This read me is designed for those intending to make contributions to ICO. The primary purpose of this document is to justify development decisions and provide information regarding the release process and repository structure. For content contributions, please see the Contributing Guidelines.
Please see the developer tools for more details regarding specific development process. At the time of this writing (early 2019) there is not a need for a high development bar for ICO. As ICO moves toward an application space, this will need to change.
- The
ICO/src/ontology/ico-edit.owlfile is the file that should be edited. - When this file is stable, and all work has been verified, run
ICO/tools/temporary_release_process.sh - Rename and move the resulting merged file to the correct file path.
- Move previous OWL file to
releases/as appropriate. - Create a new release via GitHub releases.
ICO makes use of terms from other ontologies according to the the Minimum Information to Reference an External Ontology Term principals:
M. Courtot et al., “MIREOT: the Minimum Information to Reference an External Ontology Term,” Nature Precedings, Aug. 2009.
We maintain local versions of ontologies in the imports/ folder and rely on the catalog-v001.xml to resolve owl:imports statements to local file versions rather than the full ontology specified by the purl namespace. In order to develop and maintain these files we use OntoFox. Each file has an OntoFox input specification in imports/OntoFox\ Inputs/.
Z. Xiang, M. Courtot, R. R. Brinkman, A. Ruttenberg, and Y. He, “OntoFox: web-based support for ontology reuse,” BMC Research Notes, vol. 3, no. 1, p. 175, Jun. 2010.
Where we import the entire ontology we maintain a local copy of the file and rely on the catalog-v001.xml to resolve owl:imports statements to local file. These files all have the suffix *_local.owl.
- http://purl.obolibrary.org/obo/ico.owl
- This should point to: https://raw.githubusercontent.com/ICO-ontology/ICO/master/src/ontology/ico_merged.owl
- Home: https://github.com/ICO-ontology/ICO
- Tracker: https://github.com/ICO-ontology/ICO/issues
- ICO ontology discussion mailing-list: https://groups.google.com/forum/#!forum/ico-discuss
- ICO discussion notes: https://docs.google.com/document/d/1j5HHtnm2nZn89O-EM1wsGjFTcoVMS_Ew8s4Z1uhfHsI/edit?usp=sharing
- Default browsing in Ontobee: http://www.ontobee.org/ontology/ico
- Browsing in NCBO BioPortal: https://bioportal.bioontology.org/ontologies/ICO