Princeton University
Lewis-Sigler Institute for Integrative Genomics

HELP: GENERIC GENE ONTOLOGY (GO) TERM MAPPER

Our GO Tools: Generic GO Term Finder | Generic GO Term Mapper


Contents


Description:

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.



File Tables

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 FilesVersion
gene_ontology.obo 01/26/2020
GO Term Mapper Ontology FilesVersion
goslim_generic.obo
goslim_yeast.obo
goslim_pombe.obo
goslim_plant.obo
goslim_chembl.obo
goslim_goa.obo1.854 10/19/2010


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
2778Systematic_ID
Systematic_ID
L302.10
L2256.04
LM5.39
sample list
EXP(61) IDA(230) IPI(46) IMP(123) IGI(27) IEP(2) ISS(164) ISO(5105) ISA(200) ISM(184) IGC(1) RCA(53) TAS(8) IC(5)
Malaria parasite - Plasmodium falciparum
P. falciparum GeneDB
gene_association.GeneDB_Pfalciparum
README
23705400Systematic Name
Systematic Name
PFL1830w
2277.t00366
PFL1830W
sample list
EXP(10) IDA(1890) IPI(122) IMP(32) IGI(17) IEP(5) ISS(2739) ISO(137) ISM(42) IGC(5) RCA(420) TAS(759) NAS(14) IC(56) ND(2)
Default URL template: http://www.genedb.org/genedb/Search?organism=malaria&name=
Trypanosome - Tryanosoma brucei
T. brucei GeneDB
gene_association.GeneDB_Tbrucei
README
6362Systematic Name
Gene Name
Gene Synonym
Tb927.7.4670
RRP4
TB927.7.4670
sample list
EXP(123) IDA(10016) IPI(517) IMP(794) IGI(42) IEP(14) ISS(492) ISO(476) ISA(995) ISM(3606) RCA(1145) TAS(589) NAS(4) IC(50)
Default URL template: http://www.genedb.org/genedb/Search?organism=tryp&name=
Candida - Candida albicans
CGD
gene_association.cgd
README
60197CGD_ID
Standard Name
Systematic name
CAL0004982
CaO19.6783
CA5922
Contig4-2621_0008
orf6.8848
sample list
IDA(2617) IPI(68) IMP(5897) IGI(925) IEP(46) ISS(1886) ISO(349) ISA(170) ISM(1328) TAS(48) NAS(174) IC(35) ND(16041) IEA(327870)
Default URL template: http://www.candidagenome.org/cgi-bin/locus.pl?locus=
Slime mold - Dictyostelium discoideum
DictyBase
gene_association.dictyBase
941812098DictyBase_ID
Gene Name
Alias
DdP2X
DDB_G0272004
p2xA
sample list
IDA(3624) IPI(929) IMP(2826) IGI(532) IEP(207) ISS(3423) IGC(80) TAS(419) NAS(6) IC(148) ND(6350) IEA(40190)
Default URL template: http://dictybase.org/db/cgi-bin/dictyBase/locus.pl?locus=
Fruit fly - Drosophila melanogaster
FlyBase
gene_association.fb
README
1440916085FlyBase_ID
Gene Symbol
Gene Synonym
FBGN0031491
alpha4GT1
4-N-acetylgalactosaminyltransferase-1
CG17223
alpha1
sample list
IDA(16592) IPI(3561) IMP(23151) IGI(3610) IEP(716) ISS(11227) ISO(2) ISA(138) ISM(2895) IGC(29) TAS(3615) NAS(1860) IC(1243) ND(8064) IEA(8668)
Default URL template: http://flybase.bio.indiana.edu/.bin/fbidq.html?
Bacterium coli - Escherichia coli
GOA @EBI
gene_association.goa_Ecoli
README
71877187UniProt_Accession (or Ensembl_ID)
UniProt_ID (or Ensembl_ID)
International Protein Index
A3QXC6
A3QXC6_ECOLX
sample list
IDA(10) IPI(140) IEA(45310)
Chicken - Gallus gallus
GOA @EBI
gene_association.goa_chicken
README
1946930837UniProt_Accession (or Ensembl_ID)
UniProt_ID (or Ensembl_ID)
International Protein Index
FGB
IPI00588322
FIBB_CHICK
Q02020
sample list
EXP(3) IDA(1979) IPI(470) IMP(815) IGI(16) IEP(223) ISS(5641) ISO(36) ISA(583) ISM(22) RCA(11) TAS(693) NAS(138) IC(20) ND(64) IEA(99893)
