emmo-repo · jesper-friis · Feb 28, 2021 · Feb 28, 2021 · Feb 28, 2021 · Mar 1, 2021
diff --git a/.github/emmocheck_conf.yml b/.github/emmocheck_conf.yml
@@ -2,7 +2,6 @@
 test_namespace:
   exceptions:
     - manufacturing.EngineeredMaterial
-
 test_quantity_dimension:
   exceptions:
     - emmo.ModelledQuantitativeProperty

diff --git a/.github/pages-index.html.in b/.github/pages-index.html.in
@@ -7,21 +7,21 @@
   <meta name="author" content="Jesper Friis, SINTEF">
   <meta name="author" content="Adham Hashibon, Fraunhofer IWM">
   <meta name="author" content="Georg Schmitz, ACCESS">
-  <meta name="institution" content="European Materials &#38 Modelling Council (EMMC)">
+  <meta name="institution" content="Elemental Multiperspective Material Council (EMMC)">
   <meta name="keywords" content="EMMO, materials science, modelling, characterisation, materials, ontology">
   <meta name="dcterms.date" content="${date}">
   <link rel="stylesheet" type="text/css" href="css/style.css">
   <link rel="icon" type="image/png" href="https://avatars1.githubusercontent.com/u/51194521?s=400&u=d9e0bbceb9a6e4901077e92b2426c8bca46b1009&v=4">
-  <title>Europeean Materials &#38 Modelling Ontology</title>
+  <title>Elemental Multiperspective Material Ontology (EMMO)</title>
 </head>
 <body>
 
 <div class="header">
   <img src="https://avatars1.githubusercontent.com/u/51194521?s=400&u=d9e0bbceb9a6e4901077e92b2426c8bca46b1009&v=4" class="logo" width="64" alt="EMMO">
-  <h1 class="logo">The Europeean Materials &#38 Modelling Ontology (EMMO)</h1>
+  <h1 class="logo">Elemental Multiperspective Material Ontology (EMMO)</h1>
   <img src="https://i2.wp.com/emmc.info/wp-content/uploads/2018/10/emmc_logo-low.jpg?fit=1701%2C1701&ssl=1" class="emmclogo" width="64" alt="EMMC">
 </div>
-The European Materials Modelling Ontology (EMMO) is the result of a multidisciplinary effort within the EMMC, aimed at the development of a standard representational ontology framework based on current materials modelling and characterization knowledge. Instead of starting from general upper level concepts, as done by other ontologies, the EMMO development started from the very bottom level, using the actual picture of the physical world coming from applied sciences, and in particular from physics and material sciences.
+The Elemental Multiperspective Material Ontology (EMMO) is the result of a multidisciplinary effort within the EMMC, aimed at the development of a standard representational ontology framework based on current materials modelling and characterization knowledge. Instead of starting from general upper level concepts, as done by other ontologies, the EMMO development started from the very bottom level, using the actual picture of the physical world coming from applied sciences, and in particular from physics and material sciences.
 <p>
 The EMMO has grown from the bottom (i.e. scientific application field) to the top (i.e. conceptualization), staying focused on the original scope while at the same time maintaining an approach as general as possible. The ontological framework has been built around concepts like elementary particles, wave-particle dualism, finiteness of space and time intervals coming from the perspective for experimental physics. The development of the middle and upper layers of the ontology has been functional to the respect of these low level concepts, to facilitate the understanding of the high level concepts to users with limited or no philosophical background.
 

diff --git a/.github/workflows/ci_emmocheck.yml b/.github/workflows/ci_emmocheck.yml
@@ -4,7 +4,7 @@ on: [push]
 jobs:
 
   build:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-18.04
     strategy:
       max-parallel: 1
       matrix:

diff --git a/README.md b/README.md
@@ -1,5 +1,7 @@
 [![License: CC BY 4.0](https://img.shields.io/badge/License-CC%20BY%204.0-lightgrey.svg)](https://creativecommons.org/licenses/by/4.0/)
 ![CI tests](https://github.com/emmo-repo/EMMO/workflows/Check%20conventions/badge.svg)
+[![GitHub release](https://img.shields.io/github/v/release/emmo-repo/emmo)](https://emmo-repo.github.io/)
+
 
