I have a list of about 20,000 "Accession Reference" IDs and I want to find corresponding Gene and GO information. The IDs that start with "NM_" all seem to work fine as type="refseq", but others, starting with, "S" or "AB" or "AF" can be found only as type="embl". Those with "XM" seemingly cannot be found. What information is stored in the prefix of an ID? What do NM_, S, AB, AF, or XM mean, and where is information about these prefixes? Does it make sense to have a function that returns the type of an ID? Does it make sense to have biomaRt functions automtically "know" about the various kinds of IDs? I don't see how to vectorize any of this when one must check the type of ID with each call. Below I try "embl" IDs first because after a first pass I know I can only connect about 3,000 out of 20,000 identifiers as "refseq". Overall, trying both "embl" and then "refseq" matches perhaps 90% of the dataset of 20,000, but this doesn't seem very "clean", and perhaps about 1,000 XM probes were never matched: > # Show problem in knowing type of identifier while fetching GO or Gene info > # using biomaRt. efg, 30 Jan 2006 > > library(biomaRt) Loading required package: RMySQL Loading required package: DBI Loading required package: XML Warning message: DLL attempted to change FPU control word from 8001f to 9001f > mart <- martConnect() connected to: ensembl_mart_36 > > # First five "Accession Reference" IDs from CAMDA06-related probe dataset: > # http://ecom2.mwgdna.com/download/arrays/arrays/gene_id/xls/gene_id_hum an_40k_a.xls > # (discard _N or _NN in IDs) > probe.list <- c("NM_001533", "NM_031990", "S76822", "AF232742", "AB035863") > > GeneInfo.List <- NULL > > for (i in 1:length(probe.list)) + { + probe <- probe.list[i] + + # Assume embl ID + GOinfo <- getGO(id=probe,type="embl",species="hsapiens",mart=mart) + if ( (length(GOinfo at table$GOID) == 1) & is.na(GOinfo at table$GOID[1]) ) + { + # IF embl ID fails, try as refseq (perhaps 15% refseqs with NM_ + GOinfo <- getGO( id=probe,type="refseq",species="hsapiens",mart=mart) + GeneInfo <- getGene(id=probe,type="refseq",species="hsapiens",mart=mart) + cat(i, "refseq", probe, "\n") + + + } else { + cat(i, "embl", probe, "\n") + GeneInfo <- getGene(id=probe,type="embl",species="hsapiens",mart=mart) + } + + GeneInfo.List <- rbind( GeneInfo.List, + c(probe, + unlist( GeneInfo at table[c(1,3,4,5,6,7,2)]) )) + + cat(GOinfo at id[1], GOinfo at table$GOID, "\n") + } 1 refseq NM_001533 NM_001533 GO:0000166 GO:0003723 GO:0006397 GO:0005654 GO:0030530 GO:0005634 2 refseq NM_031990 NM_031990 GO:0000166 GO:0005515 GO:0008187 GO:0000398 GO:0008380 GO:0005654 GO:0005730 GO:0030530 GO:0003676 GO:0003723 GO:0006397 GO:0005634 3 embl S76822 S76822 GO:0000287 GO:0004310 GO:0016491 GO:0016740 GO:0006695 GO:0008299 GO:0005783 GO:0016021 4 embl AF232742 AF232742 GO:0003807 GO:0004263 GO:0004295 GO:0008233 GO:0006508 GO:0006954 GO:0007596 GO:0042730 GO:0005615 5 embl AB035863 AB035863 GO:0016874 GO:0008152 GO:0004775 GO:0006099 GO:0006104 GO:0006781 GO:0005739 > > print(GeneInfo.List) symbol band chromosome start end martID [1,] "NM_001533" "HNRPL" "q13.2" "19" "44018883" "44032452" "ENSG00000104824" [2,] "NM_031990" "PTBP1" "p13.3" "19" "748411" "763327" "ENSG00000011304" [3,] "S76822" "FDFT1" "p23.1" "8" "11697664" "11734215" "ENSG00000079459" [4,] "AF232742" "KLKB1" "q35.2" "4" "187523815" "187554773" "ENSG00000164344" [5,] "AB035863" "SUCLA2" "q14.2" "13" "47414793" "47473463" "ENSG00000136143" description [1,] "Heterogeneous nuclear ribonucleoprotein L (hnRNP L). [Source:Uniprot/SWISSPROT;Acc:P14866]" [2,] "Polypyrimidine tract-binding protein 1 (PTB) (Heterogeneous nuclear ribonucleoprotein I) (hnRNP I) (57 kDa RNA-binding protein PPTB-1). [Source:Uniprot/SWISSPROT;Acc:P26599]" [3,] "Squalene synthetase (EC 2.5.1.21) (SQS) (SS) (Farnesyl- diphosphate farnesyltransferase) (FPP:FPP farnesyltransferase). [Source:Uniprot/SWISSPROT;Acc:P37268]" [4,] "Plasma kallikrein precursor (EC 3.4.21.34) (Plasma prekallikrein) (Kininogenin) (Fletcher factor) [Contains: Plasma kallikrein heavy chain; Plasma kallikrein light chain]. [Source:Uniprot/SWISSPROT;Acc:P03952]" [5,] "Succinyl-CoA ligase [ADP-forming] beta-chain, mitochondrial precursor (EC 6.2.1.5) (Succinyl-CoA synthetase, betaA chain) (SCS-betaA) (ATP- specific succinyl-CoA synthetase beta subunit). [Source:Uniprot/SWISSPROT;Acc:Q9P2R7]" > write.csv(GeneInfo.List, row.names=F, file="GeneInfo.csv") > > martDisconnect(mart) efg Bioinformatics Stowers Institute

Hi, Ideally your microarray provider should have added an extra column to the excel sheet indicating which from database each identifier comes. This is what I found on "XM_*" IDs on the NCBI website: >RefSeq Model (predicted) Sequence Records from the Human Genome annotation >process Two letters (XM, XP, or XR), an underscore bar, and six >digits, e.g.: >XM_000483 Your XM IDs have an extra underscore and digit, removing that and querying at NCBI gives (for example for ID XM_170432_1) XM_170432 Reports gi|20542485|ref|XM_170432.1|[20542485] This record was removed as a result of standard genome annotation processing. See the genome build documentation at http://www.ncbi.nlm.nih.gov/genome/guide/build.html for further information, or contact info at ncbi.nlm.nih.gov. best, Steffen > I have a list of about 20,000 "Accession Reference" IDs and I want to find > corresponding Gene and GO information. > > The IDs that start with "NM_" all seem to work fine as type="refseq", but > others, starting with, "S" or "AB" or "AF" can be found only as > type="embl". > Those with "XM" seemingly cannot be found. > > What information is stored in the prefix of an ID? What do NM_, S, AB, > AF, > or XM mean, and where is information about these prefixes? > > Does it make sense to have a function that returns the type of an ID? > Does > it make sense to have biomaRt functions automtically "know" about the > various kinds of IDs? I don't see how to vectorize any of this when one > must check the type of ID with each call. > > Below I try "embl" IDs first because after a first pass I know I can only > connect about 3,000 out of 20,000 identifiers as "refseq". Overall, > trying > both "embl" and then "refseq" matches perhaps 90% of the dataset of > 20,000, > but this doesn't seem very "clean", and perhaps about 1,000 XM probes were > never matched: > >> # Show problem in knowing type of identifier while fetching GO or Gene > info >> # using biomaRt. efg, 30 Jan 2006 >> >> library(biomaRt) > Loading required package: RMySQL > Loading required package: DBI > Loading required package: XML > Warning message: > DLL attempted to change FPU control word from 8001f to 9001f >> mart <- martConnect() > connected to: ensembl_mart_36 >> >> # First five "Accession Reference" IDs from CAMDA06-related probe >> dataset: >> # > http://ecom2.mwgdna.com/download/arrays/arrays/gene_id/xls/gene_id_h uman_40k_a.xls >> # (discard _N or _NN in IDs) >> probe.list <- c("NM_001533", "NM_031990", "S76822", "AF232742", > "AB035863") >> >> GeneInfo.List <- NULL >> >> for (i in 1:length(probe.list)) > + { > + probe <- probe.list[i] > + > + # Assume embl ID > + GOinfo <- getGO(id=probe,type="embl",species="hsapiens",mart=mart) > + if ( (length(GOinfo at table$GOID) == 1) & is.na(GOinfo at table$GOID[1]) ) > + { > + # IF embl ID fails, try as refseq (perhaps 15% refseqs with NM_ > + GOinfo <- getGO( > id=probe,type="refseq",species="hsapiens",mart=mart) > + GeneInfo <- > getGene(id=probe,type="refseq",species="hsapiens",mart=mart) > + cat(i, "refseq", probe, "\n") > + > + > + } else { > + cat(i, "embl", probe, "\n") > + GeneInfo <- > getGene(id=probe,type="embl",species="hsapiens",mart=mart) > + } > + > + GeneInfo.List <- rbind( GeneInfo.List, > + c(probe, > + unlist( GeneInfo at table[c(1,3,4,5,6,7,2)]) > )) > + > + cat(GOinfo at id[1], GOinfo at table$GOID, "\n") > + } > 1 refseq NM_001533 > NM_001533 GO:0000166 GO:0003723 GO:0006397 GO:0005654 GO:0030530 > GO:0005634 > 2 refseq NM_031990 > NM_031990 GO:0000166 GO:0005515 GO:0008187 GO:0000398 GO:0008380 > GO:0005654 > GO:0005730 GO:0030530 GO:0003676 GO:0003723 GO:0006397 GO:0005634 > 3 embl S76822 > S76822 GO:0000287 GO:0004310 GO:0016491 GO:0016740 GO:0006695 GO:0008299 > GO:0005783 GO:0016021 > 4 embl AF232742 > AF232742 GO:0003807 GO:0004263 GO:0004295 GO:0008233 GO:0006508 GO:0006954 > GO:0007596 GO:0042730 GO:0005615 > 5 embl AB035863 > AB035863 GO:0016874 GO:0008152 GO:0004775 GO:0006099 GO:0006104 GO:0006781 > GO:0005739 >> >> print(GeneInfo.List) > symbol band chromosome start end > martID > [1,] "NM_001533" "HNRPL" "q13.2" "19" "44018883" "44032452" > "ENSG00000104824" > [2,] "NM_031990" "PTBP1" "p13.3" "19" "748411" "763327" > "ENSG00000011304" > [3,] "S76822" "FDFT1" "p23.1" "8" "11697664" "11734215" > "ENSG00000079459" > [4,] "AF232742" "KLKB1" "q35.2" "4" "187523815" "187554773" > "ENSG00000164344" > [5,] "AB035863" "SUCLA2" "q14.2" "13" "47414793" "47473463" > "ENSG00000136143" > description > [1,] "Heterogeneous nuclear ribonucleoprotein L (hnRNP L). > [Source:Uniprot/SWISSPROT;Acc:P14866]" > [2,] "Polypyrimidine tract-binding protein 1 (PTB) (Heterogeneous nuclear > ribonucleoprotein I) (hnRNP I) (57 kDa RNA-binding protein PPTB-1). > [Source:Uniprot/SWISSPROT;Acc:P26599]" > [3,] "Squalene synthetase (EC 2.5.1.21) (SQS) (SS) (Farnesyl- diphosphate > farnesyltransferase) (FPP:FPP farnesyltransferase). > [Source:Uniprot/SWISSPROT;Acc:P37268]" > [4,] "Plasma kallikrein precursor (EC 3.4.21.34) (Plasma prekallikrein) > (Kininogenin) (Fletcher factor) [Contains: Plasma kallikrein heavy chain; > Plasma kallikrein light chain]. [Source:Uniprot/SWISSPROT;Acc:P03952]" > [5,] "Succinyl-CoA ligase [ADP-forming] beta-chain, mitochondrial > precursor > (EC 6.2.1.5) (Succinyl-CoA synthetase, betaA chain) (SCS-betaA) (ATP- > specific succinyl-CoA synthetase beta subunit). > [Source:Uniprot/SWISSPROT;Acc:Q9P2R7]" >> write.csv(GeneInfo.List, row.names=F, file="GeneInfo.csv") >> >> martDisconnect(mart) > > > efg > Bioinformatics > Stowers Institute > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >