Doc updates 2025 #2317
Doc updates 2025 #2317
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…nd formating to identifiers doc
…nd formating to identifiers doc
…nd formating to identifiers doc
…nd formating to identifiers doc
…nd formating to identifiers doc
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| We do not currently have any criteria for good typecodes, other than they are ideally between 3 and 6 characters in length. | ||
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| ## unresolved |
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Sierra mentioned that Mark is reviewing this today. I'll wait till he is done. Thank you! |
| share, and interpret complex datasets with consistency and clarity. The NMDC Schema is critical substrate used to facilitate | ||
| interoperability and collaboration, as it provide a common language for data exchange across systems and disciplines. | ||
| In the context of the NMDC, this schema supports the integration of microbiome data from medicine, agriculture, | ||
| bioenergy, and environmental science into a cohesive platform. |
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This is much better. I agree with all of the points that are made in the new paragraph. "foundational framework" and "critical substrate" sound a little jargony to me, but I don't think that justifies a lot of extra work in rewording.
| @@ -173,12 +173,11 @@ $(DOCDIR): | |||
| gendoc: $(DOCDIR) prefixmaps | |||
| # Copy all documentation files to the documentation directory | |||
| cp -rf $(SRC)/docs/* $(DOCDIR) | |||
| # Added copying of images and renaming of TEMP.md | |||
| cp $(SRC)/docs/*md $(DOCDIR) | |||
| cp -r $(SRC)/docs/images $(DOCDIR) | |||
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the removed lines we just redundant with cp -rf $(SRC)/docs/* $(DOCDIR), right?
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| * An annotation schema that provides a mechanism for annotating data with additional information, such as provenance, | ||
| quality, and other metadata that is not part of the core data model. | ||
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This isn't really true any more. Right now there are more than three modules (disregarding whatever "key" means), but I would like to switch to just two: one NMDC module and one GSV MIxS module
| The NMDC Schema is annotated with the set of IDs, ordered by preference, that are allowed to act as primary keys | ||
| for instances of each class. For example the class [OrthologyGroup](https://microbiomedata.github.io/nmdc-metadata/docs/OrthologyGroup) has a description of the IDs allowed | ||
| on the class web page, the first listed is [KEGG.ORTHOLOGY](https://registry.identifiers.org/registry/kegg.orthology). The full URL for each is in the jsonld context file, | ||
| [jsonschema/nmdc.context.jsonld](...). |
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I don't think I totally get this yet, but that isn't a reason to hold up the merge.
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I agree; hard to tell from the diff, but this was text from pre-reorg. We could do another pass at refining even more of this doc.
src/docs/about.md
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| ## Credits | ||
| This schema was made using the [LinkML framework](https://github.com/biolink/biolinkml). LinkML is a data modeling language that is used to create data |
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good catch - hard to tell from the diff, but this was a link in place before I began reorg - will update.
| @@ -9,10 +9,4 @@ https://linkml.io/linkml/developers/schemaview.html#schemaview | |||
| There are also several notebooks that demonstrate SchemaView usage in the LinkML-runtime repository: | |||
| https://github.com/linkml/linkml-runtime/tree/main/notebooks | |||
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| Finally, the Biolink Model Toolkit is a helper wrapper around SchemaView for use with the Biolink Model and it | |||
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@sierra-moxon you're the expert here so I trust you. Can you just say a little more about removing these lines?
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I figured for review from external sources, that this is internal documentation that someone who wants to know about writing a SchemaView wrapper could get from me (or already has gotten) and so doesn't need to be part of the official NMDC doc any longer.
Tidying up and reorganizing hand-written documentation in the NMDC schema repo and adding logos and text to help introduce the schema to new users.
microbiomedata/docs#54