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:

• Identifiers: https://raw.githubusercontent.com/pharmacome/conso/master/export/conso.belns.
• Names: https://raw.githubusercontent.com/pharmacome/conso/master/export/conso-names.belns.

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