>
> On Oct 25, 2012, at 23:03 , Robert Olson wrote:
>
>> Which KB genome(s) should these map to?
>>
>> ----- Original Message -----
>>> Hi all,
>>>
>>>
>>> From Ecogene is possible to download a file with every possible E.coli
>>> aliases/IDs
>>>
http://www.ecogene.org/ecodownload/crossref
>>>
>>>
>>> How difficult is to get this in?
>>>
>>>
>>> José
>>>
>>>
>>> On Tue, Oct 23, 2012 at 5:10 AM, Robert Olson <
olson@mcs.anl.gov >
>>> wrote:
>>>
>>>
>>> If there are IDs missing, and we have a reliable location for the
>>> definition of the IDs, we can look into the right way to get them
>>> loaded. As I pointed out in the original note, the CDM has two primary
>>> mechanisms for these mappings, and Tom's design for the translation
>>> service is probably the place where solutions other than the CDM ones
>>> would be based.
>>>
>>> --bob
>>>
>>>
>>>
>>> ----- 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
>>>>>
>>>>> _______________________________________________
>>>>> Kbase-devel mailing list
>>>>>
Kbase-devel@lists.kbase.us
>>>>>
https://lists.kbase.us/mailman/listinfo/kbase-devel