Ontology provenance for merging ontologies

[GoogleCodeExporter]

Some ontologies become inactive or deprecated because they have merged into 
another. How should we redirect users in such cases? For example, TAO and AAO 
are being merged into uberon, CL-DC has been merged into CL, there are likely 
others. 

Original issue reported on code.google.com by haen...@ohsu.edu on 17 Nov 2012 at 4:25

[GoogleCodeExporter]

Mark as inactive (as the general status) and have a 'note' column that would 
indicate if it is merged / unresponsive. 

Original comment by bjoern.p...@gmail.com on 17 Nov 2012 at 5:17

[GoogleCodeExporter]

Note that the existing ontologies.txt metadata contains a tag "replaced_by", 
documented here:

http://code.google.com/p/obo-registry/wiki/Metadata

 "Values: the 'id' of another ontology
  only used if ontology is deprecated/obsolete
  Status: retain, but use the URI of the ontology as a value"

Example:

DC-CL contains a line:

  replaced_by   CL

YPO contains:

  is_obsolete   true
  replaced_by   ascomycete_phenotype

The idea is that this tag, along with all others in ontologies.txt will receive 
a mapping to a vocabulary such as as IAO

  http://code.google.com/p/obo-registry/issues/detail?id=1

In the interim, we will keep using replaced_by in ontologies.txt until we 
switch from using ontologies.txt as the source file:

  http://code.google.com/p/obo-registry/issues/detail?id=5

Original comment by cmung...@gmail.com on 17 Nov 2012 at 10:55

[jamesaoverton]

Closing in favour of ontodev/robot#6