reason --reasoner ELK --equivalent-classes-allowed asserted-only --exclude-tautologies structural --annotate-inferred-axioms False \ + relax \ + remove --axioms equivalent \ + relax \ + filter --term-file $(SIMPLESEED) --select "annotations ontology anonymous self" --trim true --signature true \ + reduce -r ELK \ + query --update ../sparql/inject-subset-declaration.ru --update ../sparql/inject-synonymtype-declaration.ru \ + $(SHARED_ROBOT_COMMANDS) annotate --ontology-iri $(ONTBASE)/$@ $(ANNOTATE_ONTOLOGY_VERSION) --output $@.tmp.owl && mv $@.tmp.owl $@ +# ---------------------------------------- +# Debugging Tools +# ---------------------------------------- + +explain_unsat: $(EDIT_PREPROCESSED) + $(ROBOT) explain -i $< -M unsatisfiability --unsatisfiable random:10 --explanation $(TMPDIR)/$@.md + + + +RELEASE_ASSETS_AFTER_RELEASE=$(foreach n,$(RELEASE_ASSETS), ../../$(n)) +GHVERSION=v$(VERSION) + +.PHONY: public_release +public_release: + @test $(GHVERSION) + ls -alt $(RELEASE_ASSETS_AFTER_RELEASE) + gh release create $(GHVERSION) --title "$(VERSION) Release" --draft $(RELEASE_ASSETS_AFTER_RELEASE) --generate-notes + +# ---------------------------------------- +# General Validation +# ---------------------------------------- +TSV= +ALL_TSV_FILES= + +validate-tsv: $(TSV) | $(TMPDIR) + for FILE in $< ; do \ + tsvalid $$FILE > $(TMPDIR)/validate.txt; \ + if [ -s $(TMPDIR)/validate.txt ]; then cat $(TMPDIR)/validate.txt && exit 1; fi ; \ + done + +validate-all-tsv: $(ALL_TSV_FILES) + $(MAKE) validate-tsv TSV="$^" + +# ---------------------------------------- +# Editors Utilities +# ---------------------------------------- + + + +.PHONY: normalize_src +normalize_src: $(SRC) + $(ROBOT) convert -i $< -f ofn -o $(TMPDIR)/normalise && mv $(TMPDIR)/normalise $< + +.PHONY: validate_idranges +validate_idranges: + amm $(SCRIPTSDIR)/validate_id_ranges.sc geores-idranges.owl + +.PHONY: update_repo +update_repo: + sh $(SCRIPTSDIR)/update_repo.sh + + + +# Note to future generations: computing the real path relative to the +# current directory is a way to ensure we only clean up directories that +# are located below the current directory, regardless of the contents of +# the *DIR variables. +.PHONY: clean +clean: + for dir in $(MIRRORDIR) $(TMPDIR) $(UPDATEREPODIR) ; do \ + reldir=$$(realpath --relative-to=$$(pwd) $$dir) ; \ + case $$reldir in .*|"") ;; *) rm -rf $$reldir/* ;; esac \ + done + rm -f $(CLEANFILES) + +.PHONY: help +help: + @echo "$$data" + +define data +Usage: [IMAGE=(odklite|odkfull)] [ODK_DEBUG=yes] sh run.sh make [(IMP|MIR|IMP_LARGE|PAT)=(false|true)] command + +---------------------------------------- + Command reference +---------------------------------------- + +Core commands: +* prepare_release: Run the entire release pipeline. Use make IMP=false prepare_release to avoid rerunning the imports +* prepare_release_fast: Run the entire release pipeline without refreshing imports, recreating components or recompiling patterns. +* update_repo: Update the ODK repository setup using the config file geores-odk.yaml +* test: Running all validation tests +* test_fast: Runs the test suite, but without updating imports or components +* odkversion: Show the current version of the ODK Makefile and ROBOT. +* clean: Delete all temporary files +* help: Print ODK Usage information +* public_release: Uploads the release file to a release management system, such as GitHub releases. Must be configured. + + +Imports management: +* refresh-imports: Refresh all imports and mirrors. +* recreate-components: Recreate all components. +* no-mirror-refresh-imports: Refresh all imports without downloading mirrors. +* refresh-imports-excluding-large: Refresh all imports and mirrors, but skipping the ones labelled as 'is_large'. +* refresh-%: Refresh a single import, i.e. refresh-go will refresh 'imports/go_import.owl'. +* no-mirror-refresh-%: Refresh a single import without updating the mirror, i.e. refresh-go will refresh 'imports/go_import.owl'. +* mirror-%: Refresh a single mirror. + +Editor utilities: +* validate_idranges: Make sure your ID ranges file is formatted correctly +* normalize_src: Load and save your geores-edit file after you to make sure its serialised correctly +* explain_unsat: If you have unsatisfiable classes, this command will create a markdown file (tmp/explain_unsat.md) which will explain all your unsatisfiable classes +* validate-all-tsv: Check all your tsv files for possible problems in syntax. Use ALL_TSV_FILES variable to list files +* validate-tsv: Check a tsv file for syntactic problems with tsvalid. Use TSV variable to pass filepath, e.g. make TSV=../my.tsv validate-tsv. +* release_diff: Create a diff between the current release and the new release + +Additional build commands (advanced users) +* all: Run the entire pipeline (like prepare_release), but without copying the release files to the release directory. +* all_subsets: Build all subsets +* custom_reports: Generate all custom sparql reports you have configured in your geores-odk.yaml file. +* all_assets: Build all assets +* show_assets: Print a list of all assets that would be build by the release pipeline +* all_mappings: Update all SSSOM mapping sets + +Additional QC commands (advanced users) +* robot_reports: Run all configured ROBOT reports +* validate_profile_%: Run an OWL2 DL profile validation check, for example validate_profile_geores-edit.owl. +* reason_test: Run a basic reasoning test + +Examples: +* sh run.sh make IMP=false prepare_release +* sh run.sh make update_repo +* sh run.sh make test + +Tricks: +* Add -B to the end of your command to force re-running it even if nothing has changed +* Use the IMAGE parameter to the run.sh script to use a different image like odklite +* Use ODK_DEBUG=yes sh run.sh make ... to print information about timing and debugging + +endef +export data + +include geores.Makefile \ No newline at end of file diff --git a/src/ontology/README-editors.md b/src/ontology/README-editors.md new file mode 100644 index 0000000..757cee3 --- /dev/null +++ b/src/ontology/README-editors.md @@ -0,0 +1,27 @@ +These notes are for the EDITORS of geores + +This project was created using the [ontology development kit](https://github.com/INCATools/ontology-development-kit). See the site for details. + +For more details on ontology management, please see the +[OBO Academy Tutorials](https://oboacademy.github.io/obook/), the +[OBO tutorial](https://github.com/jamesaoverton/obo-tutorial) or the [Gene Ontology Editors Tutorial](https://go-protege-tutorial.readthedocs.io/en/latest/) + +This documentation has been superceded by the ODK automatic documentation, which you can +activate by adding: + +``` +documentation: + documentation_system: mkdocs +``` + +to your Makefile and running: + +``` +sh run.sh make update_repo +``` +(Unix) + +``` +run.bat make update_repo +``` +(Windows) \ No newline at end of file diff --git a/src/ontology/catalog-v001.xml b/src/ontology/catalog-v001.xml new file mode 100644 index 0000000..9631c8c --- /dev/null +++ b/src/ontology/catalog-v001.xml @@ -0,0 +1,10 @@ + + + + + + + + + + \ No newline at end of file diff --git a/src/ontology/geores-edit.owl b/src/ontology/geores-edit.owl new file mode 100644 index 0000000..073376e --- /dev/null +++ b/src/ontology/geores-edit.owl @@ -0,0 +1,681 @@ +Prefix(:=) +Prefix(dce:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) +Prefix(dcterms:=) + + +Ontology( +Import() +Import() +Annotation(dce:contributor "Alcides Lopes") +Annotation(dce:contributor "Fabrício Henrique Rodrigues") +Annotation(dce:contributor "Fernando Cicconeto") +Annotation(dce:contributor "Joel Luis Carbonera") +Annotation(dce:contributor "Luan Fonseca Garcia") +Annotation(dce:contributor "Lucas Valadares Vieira") +Annotation(dce:contributor "Mara Abel") +Annotation(dce:contributor "Renata dos Santos Alvarenga") +Annotation(dce:contributor "Tiago Agne de Oliveira") +Annotation(dce:contributor "Yuanwei Qu") +Annotation(dcterms:description "GeoReservoir is an ontology to support the description of the geometry and the lithology of deep-marine deposits. The GeoReservoir ontology provides formal and clear definitions of deep-marine depositional system entities, creating an unambiguous terminology for geometrical and lithological properties of the deposits in the scale of outcrop and seismic sections. These definitions are independent of tasks, geological interpretations, and process inferences. We created this language to make it possible to formally and uniformly describe any deep-marine occurrence in the world with an adequate level of detail for sedimentological studies and computer processing."@en) +Annotation(dcterms:license "https://creativecommons.org/licenses/by-nc/4.0/") +Annotation(dcterms:title "GeoReservoir Ontology") +Annotation(rdfs:comment "Cited references: + +1. Abel, M., Perrin, M., Carbonera, J.L.: Ontological analysis for information integration in geomodeling. Earth Science Informatics 8, 21–36 (2015) +2. Carbonera, J.L., Abel, M., Scherer, C.M.S.: Visual interpretation of events in petroleum exploration: An approach supported by well-founded ontologies. Expert Systems With Applications 42, 2749–2763 (2015) +3. Cullis, S., Colombera, L., Patacci, M., McCaffrey, W.D.: Hierarchical classifications of the sedimentary architecture of deep-marine depositional systems. Earth-Science Reviews 179, 38–71 (2018) +4. De Ros, L.F., Goldberg, K.: Reservoir petrofacies: A tool for quality characterization and prediction. In: AAPG Annual Conference and Exhibition. Long Beach (2007) +5. Garcia, L.F., Carbonera, J.L., Rodrigues, F.H., Antunes, C.R., Abel, M.: What rocks are made of: Towards an ontological pattern for material constitution in the geological domain. In: Laender, A.H.F., Pernici, B., Lim, E.P., Oliveira, J.P.M. (eds.) ER: 38th International Conference on Conceptual Modeling. pp. 275–286. Springer, Cham (2019) +6. Guarino, N., Welty, C.A.: An overview of ontoclean. In: Staab, S., Studer, R. (eds.) Handbook on Ontologies, pp. 151–171. Springer, Berlin, Heidelberg (2004) +7. McHargue, T., Pyrcz, M.J., Sullivan, M.D., Clark, J.D., Fildani, A., Romans, B.W., Covault, J.A., Levy, M., Posamentier, H.W., Drinkwater, N.J.: Architecture of turbidite channel systems on the continental slope: Patterns and predictions. Marine and Petroleum Geology 28, 728–743 (2011) +8. Middleton, G.V.: Johannes walther’s law of the correlation of facies. Bulletin of the Geological Society of America 84, 979–988 (1973) +9. Nichols, G.: Sedimentology and Stratigraphy. Wiley-Blackwell, Chichester, 2nd edn. (2009) +10. Rovetto, R.: The shape of shapes: An ontological exploration. In: Hastings, J., Kutz, O., Bhatt, M., Borgo, S. (eds.) Proceedings of the First Interdisciplinary Workshop on SHAPES. Karlsruhe (2011), http://ceur-ws.org/Vol-812/ +11. Walker, R.G., James, N.P.: Facies Models: Response to Sea Level Change. Geological Association of Canada, St. John’s (1992)"@en) +Annotation(rdfs:comment "We acknowledge the Brazilian funding agencies CNPq and CAPES for financing this work and the Research Centre of Petrobras (CENPES) for collaborating on this project."@en) + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(DataProperty()) +Declaration(DataProperty()) +Declaration(DataProperty()) +Declaration(DataProperty()) +Declaration(DataProperty()) +Declaration(DataProperty()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(AnnotationProperty(dce:license)) +Declaration(AnnotationProperty()) +############################ +# Annotation Properties +############################ + +# Annotation Property: (metaproperties) + +AnnotationAssertion( "For metaproperties, we use the following notation (Guarino and Welty, 2004; Abel et al., 2015): + +– R+ / R- / R~: rigid / not rigid / anti-rigid; +– I+ / I-: carries / does not carry identity; +– O+ / O-: provides / does not provide identity; +– U+ / U-: carries / does not carry unity; +– ED+ / ED-: existentially dependent / independent."@en) +AnnotationAssertion(rdfs:label "metaproperties"@en) + + +############################ +# Object Properties +############################ + +# Object Property: (has contact position) + +AnnotationAssertion(rdfs:label "has contact position"@en) +SubObjectPropertyOf( owl:topObjectProperty) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has contact type) + +AnnotationAssertion(rdfs:label "has contact type"@en) +SubObjectPropertyOf( owl:topObjectProperty) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has geometry type) + +AnnotationAssertion(rdfs:comment "Luan: Geometry Type talvez seja uma classe de segunda ordem cuja as instâncias são os diferentes tipos de Geometria. Por exemplo, é errado dizer que Geometria Lenticular é subtipo da Quality Geometria. Lenticular é na realidade um subtipo de Tipo de Geometria e não de Geometria."@pt) +AnnotationAssertion(rdfs:label "has geometry type"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has base geometry) + +AnnotationAssertion(rdfs:label "has base geometry"@en) +SubObjectPropertyOf( ) + +# Object Property: (has top geometry) + +AnnotationAssertion(rdfs:label "has top geometry"@en) +SubObjectPropertyOf( ) + + +############################ +# Data Properties +############################ + +# Data Property: (has value) + +AnnotationAssertion( "A relation between a Quality and its values."@en) +AnnotationAssertion(rdfs:comment "O objetivo desta data property é conectar em níveL de implementação uma qualidade com o valor em seu espaço de qualiades. Por exemplo, a qualidade dimensão tem um espaço de qualidade que é um valor real positivo para sua largura. + +A IAO possui uma propriedade has measurement datum cujo domínio é um measurement datum. Porém, o problema de usar tal propriedade é acrescentar a necessidade de criar uma instância de measurement datum."@pt) +AnnotationAssertion(rdfs:label "has value"@en) +SubDataPropertyOf( owl:topDataProperty) +DataPropertyDomain( ) + +# Data Property: (has dimension value) + +AnnotationAssertion(rdfs:label "has dimension value"@en) +SubDataPropertyOf( ) +DataPropertyDomain( ) + +# Data Property: (has lenght value) + +AnnotationAssertion(rdfs:label "has lenght value"@en) +SubDataPropertyOf( ) +DataPropertyDomain( ) +DataPropertyRange( xsd:double) + +# Data Property: (has measurement unit) + +AnnotationAssertion( "A relation between a Quality and a literal string that represents its measurement unit."@en) +AnnotationAssertion(rdfs:label "has measurement unit"@en) +SubDataPropertyOf( ) +DataPropertyDomain( ) +DataPropertyRange( xsd:string) + +# Data Property: (has thickness value) + +AnnotationAssertion(rdfs:label "has thickness value"@en) +SubDataPropertyOf( ) +DataPropertyDomain( ) +DataPropertyRange( xsd:double) + +# Data Property: (has width value) + +AnnotationAssertion(rdfs:label "has width value"@en) +SubDataPropertyOf( ) +DataPropertyDomain( ) +DataPropertyRange( xsd:double) + + + +############################ +# Classes +############################ + +# Class: (geological object) + +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (amount of rock) + +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (body of rock) + +AnnotationAssertion(rdfs:label "body of rock"@en) +AnnotationAssertion( "corpo de rocha"@pt) +AnnotationAssertion( "'body of rock' is a 'geological object' that is 'constituted by' some 'amount of rock'") +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (stratigraphic unit) + +AnnotationAssertion(rdfs:comment "Os diferentes elementos arquiteturais ocorrem dentro de uma unidade com uma idade definida que é a unidade estratigráfica. + +Ainda não sabemos se poderia ser uma unidade litoestratigráfica."@pt) +AnnotationAssertion(rdfs:label "stratigraphic unit"@en) +AnnotationAssertion( "unidade estratigráfica"@pt) +SubClassOf( ) + +# Class: (lithostratigraphic unit) + +AnnotationAssertion(rdfs:label "lithostratigraphic unit"@en) +AnnotationAssertion( "unidade litoestratigráfica"@pt) +SubClassOf( ) + +# Class: (formation) + +AnnotationAssertion(rdfs:label "formation"@en) +AnnotationAssertion( "formação"@pt) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (member) + +AnnotationAssertion(rdfs:label "member"@en) +AnnotationAssertion( "membro"@pt) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (architectural element) + +AnnotationAssertion(rdfs:comment "A restrição de partes de escala menores ainda não foi implementada."@pt) +AnnotationAssertion(rdfs:comment "Luan: Elementos arquiteturais são os objetos básicos que os geólogos vão reconhecer e descrever. Eles podem ocorrer em diversas escalas. +Um elemento pode ter outro elemento como parte, desde que de uma escala menor."@pt) +AnnotationAssertion(rdfs:label "architectural element"@en) +AnnotationAssertion( "elemento arquitetural"@pt) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (build up unit) + +AnnotationAssertion(rdfs:label "build up unit"@en) +AnnotationAssertion( "edifício"@pt) +SubClassOf( ) + +# Class: (channel unit) + +AnnotationAssertion( "An elongated Depositional Unit having some Channel Surface as its boundary and constituted by some Sediment or Sedimentary Rock that fills it (McHargue et al., 2011)."