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Verify curie map for identifier.org URIs #158

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kshefchek opened this issue Jul 6, 2015 · 4 comments
Closed

Verify curie map for identifier.org URIs #158

kshefchek opened this issue Jul 6, 2015 · 4 comments
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@kshefchek
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Verify that these URIs resolve as some look incorrect, for example:
'PomBase' : 'http://identifiers.org/PomBase:'
'TAIR' : 'http://identifiers.org/TAIR:'
'SwissProt' : 'http://identifiers.org/SwissProt:'
etc.

@kshefchek kshefchek self-assigned this Jul 6, 2015
@nlwashington
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This should be added to the testing suite.

@jmcmurry
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jmcmurry commented Oct 7, 2015

A related issue is here: https://github.com/monarch-initiative/monarch-app/issues/984
In essence, we need to not only verify that the mappings are correct, but also that they are consistent app-wide.

@jmcmurry
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Hmm. 'TAIR' : 'http://identifiers.org/TAIR:' is definitely wrong: resolution of the ID depends on knowing which type it is. I'm not sure what our identifier policy ought to be in this situation. TAIR prescribe a prefix (and a colon), but that prefix (eg. "Gene", or "AASequence") is so generic as to invite confusion (at best) and collisions (at worst).
Perhaps we could tweak their prefixes simply by prepending 'TAIR-'. Still, the locus example requires special handling as it doesn't have a prefix at all.

identifiers.org resolving nsp native resolving nsp example LRI LRI RegEx Suggested prefix tweak
http://identifiers.org/tair.gene/ http://arabidopsis.org/servlets/TairObject?accession= Gene:2200934 ^Gene:\d{7}$ TAIR-Gene
http://identifiers.org/tair.locus/ http://arabidopsis.org/servlets/TairObject?type=locus&name= AT1G01030 ^AT[1-5]G\d{5}$ TAIR-Locus
http://identifiers.org/tair.protein/ http://arabidopsis.org/servlets/TairObject?accession= AASequence:1009107926 ^AASequence:\d{10}$ TAIR-AASequence

@kshefchek
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I think @TomConlin took care of this, please reopen if there are still issues

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