----- Original Message -----
> Really nice work Bob, and great explanation.
>
> So I'd like the science users to kick the tires on this.
> Sam, does it have the plant gene IDs we need?
> Janaka, does it have gene IDs you need for all your template genomes
> used for your core model work?
> Jose, does it have blatner numbers? bsu loci for B. subtilis?
> Ben Bowen, does it have your shewenella genes?
> Gavin, how about all the gene IDs in the datasets you're loading?
> Liz, I know you in particular are an alias finatic. Do you see missing
> content?
>
> Someone should probably make a tutorial on ID querying?? The text Bob
> has below is pretty darn close.
>
> Bob, if we discover that there are important IDs we're missing, how do
> we go about getting them in? Do we do something crazy like setting up
> a git repo where poeple check in new ID sets for loading?? Or is there
> a more sane solution?
>
> On Oct 22, 2012, at 3:48 PM, Robert Olson wrote:
>
> > Since these questions come up a lot, and since we now have some
> > additional data loaded, I wanted to give some examples of doing ID
> > lookups using the KBase Central Store.
> >
> > There are two forms of external IDs loaded into the CDM.
> >
> > The first is a set of aliases that may be associated with features.
> > These are data like gene names and locus tags that for instance come
> > along with the Genbank files that originally sourced the genomes.
> >
> > These may be searched with the new script (and API function)
> > aliases_to_fids:
> >
> > $ echo b0010 | aliases_to_fids
> > b0010 kb|g.1870.peg.4458
> > $ echo dnaK | aliases_to_fids | head
> > dnaK kb|g.5.peg.1109
> > dnaK kb|g.11.peg.1619
> > dnaK kb|g.22.peg.3037
> > dnaK kb|g.27.peg.3820
> > dnaK kb|g.34.peg.1696
> > dnaK kb|g.35.peg.966
> > dnaK kb|g.37.peg.1437
> > dnaK kb|g.39.peg.2253
> > dnaK kb|g.39.peg.2487
> > dnaK kb|g.42.peg.766
> > $ echo dnaK | aliases_to_fids | wc -l
> > 1658
> >
> > (this is also available in Iris).
> >
> > The second source of external IDs is the external protein database
> > data that are loaded in the HasAssertedFunctionFrom relationship.
> > The relevant part of the schema is here:
> >
> > <PastedGraphic-1.png>
> >
> > What this tells us is if you have a feature, you can find the
> > protein sequence for that feature, and map it to the set of
> > assertions from some external database:
> >
> > $ echo 'kb|g.3785.peg.1578' | get_relationship_Produces -rel to_link
> > | get_relationship_HasAssertedFunctionFrom -rel
> > function,external_id,to_link
> > kb|g.3785.peg.1578 feb01774b3c5bb6e84ca9ae888514c5f multidrug
> > resistance protein A ref|ZP_05465429.1 NCBI
> > kb|g.3785.peg.1578 feb01774b3c5bb6e84ca9ae888514c5f multidrug
> > resistance protein A gb|EEZ16943.1 NCBI
> > kb|g.3785.peg.1578 feb01774b3c5bb6e84ca9ae888514c5f secretion
> > protein HlyD family protein gb|ADZ67367.1 NCBI
> > kb|g.3785.peg.1578 feb01774b3c5bb6e84ca9ae888514c5f secretion
> > protein HlyD family protein gb|ADZ88235.1 NCBI
> > kb|g.3785.peg.1578 feb01774b3c5bb6e84ca9ae888514c5f Multidrug
> > resistance protein gb|AEQ09823.1 NCBI
> > kb|g.3785.peg.1578 feb01774b3c5bb6e84ca9ae888514c5f Multidrug
> > resistance protein A tr|D0GC62|D0GC62_BRUML TrEMBL
> > kb|g.3785.peg.1578 feb01774b3c5bb6e84ca9ae888514c5f Multidrug
> > resistance protein tr|G4PJZ8|G4PJZ8_BRUML TrEMBL
> > kb|g.3785.peg.1578 feb01774b3c5bb6e84ca9ae888514c5f Secretion
> > protein HlyD family protein tr|F2GWN2|F2GWN2_BRUM5 TrEMBL
> > kb|g.3785.peg.1578 feb01774b3c5bb6e84ca9ae888514c5f Secretion
> > protein HlyD family protein tr|F2HWT4|F2HWT4_BRUMM TrEMBL
> >
> > Since going in the other direction requires querying on a
> > relationship field, and we may want to do prefix matches there, you
> > will need the new external_ids_to_fids script (or API routine):
> >
> > $ echo 'gb|ADZ88235.1' | external_ids_to_fids
> > gb|ADZ88235.1 kb|g.1940.peg.347
> > gb|ADZ88235.1 kb|g.2192.peg.1337
> > gb|ADZ88235.1 kb|g.29.peg.2088
> > gb|ADZ88235.1 kb|g.30.peg.1725
> > gb|ADZ88235.1 kb|g.31.peg.2171
> > gb|ADZ88235.1 kb|g.3785.peg.1578
> >
> > Or for a prefix match:
> >
> > $ echo 'gb|ADZ88235' | external_ids_to_fids -prefix
> > gb|ADZ88235 kb|g.1940.peg.347
> > gb|ADZ88235 kb|g.2192.peg.1337
> > gb|ADZ88235 kb|g.29.peg.2088
> > gb|ADZ88235 kb|g.30.peg.1725
> > gb|ADZ88235 kb|g.31.peg.2171
> > gb|ADZ88235 kb|g.3785.peg.1578
> >
> > --bob
> >
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