- Microbe - mailman3.cels.anl.gov

Re: [Microbe] nice d3 interactive visualization, fosters ideas relevant to model / phenotype reconciliation
by Adam Paul Arkin 04 Nov '12

04 Nov '12

That is really nice. Sent from my mobile device. Please excuse any seeming terseness or errors. Adam Paul Arkin Dean A. Richard Newton Memorial Chair ------------------------------------- Director, Physical Biosciences Division E.O. Lawrence Berkeley National Laboratory Professor, Department of Bioengineering University of California Berkeley, CA, 94720 PI and Co-Director, Virtual Institute of Microbial Stress and Survival, http://vimss.lbl.gov Director of Bioinformatics, The Joint Bioenergy Institute, http://jbei.lbl.gov Investigator, Energy Biosciences Institute, http://energybiosciencesinstitute.org Head, Synthetic Biology, Physical Biosciences Division, Lawrence Berkeley National Laboratory Office: 309B Hildebrand Hall (Berkeley Campus) Mailing address: E.O. Lawrence Berkeley National Laboratory 1 Cyclotron Road, MS Stanley-922 Berkeley, CA 94720 Contact: W: http://genomics.lbl.gov V: 510-495-2366 C: 510-206-1389 F: 510-486-6219 Assistant: Gwyneth A. Terry V: 510-495-2116 E: GATerry(a)lbl.gov ------------------------------------- On Nov 3, 2012, at 9:03 PM, Christopher Henry <chrisshenry(a)gmail.com> wrote: > i love it!!!! We most definitely should do it. ASAP. > Something like that could bring real shock and awe to the demo... > > On Nov 3, 2012, at 8:59 PM, Ben Bowen wrote: > >> If you go to this link and click "next" >> http://elections.nytimes.com/2012/electoral-map >> there is a nice d3 visualization. >> >> Instead of states: think media conditions (we have ~100) >> Instead of electoral votes for radius: think how many discrepancies were resolved >> Instead of dragging to explore voting outcomes: think which changes to the model you want to accept. >> Instead of tooltips with electoral votes: have option to select 1, 2, or 3 best modification to the model. >> >> Add a button at the bottom for "commit" and get a nice, shiny new model to play with. >> >> ----------------------------- >> Email: BPBowen(a)lbl.gov >> Phone: (510) 214-6683 >> MS 977-221, Lawrence Berkeley Lab >> Web: ms.lbl.gov >> _______________________________________________ >> Microbe mailing list >> Microbe(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/microbe > > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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Re: [Microbe] nice d3 interactive visualization, fosters ideas relevant to model / phenotype reconciliation
by Christopher Henry 03 Nov '12

03 Nov '12

i love it!!!! We most definitely should do it. ASAP. Something like that could bring real shock and awe to the demo... On Nov 3, 2012, at 8:59 PM, Ben Bowen wrote: > If you go to this link and click "next" > http://elections.nytimes.com/2012/electoral-map > there is a nice d3 visualization. > > Instead of states: think media conditions (we have ~100) > Instead of electoral votes for radius: think how many discrepancies were resolved > Instead of dragging to explore voting outcomes: think which changes to the model you want to accept. > Instead of tooltips with electoral votes: have option to select 1, 2, or 3 best modification to the model. > > Add a button at the bottom for "commit" and get a nice, shiny new model to play with. > > ----------------------------- > Email: BPBowen(a)lbl.gov > Phone: (510) 214-6683 > MS 977-221, Lawrence Berkeley Lab > Web: ms.lbl.gov > _______________________________________________ > Microbe mailing list > Microbe(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/microbe

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nice d3 interactive visualization, fosters ideas relevant to model / phenotype reconciliation
by Ben Bowen 03 Nov '12

03 Nov '12

If you go to this link and click "next" http://elections.nytimes.com/2012/electoral-map there is a nice d3 visualization. Instead of states: think media conditions (we have ~100) Instead of electoral votes for radius: think how many discrepancies were resolved Instead of dragging to explore voting outcomes: think which changes to the model you want to accept. Instead of tooltips with electoral votes: have option to select 1, 2, or 3 best modification to the model. Add a button at the bottom for "commit" and get a nice, shiny new model to play with. ----------------------------- Email: BPBowen(a)lbl.gov Phone: (510) 214-6683 MS 977-221, Lawrence Berkeley Lab Web: ms.lbl.gov

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Re: [Microbe] [Kbase-devel] ID mapping in KBase
by Gary Olsen 26 Oct '12

