search

information-artifact-ontology / IAO

information artifact ontology
Creative Commons Attribution 4.0 International
75 stars 26 forks source link

two terms with same URI #143

Open zhengj2007 opened 9 years ago

zhengj2007 commented 9 years ago

From zhengj2...@gmail.com on August 27, 2013 13:03:42

http://purl.obolibrary.org/obo/IAO_0000600 was used by two terms:

  1. Class: predict value
  2. Annotation Property: elucidation

Issue caused by Bjoern edited BFO preGraz release compatible version IAO version and Alan added 'elucidation' into BFO 1.1 version IAO.

Since 'elucidation' has been used by several ontologies, 'predict value' should be assigned another URI.

IAO developers should find a way to solve the conflict caused by using different versions of BFO.

------------------------------------- http://purl.obolibrary.org/obo/IAO_0010000 used in http://bfo.googlecode.com/svn/releases/owl-ruttenberg-2010-05-25/ruttenberg-relations.owl with rdf:label "axiom id"

used in https://information-artifact-ontology.googlecode.com/svn/trunk/src/ontology/ontology-metadata.owl with rdf:label "has axiom id"

Original issue: http://code.google.com/p/information-artifact-ontology/issues/detail?id=143

zhengj2007 commented 9 years ago

From mcour...@gmail.com on January 14, 2014 14:44:07

Hi Jie,

Do I understand correctly that those are two different errors? (1) http://purl.obolibrary.org/obo/IAO_0000600 - URI used by two terms (2) http://purl.obolibrary.org/obo/IAO_0010000 - less problematic, just (has) axiom id

For (1), could you clarify where is predict value defined? I am confused by different versions. For (2), is owl-ruttenberg still being used or should it just be marked as deprecated?

I think you could go ahead and make the edits if you feel comfortable doing so; probably easier that way.

Status: Started

zhengj2007 commented 9 years ago

From zhengj2...@gmail.com on January 29, 2014 07:00:30

Hi Melanie,

OBI is using owl-ruttenberg and its compatible IAO now. That's why it caused problem. 'predict value' is a testing class for distinguish data item is not coming from measurement but from prediction.

Current OBI stop editing IAO and make changes in OBI now. I submitted issue to IAO for letting IAO developers know there are two versions of IAO and changes made in both version.

zhengj2007 commented 9 years ago

From mcour...@gmail.com on January 29, 2014 11:27:24

Hi Jie,

Do you mean owl-ruttenberg is not compatible with IAO now? You say "Current OBI stop editing IAO and make changes in OBI now. I submitted issue to IAO for letting IAO developers know there are two versions of IAO and changes made in both version." Could you maybe reference those version by URIs? I'm not sure which they are, and I don't recall much SVN commits (though I may have missed some)

With respect to finding a long term plan:

Thanks for sharing your issue and comments! Melanie

zhengj2007 commented 9 years ago

From zhengj2...@gmail.com on January 29, 2014 12:16:08

Hi Melanie,

When I talked about owl-ruttenberg I mean BFO 2.0 pre-graz version. http://purl.obolibrary.org/obo/bfo/2010-05-25/ruttenberg-bfo2.owl OBI is importing this version of BFO now. Since OBI import whole IAO, for making consistency, I made a BFO 2.0 pre-graz version compatible IAO together with Alan in early 2012. But I didn't set OBO purl for this version of IAO since it is not using release version BFO. This version of IAO was made using IAO developmental SVN version: 530. Details please see the files under: https://information-artifact-ontology.googlecode.com/svn/releases/2012-01-05 OBI would like to switch to an OBO Foundry community acceptable BFO version. As what I know, many OBO Foundry ontologies like GO, PATO, UBERON, etc. are using BFO 2.0 classes and atemporal relations defined in RO including some with BFO ID (assigned in BFO 2.0 ruttenberg version), like: http://purl.obolibrary.org/obo/BFO_0000051 (has part). Following other OBO Foundry ontologies approach is lot of works for OBI due to import whole IAO and BFO. If OBO Foundry policy has guide of which version of BFO should be used, I would like to spend time on updating OBI.

OBI/IAO developers found that IAO:data item model is not correct. The discussion started in May 2012 OBI workshop. At that time, 'predicted value' was added in IAO (bfo-ruttenberg version). Since we found two versions of IAO were used and edited, we decided to make changes in OBI to avoid potential conflict. When OBO foundry finally reach agreement of which version of BFO should be used, those data model implemented in OBI can be moved to IAO.

I understand your confusion. However, the mess cannot be sorted out without solving the version of BFO version should be used in the OBO Foundry community.

Thanks,

Jie

zhengj2007 commented 9 years ago

From zhengj2...@gmail.com on March 04, 2014 13:27:02

Issue was fixed since OBI developers assigned an OBI id to 'predict value'.