NIF Standard (NIFSTD) Ontologies
Latest commit 95b59f9 Oct 16, 2017 @tgbugs tgbugs Merge pull request #120 from SciCrunch/uri-switch
uri switch, backend refactor, and 3.0

This pull request includes 3 major changes for the 3.0 release of NIFSTD.

    All NIFSTD native identifiers have been switched to use the resolver. This closes #59.
    Major reworking of the import chain (see #115 for reference), including importing most external ontologies from their canonical iris.
    All backend ObjectProperties have been switched to use BFO2/RO/IAO. This closes #39.

The current state of the ontology produces reasoning errors because of obophenotype/uberon#1370. These will persist until that issue is resolved or I complete our load time patching infrastructure.

The old backend is not completely gone since we still import an old version of pr that uses the old BFO1.1 backend. The new pr is huge and switching requires further review/planning since it cannot be dropped directly into the ontology as is and thus did not make the cut for updating the 3.0 release. ero.owl was removed from the import chain pending a review of its classes.

This pull request also starts the process of moving documentation into the repository from the GitHub wiki to reduce dependence on external systems.

Note that this pull request also moves the scigraph/ folder and associated loading and curie mapping (which defines the qnames used by the ontology) to pyontutils/scigraph.


Repository for the NIF Standard (NIFSTD) Ontologies.


NIFSTD is undergoing significant changes. Please see the issue tracker for upcoming changes. For a full record of changes please see the log or run git log for a quick overview.


Please see docs/ for documentation about how to develop NIFSTD using this repository.

Please see the GitHub wiki for documentation about the structure of the ontology and how to load and edit it.


Please fork and submit pull requests on GitHub.
Please read the docs for development processes.
See the wiki for more documentation.
In short, load ttl/nif.ttl in your favourite ontology editor, and before commit run ttlfmt on any files that you have modified.


Creative Commons License
The contents of this repository are licensed under a Creative Commons Attribution 4.0 International License. The text of the license can also be found in the LICENSE file.