 # Elementary Multiperspective Material Ontology (EMMO)
 
@@ -13,7 +15,8 @@
 
 ## Table of content
   * [About EMMO](#about-emmo)
-  * [Some words about the new name and logo](#some-words-about-the-new-name-and-logo)
+      * [Some words about the new name and logo](#some-words-about-the-new-name-and-logo)
+      * [Use of EMMO in domain ontologies](#use-of-emmo-in-domain-ontologies)
   * [EMMO in a Nutshell](#emmo-in-a-nutshell)
       * [Top Level](#top-level)
       * [Middle Level](#middle-level)
@@ -45,6 +48,26 @@ A lot can be said about the logo:
 
 
 
+### Use of EMMO in domain ontologies
+Currently there are several domain ontologies in development that use EMMO as the top and middle level ontology.
+Typically they import one of the versions of EMMO listed on [https://emmo-repo.github.io/](https://emmo-repo.github.io/).
+The following table lists the public EMMO-based domain ontologies that we are aware of.
+Please create an issue if you have a public domain ontology that you think should be listed here.
+
+| Domain ontology                            | Link                                                                                                                                      |
+| ------------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------- |
+| Battery Interface Ontology (BattINFO)      | [https://github.com/BIG-MAP/BattINFO](https://github.com/BIG-MAP/BattINFO)                                                                |
+| General Process Ontology (GPO)             | [https://github.com/General-Process-Ontology/ontology](https://github.com/General-Process-Ontology/ontology)                              |
+| Ontology for the Battery Value Chain (BVC) | [https://github.com/Battery-Value-Chain-Ontology/ontology](https://github.com/Battery-Value-Chain-Ontology/ontology)                      |
+| Crystallography                            | [https://github.com/emmo-repo/domain-crystallography](https://github.com/emmo-repo/domain-crystallography)                                |
+| Mechanical Testing                         | [https://github.com/emmo-repo/domain-mechanical-testing](https://github.com/emmo-repo/domain-mechanical-testing)                          |
+| Microstructure domain ontology             | [https://github.com/emmo-repo/domain-ontology](https://github.com/emmo-repo/domain-ontology)                                              |
+| Datamodel ontology                         | [https://github.com/emmo-repo/datamodel-ontology](https://github.com/emmo-repo/datamodel-ontology)                                        |
+| Mappings ontology                          | [https://github.com/emmo-repo/domain-mappings](https://github.com/emmo-repo/domain-mappings)                                              |
+| Atomistic and Electronic Modelling         | [https://github.com/emmo-repo/domain-atomistic](https://github.com/emmo-repo/domain-atomistic)                                            |
+| EMMO example domain ontologies             | [https://github.com/emmo-repo/EMMO/tree/master/domain](https://github.com/emmo-repo/EMMO/tree/master/domain)                              |
+
+
 ## EMMO in a Nutshell
 The EMMO ontology is structured in shells, expressed by specific ontology fragments, that extends from fundamental concepts to the application domains, following the dependency flow.
 
@@ -114,7 +137,7 @@ The fastest way to access the EMMO is to open the ontology via Protégé via the
 
 The EMMO hierarchy will be visible only after reasoning inference: use *ctrl-R* to start the reasoner and under the *Entities* tab, select the *Classes* subtab and *Inferred* in the scroll button.
 
-It is recommended to use FaCT++ as reasoner. You can select it through the menu *Reasoner*.  An instruction for how to install the FaCT++ plugin on Protege 5.5.0 on Windows can be found in the [doc subdirectory](doc/installing_factplusplus.md).
+From EMMO 1.0.0-beta4 it is recommended to use HermiT as reasoner (distributed by default with Protege).  For earlier EMMO versions is FaCT++ the recommended reasoner. You can select it through the menu *Reasoner*.  An instruction for how to install the FaCT++ plugin on Protege 5.5.0 on Windows can be found in the [doc subdirectory](doc/installing_factplusplus.md).
 
 To access EMMO from Python, we recommend [EMMO-python](https://github.com/emmo-repo/EMMO-python/).
 