@en) +AnnotationAssertion(rdfs:comment "In stratigraphic terms, a channel unit is constituted by the sediments or sedimentary rocks that fill a channel. It is important to notice that, in more general terms, a channel is a passageway for fluids or sediments, i.e., an immaterial entity. If one elaborates about the erosion and deposition processes that generate these units (McHargue et al., 2011), it is essential to have this disambiguation."@en) +AnnotationAssertion(rdfs:comment "In this work, we decided not to model the named hierarchical scales as entities (e.g., Channel Element, Channel Complex, Channel Complex Set - McHargue et al., 2011) because there exists a wide variety of hierarchical schemes in the literature, and they are not necessarily interoperable (Cullis et al., 2018). Instead, we focus on the fact that units can be fractally nested: a unit can be a Proper Spatial Part Of another unit, which can be a Proper Spatial Part Of another unit, and so forth. We consider that this approach solves the problem of implementing a solution for the repeatability of the geological objects in multiple scales. As so, a Channel Unit can be decomposed in other Channel Units many times as necessary, keeping the representation structure. In the future, we can study the integration of hierarchical schemes and try to infer scales from the spatial relations."@en) +AnnotationAssertion(rdfs:label "channel unit"@en) +AnnotationAssertion( "canal"@pt) +AnnotationAssertion( "R+ I+ O- U+ ED-") +SubClassOf( ) + +# Class: (dome unit) + +AnnotationAssertion(rdfs:label "dome unit"@en) +AnnotationAssertion( "domo"@pt) +SubClassOf( ) + +# Class: (dune unit) + +AnnotationAssertion(rdfs:label "dune unit"@en) +AnnotationAssertion( "duna"@pt) +SubClassOf( ) + +# Class: (intrusive dike) + +AnnotationAssertion(rdfs:label "intrusive dike"@en) +AnnotationAssertion( "dique intrusivo"@pt) +SubClassOf( ) + +# Class: (intrusive sill unit) + +AnnotationAssertion(rdfs:label "intrusive sill unit"@en) +AnnotationAssertion( "soleira intrusiva"@pt) +SubClassOf( ) + +# Class: (levee unit) + +AnnotationAssertion( "A Depositional Unit having Wedge Geometry and forming a bank or ridge geomorphology associated with some Channel Unit."@en) +AnnotationAssertion(rdfs:comment "This term is not consensual as some authors refer to these units as the wedge-shape embankments around channels, which is the definition that we adopt here, while other authors refer to them as not necessarily being these embankments and possibly having wing shapes, among other definitions."@en) +AnnotationAssertion(rdfs:comment "This term refers to the geomorphological association of some wegde-shaped unit with some channel unit, even if the channel does not exist at the moment of the observation by the geologist and the levee is probabilistically identified by tendencies (e.g., typical facies). In other words, the term \"levee\" ontologicallly denotes this relation even though it cannot be deterministically observed."@en) +AnnotationAssertion(rdfs:label "levee unit"@en) +AnnotationAssertion( "dique"@pt) +AnnotationAssertion( "R~ I+ O- U+ ED-") +SubClassOf( ) + +# Class: (lobe unit) + +AnnotationAssertion( "A Depositional Unit having some Lobe Geometry."@en) +AnnotationAssertion(rdfs:comment "For Lobe Unit hierarchical scales, we adopted the same approach as in Channel Unit."@en) +AnnotationAssertion(rdfs:comment "These depositional units are usually found at deep-water depositional system terminal regions, or at channel laterals as Overbank Units."@en) +AnnotationAssertion(rdfs:label "lobe unit"@en) +AnnotationAssertion( "lobo"@pt) +AnnotationAssertion( "R+ I+ O- U+ ED-") +SubClassOf( ) + +# Class: (mound unit) + +AnnotationAssertion( "A Depositional Unit having Mound Geometry with an irregular top surface and internal chaotic facies."@en) +AnnotationAssertion(rdfs:label "mound unit"@en) +AnnotationAssertion( "monte"@pt) +AnnotationAssertion( "R+ I+ O- U+ ED-") +SubClassOf( ) + +# Class: (olistrostomes unit) + +AnnotationAssertion( "megaclast"@en) +AnnotationAssertion( "megaclasto"@pt) +AnnotationAssertion(rdfs:label "olistrostomes unit"@en) +AnnotationAssertion( "olistrostomas"@pt) +SubClassOf( ) + +# Class: (sheet unit) + +AnnotationAssertion(rdfs:label "sheet unit"@en) +AnnotationAssertion( "lençol"@pt) +SubClassOf( ) + +# Class: (fossil) + +AnnotationAssertion(rdfs:label "fossil"@en) +AnnotationAssertion( "fóssil"@pt) +SubClassOf( ) + +# Class: (group) + +AnnotationAssertion(rdfs:label "group"@en) +AnnotationAssertion( "grupo"@pt) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (depositional system) + +AnnotationAssertion( "An Object Aggregate whose members are mereotopologically-linked Depositional Units."@en) +AnnotationAssertion(rdfs:label "depositional system"@en) +AnnotationAssertion( "sistema deposicional"@pt) +AnnotationAssertion( "R+ I+ O+ U+ ED-") +SubClassOf( ) + +# Class: (sedimentary environment) + +AnnotationAssertion( "The sedimentary environment is the specific depositional setting of a particular sedimentary rock and is unique in terms of physical, chemical, and biological characteristics."@en) +AnnotationAssertion( "Britannica +https://www.britannica.com/science/sedimentary-rock/Sedimentary-environments"@en) +AnnotationAssertion(rdfs:label "sedimentary environment"@en) +AnnotationAssertion( "ambiente de sedimentação"@pt) +SubClassOf( ) + +# Class: (dimension) + +AnnotationAssertion( "A Quality that inheres in an Independent Continuant by virtue of one of its one-dimensional extents. It is a category that includes at least the three dimensions defined in this ontology: Width, Length, and Thickness. All dimensions are expressed by a real number indicating its value and a literal string indicating its measurement unit."@en) +AnnotationAssertion(rdfs:label "dimension"@en) +SubClassOf( ) +SubClassOf( DataSomeValuesFrom( xsd:double)) +SubClassOf( DataSomeValuesFrom( xsd:string)) +SubClassOf( DataSomeValuesFrom( xsd:double)) +SubClassOf( DataSomeValuesFrom( xsd:double)) + +# Class: (geometry) + +AnnotationAssertion( "A Quality that inheres in a Depositional Unit by virtue of its external three-dimensional shape. It does not reflect the exact mathematical specifications of a geometric shape but abstracts and simplifies these specifications (Rovetto, 2011)."@en) +AnnotationAssertion(rdfs:label "geometry"@en) +AnnotationAssertion( "geometria"@pt) +SubClassOf( ) +SubClassOf( ObjectMinCardinality(1 )) + +# Class: (lithology) + +AnnotationAssertion(rdfs:label "lithology"@en) +AnnotationAssertion( "litologia"@pt) +SubClassOf( ) + +# Class: (statigraphic contact) + +AnnotationAssertion(rdfs:label "statigraphic contact"@en) +AnnotationAssertion( "contato estratigráfico"@pt) +SubClassOf( ) + +# Class: (bed contact) + +AnnotationAssertion(rdfs:label "bed contact"@en) +AnnotationAssertion( "contato de camada"@pt) +SubClassOf( ) +SubClassOf( ObjectExactCardinality(1 )) +SubClassOf( ObjectExactCardinality(1 )) + +# Class: (sinuosity) + +AnnotationAssertion( "A Quality that inheres in a Channel Unit by virtue of how wavy it is across its length. It is expressed by a real number given by its curved length divided by its length in a straight line."@en) +AnnotationAssertion(rdfs:label "sinuosity"@en) +SubClassOf( ) +SubClassOf( ObjectExactCardinality(1 )) +SubClassOf( DataSomeValuesFrom( DatatypeRestriction(xsd:decimal xsd:minInclusive "1"^^xsd:integer))) +SubClassOf( DataAllValuesFrom( DatatypeRestriction(xsd:decimal xsd:minInclusive "1"^^xsd:integer))) + +# Class: (facies) + +AnnotationAssertion( "A pattern of properties of Geological Objects."@en) +AnnotationAssertion(rdfs:comment "This entity is defined in the literature as a combination of features that differentiates a geological object from its adjacent geological objects (Walker and James, 1992). However, a Facies does not describe a single Geological Object’s features: it might repeat in several objects as a pattern. This particular aspect matches the definition of Generically Dependent Continuant in BFO. Another important aspect is that the features that compose facies vary depending on the research context, e.g., Sedimentary Facies, Petrofacies (De Ros and Goldberg, 2007), Lithofacies, Ichnofacies, and Biofacies (Nichols, 2009)."@en) +AnnotationAssertion(rdfs:label "facies"@en) +AnnotationAssertion( "fácies"@pt) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (sedimentary facies) + +AnnotationAssertion( "A Facies consisting of the sum of the sedimentological characteristics of Depositional Units (Middleton, 1973, Nichols, 2009, Carbonera et al., 2015)."@en) +AnnotationAssertion(rdfs:comment "As an example, if we would model Cross-bedded Sandstone (Nichols, 2009), it would be an entity subsumed by Sedimentary Facies having the following relations: (1) Generically Depends On some (Constituted By some Sandstone (a)); and (2) Has Part some Cross-bedding Structure (b). (a): Sandstone would be an entity subsumed by Sedimentary Rock. (b): Cross-bedding Structure would be an entity subsumed by Sedimentary Structure."@en) +AnnotationAssertion(rdfs:label "sedimentary facies"@en) +AnnotationAssertion( "fácies sedimentar"@pt) +SubClassOf( ) + +# Class: (facies association) + +AnnotationAssertion( "A Generically Dependent Continuant that consists of an aggregate of Facies."@en) +AnnotationAssertion(rdfs:comment "It usually describes the Facies that are typically found in specific regions or sub-environments. For example, the Channel Axis Association (McHargue et al., 2011) describes Sedimentary Facies typically found at the center part of channels (in a cross-section point of view)."@en) +AnnotationAssertion(rdfs:label "facies association"@en) +AnnotationAssertion( "associação de facies"@pt) +SubClassOf( ) +SubClassOf( ObjectMinCardinality(2 )) + +# Class: (sediment) + +AnnotationAssertion( "An Unconsolidated Earth Material constituted by some collection of sedimentary grains or particles (Garcia et al., 2019)."@en) +AnnotationAssertion(rdfs:label "sediment"@en) +AnnotationAssertion( "R+ I+ O- U- ED-") +SubClassOf( ) + +# Class: (sedimentary rock) + +AnnotationAssertion( "'sedimentary rock' is an 'amount of rock' constituted by some collection of sedimentary grains or particles (Garcia et al., 2019)."@en) +AnnotationAssertion(rdfs:label "sedimentary rock"@en) +AnnotationAssertion( "rocha sedimentar"@pt) +AnnotationAssertion( "R+ I+ O- U- ED-") +SubClassOf( ) + +# Class: (igneous rock) + +AnnotationAssertion(rdfs:isDefinedBy "https://www.britannica.com/science/igneous-rock") +AnnotationAssertion(rdfs:label "igneous rock"@en) +AnnotationAssertion( "rocha ígnea"@pt) +AnnotationAssertion( "'igneous rock' is an 'amount of rock' generated by the cooling and solidification of molten 'earth material'.") +SubClassOf( ) + +# Class: (metamorphic rock) + +AnnotationAssertion(rdfs:isDefinedBy "Adapted from Brittanica. +https://www.britannica.com/science/metamorphic-rock") +AnnotationAssertion(rdfs:label "metamorphic rock"@en) +AnnotationAssertion( "rocha metamórfica"@pt) +AnnotationAssertion( "'metamorphic rock' is an 'amount of rock' generated by the alteration of preexisting rocks in response to changing environmental conditions, such as variations in temperature, pressure, and mechanical stress, and the addition or subtraction of chemical components.") +SubClassOf( ) + +# Class: (complex architectural element) + +AnnotationAssertion(rdfs:label "complex architectural element"@en) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf( ObjectAllValuesFrom( ObjectUnionOf( )))) + +# Class: (composite architectural element) + +AnnotationAssertion(rdfs:label "composite architectural element"@en) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf( ObjectAllValuesFrom( ))) + +# Class: (individual architectural element) + +AnnotationAssertion(rdfs:label "individual architectural element"@en) +SubClassOf( ) +SubClassOf( ObjectIntersectionOf( ObjectComplementOf(ObjectSomeValuesFrom( )))) + +# Class: (channel surface) + +AnnotationAssertion( "A Geological Boundary that forms the basis of a Channel Unit, having a concave-up shape unless truncated by overlying depositional units."@en) +AnnotationAssertion(rdfs:label "channel surface"@en) +AnnotationAssertion( "R+ I+ O- U+ ED-") +SubClassOf( ) + +# Class: (basin) + +AnnotationAssertion(rdfs:label "basin"@en) +AnnotationAssertion( "bacia"@pt) +SubClassOf( ) + +# Class: (geological site) + +AnnotationAssertion(rdfs:comment "Epistemologicamente não é possível determinar os limites deste site e, portanto, cada geólogo pode posicionar sua área de interesse em uma localização e limites distintos, o que torna muito difícil tratar computacionalmente a identidade do sítio geológico. Esse problema acontece com outras entidades do tipo site: Região da Serra Gaúcha, Litoral Norte, etc, cuja delimitação é problemática, mas existe uma identidade consensual."@pt) +AnnotationAssertion(rdfs:label "geological site"@en) +AnnotationAssertion( "sítio geológico"@pt) +SubClassOf( ) + +# Class: (contact position) + +AnnotationAssertion(rdfs:label "contact position"@en) +AnnotationAssertion( "posição do contato"@pt) +EquivalentClasses( ObjectOneOf( )) + +# Class: (geometry type) + +AnnotationAssertion(rdfs:comment "Luan: Talvez tipo de Geometria seja uma classe de segunda ordem, mas em primeiro momento não utilizaremos punning para representar isto. A classe geometry tem uma relação de 'has geometry type' com um 'geometry type' e as instâncias dessa classe é que definem o tipo de geometria de fato. Caso seja necessário criar alguma subclasse de um 'body of rock' que tenha um 'geometry type' específico é possível utilizar a primitiva do owl value para isto. + +Não sabemos ainda como classificar esta classe. Do que ela seria subclasse?"@pt) +AnnotationAssertion(rdfs:label "geometry type"@en) +AnnotationAssertion( "tipo de geometria"@pt) +EquivalentClasses( ObjectOneOf( )) + +# Class: (contact type) + +AnnotationAssertion(rdfs:label "contact type"@en) +AnnotationAssertion( "tipo de contato"@pt) +EquivalentClasses( ObjectOneOf( )) + + +############################ +# Named Individuals +############################ + +# Individual: (amalgamated contact) + +AnnotationAssertion(rdfs:label "amalgamated contact"@en) +AnnotationAssertion( "contato amalgamado"@pt) +ClassAssertion( ) + +# Individual: (base position contact) + +AnnotationAssertion(rdfs:label "base position contact"@en) +AnnotationAssertion( "contato de base"@pt) +ClassAssertion( ) + +# Individual: (cryptic/covered contact) + +AnnotationAssertion(rdfs:label "cryptic/covered contact"@en) +AnnotationAssertion( "contato críptico/encoberto"@pt) +ClassAssertion( ) + +# Individual: (conformable contact) + +AnnotationAssertion(rdfs:label "conformable contact"@en) +AnnotationAssertion( "contato concordante"@pt) +ClassAssertion( ) + +# Individual: (erosive contact) + +AnnotationAssertion(rdfs:label "erosive contact"@en) +AnnotationAssertion( "contato erosivo"@pt) +ClassAssertion( ) + +# Individual: (faulted contact) + +AnnotationAssertion(rdfs:label "faulted contact"@en) +AnnotationAssertion( "contato de falha"@pt) +ClassAssertion( ) + +# Individual: (gradational contact) + +AnnotationAssertion(rdfs:label "gradational contact"@en) +AnnotationAssertion( "contato gradacional"@pt) +ClassAssertion( ) + +# Individual: (intrusive contact) + +AnnotationAssertion(rdfs:label "intrusive contact"@en) +AnnotationAssertion( "contato intrusivo"@pt) +ClassAssertion( ) + +# Individual: (sharp contact) + +AnnotationAssertion(rdfs:label "sharp contact"@en) +AnnotationAssertion( "contato abrupto"@pt) +ClassAssertion( ) + +# Individual: (irregular geometry) + +AnnotationAssertion(rdfs:label "irregular geometry"@en) +AnnotationAssertion( "geometria irregular"@pt) +ClassAssertion( ) + +# Individual: (lenticular convex top flatbed geometry) + +AnnotationAssertion(rdfs:label "lenticular convex top flatbed geometry"@en) +AnnotationAssertion( "geometria lenticular topo convexo base plana"@pt) +ClassAssertion( ) + +# Individual: (lenticular concave convex geometry) + +AnnotationAssertion(rdfs:label "lenticular concave convex geometry"@en) +AnnotationAssertion( "geometria lenticular côncavo convexa"@pt) +ClassAssertion( ) + +# Individual: (lateral position contact) + +AnnotationAssertion(rdfs:label "lateral position contact"@en) +AnnotationAssertion( "contato lateral"@pt) +ClassAssertion( ) + +# Individual: (lenticular flattop concave base geometry) + +AnnotationAssertion(rdfs:label "lenticular flattop concave base geometry"@en) +AnnotationAssertion( "geometria lenticular topo plano base convexa"@pt) +ClassAssertion( ) + +# Individual: (sheet geometry) + +AnnotationAssertion(rdfs:label "sheet geometry"@en) +AnnotationAssertion( "geometria lençoidal"@pt) +ClassAssertion( ) + +# Individual: (sigmoidal geometry) + +AnnotationAssertion(rdfs:label "sigmoidal geometry"@en) +AnnotationAssertion( "geometria sigmoidal"@pt) +ClassAssertion( ) + +# Individual: (tabular geometry) + +AnnotationAssertion(rdfs:label "tabular