Synchronization tool: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
m (adding some content)
 
m (xxx)
Line 5: Line 5:


requirements of two ontologies that need aligning:
requirements of two ontologies that need aligning:
1. xrefs in one of the ontologies
#1. xrefs in one of the ontologies
2. metadata in the header that specifies the relationship between the terms and their xref'd terms
#2. metadata in the header that specifies the relationship between the terms and their xref'd terms
3. kinds of differences that need checking:
#3. kinds of differences that need checking:


a. terms that are in both ontologies but not xref'd (could be based on structure of ontology and/or term name)
#a. terms that are in both ontologies but not xref'd (could be based on structure of ontology and/or term name)
b. terms that are in one ontology but not another (terms without xref's)
#b. terms that are in one ontology but not another (terms without xref's)
c. terms with xrefs but with different names
#c. terms with xrefs but with different names
d. topological inconsistencies (Chris has already set up an "sdiff" tool that does this)
#d. topological inconsistencies (Chris has already set up an "sdiff" tool that does this)

Revision as of 15:11, 21 August 2008

Ideas for an obo ontology synchronization tool in OE2 (largely notes from conf call on 8.21.08 with Amina, Nomi, Chris, Wasila, Peter, Melissa and Jim.)

Background: Two ontologies need to be aligned. An example is the zebrafish anatomy ontology (ZFA) and the Teleost anatomy ontology (TAO). Terms in the ZFA are in an is_a relationship to those in the TAO, since zebrafish is_a teleost. There will necessarily be terms in TAO that are not in ZFA, and there may also be terms in ZFA that are not in TAO due to level of detail that may be unnecessary for TAO.

requirements of two ontologies that need aligning:

  1. 1. xrefs in one of the ontologies
  2. 2. metadata in the header that specifies the relationship between the terms and their xref'd terms
  3. 3. kinds of differences that need checking:
  1. a. terms that are in both ontologies but not xref'd (could be based on structure of ontology and/or term name)
  2. b. terms that are in one ontology but not another (terms without xref's)
  3. c. terms with xrefs but with different names
  4. d. topological inconsistencies (Chris has already set up an "sdiff" tool that does this)