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[bioontology-support] Fwd: HIV ontology parsing issue [WAS: Ontology Upload]

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Apr 6 16:57:30 PDT 2017



Begin forwarded message:

From: Jennifer Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>>
Subject: Re: [bioontology-support] HIV ontology parsing issue [WAS: Ontology Upload]
Date: April 6, 2017 at 4:57:09 PM PDT
To: Sabrina Falcon <falcos2 at unlv.nevada.edu<mailto:falcos2 at unlv.nevada.edu>>

Hi Sabrina,


On Apr 6, 2017, at 2:50 PM, Sabrina Falcon <falcos2 at unlv.nevada.edu<mailto:falcos2 at unlv.nevada.edu>> wrote:

Yes, I think that was what we meant to do, thank you. I changed the version tags to correctly reflect that. From now on we will be using OBO format 1.4.


OK, thanks for the clarification.

After several exchanges with the OWL API developers, the conclusion is that we either need to include an OWL API compatibility module, or upgrade to a more recent version of the OWL API in order to parse your ontology.  I’m going to try the route of upgrading to a newer version of the API, and I’ve entered an issue in our tracker for this:

https://github.com/ncbo/owlapi_wrapper/issues/5

We’ll try to get this completed as soon as we’re able.

In case anyone is interested in the exchange with the OWL API developers, their mailing list archives are public:

https://sourceforge.net/p/owlapi/mailman/owlapi-developer/?viewmonth=201704



Also, I noticed in the link you sent me that in sections 8.1.2 and 8.2.2 the “part_of” tags used not as a stand-alone tag, but as something to be referenced:

8.1.2 File Comments

  *   If a frame references an identifier, and that identifier is opaque (i.e. it conforms to the Canonical-Prefixed-ID production rule), then the generator should add commments, adding a label for every opaque identifier. For example:

relationship: part_of ABC:1234567 ! hand
relationship: R:9999999 ABC:1234567 ! part_of hand


  *   All file comments should be preceded by a tag-value pair, and there should be exactly one space character on either side of the '!' character

8.2.2 Relation (Property) Identifiers

Relation identifiers should in follow the same guidelines as class identifiers. Note however that the use of symbolic identifiers such as 'part_of' is common in almost all OBO format ontologies, and has a precedent stretching back over ten years. A large body of software now expects symbolic identifiers for relations, and ontology maintainers are understandably reluctant to change these to numeric identifiers.

This specification provides a means of using numeric identifiers globally whilst retaining symbolic identifiers within the context of a single file. Refer to section 5.9.3<http://owlcollab.github.io/oboformat/doc/obo-syntax.html#5.9.3> for details.

  *   Every symbolic relation identifier (e.g. 'part_of') should have an xref tag to a formal relation identifier. E.g.

[Typedef]
id: has_part
name: has_part
xref: BFO:0000051


  *   This xref should refer to either BFO (http://purl.obolibrary.org/obo/bfo.owl) or to RO (http://purl.obolibrary.org/obo/ro.owl). Xrefs to the old RO can be provided for historic purposes, but are otherwise discouraged.
  *   According to the rules in section 5.9.3<http://owlcollab.github.io/oboformat/doc/obo-syntax.html#5.9.3>, the symbolic relation identifier can be used as a shorthand for the formal relation identifier.
  *   When roundtripping the OBO file, the symbolic identifiers should be preserved.

It was also not listed in the OBO2OWL mappings https://docs.google.com/spreadsheets/d/1VaERPs9EubExHRlU37fcBDzGRHgCrnoS28ZhDKRrX34/edit#gid=6

Although it is on the Relations Ontology http://obofoundry.org/ontology/ro.html (id: BFO:0000050)

Is the there a possibility the tag is obsolete or is there a problem with the way we integrated it?


I’m not an expert in OBO syntax.  I would suggest posting your question about the use of part_of tags on the “OBO Discuss” support list.  You can subscribe to that list here: https://lists.sourceforge.net/lists/listinfo/obo-discuss.

Best,
Jennifer


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