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Curation of Neurodegeneration Supporting Ontology (CONSO) GitHub Actions DOI

This ontology, developed during the Human Brain Pharmacome project, contains terms representing chemistry, molecular biology, epidemiology, and pathology relevant to neurodegenerative disease. A web site listing the contents is hosted by GitHub Pages at https://pharmacome.github.io/conso/.

Contents • Exports • Contributing • Build • License

Contents

classes.tsv

This tab-separated values file contains a two columns describing classes of entities in CONSO:

  1. Class
  2. BEL Encodings

typedefs.tsv

This tab-separated values file contains a six columns describing relationships used in CONSO:

  1. Identifier
  2. Name
  3. Namespace (optional)
  4. Xrefs (namespace prefixed, comma separated)
  5. Transitive (true or false)
  6. Comment

terms.tsv

This tab-separated values file contains four columns describing entities in CONSO:

  1. Identifier
  2. Author
  3. Label
  4. Class
  5. References (namespace prefixed, comma separated. Example: pmid:1234, pmid:1245, pmc:PMC1234)
  6. Description (no double quote characters allowed)

synonyms.tsv

This tab-separated values contains four columns describing synonyms for terms in CONSO:

  1. Identifier
  2. Synonym
  3. References (namespace prefixed, comma separated. Example: pubmed:1234, pubmed:1245, pmc:PMC1234)
  4. Specificity (one of EXACT, BROAD, NARROW, or RELATED. See: https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_4.html)

xrefs.tsv

This tab-separated values file contains three columns describing other databases that have listed this equivalent entity:

  1. CONSO Identifier
  2. Database (preferred using identifiers.org)
  3. Identifier

relations.tsv

This tab-separated values file describes relations between terms in CONSO:

  1. Source Namespace
  2. Source Identifier
  3. Source Name
  4. Relationship (e.g., is_a, part_of, etc.)
  5. Target Namespace
  6. Target Identifier
  7. Target Name

Exports

CONSO is automatically exported to several formats on each build in the export/ directory:

Open Biomedical Ontology

The latest OBO file can be found at https://raw.githubusercontent.com/pharmacome/conso/master/export/conso.obo.

This file can be regenerated with tox -e obo.

Web Ontology Language

The latest OWL file can be found at https://raw.githubusercontent.com/pharmacome/conso/master/export/conso.owl.

This file can be regenerated with tox -e owl.

Biological Expression Language

The Biological Expression Language (BEL) is a domain specific language for encoding biomedical relations. It relies on controlled vocabularies like CONSO to ensure semantic alignment.

A BEL namespace file for CONSO can be generated with tox -e belns, then commit to GitHub and use the commit hash to build a new URL for BEL documents following the form of: https://raw.githubusercontent.com/pharmacome/conso/{HASH GOES HERE}/export/conso.belns

The latest BEL namespace can be found at:

Contributing

Contributions are welcome! Please submit all pull requests to https://github.com/pharmacome/conso.

Tips:

  • When adding a new term, make sure that the entry has a new and unique identifier that follows the regular expression ^CONSO\d{5}$
  • Only capitalize proper nouns in term labels (e.g., Tau is a named protein, so it is capitalized but hyperphosphorylation is not)
  • Normalize greek letters to full english names, then add synonyms with the greek letter.
  • References should be written as compact URIs (CURIEs) (e.g., pubmed:1234, pubmed:1245, pmc:PMC1234, etc.)

Build

All build operations are handled by tox, which can be installed from the command line (just needed the first time) with:

$ pip install tox

First, cd into the folder for this repository, then tox can be directly run as a command. It takes care of checking the content and exporting it

$ tox

Finally, the results need to be git pushed back to GitHub.

License

  • BEL scripts in this repository are licensed under the CC BY 4.0 license.
  • Python source code in this repository is licensed under the MIT license.

Acknowledgements

Logo

Logo designed by Daniel Domingo-Fernández