This GO Term Mapper tool maps the granular GO annotations for genes in a list to a set of broader, high-level parent GO slim terms, allowing you to bin your genes into broad categories. This is possible with GO because there are parent:child relationships recorded between granular terms and more general parent GO slim terms. For a better view of parent:children relationships of GO terms, please visit the AmiGO web site.
This GO Term Mapper tool serves a different function than the GO Term Finder tool. The GO Term Mapper tool simply bins the submitted gene list to a static set of ancestor GO terms. In contrast, the GO Term Finder tool finds the GO terms significantly enriched in a submitted list of genes.
The Gene Association File Table below lists the types of identifiers in the gene association files that the GO Term Mapper program accepts as input for the list of gene names. It also provides links for tools that may help you to convert from an unsupported identifier system to one that is supported.
For example, if you have a file of gene identifiers that are a
different type than those listed in the table, you can use a tool provided
by UniProt that converts several types of identifiers into
UniProt_IDs/Accession. You can then use the GOA gene association files
that contain UniProt_IDs/Accession gene names.
Please see Gene Association File Table for the full description of the gene association files.
The generic slim ontology contains terms that are considered generally interesting across all annotations, whereas the alternative slim ontologies are provided by individual organizations and may contain (or exclude) certain terms that are considered by them to be of particular interest (or not particularly of interest) for their specific annotation.
The different slim ontologies that are used include:
Slim gene association files are created by using map2slim.pl script (part of GO::Perl). Each slim gene association file is generated using the full ontology, the slim ontology, and the annotation file.
The output page displays the GO slim term(s) to which your gene(s)
have been mapped. The HTML table includes links for the gene names
to external sites that provide more details for each gene. Also listed is the frequency with which
each GO slim term is used to annotate (directly, or indirectly, via parental relationship with a granular term) the genes
in your list as well as the frequency that same slim term annotates
the genes in the organism. The term is also a link to the external
AmiGO site which
provides more information about each term including parent-child relationships.
The gene name is appended to your entry. For example: If 'http://www.yeastgenome.org/locus/' is entered, the link for YPL250C becomes http://www.yeastgenome.org/locus/YPL250C.
As another example: 'http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=xxxx' is the GO Term Mapper program's
default gene URL for human protein, where xxxx is a UniProt_ID or UniProt_Accession (e.g.
http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=BRCA2). If you prefer to use the UniProt (the Universal
Protein Resource) site to display information about a protein
(e.g.
http://www.uniprot.org/uniprot/?query=BRCA2), you can type the
UniProt URL 'http://www.uniprot.org/uniprot/?query='
in the provided text box to override the program's default URL.
Without the advanced options, the program should finish quickly. Advanced options may increase the run time dramatically. Use of these options requires running map2slim to generate a custom gene association file based on your input.
Please remember to select the correct Ontology Aspect (step 2 in Basic Inputs section) corresponding to the slim GOID(s) in your GO slim list.
In general, the ontology and gene association files are downloaded nightly from GO FTP site. Occasionally, there may be a problem with a particular file causing a delay in updating it. For example, sometimes an association file does not conform exactly to our understanding of the specification. In such a case, the file is removed from the annotation selection pop-up menu, and a notice is printed below the pop-up menu, until the situation is resolved.
The tables below show the version, GOC validation dates (where available and applicable), and other information for files that are currently in use.