@@ -125,13 +148,8 @@ Browsable documentation and pre-inferred versions of EMMO are available on [http
 ---
 
 ## Contacts:
-Emanuele Ghedini
-University of Bologna (IT)
-email: [email protected]
+You can contact EMMO Authors via [email protected]
 
-Gerhard Goldbeck
-Goldbeck Consulting Ltd (UK)
-email: [email protected]
 
 
 ### Acknowledgement

diff --git a/doc/emmodoc/emmodoc-meta.yaml b/doc/emmodoc/emmodoc-meta.yaml
@@ -1,5 +1,5 @@
 ---
-title:  'Europeean Materials Modelling Ontology'
+title:  'Elemental Multiperspective Material Ontology (EMMO)'
 version: 1.0.0-alpha2
 author:
 - name: Emanuele Ghedini

diff --git a/domain/README.md b/domain/README.md
@@ -0,0 +1,4 @@
+Examples of how to extend EMMO in domain ontologies
+===================================================
+The owl files in this directory are intended as examples of how to extend EMMO in domain ontologies.
+These examples are not intended to be full featured domain ontologies, but might still be useful to include or copy in actual application ontologiess.
diff --git a/domain/commonmaterials.ttl b/domain/commonmaterials.ttl
@@ -35,7 +35,7 @@ email: [email protected]
 Emanuele Ghedini
 University of Bologna (IT)
 email: [email protected]"""@en ,
-                                                             "The EMMO requires FacT++ reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
+                                                             "The EMMO requires HermiT reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
                                                 owl:versionInfo "1.0.0-beta" .
 
 #################################################################

diff --git a/domain/commonperceptual.ttl b/domain/commonperceptual.ttl
@@ -35,7 +35,7 @@ email: [email protected]
 Emanuele Ghedini
 University of Bologna (IT)
 email: [email protected]"""@en ,
-                                                              "The EMMO requires FacT++ reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
+                                                              "The EMMO requires HermiT reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
                                                  owl:versionInfo "1.0.0-beta" .
 
 #################################################################

diff --git a/domain/domain.ttl b/domain/domain.ttl
@@ -34,7 +34,7 @@ email: [email protected]
 Emanuele Ghedini
 University of Bologna (IT)
 email: [email protected]"""@en ,
-                                          "The EMMO requires FacT++ reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
+                                          "The EMMO requires HermiT reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
                              owl:versionInfo "1.0.0-beta" .
 
 ###  Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi
diff --git a/emmo.ttl b/emmo.ttl
@@ -12,7 +12,7 @@
                          owl:versionIRI <http://emmo.info/emmo/1.0.0-beta> ;
                          owl:imports <http://emmo.info/emmo/1.0.0-beta/middle> ,
                                      <http://emmo.info/emmo/1.0.0-beta/top> ;
-                         dcterms:abstract """European Materials & Modelling Ontology (EMMO)
+                         dcterms:abstract """Elemental Multiperspective Material Ontology (EMMO)
 
 EMMO is a multidisciplinary effort to develop a standard representational framework (the ontology) based on current materials modelling knowledge, including physical sciences, analytical philosophy and information and communication technologies.
 
@@ -31,7 +31,7 @@ EMMO is released under a Creative Commons license Attribution 4.0 International
                                          "Jesper Friis" ;
                          dcterms:license "https://creativecommons.org/licenses/by/4.0/legalcode" ;
                          dcterms:publisher "EMMC ASBL" ;
-                         dcterms:title "European Materials & Modelling Ontology"@en ;
+                         dcterms:title "Elemental Multiperspective Material Ontology"@en ;
                          rdfs:comment """Contacts:
 Gerhard Goldbeck
 Goldbeck Consulting Ltd (UK)
@@ -40,7 +40,7 @@ email: [email protected]
 Emanuele Ghedini
 University of Bologna (IT)
 email: [email protected]"""@en ,
-                                      "The EMMO requires FacT++ reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
+                                      "The EMMO requires HermiT reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
                          owl:versionInfo "1.0.0-beta" .
 
 ###  Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi
diff --git a/middle/holistic.ttl b/middle/holistic.ttl
@@ -36,7 +36,7 @@ email: [email protected]
 Emanuele Ghedini
 University of Bologna (IT)
 email: [email protected]"""@en ,
-                                                      "The EMMO requires FacT++ reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
+                                                      "The EMMO requires HermiT reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
                                          owl:versionInfo "1.0.0-beta" .
 
 #################################################################

diff --git a/middle/isq.ttl b/middle/isq.ttl
@@ -42,7 +42,7 @@ University of Bologna (IT)
 email: [email protected]"""@en ;
                                     dcterms:license "https://creativecommons.org/licenses/by/4.0/legalcode" ;
                                     owl:versionInfo "1.0.0-beta" ;
-                                    dcterms:abstract """European Materials & Modelling Ontology (EMMO)
+                                    dcterms:abstract """Elemental Multiperspective Material Ontology (EMMO)
 
 EMMO is a multidisciplinary effort to develop a standard representational framework (the ontology) based on current materials modelling knowledge, including physical sciences, analytical philosophy and information and communication technologies.
 
