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Terminology Travis CI

This is a terminology for the Human Brain Pharmacome (HBP) project, containing terms representing the molecular biology relevant to neurodegenerative disease.

Contents • Contributing • Exports

Contents

terms.tsv

This tab-separated values file contains four columns describing entities in the HBP terminology:

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

synonyms.tsv

This tab-separated values contains four columns describing synonyms for terms in the HBP terminology:

  1. Identifier
  2. Synonym
  3. References (namespace prefixed, comma separated. Example: pmid:1234, pmid: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. HBP Identifier
  2. Database (preferred using identifiers.org)
  3. Identifier

relations.tsv

This tab-separated values file describes relations between terms in the HBP terminology:

  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

Contributing

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

Tips:

  • When adding a new term, make sure that the entry has a new and unique identifier that follows the regular expression ^HBP\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 follow the https://identifiers.org semantic web style (e.g., pmid:1234, pmid:1245, pmc:PMC1234, etc.)

Exports

For generating a BEL namespace and other resources, see: https://github.com/pharmacome/terminology/tree/master/export