| GO Term Finder Ontology Files | Version |
|---|---|
| go-basic.obo | releases/2024-03-28 |
| GO Term Mapper Ontology Files | Version |
| goslim_generic.obo | go/2024-03-28/subsets/goslim_generic.owl |
| goslim_yeast.obo | go/2024-03-28/subsets/goslim_yeast.owl |
| goslim_pombe.obo | |
| goslim_plant.obo | |
| goslim_chembl.obo | |
| goslim_goa.obo | 1.854 |
| Organism, Gene Associations, and Authority |
Total Annotated Gene Products |
Total Estimated Gene Products |
Identifiers | Example IDs | Identifier Conversion Tool(s) | Evidence Code Counts |
|---|---|---|---|---|---|---|
| Skin parasite - Leishmania major L. major GeneDB gene_association.GeneDB_Lmajor README | 4132 | Systematic_ID Systematic_ID | L302.10 L2256.04 LM5.39 sample list | EXP(41) IDA(216) IPI(45) IMP(104) IGI(26) IEP(2) ISS(160) ISO(8696) ISA(182) ISM(184) IGC(1) RCA(46) TAS(8) IC(4) IEA(4) | ||
| Trypanosome - Tryanosoma brucei T. brucei GeneDB gene_association.GeneDB_Tbrucei README | 6301 | Systematic Name Gene Name Gene Synonym | Tb927.7.4670 RRP4 TB927.7.4670 sample list | EXP(124) IDA(10762) IPI(539) IMP(1061) IGI(47) IEP(16) ISS(461) ISO(465) ISA(956) ISM(3599) RCA(1132) TAS(582) NAS(4) IC(47) | ||
| Default URL template: http://www.genedb.org/genedb/Search?organism=tryp&name= | ||||||
| Candida - Candida albicans CGD gene_association.cgd README | 60318 | CGD_ID Standard Name Systematic name | CAL0004982 CaO19.6783 CA5922 Contig4-2621_0008 orf6.8848 sample list | IDA(3429) IPI(72) IMP(6121) IGI(939) IEP(38) ISS(1883) ISO(344) ISA(162) ISM(1328) RCA(6837) TAS(47) NAS(168) IC(23) ND(16098) IEA(312232) | ||
| Default URL template: http://www.candidagenome.org/cgi-bin/locus.pl?locus= | ||||||
| Slime mold - Dictyostelium discoideum DictyBase gene_association.dictyBase | 9641 | 12098 | DictyBase_ID Gene Name Alias | DdP2X DDB_G0272004 p2xA sample list | IDA(4284) IPI(1210) IMP(3204) IGI(570) IEP(230) ISS(3450) IGC(79) TAS(447) NAS(6) IC(145) ND(6326) IEA(35408) | |
| Default URL template: http://dictybase.org/db/cgi-bin/dictyBase/locus.pl?locus= | ||||||
| Fruit fly - Drosophila melanogaster FlyBase gene_association.fb README | 14769 | 16085 | FlyBase_ID Gene Symbol Gene Synonym | FBGN0031491 alpha4GT1 4-N-acetylgalactosaminyltransferase-1 CG17223 alpha1 sample list | EXP(1) IDA(19113) IPI(3887) IMP(24639) IGI(4054) IEP(781) ISS(11178) ISO(3) ISA(34) ISM(2950) IGC(29) TAS(2647) NAS(1457) IC(1398) ND(7622) IEA(21119) | |
| Default URL template: http://flybase.bio.indiana.edu/.bin/fbidq.html? | ||||||
| Chicken - Gallus gallus GOA @EBI gene_association.goa_chicken README | 24742 | 30837 | UniProt_Accession (or Ensembl_ID) UniProt_ID (or Ensembl_ID) International Protein Index | FGB IPI00588322 FIBB_CHICK Q02020 sample list | EXP(14) IDA(1730) IPI(441) IMP(698) IGI(21) IEP(172) ISS(6306) ISO(36) ISA(326) ISM(23) RCA(3) TAS(588) NAS(115) IC(21) ND(51) IEA(55875) | |
| Cow - Bos taurus GOA @EBI gene_association.goa_cow README | 19014 | 37225 | UniProt_Accession (or Ensembl_ID) UniProt_ID (or Ensembl_ID) International Protein Index | FGG P12799 IPI00699860 FIBG_BOVIN sample list | EXP(26) IDA(1981) IPI(653) IMP(271) IGI(13) IEP(7) ISS(21755) ISO(9) ISA(149) RCA(2) TAS(672) NAS(65) IC(40) ND(104) IEA(82011) | |