@@ -52,7 +52,7 @@ EMMO is released under a Creative Commons license Attribution 4.0 International
                                     dcterms:contributor "Access, DE" ;
                                     dcterms:creator "Gerhard Goldbeck" ,
                                                     "Jesper Friis" ;
-                                    rdfs:comment "The EMMO requires FacT++ reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en .
+                                    rdfs:comment "The EMMO requires HermiT reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en .
 
 #################################################################
 #    Annotation properties
@@ -681,7 +681,7 @@ It defines the base unit mole in the SI system."""@en ;
                                            :EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 """An objective comparative measure of hot or cold.
 
 Temperature is a relative quantity that can be used to express temperature differences. Unlike ThermodynamicTemperature, it cannot express absolute temperatures."""@en ;
-                                           :EMMO_de178b12_5d35_4bca_8efa_a4193162571d "T-1 L0 M0 I0 Θ0 N+1 J0" ;
+                                           :EMMO_de178b12_5d35_4bca_8efa_a4193162571d "T0 L0 M0 I0 Θ+1 N0 J0" ;
                                            :EMMO_fe015383_afb3_44a6_ae86_043628697aa2 "https://doi.org/10.1351/goldbook.T06261" ;
                                            skos:prefLabel "CelsiusTemperature"@en .
 

diff --git a/middle/manufacturing.ttl b/middle/manufacturing.ttl
@@ -34,7 +34,7 @@ email: [email protected]
 Emanuele Ghedini
 University of Bologna (IT)
 email: [email protected]"""@en ,
-                                                           "The EMMO requires FacT++ reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
+                                                           "The EMMO requires HermiT reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
                                               owl:versionInfo "1.0.0-beta" .
 
 #################################################################

diff --git a/middle/materials.ttl b/middle/materials.ttl
@@ -34,7 +34,7 @@ email: [email protected]
 Emanuele Ghedini
 University of Bologna (IT)
 email: [email protected]"""@en ,
-                                                       "The EMMO requires FacT++ reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
+                                                       "The EMMO requires HermiT reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
                                           owl:versionInfo "1.0.0-beta" .
 
 #################################################################
@@ -313,7 +313,7 @@ e.g. you cannot remove H from H20 without changing the molecule type (essential)
 :EMMO_5cb107ba_7daa_46dd_8f9f_da22a6eac676 rdf:type owl:Class ;
                                            rdfs:subClassOf :EMMO_4b3e2374_52a1_4420_8e3f_3ae6b9bf7dff ;
                                            :EMMO_967080e5_2f42_4eb2_a3a9_c58143e835f9 "A liquid solution in which the solvent is water."@en ;
-                                           skos:prefLabel "AcqueousSolution"@en .
+                                           skos:prefLabel "AqueousSolution"@en .
 
 
 ###  http://emmo.info/emmo#EMMO_5d659e25_a508_43ed_903c_3707c7c7cd4b

diff --git a/middle/math.ttl b/middle/math.ttl
@@ -35,7 +35,7 @@ email: [email protected]
 Emanuele Ghedini
 University of Bologna (IT)
 email: [email protected]"""@en ,
-                                                  "The EMMO requires FacT++ reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
+                                                  "The EMMO requires HermiT reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
                                      owl:versionInfo "1.0.0-beta" .
 
 #################################################################

diff --git a/middle/metrology.ttl b/middle/metrology.ttl
@@ -37,7 +37,7 @@ email: [email protected]
 Emanuele Ghedini
 University of Bologna (IT)
 email: [email protected]"""@en ,
-                                                       "The EMMO requires FacT++ reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
+                                                       "The EMMO requires HermiT reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
                                           owl:versionInfo "1.0.0-beta" .
 
 #################################################################

diff --git a/middle/middle.ttl b/middle/middle.ttl
@@ -54,7 +54,7 @@ email: [email protected]
 Emanuele Ghedini
 University of Bologna (IT)
 email: [email protected]"""@en ,
-                                             "The EMMO requires FacT++ reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
+                                             "The EMMO requires HermiT reasoner plugin in order to visualize all inferences and class hierarchy (ctrl+R hotkey in Protege)."@en ;
                                 owl:versionInfo "1.0.0-beta" .
 
 ###  Generated by the OWL API (version 4.5.9.2019-02-01T07:24:44Z) https://github.com/owlcs/owlapi