geometry"@en) +AnnotationAssertion( "geometria tabular"@pt) +ClassAssertion( ) + +# Individual: (top position contact) + +AnnotationAssertion(rdfs:label "top position contact"@en) +AnnotationAssertion( "contato de topo"@pt) +ClassAssertion( ) + +# Individual: (wedge shape geometry) + +AnnotationAssertion(rdfs:label "wedge shape geometry"@en) +AnnotationAssertion( "geometria de cunha"@pt) +ClassAssertion( ) + + +DisjointClasses( ) +DisjointClasses( ) +DisjointClasses( ) +DisjointClasses( ) +) \ No newline at end of file diff --git a/src/ontology/geores-idranges.owl b/src/ontology/geores-idranges.owl new file mode 100644 index 0000000..4a8496b --- /dev/null +++ b/src/ontology/geores-idranges.owl @@ -0,0 +1,53 @@ +## ID Ranges File +Prefix: rdf: +Prefix: idsfor: +Prefix: dce: +Prefix: xsd: +Prefix: allocatedto: +Prefix: xml: +Prefix: idprefix: +Prefix: iddigits: +Prefix: rdfs: +Prefix: idrange: +Prefix: owl: + +Ontology: + + +Annotations: + idsfor: "GEORES", + idprefix: "https://www.inf.ufrgs.br/bdi/ontologies/GEORES_", + iddigits: 7 + +AnnotationProperty: idprefix: + + +AnnotationProperty: iddigits: + + +AnnotationProperty: idsfor: + + +AnnotationProperty: allocatedto: + +Datatype: idrange:1 + + Annotations: + allocatedto: "Luan Garcia" + + EquivalentTo: + xsd:integer[>= 1 , <= 300] + + +Datatype: idrange:2 + + Annotations: + allocatedto: "Alcides Lopes" + + EquivalentTo: + xsd:integer[>= 301 , <= 600] + + +Datatype: xsd:integer +Datatype: rdf:PlainLiteral + diff --git a/src/ontology/geores-odk.yaml b/src/ontology/geores-odk.yaml new file mode 100644 index 0000000..c03dc82 --- /dev/null +++ b/src/ontology/geores-odk.yaml @@ -0,0 +1,22 @@ +id: geores +title: GeoReservoir Ontology +github_org: BDI-UFRGS +git_main_branch: master +repo: GeoReservoirOntology +uribase: https://www.inf.ufrgs.br/bdi/ontologies +license: https://creativecommons.org/licenses/by-nc/4.0/ +release_artefacts: + - base + - full + - simple +primary_release: full +ci: + - github_actions +import_group: + products: + - id: bfo2020 + mirror_from: http://purl.obolibrary.org/obo/bfo/2020/bfo-core.owl + - id: geocore + mirror_from: https://www.inf.ufrgs.br/bdi/ontologies/geocore/releases/2024-04-06/geocore.owl + module_type: SLME + module_type_slme: TOP \ No newline at end of file diff --git a/src/ontology/geores.Makefile b/src/ontology/geores.Makefile new file mode 100644 index 0000000..159eb92 --- /dev/null +++ b/src/ontology/geores.Makefile @@ -0,0 +1,7 @@ +## Customize Makefile settings for geores +## +## If you need to customize your Makefile, make +## changes here rather than in the main Makefile + + + diff --git a/src/ontology/imports/bfo2020_import.owl b/src/ontology/imports/bfo2020_import.owl new file mode 100644 index 0000000..1b949ee --- /dev/null +++ b/src/ontology/imports/bfo2020_import.owl @@ -0,0 +1,273 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2024-04-07") + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) + +############################ +# Object Properties +############################ + +# Object Property: (generically depends on) + +AnnotationAssertion( "252-BFO") +AnnotationAssertion(rdfs:label "generically depends on"@en) +AnnotationAssertion( "g-depends on"@en) +AnnotationAssertion( "b generically depends on c =Def b is a generically dependent continuant & c is an independent continuant that is not a spatial region & at some time t there inheres in c a specifically dependent continuant which concretizes b at t"@en) +AnnotationAssertion( "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: "@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf())) + +# Object Property: (is carrier of) + +AnnotationAssertion( "254-BFO") +AnnotationAssertion(rdfs:label "is carrier of"@en) +AnnotationAssertion( "b is carrier of c =Def there is some time t such that c generically depends on b at t"@en) +AnnotationAssertion( "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: "@en) +ObjectPropertyDomain( ObjectIntersectionOf( ObjectComplementOf())) +ObjectPropertyRange( ) + +# Object Property: (has member part) + +AnnotationAssertion( "230-BFO") +AnnotationAssertion(rdfs:label "has member part"@en) +AnnotationAssertion( "b has member part c =Def c member part of b"@en) +AnnotationAssertion( "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: "@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (member part of) + +AnnotationAssertion( "228-BFO") +AnnotationAssertion(rdfs:label "member part of"@en) +AnnotationAssertion( "b member part of c =Def b is an object & c is a material entity & there is some time t such that b continuant part of c at t & there is a mutually exhaustive and pairwise disjoint partition of c into objects x1, ..., xn (for some n ≠ 1) with b = xi (for some 1 <= i <= n)"@en) +AnnotationAssertion( "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: "@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (continuant part of) + +AnnotationAssertion( "221-BFO") +AnnotationAssertion(rdfs:label "continuant part of"@en) +AnnotationAssertion( "b continuant part of c =Def b and c are continuants & there is some time t such that b and c exist at t & b continuant part of c at t"@en) +AnnotationAssertion( "Milk teeth continuant part of human; surgically removed tumour continuant part of organism"@en) +AnnotationAssertion( "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: "@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has continuant part) + +AnnotationAssertion( "271-BFO") +AnnotationAssertion(rdfs:label "has continuant part"@en) +AnnotationAssertion( "b has continuant part c =Def c continuant part of b"@en) +AnnotationAssertion( "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: "@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (specifically depended on by) + +AnnotationAssertion( "260-BFO") +AnnotationAssertion(rdfs:label "specifically depended on by"@en) +AnnotationAssertion( "s-depended on by"@en) +AnnotationAssertion( "b specifically depended on by c =Def c specifically depends on b"@en) +AnnotationAssertion( "Coloured object specifically depended on by colour"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ObjectUnionOf( ObjectIntersectionOf( ObjectComplementOf()))) +ObjectPropertyRange( ) + +# Object Property: (specifically depends on) + +AnnotationAssertion( "012-BFO") +AnnotationAssertion(rdfs:label "specifically depends on"@en) +AnnotationAssertion( "s-depends on"@en) +AnnotationAssertion( "(Elucidation) specifically depends on is a relation between a specifically dependent continuant b and specifically dependent continuant or independent continuant that is not a spatial region c such that b and c share no parts in common & b is of a nature such that at all times t it cannot exist unless c exists & b is not a boundary of c"@en) +AnnotationAssertion( "A shape specifically depends on the shaped object; hue, saturation and brightness of a colour sample specifically depends on each other"@en) +AnnotationAssertion( "The analogue of specifically depends on for occurrents is has participant."@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ObjectUnionOf( ObjectIntersectionOf( ObjectComplementOf()))) + +# Object Property: (bearer of) + +AnnotationAssertion( "053-BFO") +AnnotationAssertion(rdfs:label "bearer of"@en) +AnnotationAssertion( "b bearer of c =Def c inheres in b"@en) +AnnotationAssertion( "A patch of ink is the bearer of a colour quality; an organism is the bearer of a temperature quality"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ObjectIntersectionOf( ObjectComplementOf())) +ObjectPropertyRange( ) + +# Object Property: (inheres in) + +AnnotationAssertion( "051-BFO") +AnnotationAssertion(rdfs:label "inheres in"@en) +AnnotationAssertion( "b inheres in c =Def b is a specifically dependent continuant & c is an independent continuant that is not a spatial region & b specifically depends on c"@en) +AnnotationAssertion( "A shape inheres in a shaped object; a mass inheres in a material entity"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf())) + + + +############################ +# Classes +############################ + +# Class: (entity) + +AnnotationAssertion( "001-BFO") +AnnotationAssertion(rdfs:label "entity"@en) +AnnotationAssertion( "(Elucidation) An entity is anything that exists or has existed or will exist"@en) +AnnotationAssertion( "Julius Caesar; the Second World War; your body mass index; Verdi's Requiem"@en) + +# Class: (continuant) + +AnnotationAssertion( "008-BFO") +AnnotationAssertion(rdfs:label "continuant"@en) +AnnotationAssertion( "(Elucidation) A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity"@en) +AnnotationAssertion( "A human being; a tennis ball; a cave; a region of space; someone's temperature"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (independent continuant) + +AnnotationAssertion( "017-BFO") +AnnotationAssertion(rdfs:label "independent continuant"@en) +AnnotationAssertion( "b is an independent continuant =Def b is a continuant & there is no c such that b specifically depends on c or b generically depends on c"@en) +AnnotationAssertion( "An atom; a molecule; an organism; a heart; a chair; the bottom right portion of a human torso; a leg; the interior of your mouth; a spatial region; an orchestra"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (spatial region) + +AnnotationAssertion( "035-BFO") +AnnotationAssertion(rdfs:label "spatial region"@en) +AnnotationAssertion( "(Elucidation) A spatial region is a continuant entity that is a continuant part of the spatial projection of a portion of spacetime at a given time"@en) +AnnotationAssertion( "As for zero-dimensional spatial region, one-dimensional spatial region, two-dimensional spatial region, three-dimensional spatial region"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (quality) + +AnnotationAssertion( "055-BFO") +AnnotationAssertion(rdfs:label "quality"@en) +AnnotationAssertion( "(Elucidation) A quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized"@en) +AnnotationAssertion( "The colour of a tomato; the ambient temperature of this portion of air; the length of the circumference of your waist; the shape of your nose; the shape of your nostril; the mass of this piece of gold"@en) +SubClassOf( ) + +# Class: (specifically dependent continuant) + +AnnotationAssertion( "050-BFO") +AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) +AnnotationAssertion( "b is a specifically dependent continuant =Def b is a continuant & there is some independent continuant c which is not a spatial region & which is such that b specifically depends on c"@en) +AnnotationAssertion( "(with multiple bearers) John's love for Mary; the ownership relation between John and this statue; the relation of authority between John and his subordinates"@en) +AnnotationAssertion( "(with one bearer) The mass of this tomato; the pink colour of a medium rare piece of grilled filet mignon at its centre; the smell of this portion of mozzarella; the disposition of this fish to decay; the role of being a doctor; the function of this heart to pump blood; the shape of this hole"@en) +SubClassOf( ) + +# Class: (object aggregate) + +AnnotationAssertion( "025-BFO") +AnnotationAssertion(rdfs:label "object aggregate"@en) +AnnotationAssertion( "(Elucidation) An object aggregate is a material entity consisting exactly of a plurality (≥1) of objects as member parts which together form a unit"@en) +AnnotationAssertion( "The aggregate of the musicians in a symphony orchestra and their instruments; the aggregate of bearings in a constant velocity axle joint; the nitrogen atoms in the atmosphere; a collection of cells in a blood biobank"@en) +AnnotationAssertion( "'Exactly' means that there are no parts of the object aggregate other than its member parts.") +AnnotationAssertion( "The unit can, at certain times, consist of exactly one object, for example, when a wolf litter loses all but one of its pups, but it must at some time have a plurality of member parts.") +SubClassOf( ) + +# Class: (site) + +AnnotationAssertion( "034-BFO") +AnnotationAssertion(rdfs:label "site"@en) +AnnotationAssertion( "(Elucidation) A site is a three-dimensional immaterial entity whose boundaries either (partially or wholly) coincide with the boundaries of one or more material entities or have locations determined in relation to some material entity"@en) +AnnotationAssertion( "A hole in a portion of cheese; a rabbit hole; the Grand Canyon; the Piazza San Marco; the kangaroo-joey-containing hole of a kangaroo pouch; your left nostril (a fiat part - the opening - of your left nasal cavity); the lumen of your gut; the hold of a ship; the interior of the trunk of your car; hole in an engineered floor joist"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( ObjectUnionOf( ))) +SubClassOf( ObjectAllValuesFrom( ObjectUnionOf( ))) + +# Class: (generically dependent continuant) + +AnnotationAssertion( "074-BFO") +AnnotationAssertion(rdfs:label "generically dependent continuant"@en) +AnnotationAssertion( "g-dependent continuant"@en) +AnnotationAssertion( "(Elucidation) A generically dependent continuant is an entity that exists in virtue of the fact that there is at least one of what may be multiple copies which is the content or the pattern that multiple copies would share"@en) +AnnotationAssertion( "The pdf file on your laptop; the pdf file that is a copy thereof on my laptop; the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule; the content that is shared by a string of dots and dashes written on a page and the transmitted Morse code signal; the content of a sentence; an engineering blueprint"@en) +SubClassOf( ) + +# Class: (material entity) + +AnnotationAssertion( "019-BFO") +AnnotationAssertion(rdfs:label "material entity"@en) +AnnotationAssertion( "(Elucidation) A material entity is an independent continuant has some portion of matter as continuant part"@en) +AnnotationAssertion( "A human being; the undetached arm of a human being; an aggregate of human beings"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) +SubClassOf( ObjectAllValuesFrom( ObjectUnionOf( ))) +DisjointClasses( ) + +# Class: (continuant fiat boundary) + +AnnotationAssertion( "029-BFO") +AnnotationAssertion(rdfs:label "continuant fiat boundary"@en) +AnnotationAssertion( "(Elucidation) A continuant fiat boundary b is an immaterial entity that is of zero, one or two dimensions & such that there is no time t when b has a spatial region as continuant part & whose location is determined in relation to some material entity"@en) +AnnotationAssertion( "As for fiat point, fiat line, fiat surface"@en) +SubClassOf( ) +SubClassOf( ObjectAllValuesFrom( )) + +# Class: (immaterial entity) + +AnnotationAssertion( "028-BFO") +AnnotationAssertion(rdfs:label "immaterial entity"@en) +AnnotationAssertion( "b is an immaterial entity =Def b is an independent continuant which is such that there is no time t when it has a material entity as continuant part"@en) +AnnotationAssertion( "As for fiat point, fiat line, fiat surface, site"@en) +SubClassOf( ) + + +DisjointClasses( ) +DisjointClasses( ) +) \ No newline at end of file diff --git a/src/ontology/imports/bfo2020_terms.txt b/src/ontology/imports/bfo2020_terms.txt new file mode 100644 index 0000000..bddd81b --- /dev/null +++ b/src/ontology/imports/bfo2020_terms.txt @@ -0,0 +1,3 @@ +BFO:0000084 #generically depends on +BFO:0000197 #inheres in +BFO:0000129 #member_part_of \ No newline at end of file diff --git a/src/ontology/imports/geocore_import.owl b/src/ontology/imports/geocore_import.owl new file mode 100644 index 0000000..c5a0d74 --- /dev/null +++ b/src/ontology/imports/geocore_import.owl @@ -0,0 +1,471 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2024-04-07") + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) + +############################ +# Object Properties +############################ + +# Object Property: (generically depends on) + +AnnotationAssertion( "252-BFO") +AnnotationAssertion(rdfs:label "generically depends on"@en) +AnnotationAssertion( "g-depends on"@en) +AnnotationAssertion( "b generically depends on c =Def b is a generically dependent continuant & c is an independent continuant that is not a spatial region & at some time t there inheres in c a specifically dependent continuant which concretizes b at t"@en) +AnnotationAssertion( "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: "@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf())) + +# Object Property: (is carrier of) + +AnnotationAssertion( "254-BFO") +AnnotationAssertion(rdfs:label "is carrier of"@en) +AnnotationAssertion( "b is carrier of c =Def there is some time t such that c generically depends on b at t"@en) +AnnotationAssertion( "Users that require more sophisticated representations of time are encouraged to import a temporal extension of BFO-Core provided by the BFO development team. See documentation for guidance: "@en) +ObjectPropertyDomain( ObjectIntersectionOf( ObjectComplementOf())) +ObjectPropertyRange( ) + +# Object Property: (specifically depended on by) + +AnnotationAssertion( "260-BFO") +AnnotationAssertion(rdfs:label "specifically depended on by"@en) +AnnotationAssertion( "s-depended on by"@en) +AnnotationAssertion( "b specifically depended on by c =Def c specifically depends on b"@en) +AnnotationAssertion( "Coloured object specifically depended on by colour"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ObjectUnionOf( ObjectIntersectionOf( ObjectComplementOf()))) +ObjectPropertyRange( ) + +# Object Property: (specifically depends on) + +AnnotationAssertion( "012-BFO") +AnnotationAssertion(rdfs:label "specifically depends on"@en) +AnnotationAssertion( "s-depends on"@en) +AnnotationAssertion( "(Elucidation) specifically depends on is a relation between a specifically dependent continuant b and specifically dependent continuant or independent continuant that is not a spatial region c such that b and c share no parts in common & b is of a nature such that at all times t it cannot exist unless c exists & b is not a boundary of c"@en) +AnnotationAssertion( "A shape specifically depends on the shaped object; hue, saturation and brightness of a colour sample specifically depends on each other"@en) +AnnotationAssertion( "The analogue of specifically depends on for occurrents is has participant."