| Human - Homo sapiens GOA @EBI gene_association.goa_human README | 19635 | UniProt_Accession (or Ensembl_ID) UniProt_ID (or Ensembl_ID) International Protein Index | TGFR1_HUMAN IPI00005733 P36897 TGFBR1 sample list | EXP(992) IDA(97427) IPI(220449) IMP(25904) IGI(1974) IEP(927) ISS(29793) ISO(319) ISA(1439) ISM(3) RCA(471) TAS(98309) NAS(12683) IC(1487) ND(1695) IEA(71402) | ||
| Default URL template: http://www.ensembl.org/Homo_sapiens/geneview?gene= | ||||||
| Human - Homo sapiens GOA @EBI + Ensembl gene_association.goa_human_ensembl README | 19817 | UniProt_Accession (or Ensembl_ID) UniProt_ID (or Ensembl_ID) International Protein Index with additional crossreferenced gene symbols | FZD6 B4DRN0_HUMAN ENSG00000164930 B4DRN0 sample list | EXP(613) IDA(88710) IPI(213005) IMP(25206) IGI(2047) IEP(933) ISS(28265) ISO(11) ISA(1439) ISM(3) RCA(470) TAS(95949) NAS(7152) IC(6837) ND(1706) IEA(73570) | ||
| Default URL template: http://www.ensembl.org/Homo_sapiens/geneview?gene= | ||||||
| Human - Homo sapiens GOA @EBI + XREFs gene_association.goa_human_hgnc README | 19817 | UniProt_Accession (or Ensembl_ID) UniProt_ID (or Ensembl_ID) International Protein Index with additional crossreferenced gene symbols | HGNC:4854 FZD6 O60353 HGNC:4044 4044 FZD6_HUMAN sample list | EXP(613) IDA(88710) IPI(213005) IMP(25206) IGI(2047) IEP(933) ISS(28265) ISO(11) ISA(1439) ISM(3) RCA(470) TAS(95949) NAS(7152) IC(6837) ND(1706) IEA(73570) | ||
| Default URL template: http://www.genenames.org/data/hgnc_data.php?hgnc_id= | ||||||
| Mouse - Mus musculus MGI gene_association.mgi README | 31925 | MGI_ID Gene Symbol Gene_Symbol (old) | P2ry12 MGI:1918089 P2Y12 sample list | EXP(701) IDA(72243) IPI(20894) IMP(61978) IGI(15812) IEP(2226) ISS(1830) ISO(147792) ISA(5083) ISM(32) RCA(306) TAS(7979) NAS(4350) IC(701) ND(45158) IEA(69374) | ||
| Default URL template: http://www.informatics.jax.org/searches/accession_report.cgi?id= | ||||||
| Yeast - Schizosaccharomyces pombe PomBase gene_association.pombase README | 5364 | Systematic Name Gene Name Gene Synonym | SPCC191.07 cyc1 sample list | EXP(1828) IDA(8565) IPI(3435) IMP(4746) IGI(695) IEP(19) ISS(931) ISO(2973) ISM(1200) TAS(360) NAS(510) IC(1638) ND(1766) IEA(3387) | ||
| Default URL template: http://www.pombase.org/gene/ | ||||||
| Pseudomonas - Pseudomonas aeruginosa PAO1 PseudoCAP gene_association.pseudocap | 1505 | PA# Gene Name Alt. Gene Name (opt.) | fliD PA1094 hook-associated protein sample list | EXP(40) IDA(866) IPI(42) IMP(1139) IGI(61) IEP(13) ISS(1229) ISO(13) ISA(10) IGC(48) TAS(11) NAS(18) | ||
| Default URL template: http://www.pseudomonas.com/AnnotationByPAU.asp?PA= | ||||||
| Rat - Rattus norvegicus RGD gene_association.rgd README | 23743 | RGD_ID (or Ensembl Id, or UniProt accession) Gene Symbol (or UniProt Entry Name) if GOA-provided, an International Protein Index identifier | Fgb D3Z8Y5_RAT D3Z8Y5 IPI00948614 sample list | EXP(424) IDA(27357) IPI(8115) IMP(10330) IGI(325) IEP(10846) ISS(27269) ISO(206603) RCA(5) TAS(3229) NAS(731) IC(180) ND(2040) IEA(92095) | ||
