Re: [Obo-discuss] Requesting a dbxref prefix for taxa in PaleoDB

[Walls, R. <rw...@ny...>]

It may depend on if and how you plan to link to the dbxrefs (see http://www.geneontology.org/cgi-bin/xrefs.cgi). If you require a separate url syntax for each different type of object at the Paleobotany Database, then you need to give each type of data object a different abbreviation. However, I can tell you from experience that this can make life difficult. At the PO, we are trying to move toward a single abbreviation for each database. This requires the database to be set up in such a way that each object has a unique id (regardless of its type) and they must also supply you with a url syntax that will link to any of their objects. Our supplying databases have been extremely helpful in this regard. How about using Paleodb as an abbreviation? It matches their generic url, and it is clear to users what it stands for.

Ramona

_____________________________
Ramona Walls
Post-doctoral Researcher/Plant Ontology Curator
New York Botanical Garden
2900th Southern Blvd.
Bronx, NY 10458
(718)817-8173
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-----Original Message-----
From: Peter Midford [mailto:pet...@gm...]
Sent: Tue 11/1/2011 2:01 PM
To: obo...@li...
Subject: [Obo-discuss] Requesting a dbxref prefix for taxa in PaleoDB
 
Hi everyone,
                      I am importing a lot of taxa from the Paleobiology Database (paleodb.org) into our new vertebrate taxonomy ontology (and they will be added into TTO as well).   Although incomplete, this taxonomy fills an important complementary role to NCBI and is arguably the best source for taxa outside the scope of NCBI (e.g., fossils w/o molecular traces).  So, what would be an appropriate dbxref for these taxa?  PBDB is too close to PDB and since there are other types of data in this database, I would suggest either PBDBTaxon or PaleoDBTaxon as prefixes, though I appreciate that these are longer than most such prefixes.

I hope this issue can be resolved quickly, as there is a fairly urgent need to incorporate these fossil taxa.

Thanks,
Peter

Peter E.  Midford
Phenoscape Taxonomy Curator
Pet...@gm...