Skip to content
The Curation of Neurodegeneration Supporting Ontology (CONSO)
Jupyter Notebook Python HTML
Branch: master
Clone or download

Latest commit

Fetching latest commit…
Cannot retrieve the latest commit at this time.

Files

Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
docs
export
external
notebooks
src/conso
.flake8
.gitignore
.travis.yml
LICENSE
README.md
authors.tsv
classes.tsv
relations.tsv
setup.cfg
setup.py
synonyms.tsv
terms.tsv
tox.ini
typedefs.tsv
xrefs.tsv

README.md


Curation of Neurodegeneration Supporting Ontology (CONSO) Travis CI

This ontology, developed during the Human Brain Pharmacome project, contains terms representing chemistry, molecular biology, epidemiology, and pathology relevant to neurodegenerative disease.

ContentsContributingBuildLicense

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: 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. 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

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 follow the https://identifiers.org semantic web style (e.g., pmid:1234, pmid: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:

$ pip3 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.
You can’t perform that action at this time.