@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ObjectUnionOf( ObjectIntersectionOf( ObjectComplementOf()))) + +# Object Property: (bearer of) + +AnnotationAssertion( "053-BFO") +AnnotationAssertion(rdfs:label "bearer of"@en) +AnnotationAssertion( "b bearer of c =Def c inheres in b"@en) +AnnotationAssertion( "A patch of ink is the bearer of a colour quality; an organism is the bearer of a temperature quality"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ObjectIntersectionOf( ObjectComplementOf())) +ObjectPropertyRange( ) + +# Object Property: (inheres in) + +AnnotationAssertion( "051-BFO") +AnnotationAssertion(rdfs:label "inheres in"@en) +AnnotationAssertion( "b inheres in c =Def b is a specifically dependent continuant & c is an independent continuant that is not a spatial region & b specifically depends on c"@en) +AnnotationAssertion( "A shape inheres in a shaped object; a mass inheres in a material entity"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ObjectIntersectionOf( ObjectComplementOf())) + +# Object Property: (occupies temporal region) + +AnnotationAssertion( "132-BFO") +AnnotationAssertion(rdfs:label "occupies temporal region"@en) +AnnotationAssertion( "p occupies temporal region t =Def p is a process or process boundary & the spatiotemporal region occupied by p temporally projects onto t"@en) +AnnotationAssertion( "The Second World War occupies the temporal region September 1, 1939 - September 2, 1945"@en) +FunctionalObjectProperty() +ObjectPropertyDomain( ObjectUnionOf( )) +ObjectPropertyRange( ) + +# Object Property: (has age) + +AnnotationAssertion( "The relation between a Geological Object and its Geological Age."@en) +AnnotationAssertion(rdfs:label "has age"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (age of) + +AnnotationAssertion( "The relation between a Geological Age and a Geological Object. Inverse of has age relation."@en) +AnnotationAssertion(rdfs:label "age of"@en) +SubObjectPropertyOf( ) + +# Object Property: (constituted by) + +AnnotationAssertion( "The relation between some material entity and the material that it is made of.") +AnnotationAssertion( "This is a material constitution relation intended to represent the relationship between material objects, such as geological objects and earth materials, or aggregates of them."@en) +AnnotationAssertion( "Evnine, S. J. (2011). Constitution and composition: Three approaches to their relation. ProtoSociology, 27, 212-235.") +AnnotationAssertion(rdfs:label "constituted by"@en) +AsymmetricObjectProperty() +IrreflexiveObjectProperty() + + + +############################ +# Classes +############################ + +# Class: (entity) + +AnnotationAssertion( "001-BFO") +AnnotationAssertion(rdfs:label "entity"@en) +AnnotationAssertion( "(Elucidation) An entity is anything that exists or has existed or will exist"@en) +AnnotationAssertion( "Julius Caesar; the Second World War; your body mass index; Verdi's Requiem"@en) + +# Class: (continuant) + +AnnotationAssertion( "008-BFO") +AnnotationAssertion(rdfs:label "continuant"@en) +AnnotationAssertion( "(Elucidation) A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity"@en) +AnnotationAssertion( "A human being; a tennis ball; a cave; a region of space; someone's temperature"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (occurrent) + +AnnotationAssertion( "077-BFO") +AnnotationAssertion(rdfs:label "occurrent"@en) +AnnotationAssertion( "(Elucidation) An occurrent is an entity that unfolds itself in time or it is the start or end of such an entity or it is a temporal or spatiotemporal region"@en) +AnnotationAssertion( "As for process, history, process boundary, spatiotemporal region, zero-dimensional temporal region, one-dimensional temporal region, temporal interval, temporal instant."@en) +SubClassOf( ) + +# Class: (independent continuant) + +AnnotationAssertion( "017-BFO") +AnnotationAssertion(rdfs:label "independent continuant"@en) +AnnotationAssertion( "b is an independent continuant =Def b is a continuant & there is no c such that b specifically depends on c or b generically depends on c"@en) +AnnotationAssertion( "An atom; a molecule; an organism; a heart; a chair; the bottom right portion of a human torso; a leg; the interior of your mouth; a spatial region; an orchestra"@en) +SubClassOf( ) + +# Class: (spatial region) + +AnnotationAssertion( "035-BFO") +AnnotationAssertion(rdfs:label "spatial region"@en) +AnnotationAssertion( "(Elucidation) A spatial region is a continuant entity that is a continuant part of the spatial projection of a portion of spacetime at a given time"@en) +AnnotationAssertion( "As for zero-dimensional spatial region, one-dimensional spatial region, two-dimensional spatial region, three-dimensional spatial region"@en) +SubClassOf( ) + +# Class: (temporal region) + +AnnotationAssertion( "100-BFO") +AnnotationAssertion(rdfs:label "temporal region"@en) +AnnotationAssertion( "(Elucidation) A temporal region is an occurrent over which processes can unfold"@en) +AnnotationAssertion( "As for zero-dimensional temporal region and one-dimensional temporal region"@en) +SubClassOf( ) + +# Class: (spatiotemporal region) + +AnnotationAssertion( "095-BFO") +AnnotationAssertion(rdfs:label "spatiotemporal region"@en) +AnnotationAssertion( "(Elucidation) A spatiotemporal region is an occurrent that is an occurrent part of spacetime"@en) +AnnotationAssertion( "The spatiotemporal region occupied by the development of a cancer tumour; the spatiotemporal region occupied by an orbiting satellite"@en) +AnnotationAssertion( "'Spacetime' here refers to the maximal instance of the universal spatiotemporal region."@en) +SubClassOf( ) + +# Class: (process) + +AnnotationAssertion( "083-BFO") +AnnotationAssertion(rdfs:label "process"@en) +AnnotationAssertion( "event"@en) +AnnotationAssertion( "(Elucidation) p is a process means p is an occurrent that has some temporal proper part and for some time t, p has some material entity as participant"@en) +AnnotationAssertion( "An act of selling; the life of an organism; a process of sleeping; a process of cell-division; a beating of the heart; a process of meiosis; the taxiing of an aircraft; the programming of a computer"@en) +SubClassOf( ) + +# Class: (quality) + +AnnotationAssertion( "055-BFO") +AnnotationAssertion(rdfs:label "quality"@en) +AnnotationAssertion( "(Elucidation) A quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized"@en) +AnnotationAssertion( "The colour of a tomato; the ambient temperature of this portion of air; the length of the circumference of your waist; the shape of your nose; the shape of your nostril; the mass of this piece of gold"@en) +SubClassOf( ) + +# Class: (specifically dependent continuant) + +AnnotationAssertion( "050-BFO") +AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) +AnnotationAssertion( "b is a specifically dependent continuant =Def b is a continuant & there is some independent continuant c which is not a spatial region & which is such that b specifically depends on c"@en) +AnnotationAssertion( "(with multiple bearers) John's love for Mary; the ownership relation between John and this statue; the relation of authority between John and his subordinates"@en) +AnnotationAssertion( "(with one bearer) The mass of this tomato; the pink colour of a medium rare piece of grilled filet mignon at its centre; the smell of this portion of mozzarella; the disposition of this fish to decay; the role of being a doctor; the function of this heart to pump blood; the shape of this hole"@en) +SubClassOf( ) + +# Class: (object aggregate) + +AnnotationAssertion( "025-BFO") +AnnotationAssertion(rdfs:label "object aggregate"@en) +AnnotationAssertion( "(Elucidation) An object aggregate is a material entity consisting exactly of a plurality (≥1) of objects as member parts which together form a unit"@en) +AnnotationAssertion( "The aggregate of the musicians in a symphony orchestra and their instruments; the aggregate of bearings in a constant velocity axle joint; the nitrogen atoms in the atmosphere; a collection of cells in a blood biobank"@en) +AnnotationAssertion( "'Exactly' means that there are no parts of the object aggregate other than its member parts.") +AnnotationAssertion( "The unit can, at certain times, consist of exactly one object, for example, when a wolf litter loses all but one of its pups, but it must at some time have a plurality of member parts.") +SubClassOf( ) + +# Class: (site) + +AnnotationAssertion( "034-BFO") +AnnotationAssertion(rdfs:label "site"@en) +AnnotationAssertion( "(Elucidation) A site is a three-dimensional immaterial entity whose boundaries either (partially or wholly) coincide with the boundaries of one or more material entities or have locations determined in relation to some material entity"@en) +AnnotationAssertion( "A hole in a portion of cheese; a rabbit hole; the Grand Canyon; the Piazza San Marco; the kangaroo-joey-containing hole of a kangaroo pouch; your left nostril (a fiat part - the opening - of your left nasal cavity); the lumen of your gut; the hold of a ship; the interior of the trunk of your car; hole in an engineered floor joist"@en) +SubClassOf( ) + +# Class: (object) + +AnnotationAssertion( "024-BFO") +AnnotationAssertion(rdfs:label "object"@en) +AnnotationAssertion( "(Elucidation) An object is a material entity which manifests causal unity & is of a type instances of which are maximal relative to the sort of causal unity manifested"@en) +AnnotationAssertion( "An organism; a fish tank; a planet; a laptop; a valve; a block of marble; an ice cube"@en) +AnnotationAssertion( "A description of three primary sorts of causal unity is provided in Basic Formal Ontology 2.0. Specification and User Guide"@en) +SubClassOf( ) + +# Class: (generically dependent continuant) + +AnnotationAssertion( "074-BFO") +AnnotationAssertion(rdfs:label "generically dependent continuant"@en) +AnnotationAssertion( "g-dependent continuant"@en) +AnnotationAssertion( "(Elucidation) A generically dependent continuant is an entity that exists in virtue of the fact that there is at least one of what may be multiple copies which is the content or the pattern that multiple copies would share"@en) +AnnotationAssertion( "The pdf file on your laptop; the pdf file that is a copy thereof on my laptop; the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule; the content that is shared by a string of dots and dashes written on a page and the transmitted Morse code signal; the content of a sentence; an engineering blueprint"@en) +SubClassOf( ) + +# Class: (process boundary) + +AnnotationAssertion( "084-BFO") +AnnotationAssertion(rdfs:label "process boundary"@en) +AnnotationAssertion( "p is a process boundary =Def p is a temporal part of a process & p has no proper temporal parts"@en) +AnnotationAssertion( "The boundary between the 2nd and 3rd year of your life"@en) +SubClassOf( ) + +# Class: (one-dimensional temporal region) + +AnnotationAssertion( "103-BFO") +AnnotationAssertion(rdfs:label "one-dimensional temporal region"@en) +AnnotationAssertion( "(Elucidation) A one-dimensional temporal region is a temporal region that is a whole that has a temporal interval and zero or more temporal intervals and temporal instants as parts"@en) +AnnotationAssertion( "The temporal region during which a process occurs"@en) +SubClassOf( ) + +# Class: (material entity) + +AnnotationAssertion( "019-BFO") +AnnotationAssertion(rdfs:label "material entity"@en) +AnnotationAssertion( "(Elucidation) A material entity is an independent continuant has some portion of matter as continuant part"@en) +AnnotationAssertion( "A human being; the undetached arm of a human being; an aggregate of human beings"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (continuant fiat boundary) + +AnnotationAssertion( "029-BFO") +AnnotationAssertion(rdfs:label "continuant fiat boundary"@en) +AnnotationAssertion( "(Elucidation) A continuant fiat boundary b is an immaterial entity that is of zero, one or two dimensions & such that there is no time t when b has a spatial region as continuant part & whose location is determined in relation to some material entity"@en) +AnnotationAssertion( "As for fiat point, fiat line, fiat surface"@en) +SubClassOf( ) + +# Class: (immaterial entity) + +AnnotationAssertion( "028-BFO") +AnnotationAssertion(rdfs:label "immaterial entity"@en) +AnnotationAssertion( "b is an immaterial entity =Def b is an independent continuant which is such that there is no time t when it has a material entity as continuant part"@en) +AnnotationAssertion( "As for fiat point, fiat line, fiat surface, site"@en) +SubClassOf( ) + +# Class: (relational quality) + +AnnotationAssertion( "057-BFO") +AnnotationAssertion(rdfs:label "relational quality"@en) +AnnotationAssertion( "b is a relational quality =Def b is a quality & there exists c and d such that c and d are not identical & b specifically depends on c & b specifically depends on d"@en) +AnnotationAssertion( "A marriage bond; an instance of love; an obligation between one person and another"@en) +SubClassOf( ) + +# Class: (fiat surface) + +AnnotationAssertion( "033-BFO") +AnnotationAssertion(rdfs:label "fiat surface"@en) +AnnotationAssertion( "(Elucidation) A fiat surface is a two-dimensional continuant fiat boundary that is self-connected"@en) +AnnotationAssertion( "The surface of the Earth; the plane separating the smoking from the non-smoking zone in a restaurant"@en) +SubClassOf( ) + +# Class: (geological object) + +AnnotationAssertion( "An object that is 'generated by' some 'geological process' and has at least one part 'constituted by' some 'earth material' that is not an 'earth fluid'."@en) +AnnotationAssertion( "A geological object is a naturally occurring entity because a geological process +generates it, and some earth material constitutes it. Thus, we can differentiate geological objects from artificial objects, such as a well-core, because even though some earth material constitutes artificial objects, they are human-made rather than generated by some geological process. Furthermore, Geological Objects are specializations of BFO Objects, meaning they must necessarily have some unity criteria. The unity is what differentiates geological objects from Earth Materials."@en) +AnnotationAssertion(rdfs:label "geological object"@en) +AnnotationAssertion( "objeto geológico"@pt) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectComplementOf()))) +DisjointClasses( ) + +# Class: (geological process) + +AnnotationAssertion( "Examples are the process of deposition, the process of folding, a tectonic process, a sedimentary process."@en) +AnnotationAssertion( "It is a physical, or chemical, or biological, naturally occurring process that occurs on the Earth’s surface or subsurface and occupies some 'geological time interval'"@en) +AnnotationAssertion( "Geological processes are macro processes that generate, transform, deform, transport, or destroy geological objects and earth materials. These processes are not necessarily atomic and may have other geological processes as parts."@en) +AnnotationAssertion(rdfs:label "geological process"@en) +AnnotationAssertion( "processo geológico"@pt) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (geological age) + +AnnotationAssertion( "It is a quality that 'inheres in' a 'geological object' or 'earth material' that corresponds to the 'geological time interval' in which the 'geological process' that it was 'generated by' occupied."@en) +AnnotationAssertion(rdfs:label "geological age"@en) +AnnotationAssertion( "idade geológica"@pt) +SubClassOf( ) + +# Class: (geological structure) + +AnnotationAssertion( "It is a 'generically dependent continuant' that is the pattern of a non-atomic 'geological object''s internal arrangement."