add OBO Foundry annotations

[wdduncan]

I work with a number of OBO Foundry ontology. These ontologies often has annotations such as:

• http://purl.obolibrary.org/obo/IAO_0000115 (definition)
• http://purl.obolibrary.org/obo/IAO_0000112 (example of usage)
• http://purl.obolibrary.org/obo/IAO_0000116 (editor note)
  etc.

I tried reading the instructions for supermodel, but couldn't figure out how to use it (sorry). Is there a way add these annotations to the pyLODE output?

[nicholascar]

I think you should avoid the Supermodel profile: that's for multi-part things.

You probably just need an alternate profile for OntPub - annotated ontologies - or just support for OBO Foundry predicates within OntPub.

Since I'm actively developing this again. @wdduncan, if you can add a more complete list of all the annotations you'd want supported, I'll pick one of the two implementation options and implement it!

[nicholascar]

Perhaps all these from the OBO Metadata Ontology:

• http://purl.obolibrary.org/obo/OMO_0003010, International Nonproprietary Name
• http://purl.obolibrary.org/obo/OMO_0003005, UK spelling synonym
• http://purl.obolibrary.org/obo/OMO_0003000, abbreviation
• http://purl.obolibrary.org/obo/OMO_0003012, acronym
• http://purl.obolibrary.org/obo/OMO_0003001, ambiguous synonym
• http://purl.obolibrary.org/obo/OMO_0002000, defined by construct
• http://purl.obolibrary.org/obo/OMO_0003002, dubious synonym
• http://www.geneontology.org/formats/oboInOwl#hasDbXref, has cross-reference
• http://purl.obolibrary.org/obo/OMO_0003014, has ontology hierarchical property
• http://purl.obolibrary.org/obo/OMO_0004000, has symbol
• http://purl.obolibrary.org/obo/OMO_0003011, latin term
• http://purl.obolibrary.org/obo/OMO_0003003, layperson synonym
• http://purl.obolibrary.org/obo/OMO_0003009, legal name
• http://purl.obolibrary.org/obo/OMO_0001001, logical characteristic of object property
• http://purl.obolibrary.org/obo/OMO_0003007, misnomer
• http://purl.obolibrary.org/obo/OMO_0003006, misspelling
• http://purl.obolibrary.org/obo/OMO_0003004, plural form
• http://purl.obolibrary.org/obo/OMO_0002001, preferred label for community
• http://purl.obolibrary.org/obo/OMO_0003008, previous name
• http://purl.obolibrary.org/obo/IAO_0000589, OBO foundry unique label
• http://purl.obolibrary.org/obo/IAO_0000118, alternative label
• http://purl.obolibrary.org/obo/IAO_0000427, antisymmetric property
• http://purl.obolibrary.org/obo/IAO_0000232, curator note
• http://purl.obolibrary.org/obo/IAO_0000115, definition
• http://purl.obolibrary.org/obo/IAO_0000119, definition source
• http://purl.obolibrary.org/obo/IAO_0000116, editor note
• http://purl.obolibrary.org/obo/IAO_0000111, editor preferred term
• http://purl.obolibrary.org/obo/IAO_0000600, elucidation
• http://purl.obolibrary.org/obo/IAO_0000112, example of usage
• http://purl.obolibrary.org/obo/IAO_0000425, expand assertion to
• http://purl.obolibrary.org/obo/IAO_0000424, expand expression to
• http://purl.obolibrary.org/obo/IAO_0000426, first order logic expression
• http://purl.obolibrary.org/obo/IAO_0000596, has ID digit count
• http://purl.obolibrary.org/obo/IAO_0000598, has ID policy for
• http://purl.obolibrary.org/obo/IAO_0000599, has ID prefix
• http://purl.obolibrary.org/obo/IAO_0000597, has ID range allocated to
• http://purl.obolibrary.org/obo/IAO_0000602, has associated axiom(fol)
• http://purl.obolibrary.org/obo/IAO_0000601, has associated axiom(nl)
• http://purl.obolibrary.org/obo/IAO_0010000, has axiom label
• http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym, has broad synonym
• http://purl.obolibrary.org/obo/IAO_0000114, has curation status
• http://www.geneontology.org/formats/oboInOwl#hasExactSynonym, has exact synonym
• http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym, has narrow synonym
• http://purl.obolibrary.org/obo/IAO_0000231, has obsolescence reason
• http://purl.obolibrary.org/obo/IAO_0000700, has ontology root term
• http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym, has related synonym
• http://purl.obolibrary.org/obo/IAO_0000412, imported from
• http://purl.obolibrary.org/obo/IAO_0000113, in branch
• http://purl.obolibrary.org/obo/IAO_0000603, is allocated id range
• http://purl.obolibrary.org/obo/IAO_0000411, is denotator type
• http://purl.obolibrary.org/obo/IAO_0006011, may be identical to
• http://purl.obolibrary.org/obo/IAO_0000234, ontology term requester
• http://purl.obolibrary.org/obo/IAO_0006012, scheduled for obsoletion on or after
• http://purl.obolibrary.org/obo/IAO_0000117, term editor
• http://purl.obolibrary.org/obo/IAO_0100001, term replaced by
• http://purl.obolibrary.org/obo/IAO_0000233, term tracker item

With these values:

• http://purl.obolibrary.org/obo/OMO_0001002, domain entity does not exist
• http://purl.obolibrary.org/obo/OMO_0001000, out of scope
• http://purl.obolibrary.org/obo/IAO_0000420, defined class
• http://purl.obolibrary.org/obo/IAO_0000002, example to be eventually removed
• http://purl.obolibrary.org/obo/IAO_0000103, failed exploratory term
• http://purl.obolibrary.org/obo/IAO_0000120, metadata complete
• http://purl.obolibrary.org/obo/IAO_0000123, metadata incomplete
• http://purl.obolibrary.org/obo/IAO_0000421, named class expression
• http://purl.obolibrary.org/obo/IAO_0000224, obsolete_core
• http://purl.obolibrary.org/obo/IAO_0000121, organizational term
• http://purl.obolibrary.org/obo/IAO_0000125, pending final vetting
• http://purl.obolibrary.org/obo/IAO_0000226, placeholder removed
• http://purl.obolibrary.org/obo/IAO_0000122, ready for release
• http://purl.obolibrary.org/obo/IAO_0000428, requires discussion
• http://purl.obolibrary.org/obo/IAO_0000228, term imported
• http://purl.obolibrary.org/obo/IAO_0000229, term split
• http://purl.obolibrary.org/obo/IAO_0000227, terms merged
• http://purl.obolibrary.org/obo/IAO_0000423, to be replaced with external ontology term
• http://purl.obolibrary.org/obo/IAO_0000124, uncurated
• http://purl.obolibrary.org/obo/IAO_0000410, universal

[wdduncan]

Thanks for responding. I had forgotten about this. What is "OntoPub"?

[nicholascar]

OntPub is the profile of ontologies that we use for documentation generation - publication.

It just mandates some basic annotation properties such as schema:name / rdfs:label, skos:example, rdfs:isDefinedBy etc.

[wdduncan]

Thanks! How do I add relations to the profile?
Do I make a PR on https://github.com/AGLDWG/ontpub-profile?
Sorry if I am missing something in the docs.