26 Oct '12

kb|g.1870 Escherichia coli str. K-12 substr. MG1655 is one of the two genome versions that you can download from their FTP site. The treat this as their gold standard sequence. The other available from their WWW site is the .1 version of the above (though it differs in length by about 300 bp, go figure). kb|g.0 Escherichia coli K12 was a very closely related genome, published still earlier. I have not done the experiment, but I suggest that if we want the features to line-up to the nucleotide, we use kb|g.1870. Otherwise we need to go by sequence, and there will be some features with identical sequence. Gary On Oct 26, 2012, at 00:33 , José Pedro Lopes Faria wrote: > I am guessing its E. coli K12 since one of the aliases available from that list is "K-12 Gene Accession (ECK)" > And K12 in the SEED is 83333.1 right? > > I can dig deeper in this data, but seems pretty good, has ECK numbers Blat numbers, several synonyms, etc. > I got this info as an answer from http://ecoliwiki.net/colipedia/index.php/Welcome_to_EcoliWiki to an email I sent asking for a complete/updated file with all E.coli aliases. > > José > > > > On Fri, Oct 26, 2012 at 5:31 AM, Gary Olsen <gary(a)life.illinois.edu> wrote: > Sorry, I did not copy anyone else. > > Gary > > Begin forwarded message: > > > From: Gary Olsen <gary(a)life.illinois.edu> > > Subject: Re: [Microbe] [Kbase-devel] ID mapping in KBase > > Date: October 25, 2012 23:29:05 CDT > > To: Robert Olson <olson(a)mcs.anl.gov> > > > > kb|g.1870 Escherichia coli str. K-12 substr. MG1655 > > > > Gary > > > > 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(a)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(a)lists.kbase.us > >>>>> https://lists.kbase.us/mailman/listinfo/kbase-devel > >> _______________________________________________ > >> Microbe mailing list > >> Microbe(a)lists.kbase.us > >> https://lists.kbase.us/mailman/listinfo/microbe > > > >

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Re: [Microbe] [Kbase-devel] ID mapping in KBase
by José Pedro Lopes Faria 26 Oct '12

26 Oct '12

I am guessing its E. coli K12 since one of the aliases available from that list is "K-12 Gene Accession (ECK)" And K12 in the SEED is 83333.1 right? I can dig deeper in this data, but seems pretty good, has ECK numbers Blat numbers, several synonyms, etc. I got this info as an answer from http://ecoliwiki.net/colipedia/index.php/Welcome_to_EcoliWiki to an email I sent asking for a complete/updated file with all E.coli aliases. José On Fri, Oct 26, 2012 at 5:31 AM, Gary Olsen <gary(a)life.illinois.edu> wrote: > Sorry, I did not copy anyone else. > > Gary > > Begin forwarded message: > > > From: Gary Olsen <gary(a)life.illinois.edu> > > Subject: Re: [Microbe] [Kbase-devel] ID mapping in KBase > > Date: October 25, 2012 23:29:05 CDT > > To: Robert Olson <olson(a)mcs.anl.gov> > > > > kb|g.1870 Escherichia coli str. K-12 substr. MG1655 > > > > Gary > > > > 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(a)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(a)lists.kbase.us > >>>>> https://lists.kbase.us/mailman/listinfo/kbase-devel > >> _______________________________________________ > >> Microbe mailing list > >> Microbe(a)lists.kbase.us > >> https://lists.kbase.us/mailman/listinfo/microbe > > > >

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Fwd: [Kbase-devel] ID mapping in KBase
by Gary Olsen 25 Oct '12

25 Oct '12

Sorry, I did not copy anyone else. Gary Begin forwarded message: > From: Gary Olsen <gary(a)life.illinois.edu> > Subject: Re: [Microbe] [Kbase-devel] ID mapping in KBase > Date: October 25, 2012 23:29:05 CDT > To: Robert Olson <olson(a)mcs.anl.gov> > > kb|g.1870 Escherichia coli str. K-12 substr. MG1655 > > Gary > > 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(a)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(a)lists.kbase.us >>>>> https://lists.kbase.us/mailman/listinfo/kbase-devel >> _______________________________________________ >> Microbe mailing list >> Microbe(a)lists.kbase.us >> https://lists.kbase.us/mailman/listinfo/microbe >

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Re: [Microbe] [Kbase-devel] ID mapping in KBase
by Robert Olson 25 Oct '12

25 Oct '12

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(a)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(a)lists.kbase.us > > > https://lists.kbase.us/mailman/listinfo/kbase-devel

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Re: [Microbe] [Kbase-devel] ID mapping in KBase
by José Pedro Lopes Faria 25 Oct '12

25 Oct '12

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(a)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(a)lists.kbase.us > > > https://lists.kbase.us/mailman/listinfo/kbase-devel >

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Re: [Microbe] [Kbase-devel] ID mapping in KBase
by Robert Olson 22 Oct '12

22 Oct '12

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(a)lists.kbase.us > > https://lists.kbase.us/mailman/listinfo/kbase-devel

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Re: [Microbe] [Kbase-devel] ID mapping in KBase
by Christopher Henry 22 Oct '12

22 Oct '12

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(a)lists.kbase.us > https://lists.kbase.us/mailman/listinfo/kbase-devel

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