@en) +AnnotationAssertion( "Geological structures are general material patterns repeated in many geological +objects. The pattern comprises the material configuration and the mutual relationships of the object’s different parts. Structures result from one or a series of geological processes that generated or transformed the geological object they generically depend on. Thus, there is some historical dependence relation between the structure and this geological process, but what concretizes the structure is some complex quality inhering in the object, not the process."@en) +AnnotationAssertion(rdfs:label "geological structure"@en) +AnnotationAssertion( "estrutura geológica"@pt) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (geological time interval) + +AnnotationAssertion( "It is a BFO temporal interval that corresponds to a time interval within the Geological Time Scale."@en) +AnnotationAssertion(rdfs:label "geological time interval"@en) +AnnotationAssertion( "intervalo de tempo geológico"@pt) +SubClassOf( ) + +# Class: (earth material) + +AnnotationAssertion( "Examples are an amount of sandstone, an amount of petroleum, an amount of +natural gas."@en) +AnnotationAssertion( "It is a natural amount of matter 'generated by' some 'geological process'."@en) +AnnotationAssertion( "Earth Materials are natural amounts of matter. Thus, they come into existence by nature, without any artificial aid. Since they are amounts, they don’t hold unity criteria, but they are ontologically rigid and provide an identity criteria. Earth Materials and BFO Objects are disjoint. They are either solid, fluid, or unconsolidated. We usually observe earth materials when constituting other objects, such as an amount of rock constituting a geological unity or an amount of sand constituting a dune."@en) +AnnotationAssertion(rdfs:label "earth material"@en) +AnnotationAssertion( "material geologico"@pt) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (amount of mineral) + +AnnotationAssertion( "The amount of quarts that constitutes some grain, the amount of feldspar that is part of an amount of rock."@en) +AnnotationAssertion( "An amount of rock is an 'earth material' that is a naturally occuring, inorganic, solid, homogeneous chemical compound with a crystalline structure."@en) +AnnotationAssertion( "Amounts of mineral lack a unity criteria as every other 'earth material'. We usually observe them when they are constitution objects such as crystals or grains."@en) +AnnotationAssertion(rdfs:label "amount of mineral"@en) +AnnotationAssertion( "quantidade de mineral"@pt) +SubClassOf( ) + +# Class: (amount of rock) + +AnnotationAssertion( "The amount of sandstone that constitutes a lithostratigraphic unit."@en) +AnnotationAssertion( "An amount of rock is a solid consolidated 'earth material' that is 'constituted by' an aggregate of particles made of mineral matter or material of biological origin."@en) +AnnotationAssertion( "Geologists define rocks at a scale of observation where they consider them homogeneous, even though an aggregate of solid particles constitutes it. These particles are usually geological objects, such as grains or crystals, or the rest of dead animals or plants. + +Amounts of rock, like other earth materials, are independent rigid entities that do not hold any unity criteria. We can observe them in nature when they are constituting objects such as geological unities."@en) +AnnotationAssertion(rdfs:label "amount of rock"@en) +AnnotationAssertion( "quantidade de rocha"@pt) +SubClassOf( ) +DisjointClasses( ) + +# Class: (earth fluid) + +AnnotationAssertion( "Earth fluid is an 'earth material' that is fluild."@en) +AnnotationAssertion( "Earth fluids can be water, oil, gas or a mixture of those fluids."@en) +AnnotationAssertion(rdfs:label "earth fluid"@en) +AnnotationAssertion( "fluido da terra"@pt) +SubClassOf( ) + +# Class: (unconsolidated earth material) + +AnnotationAssertion( "Unconsolidated earth material is an 'earth material' that is consituted by an aggregate of solid particles but is not consolidated into a 'rock' it self."@en) +AnnotationAssertion(rdfs:label "unconsolidated earth material"@en) +AnnotationAssertion( "material geológico inconsolidado"@pt) +SubClassOf( ) + +# Class: (geological boundary) + +AnnotationAssertion( "It is a fiat surface that is 'located in' the external surface of a 'geological object'."@en) +AnnotationAssertion( "The 'geological boundary' of a 'geological object' coincides with the complete physical discontinuity that delimits it."@en) +AnnotationAssertion(rdfs:label "geological boundary"@en) +AnnotationAssertion( "limite geológico"@pt) +SubClassOf( ) + +# Class: (geological contact) + +AnnotationAssertion( "It is a 'relational quality' that 'inheres in' two distinct 'geological object' that are 'externally connected with'"@en) +AnnotationAssertion( "A geological contact exists when two distinct geological objects are externally +connected with, i.e., their external boundaries are physically adjacent. Objects that are in contact do not have any kind of proper parthood relationship between them."@en) +AnnotationAssertion(rdfs:label "geological contact"@en) +AnnotationAssertion( "contato geológico"@pt) +SubClassOf( ) +SubClassOf( ObjectExactCardinality(2 )) + + +DisjointClasses( ) +DisjointClasses( ) +DisjointClasses( ) +DisjointClasses( ) +DisjointClasses( ) +) \ No newline at end of file diff --git a/src/ontology/imports/geocore_terms.txt b/src/ontology/imports/geocore_terms.txt new file mode 100644 index 0000000..90e3f8f --- /dev/null +++ b/src/ontology/imports/geocore_terms.txt @@ -0,0 +1,9 @@ +https://www.inf.ufrgs.br/bdi/ontologies/GEOCORE_0000001 #geolocical object +https://www.inf.ufrgs.br/bdi/ontologies/GEOCORE_0000002 #geological process +https://www.inf.ufrgs.br/bdi/ontologies/GEOCORE_0000004 #geological structure +https://www.inf.ufrgs.br/bdi/ontologies/GEOCORE_0000005 #geological time interval +https://www.inf.ufrgs.br/bdi/ontologies/GEOCORE_0000008 #amount of rock +https://www.inf.ufrgs.br/bdi/ontologies/GEOCORE_0000010 #unconsolidated earth material +https://www.inf.ufrgs.br/bdi/ontologies/GEOCORE_0000011 #geological boundary +https://www.inf.ufrgs.br/bdi/ontologies/GEOCORE_0000012 #geological contact + diff --git a/src/ontology/imports/iao_import.owl b/src/ontology/imports/iao_import.owl new file mode 100644 index 0000000..7b28855 --- /dev/null +++ b/src/ontology/imports/iao_import.owl @@ -0,0 +1,1182 @@ +Prefix(:=) +Prefix(owl:=) +Prefix(rdf:=) +Prefix(xml:=) +Prefix(xsd:=) +Prefix(rdfs:=) + + +Ontology( + +Annotation( ) +Annotation(owl:versionInfo "2024-04-07") + +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) +Declaration(DataProperty()) +Declaration(DataProperty()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(NamedIndividual()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) +############################ +# Annotation Properties +############################ + +# Annotation Property: (definition) + +AnnotationAssertion( "definition"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions."@en) +AnnotationAssertion( "2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. "@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "definition"@en) + +# Annotation Property: (alternative label) + +AnnotationAssertion( "alternative label"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like."@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "OBO Operations committee") +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:comment "Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).") +AnnotationAssertion(rdfs:label "alternative label"@en) + +# Annotation Property: (definition source) + +AnnotationAssertion( "definition source"@en) +AnnotationAssertion( ) +AnnotationAssertion( "Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007"@en) +AnnotationAssertion( "PERSON:Daniel Schober"@en) +AnnotationAssertion( "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "definition source"@en) + + +############################ +# Object Properties +############################ + +# Object Property: (part of) + +AnnotationAssertion( "is part of"@en) +AnnotationAssertion( "my brain is part of my body (continuant parthood, two material entities)"@en) +AnnotationAssertion( "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)"@en) +AnnotationAssertion( "this day is part of this year (occurrent parthood)"@en) +AnnotationAssertion( "a core relation that holds between a part and its whole"@en) +AnnotationAssertion( "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other."@en) +AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) +AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) + +A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'."@en) +AnnotationAssertion( "part_of"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "part of"@en) +AnnotationAssertion(rdfs:seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of") +InverseObjectProperties( ) +TransitiveObjectProperty() + +# Object Property: (has part) + +AnnotationAssertion( "has part"@en) +AnnotationAssertion( "my body has part my brain (continuant parthood, two material entities)"@en) +AnnotationAssertion( "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"@en) +AnnotationAssertion( "this year has part this day (occurrent parthood)"@en) +AnnotationAssertion( "a core relation that holds between a whole and its part"@en) +AnnotationAssertion( "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part."@en) +AnnotationAssertion( "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/"@en) +AnnotationAssertion( "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'."@en) +AnnotationAssertion( "has_part"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has part"@en) +TransitiveObjectProperty() + +# Object Property: (is about) + +AnnotationAssertion( "This document is about information artifacts and their representations"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A (currently) primitive relation that relates an information artifact to an entity."@en) +AnnotationAssertion( "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. + +We will try to build it back up by elaborating the various subproperties that are more precisely defined. + +Some currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic."@en) +AnnotationAssertion( "person:Alan Ruttenberg"@en) +AnnotationAssertion( "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"@en) +AnnotationAssertion(rdfs:label "is about"@en) +ObjectPropertyDomain( ) + +# Object Property: (denotes) + +AnnotationAssertion( "A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance \"Alan\" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between \"Alan\" and the person that is being named."@en) +AnnotationAssertion( "A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically"@en) +AnnotationAssertion( "2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. +g denotes r =def +r is a portion of reality +there is some c that is a concretization of g +every c that is a concretization of g specifically denotes r"@en) +AnnotationAssertion( "person:Alan Ruttenberg"@en) +AnnotationAssertion( "Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan"@en) +AnnotationAssertion(rdfs:comment ""@en) +AnnotationAssertion(rdfs:label "denotes"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (denoted by) + +AnnotationAssertion( "inverse of the relation 'denotes'"@en) +AnnotationAssertion( "Person: Jie Zheng, Chris Stoeckert, Mike Conlon"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "denoted by"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has coordinate unit label) + +AnnotationAssertion(rdfs:comment "relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point"@en) +AnnotationAssertion(rdfs:label "has coordinate unit label"@en) +SubObjectPropertyOf( ) +FunctionalObjectProperty() +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (characteristic of) + +AnnotationAssertion( "inheres in"@en) +AnnotationAssertion( "this fragility is a characteristic of this vase"@en) +AnnotationAssertion( "this red color is a characteristic of this apple"@en) +AnnotationAssertion( "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence."@en) +AnnotationAssertion( "inheres_in"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:comment "Note that this relation was previously called \"inheres in\", but was changed to be called \"characteristic of\" because BFO2 uses \"inheres in\" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing.") +AnnotationAssertion(rdfs:label "characteristic of"@en) +InverseObjectProperties( ) +FunctionalObjectProperty() + +# Object Property: (has characteristic) + +AnnotationAssertion( "bearer of"@en) +AnnotationAssertion( "this apple is bearer of this red color"@en) +AnnotationAssertion( "this vase is bearer of this fragility"@en) +AnnotationAssertion( "Inverse of characteristic_of"@en) +AnnotationAssertion( "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist."@en) +AnnotationAssertion( "bearer_of"@en) +AnnotationAssertion( "is bearer of"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has characteristic"@en) +InverseFunctionalObjectProperty() +ObjectPropertyRange( ) + +# Object Property: (is concretized as) + +AnnotationAssertion( "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."@en) +AnnotationAssertion( "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."@en) +AnnotationAssertion( "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants."@en) +AnnotationAssertion(rdfs:label "is concretized as"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (concretizes) + +AnnotationAssertion( "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)."@en) +AnnotationAssertion( "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)."@en) +AnnotationAssertion( "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant."@en) +AnnotationAssertion(rdfs:label "concretizes"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (function of) + +AnnotationAssertion( "this catalysis function is a function of this enzyme"@en) +AnnotationAssertion( "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists."@en) +AnnotationAssertion( "function_of"@en) +AnnotationAssertion( "is function of"@en) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "function of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) + +# Object Property: (quality of) + +AnnotationAssertion( "this red color is a quality of this apple"@en) +AnnotationAssertion( "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A quality inheres in its bearer at all times for which the quality exists."@en) +AnnotationAssertion( "is quality of"@en) +AnnotationAssertion( "quality_of"@en) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "quality of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (role of) + +AnnotationAssertion( "this investigator role is a role of this person"@en) +AnnotationAssertion( "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists."@en) +AnnotationAssertion( "is role of"@en) +AnnotationAssertion( "role_of"@en) +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "role of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has function) + +AnnotationAssertion( "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists."@en) +AnnotationAssertion( "has_function"@en) +AnnotationAssertion(rdfs:label "has function"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has quality) + +AnnotationAssertion( "this apple has quality this red color"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist."@en) +AnnotationAssertion( "has_quality"@en) +AnnotationAssertion(rdfs:label "has quality"@en) +SubObjectPropertyOf( ) +ObjectPropertyRange( ) + +# Object Property: (has role) + +AnnotationAssertion( "this person has role this investigator role (more colloquially: this person has this role of investigator)"@en) +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence"@en) +AnnotationAssertion( "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists."@en) +AnnotationAssertion( "has_role"@en) +AnnotationAssertion(rdfs:label "has role"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (has disposition) + +AnnotationAssertion( "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence"@en) +AnnotationAssertion(rdfs:label "has disposition"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (disposition of) + +AnnotationAssertion(rdfs:comment "This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020.") +AnnotationAssertion(rdfs:label "disposition of"@en) +SubObjectPropertyOf( ) + +# Object Property: (2D boundary of) + +AnnotationAssertion( "the surface of my skin is a 2D boundary of my body"@en) +AnnotationAssertion( "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity"@en) +AnnotationAssertion( "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts."@en) +AnnotationAssertion( "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape."