https://github.com/cmungall/obo-metadata

EXPERIMENTAL obo metadata repo
https://github.com/cmungall/obo-metadata

linkml metadata obofoundry

Last synced: about 1 month ago
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EXPERIMENTAL obo metadata repo

• Host: GitHub
• URL: https://github.com/cmungall/obo-metadata
• Owner: cmungall
• License: mit
• Created: 2022-04-11T15:03:02.000Z (almost 3 years ago)
• Default Branch: main
• Last Pushed: 2022-04-12T15:29:20.000Z (almost 3 years ago)
• Last Synced: 2024-10-30T11:24:47.974Z (3 months ago)
• Topics: linkml, metadata, obofoundry
• Language: Jupyter Notebook
• Homepage: https://cmungall.github.io/obo-metadata/
• Size: 1.2 MB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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README

        
# obo-metadata

This is a demonstration project on how to create a metadata SCHEMA for OBO that can be

used for constraint checking.

The intended workflow is:

 * The core properties are [maintained in a google sheet](https://docs.google.com/spreadsheets/d/1YU_58PB-TaxlvJ5oIneUig8kB8CbmHyR30hUqfD0ZtE/edit) and synced with COGs

 * The sheet is compiled to different products including:

     1. a SCHEMA that can be used for VALIDATION

     2. OWL AnnotationProperties (omo.owl) that can be IMPORTED in different ontologies

Currently, the format of the schema is LinkML yaml. This can be used to generate different

valdation schemas

 - SHACL

 - JSON-Schema

 - LinkML itself

As a DEMO FLAGSHIP APPLICATION the

[OAK](https://incatools.github.io/ontology-access-kit/) library and

command line tool implements an efficient OMO checker that takes as input:

 1. the OMO LinkML schema

 2. a SQLite version of an ontology created using rdftab

And produces a report

## Schema

- [google sheets](https://docs.google.com/spreadsheets/d/1YU_58PB-TaxlvJ5oIneUig8kB8CbmHyR30hUqfD0ZtE/edit) (partial)

- [obo-metadata.yaml](src/linkml/obo-metadata.yaml)

## Examples

See [examples](examples)

## OBO Report

PRELIMINARY!!!

- [sheet](https://docs.google.com/spreadsheets/d/1Er8xYeKMvKKo-MGQf7w9jUgCWTOZwprDq9Td2Nuu4Po/edit#gid=488211236)

- analysis [notebooks](notebooks)

## Manifest

 * Generated docs: [cmungall.github.io/obo-metadata/](https://cmungall.github.io/obo-metadata/)

     * Example property: https://cmungall.github.io/obo-metadata/definition/

     * Example metaclass: https://cmungall.github.io/obo-metadata/Class/

 * Source: [src/linkml/](src/linkml/)

 * Analysis (v preliminary)

     * [notebooks](notebooks)

 * Derived files: [project](https://github.com/cmungall/obo-metadata/tree/main/project)

     * Schemasheets: TODO: sync w COGS [project/sheets](project/sheets)

     * JSON-Schema [project/json-schema](project/jsonschema)

     * etc

## How to validate

You will need to:

 1. Install OAK

 2. Obtain the SQLite version of the ontology(ies) to be validated

 3. Run on command line

See:

 * [howtos/validate-an-obo-ontology](https://incatools.github.io/ontology-access-kit/howtos/validate-an-obo-ontology.html)

 * In: [OAK](https://github.com/INCATools/ontology-access-kit/)