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Merge pull request #300 from JervenBolleman/patch-1
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Use UniProt purl's for UniProt data
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@jmcmurry
jmcmurry committed May 2, 2016
2 parents cee3a2e + 3a66857 commit cd5b1d3
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions dipper/curie_map.yaml
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Expand Up @@ -157,9 +157,9 @@
'HPRD' : 'http://www.hprd.org/protein/'
'NCBIProtein' : 'http://www.ncbi.nlm.nih.gov/protein/'
'PDB' : 'http://identifiers.org/PDB:'
'SwissProt' : 'http://identifiers.org/SwissProt:'
'TrEMBL' : 'http://www.uniprot.org/uniprot/'
'UniProtKB' : 'http://identifiers.org/uniprot/'
'SwissProt' : 'http://purl.uniprot.org/uniprot/'
'TrEMBL' : 'http://purl.uniprot.org/uniprot/'
'UniProtKB' : 'http://purl.uniprot.org/uniprot/'

#chemicals
'CID' : 'http://pubchem.ncbi.nlm.nih.gov/compound/'
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8 comments on commit cd5b1d3

@jnguyenx
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This PR broke SciGraph, because two CURIEs resolve to the same prefix. SciGraph is not able to do the inverse resolution (IRI to CURIE).

In general I don't think it makes much sense to have duplicates in either the keys or values, we have to be able to convert in both directions.

@cmungall
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Yep, we need this to be 1:1

For general registration of alternate prefixes, consider https://github.com/prefixcommons/

@jnguyenx
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PR reverted.

@jmcmurry
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Arg. Didn't think to check that, sorry. Is the distinction between SwissProt,/Trembl/UniprotKB even useful to us? If not, we could collapse these prefixes to just 'UniProt' and keep it simple.

@cmungall
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@cmungall cmungall commented on cd5b1d3 May 4, 2016 via email

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@jmcmurry
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'UniProtKB' is fine with me, but do you agree we could collapse to that prefix? What would be involved on the data side? @kshefchek

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We would just need to convert any TrEMBL or SwissProt prefixes to UniProtKB, we'll have to examine the sources to see where these are used.

@cmungall
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@cmungall cmungall commented on cd5b1d3 May 4, 2016 via email

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