| Default URL template: http://rgd.mcw.edu/tools/genes/genes_view.cgi?id= | ||||||
| Yeast - Saccharomyces cerevisiae SGD gene_association.sgd README | 6895 | 7166 | SGD_ID Gene Name Systematic ORF Name | YJL166W S000003702 COR5 QCR8 sample list | EXP(11) IDA(17973) IPI(3064) IMP(13980) IGI(5319) IEP(23) ISS(957) ISO(15) ISA(251) ISM(435) RCA(580) TAS(242) NAS(82) IC(1004) ND(3542) IEA(46537) | |
| Default URL template: http://www.yeastgenome.org/locus/ | ||||||
| Common wallcress - Arabidopsis thaliana TAIR gene_association.tair README | 43753 | TAIR Accession Gene Name Gene Alias | AT4G31210 AT4G31210.1 LOCUS:2128101 F8F16.30 F8F16_30 sample list | IDA(22366) IPI(24892) IMP(17948) IGI(4193) IEP(4801) ISS(8174) ISM(37753) RCA(868) TAS(6686) NAS(710) IC(184) ND(26895) IEA(22959) | ||
| Default URL template: http://www.arabidopsis.org/servlets/Search?type=general&search_action=detail&method=1&show_obsolete=F&sub_type=gene&SEARCH_EXACT=4&SEARCH_CONTAINS=1&name= | ||||||
| Worm - Caenorhabditis elegans WormBase gene_association.wb README | 14619 | 22246 | Protein Name Gene Name Gene Symbol | casy-1 B0034.3 cdh-11 WBGENE00000403 sample list | EXP(2) IDA(7838) IPI(4259) IMP(10404) IGI(4653) IEP(169) ISS(1910) ISO(1) ISM(9) RCA(13) TAS(173) NAS(180) IC(115) ND(430) IEA(67437) | |
| Default URL template: http://www.wormbase.org/db/gene/gene?name= | ||||||
| Zebrafish - Danio rerio ZFIN gene_association.zfin README | 25443 | 25849 | ZFIN_ID Gene Symbol | ZDB-GENE-030131-6506 mobkl1b sample list | IDA(4623) IPI(1220) IMP(19983) IGI(5466) IEP(154) ISS(7001) ISO(13) ISM(1) TAS(111) NAS(127) IC(119) ND(7290) IEA(127138) | |
| Default URL template: http://zfin.org/cgi-bin/webdriver?MIval=aa-markerview.apg&OID= | ||||||
Included in the above table are augmented association files which contain additional synonyms from other sources. These files and their sources are:
| Augmented Association File | Source of Additional Synonyms |
|---|---|
| goa_human_hgnc |
Human
Xrefs from EBI
Integr8 from EBI |
Please note that the additional synonyms may
result in greater ambiguity of terms.
For background and description of GO Term Mapper, please see the:
For background and description of GO-TermFinder, please see Boyle et al, Bioinformatics (2004)
Please cite the original manuscript for GO-TermFinder (the perl module with several supporting methods used by this tool):
"GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes." Boyle et al, Bioninformatics (2004)
which can be accessed at PubMed here.This tool uses map2slim, which should be referenced by the URL (http://search.cpan.org/~cmungall/go-perl) for go-perl and/or the paper:
"The Gene Ontology (GO) database and informatics resource." Harris et al, Nucleic Acids Res. (2004)
which can also be accessed at PubMed here.Please also include the URL for GOTermMapper or the Princeton GO home page:
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