@en) +AnnotationAssertion( "2D_boundary_of"@en) +AnnotationAssertion( "boundary of"@en) +AnnotationAssertion( "is 2D boundary of"@en) +AnnotationAssertion( "is boundary of"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "2D boundary of"@en) +InverseObjectProperties( ) + +# Object Property: (has 2D boundary) + +AnnotationAssertion( "my body has 2D boundary the surface of my skin"@en) +AnnotationAssertion( "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity"@en) +AnnotationAssertion( "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts."@en) +AnnotationAssertion( "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape."@en) +AnnotationAssertion( "has boundary"@en) +AnnotationAssertion( "has_2D_boundary"@en) +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has 2D boundary"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (member of) + +AnnotationAssertion( "An organism that is a member of a population of organisms") +AnnotationAssertion( "is member of is a mereological relation between a item and a collection.") +AnnotationAssertion( "is member of") +AnnotationAssertion( "member part of") +AnnotationAssertion( "SIO") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "member of"@en) +SubObjectPropertyOf( ) +InverseObjectProperties( ) + +# Object Property: (has member) + +AnnotationAssertion( "has member is a mereological relation between a collection and an item.") +AnnotationAssertion( "SIO") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "has member"@en) +SubObjectPropertyOf( ) +IrreflexiveObjectProperty() + + +############################ +# Data Properties +############################ + +# Data Property: (has x coordinate value) + +AnnotationAssertion(rdfs:label "has x coordinate value"@en) +FunctionalDataProperty() +DataPropertyDomain( ) +DataPropertyRange( xsd:float) + +# Data Property: (has y coordinate value) + +AnnotationAssertion(rdfs:label "has y coordinate value"@en) +FunctionalDataProperty() +DataPropertyDomain( ) +DataPropertyRange( xsd:float) + + + +############################ +# Classes +############################ + +# Class: (entity) + +AnnotationAssertion( "entity") +AnnotationAssertion( "Entity") +AnnotationAssertion( "Julius Caesar"@en) +AnnotationAssertion( "Verdi’s Requiem"@en) +AnnotationAssertion( "the Second World War"@en) +AnnotationAssertion( "your body mass index"@en) +AnnotationAssertion( "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81"@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") Annotation(rdfs:seeAlso ) "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"@en) +AnnotationAssertion(Annotation( ) "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "entity"@en) + +# Class: (continuant) + +AnnotationAssertion( "continuant") +AnnotationAssertion( "Continuant") +AnnotationAssertion( "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts."@en) +AnnotationAssertion( "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240"@en) +AnnotationAssertion(Annotation( ) "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants"@en) +AnnotationAssertion(Annotation( ) "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])"@en) +AnnotationAssertion(Annotation( ) "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])"@en) +AnnotationAssertion(Annotation( ) "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])"@en) +AnnotationAssertion(Annotation( ) "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] ") +AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "continuant"@en) +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (occurrent) + +AnnotationAssertion( "occurrent") +AnnotationAssertion( "Occurrent") +AnnotationAssertion( "An entity that has temporal parts and that happens, unfolds or develops through time."@en) +AnnotationAssertion( "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region"@en) +AnnotationAssertion( "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players."@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process."@en) +AnnotationAssertion(Annotation( ) "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.") +AnnotationAssertion(Annotation( ) "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])"@en) +AnnotationAssertion(Annotation( ) "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])"@en) +AnnotationAssertion(Annotation( ) "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "occurrent"@en) +SubClassOf( ) +DisjointClasses( ObjectSomeValuesFrom( )) + +# Class: (independent continuant) + +AnnotationAssertion( "ic") +AnnotationAssertion( "IndependentContinuant") +AnnotationAssertion( "a chair"@en) +AnnotationAssertion( "a heart"@en) +AnnotationAssertion( "a leg"@en) +AnnotationAssertion( "a molecule"@en) +AnnotationAssertion( "a spatial region"@en) +AnnotationAssertion( "an atom"@en) +AnnotationAssertion( "an orchestra."@en) +AnnotationAssertion( "an organism"@en) +AnnotationAssertion( "the bottom right portion of a human torso"@en) +AnnotationAssertion( "the interior of your mouth"@en) +AnnotationAssertion(Annotation( ) "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en) +AnnotationAssertion(Annotation( ) "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])"@en) +AnnotationAssertion(Annotation( ) "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] ") +AnnotationAssertion(Annotation( ) "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] ") +AnnotationAssertion(Annotation( ) "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "independent continuant"@en) +SubClassOf( ) +DisjointClasses( ) +DisjointClasses( ) + +# Class: (spatial region) + +AnnotationAssertion( "s-region") +AnnotationAssertion( "SpatialRegion") +AnnotationAssertion( "BFO 2 Reference: Spatial regions do not participate in processes."@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional."@en) +AnnotationAssertion(Annotation( ) "A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])"@en) +AnnotationAssertion(Annotation( ) "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "spatial region"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (temporal region) + +AnnotationAssertion( "t-region") +AnnotationAssertion( "TemporalRegion") +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional"@en) +AnnotationAssertion(Annotation( ) "A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])"@en) +AnnotationAssertion(Annotation( ) "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])"@en) +AnnotationAssertion(Annotation( ) "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] ") +AnnotationAssertion(Annotation( ) "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "temporal region"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (two-dimensional spatial region) + +AnnotationAssertion( "2d-s-region") +AnnotationAssertion( "TwoDimensionalSpatialRegion") +AnnotationAssertion( "an infinitely thin plane in space."@en) +AnnotationAssertion( "the surface of a sphere-shaped part of space"@en) +AnnotationAssertion(Annotation( ) "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "two-dimensional spatial region"@en) +SubClassOf( ) + +# Class: (process) + +AnnotationAssertion( "process") +AnnotationAssertion( "Process") +AnnotationAssertion( "a process of cell-division, \\ a beating of the heart"@en) +AnnotationAssertion( "a process of meiosis"@en) +AnnotationAssertion( "a process of sleeping"@en) +AnnotationAssertion( "the course of a disease"@en) +AnnotationAssertion( "the flight of a bird"@en) +AnnotationAssertion( "the life of an organism"@en) +AnnotationAssertion( "your process of aging."@en) +AnnotationAssertion(Annotation( ) "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en) +AnnotationAssertion( "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)"@en) +AnnotationAssertion(Annotation( ) "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "process"@en) +SubClassOf( ) + +# Class: (disposition) + +AnnotationAssertion( "disposition") +AnnotationAssertion( "Disposition") +AnnotationAssertion( "an atom of element X has the disposition to decay to an atom of element Y"@en) +AnnotationAssertion( "certain people have a predisposition to colon cancer"@en) +AnnotationAssertion( "children are innately disposed to categorize objects in certain ways."@en) +AnnotationAssertion( "the cell wall is disposed to filter chemicals in endocytosis and exocytosis"@en) +AnnotationAssertion( "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type."@en) +AnnotationAssertion(Annotation( ) "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])"@en) +AnnotationAssertion(Annotation( ) "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "disposition"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (realizable entity) + +AnnotationAssertion( "realizable") +AnnotationAssertion( "RealizableEntity") +AnnotationAssertion( "the disposition of this piece of metal to conduct electricity."@en) +AnnotationAssertion( "the disposition of your blood to coagulate"@en) +AnnotationAssertion( "the function of your reproductive organs"@en) +AnnotationAssertion( "the role of being a doctor"@en) +AnnotationAssertion( "the role of this boundary to delineate where Utah and Colorado meet"@en) +AnnotationAssertion( "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en) +AnnotationAssertion(Annotation( ) "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])"@en) +AnnotationAssertion(Annotation( ) "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "realizable entity"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (zero-dimensional spatial region) + +AnnotationAssertion( "0d-s-region") +AnnotationAssertion( "ZeroDimensionalSpatialRegion") +AnnotationAssertion(Annotation( ) "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "zero-dimensional spatial region"@en) +SubClassOf( ) + +# Class: (quality) + +AnnotationAssertion( "quality") +AnnotationAssertion( "Quality") +AnnotationAssertion( "the ambient temperature of this portion of air"@en) +AnnotationAssertion( "the color of a tomato"@en) +AnnotationAssertion( "the length of the circumference of your waist"@en) +AnnotationAssertion( "the mass of this piece of gold."@en) +AnnotationAssertion( "the shape of your nose"@en) +AnnotationAssertion( "the shape of your nostril"@en) +AnnotationAssertion(Annotation( ) "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])"@en) +AnnotationAssertion(Annotation( ) "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "quality"@en) +SubClassOf( ) + +# Class: (specifically dependent continuant) + +AnnotationAssertion( "sdc") +AnnotationAssertion( "SpecificallyDependentContinuant") +AnnotationAssertion( "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key"@en) +AnnotationAssertion( "of one-sided specifically dependent continuants: the mass of this tomato"@en) +AnnotationAssertion( "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates."@en) +AnnotationAssertion( "the disposition of this fish to decay"@en) +AnnotationAssertion( "the function of this heart: to pump blood"@en) +AnnotationAssertion( "the mutual dependence of proton donors and acceptors in chemical reactions [79"@en) +AnnotationAssertion( "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction"@en) +AnnotationAssertion( "the pink color of a medium rare piece of grilled filet mignon at its center"@en) +AnnotationAssertion( "the role of being a doctor"@en) +AnnotationAssertion( "the shape of this hole."@en) +AnnotationAssertion( "the smell of this portion of mozzarella"@en) +AnnotationAssertion(Annotation( ) "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en) +AnnotationAssertion(Annotation( ) Annotation(rdfs:comment "per discussion with Barry Smith") "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc."@en) +AnnotationAssertion(Annotation( ) "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "specifically dependent continuant"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (role) + +AnnotationAssertion( "role") +AnnotationAssertion( "Role") +AnnotationAssertion( "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married."@en) +AnnotationAssertion( "the priest role"@en) +AnnotationAssertion( "the role of a boundary to demarcate two neighboring administrative territories"@en) +AnnotationAssertion( "the role of a building in serving as a military target"@en) +AnnotationAssertion( "the role of a stone in marking a property boundary"@en) +AnnotationAssertion( "the role of subject in a clinical trial"@en) +AnnotationAssertion( "the student role"@en) +AnnotationAssertion( "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts."@en) +AnnotationAssertion( "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives."@en) +AnnotationAssertion(Annotation( ) "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "role"@en) +SubClassOf( ) + +# Class: (object aggregate) + +AnnotationAssertion( "object-aggregate") +AnnotationAssertion( "ObjectAggregate") +AnnotationAssertion( "a collection of cells in a blood biobank."@en) +AnnotationAssertion( "a swarm of bees is an aggregate of members who are linked together through natural bonds"@en) +AnnotationAssertion( "a symphony orchestra"@en) +AnnotationAssertion( "an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)"@en) +AnnotationAssertion( "defined by fiat: the aggregate of members of an organization"@en) +AnnotationAssertion( "defined through physical attachment: the aggregate of atoms in a lump of granite"@en) +AnnotationAssertion( "defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container"@en) +AnnotationAssertion( "defined via attributive delimitations such as: the patients in this hospital"@en) +AnnotationAssertion( "the aggregate of bearings in a constant velocity axle joint"@en) +AnnotationAssertion( "the aggregate of blood cells in your body"@en) +AnnotationAssertion( "the nitrogen atoms in the atmosphere"@en) +AnnotationAssertion( "the restaurants in Palo Alto"@en) +AnnotationAssertion( "your collection of Meissen ceramic plates."@en) +AnnotationAssertion( "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)."@en) +AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") +AnnotationAssertion(Annotation( ) "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ") +AnnotationAssertion(Annotation( ) "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158.") +AnnotationAssertion(Annotation( ) "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "object aggregate"@en) +SubClassOf( ) + +# Class: (site) + +AnnotationAssertion( "site") +AnnotationAssertion( "Site") +AnnotationAssertion( "Manhattan Canyon)"@en) +AnnotationAssertion( "a hole in the interior of a portion of cheese"@en) +AnnotationAssertion( "a rabbit hole"@en) +AnnotationAssertion( "an air traffic control region defined in the airspace above an airport"@en) +AnnotationAssertion( "the Grand Canyon"@en) +AnnotationAssertion( "the Piazza San Marco"@en) +AnnotationAssertion( "the cockpit of an aircraft"@en) +AnnotationAssertion( "the hold of a ship"@en) +AnnotationAssertion( "the interior of a kangaroo pouch"@en) +AnnotationAssertion( "the interior of the trunk of your car"@en) +AnnotationAssertion( "the interior of your bedroom"@en) +AnnotationAssertion( "the interior of your office"@en) +AnnotationAssertion( "the interior of your refrigerator"@en) +AnnotationAssertion( "the lumen of your gut"@en) +AnnotationAssertion( "your left nostril (a fiat part – the opening – of your left nasal cavity)"@en) +AnnotationAssertion(Annotation( ) "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "site"@en) +SubClassOf( ) + +# Class: (generically dependent continuant) + +AnnotationAssertion( "gdc") +AnnotationAssertion( "GenericallyDependentContinuant") +AnnotationAssertion( "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity."@en) +AnnotationAssertion( "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop"@en) +AnnotationAssertion( "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule."@en) +AnnotationAssertion(Annotation( ) "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en) +AnnotationAssertion(Annotation( ) "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "generically dependent continuant"@en) +SubClassOf( ) + +# Class: (function) + +AnnotationAssertion( "function") +AnnotationAssertion( "Function") +AnnotationAssertion( "the function of a hammer to drive in nails"@en) +AnnotationAssertion( "the function of a heart pacemaker to regulate the beating of a heart through electricity"@en) +AnnotationAssertion( "the function of amylase in saliva to break down starch into sugar"@en) +AnnotationAssertion( "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc."@en) +AnnotationAssertion(Annotation( ) "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "function"@en) +SubClassOf( ) + +# Class: (material entity) + +AnnotationAssertion( "material") +AnnotationAssertion( "MaterialEntity") +AnnotationAssertion( "a flame"@en) +AnnotationAssertion( "a forest fire"@en) +AnnotationAssertion( "a human being"@en) +AnnotationAssertion( "a hurricane"@en) +AnnotationAssertion( "a photon"@en) +AnnotationAssertion( "a puff of smoke"@en) +AnnotationAssertion( "a sea wave"@en) +AnnotationAssertion( "a tornado"@en) +AnnotationAssertion( "an aggregate of human beings."@en) +AnnotationAssertion( "an energy wave"@en) +AnnotationAssertion( "an epidemic"@en) +AnnotationAssertion( "the undetached arm of a human being"@en) +AnnotationAssertion( "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en) +AnnotationAssertion( "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60"@en) +AnnotationAssertion( "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity."@en) +AnnotationAssertion( "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here."@en) +AnnotationAssertion(Annotation( ) "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])"@en) +AnnotationAssertion(Annotation( ) "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])"@en) +AnnotationAssertion(Annotation( ) "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])"@en) +AnnotationAssertion(Annotation( ) "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] ") +AnnotationAssertion(Annotation( ) "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] ") +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "material entity"@en) +SubClassOf( ) +DisjointClasses( ) + +# Class: (immaterial entity) + +AnnotationAssertion( "immaterial") +AnnotationAssertion( "ImmaterialEntity") +AnnotationAssertion( "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10"@en) +AnnotationAssertion(rdfs:isDefinedBy ) +AnnotationAssertion(rdfs:label "immaterial entity"@en) +SubClassOf( ) + +# Class: (measurement unit label) + +AnnotationAssertion( "measurement unit label"@en) +AnnotationAssertion( "Examples of measurement unit labels are liters, inches, weight per volume."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure."@en) +AnnotationAssertion( "2009-03-16: provenance: a term measurement unit was +proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and +Cristian Cocos, and subsequently moved to IAO where the objective for +which the original term was defined was satisfied with the definition +of this, different, term."@en) +AnnotationAssertion( "2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "measurement unit label"@en) +SubClassOf( ) + +# Class: (datum label) + +AnnotationAssertion( "datum label"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label"@en) +AnnotationAssertion( "http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n"@en) +AnnotationAssertion( "GROUP: IAO"@en) +AnnotationAssertion( "9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. +") +AnnotationAssertion(rdfs:label "datum label"@en) +SubClassOf( ) + +# Class: (information carrier) + +AnnotationAssertion( "information carrier"@en) +AnnotationAssertion( "In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A quality of an information bearer that imparts the information content"@en) +AnnotationAssertion( "12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'."@en) +AnnotationAssertion( "2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it.") +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "Smith, Ceusters, Ruttenberg, 2000 years of philosophy"@en) +AnnotationAssertion(rdfs:label "information carrier"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +SubClassOf( ) + +# Class: (data item) + +AnnotationAssertion( "data item"@en) +AnnotationAssertion( "Data items include counts of things, analyte concentrations, and statistical summaries."@en) +AnnotationAssertion( ) +AnnotationAssertion( "An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements."@en) +AnnotationAssertion( "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers."@en) +AnnotationAssertion( "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum."@en) +AnnotationAssertion( "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym."@en) +AnnotationAssertion( "JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith + +JAR: A data item is an approximately justified approximately true approximate belief"@en) +AnnotationAssertion( "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/") +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Chris Stoeckert"@en) +AnnotationAssertion( "PERSON: Jonathan Rees"@en) +AnnotationAssertion( "data"@en) +AnnotationAssertion(rdfs:label "data item"@en) +SubClassOf( ) + +# Class: (information content entity) + +AnnotationAssertion( "information content entity"@en) +AnnotationAssertion( "Examples of information content entites include journal articles, data, graphical layouts, and graphs."@en) +AnnotationAssertion( ) +AnnotationAssertion( "A generically dependent continuant that is about some thing."@en) +AnnotationAssertion( "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)."@en) +AnnotationAssertion( "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity."@en) +AnnotationAssertion( "PERSON: Chris Stoeckert"@en) +AnnotationAssertion( "OBI_0000142"@en) +AnnotationAssertion(rdfs:label "information content entity"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) + +# Class: (curation status specification) + +AnnotationAssertion( "curation status specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) +AnnotationAssertion( "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)"@en) +AnnotationAssertion( "PERSON:Bill Bug"@en) +AnnotationAssertion( "GROUP:OBI:"@en) +AnnotationAssertion( "OBI_0000266"@en) +AnnotationAssertion(rdfs:label "curation status specification"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (data about an ontology part) + +AnnotationAssertion( "data about an ontology part"@en) +AnnotationAssertion( "Data about an ontology part is a data item about a part of an ontology, for example a term"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "data about an ontology part"@en) +SubClassOf( ) + +# Class: (material information bearer) + +AnnotationAssertion( "material information bearer"@en) +AnnotationAssertion( "A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier."@en) +AnnotationAssertion( "a brain"@en) +AnnotationAssertion( "a hard drive"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A material entity in which a concretization of an information content entity inheres."@en) +AnnotationAssertion( "GROUP: IAO"@en) +AnnotationAssertion(rdfs:label "material information bearer"@en) +EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))) +SubClassOf( ) + +# Class: (obsolescence reason specification) + +AnnotationAssertion( "obsolescence reason specification"@en) +AnnotationAssertion( ) +AnnotationAssertion( "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en) +AnnotationAssertion( "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology."@en) +AnnotationAssertion( "PERSON: Alan Ruttenberg"@en) +AnnotationAssertion( "PERSON: Melanie Courtot"@en) +AnnotationAssertion(rdfs:label "obsolescence reason specification"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (textual entity) + +AnnotationAssertion( "textual entity"@en) +AnnotationAssertion( "Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities"@en) +AnnotationAssertion( ) +AnnotationAssertion( "A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc."@en) +AnnotationAssertion( "AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc."@en) +AnnotationAssertion( "MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities."@en) +AnnotationAssertion( "PERSON: Lawrence Hunter"@en) +AnnotationAssertion( "text"@en) +AnnotationAssertion(rdfs:label "textual entity"@en) +SubClassOf( ) + +# Class: (cartesian spatial coordinate datum) + +AnnotationAssertion( ) +AnnotationAssertion( "A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude"@en) +AnnotationAssertion( "2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "AR notes: We need to discuss whether it should include site.") +AnnotationAssertion(rdfs:label "cartesian spatial coordinate datum"@en) +AnnotationAssertion(rdfs:seeAlso "http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) +SubClassOf( ObjectExactCardinality(1 )) + +# Class: (two dimensional cartesian spatial coordinate datum) + +AnnotationAssertion( ) +AnnotationAssertion( "A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "two dimensional cartesian spatial coordinate datum"@en) +SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))) +SubClassOf( DataExactCardinality(1 )) +SubClassOf( DataExactCardinality(1 )) + +# Class: (denotator type) + +AnnotationAssertion( "denotator type"@en) +AnnotationAssertion( "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities."@en) +AnnotationAssertion( "A denotator type indicates how a term should be interpreted from an ontological perspective."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "Barry Smith, Werner Ceusters"@en) +AnnotationAssertion(rdfs:label "denotator type"@en) +EquivalentClasses( ObjectOneOf( )) +SubClassOf( ) + +# Class: (written name) + +AnnotationAssertion( "written name"@en) +AnnotationAssertion( "\"Bill Clinton\""@en) +AnnotationAssertion( "\"The Eiffel Tower\""@en) +AnnotationAssertion( "\"United States of America\""@en) +AnnotationAssertion( ) +AnnotationAssertion( "A textual entity that denotes a particular in reality."@en) +AnnotationAssertion( "PERSON: Bill Hogan"@en) +AnnotationAssertion( "https://github.com/information-artifact-ontology/IAO/issues/114"@en) +AnnotationAssertion( "The qualifier \"written\" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so \"All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT\" would be a name."@en) +AnnotationAssertion(rdfs:label "written name"@en) +SubClassOf( ) + +# Class: (length unit) + +AnnotationAssertion( "length unit") +AnnotationAssertion( ) +AnnotationAssertion(rdfs:label "length unit") +SubClassOf( ) + + +############################ +# Named Individuals +############################ + +# Individual: (example to be eventually removed) + +AnnotationAssertion( "example to be eventually removed"@en) +AnnotationAssertion(rdfs:label "example to be eventually removed"@en) +ClassAssertion( ) + +# Individual: (failed exploratory term) + +AnnotationAssertion( "failed exploratory term"@en) +AnnotationAssertion( "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job"@en) +AnnotationAssertion( "Person:Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "failed exploratory term"@en) +ClassAssertion( ) + +# Individual: (metadata complete) + +AnnotationAssertion( "metadata complete"@en) +AnnotationAssertion( "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete."@en) +AnnotationAssertion(rdfs:label "metadata complete"@en) +ClassAssertion( ) + +# Individual: (organizational term) + +AnnotationAssertion( "organizational term"@en) +AnnotationAssertion( "Term created to ease viewing/sort terms for development purpose, and will not be included in a release"@en) +AnnotationAssertion(rdfs:label "organizational term"@en) +ClassAssertion( ) + +# Individual: (ready for release) + +AnnotationAssertion( "ready for release"@en) +AnnotationAssertion( "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\""@en) +AnnotationAssertion(rdfs:label "ready for release"@en) +ClassAssertion( ) + +# Individual: (metadata incomplete) + +AnnotationAssertion( "metadata incomplete"@en) +AnnotationAssertion( "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors."@en) +AnnotationAssertion(rdfs:label "metadata incomplete"@en) +ClassAssertion( ) + +# Individual: (uncurated) + +AnnotationAssertion( "uncurated"@en) +AnnotationAssertion( "Nothing done yet beyond assigning a unique class ID and proposing a preferred term."@en) +AnnotationAssertion(rdfs:label "uncurated"@en) +ClassAssertion( ) + +# Individual: (pending final vetting) + +AnnotationAssertion( "pending final vetting"@en) +AnnotationAssertion( "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor."@en) +AnnotationAssertion(rdfs:label "pending final vetting"@en) +ClassAssertion( ) + +# Individual: (placeholder removed) + +AnnotationAssertion( "placeholder removed"@en) +AnnotationAssertion(rdfs:label "placeholder removed"@en) +ClassAssertion( ) + +# Individual: (terms merged) + +AnnotationAssertion( "terms merged"@en) +AnnotationAssertion( "An editor note should explain what were the merged terms and the reason for the merge."@en) +AnnotationAssertion(rdfs:label "terms merged"@en) +ClassAssertion( ) + +# Individual: (term imported) + +AnnotationAssertion( "term imported"@en) +AnnotationAssertion( "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use."@en) +AnnotationAssertion(rdfs:label "term imported"@en) +ClassAssertion( ) + +# Individual: (term split) + +AnnotationAssertion( "term split"@en) +AnnotationAssertion( "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created."@en) +AnnotationAssertion(rdfs:label "term split"@en) +ClassAssertion( ) + +# Individual: (universal) + +AnnotationAssertion( "universal"@en) +AnnotationAssertion( "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf"@en) +AnnotationAssertion(rdfs:label "universal"@en) +ClassAssertion( ) + +# Individual: (defined class) + +AnnotationAssertion( "defined class"@en) +AnnotationAssertion( "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal"@en) +AnnotationAssertion( "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "defined class"@en) +ClassAssertion( ) + +# Individual: (named class expression) + +AnnotationAssertion( "named class expression"@en) +AnnotationAssertion( "A named class expression is a logical expression that is given a name. The name can be used in place of the expression."@en) +AnnotationAssertion( "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions"@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion(rdfs:label "named class expression"@en) +ClassAssertion( ) + +# Individual: (to be replaced with external ontology term) + +AnnotationAssertion( "to be replaced with external ontology term"@en) +AnnotationAssertion( "Terms with this status should eventually replaced with a term from another ontology."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "to be replaced with external ontology term"@en) +ClassAssertion( ) + +# Individual: (requires discussion) + +AnnotationAssertion( "requires discussion"@en) +AnnotationAssertion( "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues."@en) +AnnotationAssertion( "Alan Ruttenberg"@en) +AnnotationAssertion( "group:OBI"@en) +AnnotationAssertion(rdfs:label "requires discussion"@en) +ClassAssertion( ) + +# Individual: (out of scope) + +AnnotationAssertion( "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not."@en) +AnnotationAssertion( "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease."@en) +AnnotationAssertion( ) +AnnotationAssertion( "https://github.com/information-artifact-ontology/ontology-metadata/issues/77") +AnnotationAssertion( "https://orcid.org/0000-0001-5208-3432") +AnnotationAssertion(rdfs:label "out of scope") +ClassAssertion( ) + + +DifferentIndividuals( ) +DifferentIndividuals( ) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) +) \ No newline at end of file diff --git a/src/ontology/imports/iao_terms.txt b/src/ontology/imports/iao_terms.txt new file mode 100644 index 0000000..e69de29 diff --git a/src/ontology/run.bat b/src/ontology/run.bat new file mode 100644 index 0000000..571d189 --- /dev/null +++ b/src/ontology/run.bat @@ -0,0 +1 @@ +docker run -v %cd%\..\..\:/work -w /work/src/ontology -e 'ROBOT_JAVA_ARGS=' -e 'JAVA_OPTS=' --rm -ti obolibrary/odkfull %* \ No newline at end of file diff --git a/src/ontology/run.sh b/src/ontology/run.sh new file mode 100644 index 0000000..873e9bd --- /dev/null +++ b/src/ontology/run.sh @@ -0,0 +1,107 @@ +#!/bin/sh +# Wrapper script for docker. +# +# This is used primarily for wrapping the GNU Make workflow. +# Instead of typing "make TARGET", type "./run.sh make TARGET". +# This will run the make workflow within a docker container. +# +# The assumption is that you are working in the src/ontology folder; +# we therefore map the whole repo (../..) to a docker volume. +# +# To use singularity instead of docker, please issue +# export USE_SINGULARITY= +# before running this script. +# +# See README-editors.md for more details. + +set -e + +if [ -f run.sh.conf ]; then + . ./run.sh.conf +fi + +# Look for a GitHub token +if [ -n "$GH_TOKEN" ]; then + : +elif [ -f ../../.github/token.txt ]; then + GH_TOKEN=$(cat ../../.github/token.txt) +elif [ -f $XDG_CONFIG_HOME/ontology-development-kit/github/token ]; then + GH_TOKEN=$(cat $XDG_CONFIG_HOME/ontology-development-kit/github/token) +elif [ -f "$HOME/Library/Application Support/ontology-development-kit/github/token" ]; then + GH_TOKEN=$(cat "$HOME/Library/Application Support/ontology-development-kit/github/token") +fi + +# SSH agent socket +# On macOS, we cannot use $SSH_AUTH_SOCK directly, +# we need to use a "magic" socket instead. +case "$(uname)" in +Darwin) + ODK_SSH_AUTH_SOCKET=/run/host-services/ssh-auth.sock + ;; +*) + ODK_SSH_AUTH_SOCKET=$SSH_AUTH_SOCK + ;; +esac +ODK_SSH_BIND= +if [ -n "$ODK_SSH_AUTH_SOCKET" ]; then + ODK_SSH_BIND=",$ODK_SSH_AUTH_SOCKET:/run/host-services/ssh-auth.sock" +fi + +ODK_IMAGE=${ODK_IMAGE:-odkfull} +TAG_IN_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $2 }') +if [ -n "$TAG_IN_IMAGE" ]; then + # Override ODK_TAG env var if IMAGE already includes a tag + ODK_TAG=$TAG_IN_IMAGE + ODK_IMAGE=$(echo $ODK_IMAGE | awk -F':' '{ print $1 }') +fi +ODK_TAG=${ODK_TAG:-latest} +ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx8G} +ODK_DEBUG=${ODK_DEBUG:-no} + +ODK_USER_ID=${ODK_USER_ID:-$(id -u)} +ODK_GROUP_ID=${ODK_GROUP_ID:-$(id -g)} + +# Convert OWLAPI_* environment variables to the OWLAPI as Java options +# See http://owlcs.github.io/owlapi/apidocs_4/org/semanticweb/owlapi/model/parameters/ConfigurationOptions.html +# for a list of allowed options +OWLAPI_OPTIONS_NAMESPACE=org.semanticweb.owlapi.model.parameters.ConfigurationOptions +for owlapi_var in $(env | sed -n s/^OWLAPI_//p) ; do + ODK_JAVA_OPTS="$ODK_JAVA_OPTS -D$OWLAPI_OPTIONS_NAMESPACE.