OBO Foundry namespace for orphan terms

[GoogleCodeExporter]

This is an idea that came out of the OFOC outreach call last week, but also 
from discussions at the National Center for Ecological Analysis and Synthesis 
(NCEAS). The goal is to have a place where ontology developers can go to 
request a new term, 1) when they are not sure where it should live or 2) the 
apparent best home is not responsive to requests.

An application (maybe something like TermGenie) would create a new term id 
quickly. The requester should either suggest which ontology(ies) it belongs in 
or say that they don't know of one. Developers of existing ontologies could 
"adopt" terms form the orphan name space. 

This is an alternative to what many application ontologies do now, which is 
create the term in their own namespace with the idea of eventually moving them 
into a domain ontology.

Original issue reported on code.google.com by rlwalls2...@gmail.com on 1 Jun 2015 at 10:16

[GoogleCodeExporter]

An essential element is that the recipient be prepared to substitute a new id 
for the generated ID. Users inexperienced in finding correct terms (for example 
they don't happen to know any of the existing synonyms) will typically create 
redundant terms. Rather than making the substitution optional I would make it 
mandatory.

Awareness of this will be an education task. Perhaps we have a server that maps 
temporary ids to new ids and recommend a script for checking and substituting 
updated ids   as part of a build process so that downstream clients can make 
changes as well. Associating a date after which the temporary ID will no longer 
resolve (once the new term is allocated) would be polite.

Original comment by alanruttenberg@gmail.com on 2 Jun 2015 at 5:05

[GoogleCodeExporter]

I'm with Ramona on this one - this would be useful for me as I find ontologies 
I work on end up accumulating a penumbra of classes that don't entirely belong 
there and don't really belong in ChEBI, say.

I think an OBO or ONTO namespace would work well for this.

I am also with Alan on the redundancy front.  Not quite sure about the expiry 
business but we can discuss.

Original comment by batchelorc@rsc.org on 2 Jun 2015 at 10:32

[GoogleCodeExporter]

Just chiming in: I think this is a good idea, in general, and something I would 
like to work on. But there are many policy and implementation details to 
consider, and we'd need tools and developer hours to implement it.

Original comment by ja...@overton.ca on 5 Jun 2015 at 3:22

[jamesaoverton]

This issue was moved to OBOFoundry/OBOFoundry.github.io#596