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#23 "ncbiest" for NCBI Expressed Sequence Tags database?

pending
Nick Juty
None
2015-11-23
2015-11-23
Jon Olav Vik
No

It would be nice to have http://identifiers.org/ncbiest (for expressed sequence tags) as a complement to http://identifiers.org/ncbigene and http://identifiers.org/ncbiprotein. I don't have any strong opinion on what the namespace should be called, nor whether the name of the collection is EST (as it would seem from their frontpage), dbEST (as it says in their breadcrumb and on Wikipedia) or nucest (as it says in their URL scheme) or NCBI EST (by analogy to NCBI Gene and NCBI Protein).

Related

Request new collection: #23

Discussion

  • Nick Juty

    Nick Juty - 2015-11-23
    • status: open --> accepted
    • assigned_to: Nick Juty
    • Collection name: [u'NCBI Database of Expressed Sequence Tags (dbEST), a.k.a. EST', u'ncbiest'] --> [u"[u'NCBI Database of Expressed Sequence Tags (dbEST), a.k.a. EST', u'ncbiest']", u"[u'NCBI Database of Expressed Sequence Tags (dbEST), a.k.a. EST', u'ncbiest']"]
    • Priority: low --> normal
     

  • Nick Juty

    Nick Juty - 2015-11-23
    • status: accepted --> pending
    • Collection name: [u"[u'NCBI Database of Expressed Sequence Tags (dbEST), a.k.a. EST', u'ncbiest']", u"[u'NCBI Database of Expressed Sequence Tags (dbEST), a.k.a. EST', u'ncbiest']"] --> [u'[u"[u\'NCBI Database of Expressed Sequence Tags (dbEST), a.k.a. EST\', u\'ncbiest\']", u"[u\'NCBI Database of Expressed Sequence Tags (dbEST), a.k.a. EST\', u\'ncbiest\']"]', u'[u"[u\'NCBI Database of Expressed Sequence Tags (dbEST), a.k.a. EST\', u\'ncbiest\']", u"[u\'NCBI Database of Expressed Sequence Tags (dbEST), a.k.a. EST\', u\'ncbiest\']"]']
     

  • Nick Juty

    Nick Juty - 2015-11-23

    Hi Jon,

    I confess to hoping you would use the dbest 'name' which seems much more unique that the dbest id (for instance if you search across ncbi databases with BP100000 you will get only one result). In any case, I've now relaxed the regex to allow purely numerical ids. You should note however that if you enter an erroneous numerical id, due to the redirection that ncbi use, you could end up referencing a protein or other entity type. So use with care...

    cheers!

    Nick

     

    Last edit: Nick Juty 2015-11-23

    • Jon Olav Vik

      Jon Olav Vik - 2015-11-23

      On Mon, Nov 23, 2015 at 12:38 PM, Nick Juty njuty@users.sf.net wrote:

      Hi Jon,

      I confess to hoping you would use the dbest 'name' which seems much more
      unique

      In this case I'm getting the IDs from a collaborator. It is indeed often
      hard for a newcomer such as myself to determine what is the "primary key"
      for each database. As long as people are clear about which ontology they're
      using, and the ontology/identifier pair is unique, I am happy.

      that the dbest id (for instance if you search across ncbi databases with
      BP100000 you will get only one result). In any case, I've now relaxed the
      regex to allow purely numerical ids.

      Thanks, that was quick! It's working nicely now.

      You should note however that if you enter an erroneous numerical id, due
      to the redirection that ncbi use, you could end up referencing a protein or
      entity type. So use with care...

      Argh. Thanks for the heads-up.

      Best regards,
      Jon Olav

       
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