${owlapi_var%=*}=${owlapi_var#*=}" +done + +TIMECMD= +if [ x$ODK_DEBUG = xyes ]; then + # If you wish to change the format string, take care of using + # non-breaking spaces (U+00A0) instead of normal spaces, to + # prevent the shell from tokenizing the format string. + echo "Running obolibrary/${ODK_IMAGE}:${ODK_TAG} with '${ODK_JAVA_OPTS}' as options for ROBOT and other Java-based pipeline steps." + TIMECMD="/usr/bin/time -f ### DEBUG STATS ###\nElapsed time: %E\nPeak memory: %M kb" +fi +rm -f tmp/debug.log + +VOLUME_BIND=$PWD/../../:/work$ODK_SSH_BIND +WORK_DIR=/work/src/ontology + +if [ -n "$ODK_BINDS" ]; then + VOLUME_BIND="$VOLUME_BIND,$ODK_BINDS" +fi + +if [ -n "$USE_SINGULARITY" ]; then + + singularity exec --cleanenv $ODK_SINGULARITY_OPTIONS \ + --env "ROBOT_JAVA_ARGS=$ODK_JAVA_OPTS,JAVA_OPTS=$ODK_JAVA_OPTS,SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock,ODK_USER_ID=$ODK_USER_ID,ODK_GROUP_ID=$ODK_GROUP_ID,ODK_DEBUG=$ODK_DEBUG" \ + --bind $VOLUME_BIND \ + -W $WORK_DIR \ + docker://obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@" +else + BIND_OPTIONS="-v $(echo $VOLUME_BIND | sed 's/,/ -v /')" + docker run $ODK_DOCKER_OPTIONS $BIND_OPTIONS -w $WORK_DIR \ + -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" -e SSH_AUTH_SOCK=/run/host-services/ssh-auth.sock -e ODK_USER_ID=$ODK_USER_ID -e ODK_GROUP_ID=$ODK_GROUP_ID -e ODK_DEBUG=$ODK_DEBUG \ + --rm -ti obolibrary/$ODK_IMAGE:$ODK_TAG $TIMECMD "$@" +fi + +case "$@" in +*update_repo*|*release*) + echo "Please remember to update your ODK image from time to time: https://oboacademy.github.io/obook/howto/odk-update/." + ;; +esac \ No newline at end of file diff --git a/src/ontology/tmp/.gitkeep b/src/ontology/tmp/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/src/scripts/run-command.sh b/src/scripts/run-command.sh new file mode 100644 index 0000000..45d431d --- /dev/null +++ b/src/scripts/run-command.sh @@ -0,0 +1,4 @@ +#!/bin/sh +ODK_DEBUG_FILE=${ODK_DEBUG_FILE:-debug.log} +echo "Command: sh $@" >> $ODK_DEBUG_FILE +/usr/bin/time -a -o $ODK_DEBUG_FILE -f "Elapsed time: %E\nPeak memory: %M kb" /bin/sh "$@" diff --git a/src/scripts/update_repo.sh b/src/scripts/update_repo.sh new file mode 100644 index 0000000..68b9d9b --- /dev/null +++ b/src/scripts/update_repo.sh @@ -0,0 +1,31 @@ +echo "This (experimental) update script will create a new repo according to your config file. It will:" +echo "(1) overwrite your repositories Makefile, ODK sparql queries (your custom queries wont be touched) and docker wrapper (run.sh)." +echo "(2) and add missing files, if any." + +set -e + +OID=geores +ROOTDIR=../.. +SRCDIR=.. +CONFIG=$OID"-odk.yaml" + +rm -rf target +mkdir target +/tools/odk.py seed -c -g -C $CONFIG +ls -l target/$OID/src +ls -l $SRCDIR/ +cp target/$OID/src/scripts/update_repo.sh $SRCDIR/scripts/ +rsync -r -u --ignore-existing --exclude 'patterns/data/default/example.tsv' --exclude 'patterns/dosdp-patterns/example.yaml' target/$OID/src/ $SRCDIR/ +cp target/$OID/src/ontology/Makefile $SRCDIR/ontology/ +cp target/$OID/src/ontology/run.sh $SRCDIR/ontology/ +cp -r target/$OID/src/sparql/* $SRCDIR/sparql/ +mkdir -p $ROOTDIR/.github +mkdir -p $ROOTDIR/.github/workflows +cp target/$OID/.github/workflows/qc.yml $ROOTDIR/.github/workflows/qc.yml + + + + +echo "WARNING: These files should be manually migrated: mkdocs.yaml, .gitignore, src/ontology/catalog.xml (if you added a new import or component)" + +echo "Ontology repository update successfully completed." \ No newline at end of file diff --git a/src/scripts/validate_id_ranges.sc b/src/scripts/validate_id_ranges.sc new file mode 100644 index 0000000..1785e8d --- /dev/null +++ b/src/scripts/validate_id_ranges.sc @@ -0,0 +1,75 @@ +import $ivy.`net.sourceforge.owlapi:owlapi-distribution:4.5.16` +import $ivy.`com.outr::scribe-slf4j:2.7.12` +import org.semanticweb.owlapi.apibinding.OWLManager +import org.semanticweb.owlapi.model._ +import org.semanticweb.owlapi.vocab.OWLFacet +import java.io.File +import scala.collection +import scala.collection.mutable +import scala.jdk.CollectionConverters._ +@main +def main(id_range_file: os.Path) = { + val o = OWLManager.createOWLOntologyManager().loadOntology(IRI.create(id_range_file.toIO)) + val allMyFacets = mutable.ListBuffer.empty[MyFacet] + for (dt <- o.getDatatypesInSignature().asScala) { + val defs = o.getAxioms(dt) + for (ax <- defs.asScala) { + val range = ax.getDataRange() + val f = new MyFacet() + f.id = dt.toString() + range.accept(new OWLDataRangeVisitor() { + override + def visit(owlDatatype: OWLDatatype) = () + override + def visit(owlDataOneOf: OWLDataOneOf) = () + override + def visit(owlDataComplementOf: OWLDataComplementOf) = () + override + def visit(owlDataIntersectionOf: OWLDataIntersectionOf) = () + override + def visit(owlDataUnionOf: OWLDataUnionOf) = () + override + def visit(owlDatatypeRestriction: OWLDatatypeRestriction) = { + for (fr <- owlDatatypeRestriction.getFacetRestrictions().asScala) { + var i = fr.getFacetValue().parseInteger() + if(fr.getFacet().equals(OWLFacet.MIN_INCLUSIVE)) { + f.min = i + } else if(fr.getFacet().equals(OWLFacet.MAX_INCLUSIVE)) { + f.max = i + } else if(fr.getFacet().equals(OWLFacet.MIN_EXCLUSIVE)) { + i += 1 + f.min = i + } else if(fr.getFacet().equals(OWLFacet.MAX_EXCLUSIVE)) { + i -= 1 + f.max = i + } else { + log("Unknown range restriction: "+fr) + } + } + } + }) + log("Testing range: "+f) + testFacetViolation(f,allMyFacets) + allMyFacets.append(f) + } + } +} +def testFacetViolation(f: MyFacet , allMyFacets: collection.Seq[MyFacet]) = { + for (f_p <- allMyFacets) { + if (((f.min <= f_p.max) && (f_p.min <= f.max))) { + throw new IllegalStateException(f + " overlaps with " + f_p + "!") + } + } +} +def log(o: Object) = { + println(o.toString()) +} +class MyFacet { + var min: Int = _ + var max: Int = _ + var id: String = _ + override + def toString(): String = { + return "Facet{" + id + "}[min:" + min + " max:" + max + "]" + } +} \ No newline at end of file diff --git a/src/sparql/README.md b/src/sparql/README.md new file mode 100644 index 0000000..fd5733f --- /dev/null +++ b/src/sparql/README.md @@ -0,0 +1,32 @@ +# Sparql checks + +[SPARQL](https://www.w3.org/TR/rdf-sparql-query/) is a W3C standard +query language for RDF. This directory contains useful SPARQL queries +for perfoming over the ontology. + +SPARQL can be executed on a triplestore or directly on any OWL +file. The queries here are all executed on either geores-edit.obo or +downstream products in the [ontology](../ontology/) folder. We use +`robot` as this allows easy execution over any Obo-format or OWL file. + +We break the queries into 3 categories: + +## Constraint Violation checks + +These are all named `*violation.sparql`. A subset of these are +configured to be executed via travis. If these return any results, +then the build will fail. + +Consult the individual sparql files to see the intent of the check + +## Construct queries + +These are named `construct*.sparql`, and always have the form `CONSTRUCT ...`. + +These are used to generate new OWL axioms that can be inserted back +into the ontology. + +## Reports + +The remaining SPARQL queries are for informative purposes. A subset +may be executed with each release. \ No newline at end of file diff --git a/src/sparql/basic-report.sparql b/src/sparql/basic-report.sparql new file mode 100644 index 0000000..cff9773 --- /dev/null +++ b/src/sparql/basic-report.sparql @@ -0,0 +1,12 @@ +prefix oio: +prefix def: +prefix owl: + +SELECT ?cls ?def (group_concat(?xref) as ?xrefs) WHERE +{ + ?cls a owl:Class . + OPTIONAL { ?cls oio:hasDbXref ?xref } . + OPTIONAL { ?cls def: ?def } . + FILTER (!isBlank(?cls)) +} +GROUP BY ?cls ?def diff --git a/src/sparql/dc-properties-violation.sparql b/src/sparql/dc-properties-violation.sparql new file mode 100644 index 0000000..7409b92 --- /dev/null +++ b/src/sparql/dc-properties-violation.sparql @@ -0,0 +1,11 @@ +# The purpose of this violation is to make sure people update +# from using the deprecated DC Elements 1.1 namespace (http://purl.org/dc/elements/1.1/) +# to using the recommended DC Terms namespace (http://purl.org/dc/terms/) +# See also discussion on https://github.com/oborel/obo-relations/pull/692 + +SELECT ?term ?predicate WHERE { + ?term ?predicate ?value . + FILTER(STRSTARTS(STR(?predicate), "http://purl.org/dc/elements/1.1/")) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "https://www.inf.ufrgs.br/bdi/ontologies/GEORES_"))) +} + diff --git a/src/sparql/edges.sparql b/src/sparql/edges.sparql new file mode 100644 index 0000000..edf658b --- /dev/null +++ b/src/sparql/edges.sparql @@ -0,0 +1,18 @@ +prefix owl: +prefix rdfs: +prefix rdf: + +SELECT ?x ?p ?y +WHERE { + {?x rdfs:subClassOf [ + a owl:Restriction ; + owl:onProperty ?p ; + owl:someValuesFrom ?y ] + } + UNION { + ?x rdfs:subClassOf ?y . + BIND(rdfs:subClassOf AS ?p) + } + ?x a owl:Class . + ?y a owl:Class . +} diff --git a/src/sparql/geores_terms.sparql b/src/sparql/geores_terms.sparql new file mode 100644 index 0000000..ad19423 --- /dev/null +++ b/src/sparql/geores_terms.sparql @@ -0,0 +1,7 @@ +SELECT DISTINCT ?term +WHERE { + { ?s1 ?p1 ?term . } + UNION + { ?term ?p2 ?o2 . } + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "https://www.inf.ufrgs.br/bdi/ontologies/GEORES_"))) +} diff --git a/src/sparql/inject-subset-declaration.ru b/src/sparql/inject-subset-declaration.ru new file mode 100644 index 0000000..93dc9e8 --- /dev/null +++ b/src/sparql/inject-subset-declaration.ru @@ -0,0 +1,11 @@ +PREFIX : +PREFIX rdf: +PREFIX rdfs: + +INSERT { ?y rdfs:subPropertyOf . } + +WHERE { + ?x ?y . + FILTER(isIRI(?y)) + FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)") || regex(str(?y),"^(https://www.inf.ufrgs.br/bdi/ontologies)")) +} \ No newline at end of file diff --git a/src/sparql/inject-synonymtype-declaration.ru b/src/sparql/inject-synonymtype-declaration.ru new file mode 100644 index 0000000..300ce36 --- /dev/null +++ b/src/sparql/inject-synonymtype-declaration.ru @@ -0,0 +1,11 @@ +PREFIX : +PREFIX rdf: +PREFIX rdfs: + +INSERT { ?y rdfs:subPropertyOf . } + +WHERE { + ?x ?y . + FILTER(isIRI(?y)) + FILTER(regex(str(?y),"^(http://purl.obolibrary.org/obo/)") || regex(str(?y),"^(http://www.ebi.ac.uk/efo/)") || regex(str(?y),"^(https://w3id.org/biolink/)") || regex(str(?y),"^(https://www.inf.ufrgs.br/bdi/ontologies)")) +} \ No newline at end of file diff --git a/src/sparql/iri-range-violation.sparql b/src/sparql/iri-range-violation.sparql new file mode 100644 index 0000000..c1099d7 --- /dev/null +++ b/src/sparql/iri-range-violation.sparql @@ -0,0 +1,19 @@ +PREFIX never_in_taxon: +PREFIX present_in_taxon: +PREFIX oboInOwl: +PREFIX dcterms: +PREFIX foaf: + +SELECT ?term ?property ?value +WHERE { + VALUES ?property { + never_in_taxon: + present_in_taxon: + foaf:depicted_by + oboInOwl:inSubset + dcterms:contributor } + ?term ?property ?value . + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "https://www.inf.ufrgs.br/bdi/ontologies/GEORES_"))) + FILTER (!isIRI(?value)) +} + diff --git a/src/sparql/label-with-iri-violation.sparql b/src/sparql/label-with-iri-violation.sparql new file mode 100644 index 0000000..afbe32a --- /dev/null +++ b/src/sparql/label-with-iri-violation.sparql @@ -0,0 +1,9 @@ +PREFIX rdfs: + +SELECT ?term ?value +WHERE { + ?term rdfs:label ?value . + FILTER (REGEX(?value, "http[s]?[:]")) + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "https://www.inf.ufrgs.br/bdi/ontologies/GEORES_"))) +} + diff --git a/src/sparql/labels.sparql b/src/sparql/labels.sparql new file mode 100644 index 0000000..89e9ec7 --- /dev/null +++ b/src/sparql/labels.sparql @@ -0,0 +1,9 @@ +PREFIX owl: +PREFIX rdf: +PREFIX rdfs: + +SELECT ?x (STR(?lab) AS ?label) WHERE { + ?x rdf:type owl:Class . + OPTIONAL {?x rdfs:label ?lab} +} +ORDER BY ?x diff --git a/src/sparql/multiple-replaced_by-violation.sparql b/src/sparql/multiple-replaced_by-violation.sparql new file mode 100644 index 0000000..65bb8de --- /dev/null +++ b/src/sparql/multiple-replaced_by-violation.sparql @@ -0,0 +1,12 @@ +PREFIX replaced_by: + +SELECT DISTINCT ?entity ?property ?value WHERE { + VALUES ?property { + replaced_by: + } + ?entity ?property ?value1 . + ?entity ?property ?value2 . + FILTER(?value1!=?value2) + BIND(CONCAT(str(?value1), CONCAT("|", str(?value2))) as ?value) +} + diff --git a/src/sparql/obsoletes.sparql b/src/sparql/obsoletes.sparql new file mode 100644 index 0000000..7aff433 --- /dev/null +++ b/src/sparql/obsoletes.sparql @@ -0,0 +1,14 @@ +prefix xsd: +PREFIX owl: +PREFIX rdf: +PREFIX rdfs: +PREFIX replaced_by: +PREFIX consider: + +SELECT ?cls ?replCls ?consCls WHERE { + ?cls a owl:Class ; + owl:deprecated "true"^^xsd:boolean . + OPTIONAL {?cls replaced_by: ?replCls} + OPTIONAL {?cls consider: ?consCls} +} +ORDER BY ?cls diff --git a/src/sparql/owldef-self-reference-violation.sparql b/src/sparql/owldef-self-reference-violation.sparql new file mode 100644 index 0000000..42aa3ed --- /dev/null +++ b/src/sparql/owldef-self-reference-violation.sparql @@ -0,0 +1,12 @@ +PREFIX rdf: +PREFIX oio: +PREFIX owl: +PREFIX rdfs: + +SELECT ?term WHERE { + { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first ?term ] ] } + UNION + { ?term owl:equivalentClass [ owl:intersectionOf [ rdf:rest*/rdf:first [ owl:someValuesFrom ?term ] ] ] } + FILTER(isIRI(?term) && (STRSTARTS(str(?term), "https://www.inf.ufrgs.br/bdi/ontologies/GEORES_"))) +} + diff --git a/src/sparql/postprocess-module.ru b/src/sparql/postprocess-module.ru new file mode 100644 index 0000000..0767af1 --- /dev/null +++ b/src/sparql/postprocess-module.ru @@ -0,0 +1,16 @@ +PREFIX rdf: +PREFIX rdfs: +PREFIX dc: +PREFIX owl: + + +DELETE { + ?ontology ?ontology_annotation_property ?ontology_annotation_value . +} + +WHERE { + ?ontology rdf:type owl:Ontology . + ?ontology ?ontology_annotation_property ?ontology_annotation_value . + FILTER(?ontology_annotation_property != dc:source && ?ontology_annotation_property != rdf:type) + +} \ No newline at end of file diff --git a/src/sparql/preprocess-module.ru b/src/sparql/preprocess-module.ru new file mode 100644 index 0000000..99120a0 --- /dev/null +++ b/src/sparql/preprocess-module.ru @@ -0,0 +1,22 @@ +PREFIX rdf: +PREFIX rdfs: +PREFIX dc: +PREFIX owl: + + +#DELETE { +# ?ontology ?ontology_annotation_property ?ontology_annotation_value . +#} + +INSERT { + ?ontology dc:source ?version_iri . +} + +WHERE { + ?ontology rdf:type owl:Ontology ; + owl:versionIRI ?version_iri . + #OPTIONAL { + # ?ontology ?ontology_annotation_property ?ontology_annotation_value . + #} + +} \ No newline at end of file diff --git a/src/sparql/simple-seed.sparql b/src/sparql/simple-seed.sparql new file mode 100644 index 0000000..247fbde --- /dev/null +++ b/src/sparql/simple-seed.sparql @@ -0,0 +1,13 @@ +prefix owl: + +SELECT DISTINCT ?cls WHERE +{ + {?cls a owl:AnnotationProperty .} + UNION + {?cls a owl:ObjectProperty .} + UNION + {?x ?cls} + UNION + {?x ?cls} + FILTER (!isBlank(?cls)) +} diff --git a/src/sparql/subsets-labeled.sparql b/src/sparql/subsets-labeled.sparql new file mode 100644 index 0000000..5ca7e31 --- /dev/null +++ b/src/sparql/subsets-labeled.sparql @@ -0,0 +1,13 @@ +prefix oio: +prefix owl: +prefix inSubset: +prefix rdfs: + +SELECT ?subset ?clsLabel +WHERE +{ + ?cls a owl:Class ; + inSubset: ?subset ; + rdfs:label ?clsLabel +} +ORDER BY ?subset ?cls diff --git a/src/sparql/synonyms.sparql b/src/sparql/synonyms.sparql new file mode 100644 index 0000000..ba6b03a --- /dev/null +++ b/src/sparql/synonyms.sparql @@ -0,0 +1,26 @@ +prefix owl: +prefix oboInOwl: +prefix rdfs: + +SELECT ?cls ?pred ?val ?synType +WHERE + { ?cls ?pred ?val ; + a owl:Class . + FILTER ( + ?pred = rdfs:label || + ?pred = oboInOwl:hasRelatedSynonym || + ?pred = oboInOwl:hasNarrowSynonym || + ?pred = oboInOwl:hasBroadSynonym || + ?pred = oboInOwl:hasExactSynonym + ) + + OPTIONAL { + [ + a owl:Axiom ; + owl:annotatedSource ?cls ; + owl:annotatedProperty ?pred ; + owl:annotatedTarget ?val ; + oboInOwl:hasSynonymType ?synType + ] + } + } diff --git a/src/sparql/terms.sparql b/src/sparql/terms.sparql new file mode 100644 index 0000000..ec58b4c --- /dev/null +++ b/src/sparql/terms.sparql @@ -0,0 +1,15 @@ +PREFIX rdf: +prefix owl: +SELECT DISTINCT ?term +WHERE { + { + ?s1 ?p1 ?term . + FILTER(?p1!=rdf:type) + } + UNION + { + ?term ?p2 ?o2 . + FILTER(?o2!=owl:Ontology) + } + FILTER(isIRI(?term)) +} \ No newline at end of file diff --git a/src/sparql/xrefs.sparql b/src/sparql/xrefs.sparql new file mode 100644 index 0000000..bde8fc9 --- /dev/null +++ b/src/sparql/xrefs.sparql @@ -0,0 +1,8 @@ +prefix oio: +prefix owl: + +SELECT ?cls ?xref WHERE +{ + ?cls a owl:Class ; + oio:hasDbXref ?xref +}