Cow - Bos taurus
GOA @EBI
gene_association.goa_cow
README
2028137225UniProt_Accession (or Ensembl_ID)
UniProt_ID (or Ensembl_ID)
International Protein Index
FGG
P12799
IPI00699860
FIBG_BOVIN
sample list
EXP(4) IDA(1590) IPI(590) IMP(251) IGI(1) IEP(5) ISS(18060) ISA(151) RCA(2) TAS(677) NAS(55) IC(11) ND(103) IEA(123367)
Human - Homo sapiens
GOA @EBI
gene_association.goa_human
README
19693UniProt_Accession (or Ensembl_ID)
UniProt_ID (or Ensembl_ID)
International Protein Index
TGFR1_HUMAN
IPI00005733
P36897
TGFBR1
sample list
EXP(457) IDA(75787) IPI(99083) IMP(22102) IGI(1700) IEP(898) ISS(24792) ISO(7) ISA(1487) ISM(757) RCA(458) TAS(104186) NAS(8070) IC(1401) ND(1803) IEA(77918)
Default URL template: http://www.ensembl.org/Homo_sapiens/geneview?gene=
Human - Homo sapiens
GOA @EBI + Ensembl
gene_association.goa_human_ensembl
README
19499UniProt_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(1271) IDA(70458) IPI(90026) IMP(19988) IGI(1469) IEP(893) ISS(21741) ISA(2) ISM(1) TAS(107837) NAS(7482) IC(1410) ND(1885) IEA(81176)
Default URL template: http://www.ensembl.org/Homo_sapiens/geneview?gene=
Human - Homo sapiens
GOA @EBI + XREFs
gene_association.goa_human_hgnc
README
19663UniProt_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(1273) IDA(70998) IPI(97274) IMP(20223) IGI(1533) IEP(900) ISS(22483) ISO(8) ISA(1449) ISM(769) TAS(104438) NAS(8120) IC(1417) ND(1874) IEA(80560)
Default URL template: http://www.genenames.org/data/hgnc_data.php?hgnc_id=
Rice - Oryza sativa
Gramene
gene_association.gramene_oryza
README
4114241521Swiss-Prot/TrEMBL_ID
Gene Name/Symbol
O04138
LOC_Os04g41620
PR-3 CLASS IV CHITINASE
Os04g0493400
CHT4
sample list
IDA(122) IPI(6) IMP(151) IGI(44) IEP(65) ISS(374) RCA(46617) TAS(13) IC(2572)
Default URL template: http://www.gramene.org/perl/protein_search?acc=
Bacillus anthracis
gene_association.jcvi_Banthracis (1.47 03/18/2011)
README
52805507JCVI Locus Name
Gene Symbol
dnaN-2
BA_2684
sample list
IDA(3) IMP(2) ISS(5955) TAS(15) NAS(4) ND(7054)
Coxiella burnetii
gene_association.jcvi_Cburnetii (1.39 03/18/2011)
README
20332095JCVI Locus Name
Gene Symbol
CBU1815
CBU0002
sample list
ISS(2148) TAS(2) ND(2984)
Campylobacter jejuni
gene_association.jcvi_Cjejuni (1.40 03/18/2011)
README
1829flaB
CJE_1526
sample list
IDA(1) IMP(15) IGI(15) ISS(2577) TAS(1) ND(1985)
Dehalococcoides ethenogenes
gene_association.jcvi_Dethenogenes (1.30 03/18/2011)
1584DET_0079
tceA
sample list
ISS(2139) TAS(4) ND(1780)
Geobacter - Geobacter sulfurreducens PCA
gene_association.jcvi_Gsulfurreducens (1.39 03/18/2011)
README
34103533JCVI Locus Name
Gene Symbol
GSU_0001
dnaN
sample list
IDA(4) ISS(4148) TAS(2) NAS(8) ND(3988)
Listeria monocytogenes
gene_association.jcvi_Lmonocytogenes (1.46 03/18/2011)
README
2822LMOF2365_1337
polC
LMOf2365_1337
sample list
IMP(2) ISS(4198) TAS(9) ND(2963)
Methylococcus capsulatus
gene_association.jcvi_Mcapsulatus (1.41 03/18/2011)
README
2925MCA_1120
sample list
IDA(2) ISS(3981) TAS(8) ND(3250)
Pseudomonas syringae
gene_association.jcvi_Psyringae (1.48 03/18/2011)
README
40125763JCVI Locus Name
Gene Symbol
flgI
PSPTO_1942
sample list
IDA(377) IPI(20) IMP(7) IGI(22) IEP(3) ISS(4348) IGC(31) TAS(41) IC(45) ND(5401)
Shewanella oneidensis
gene_association.jcvi_Soneidensis (1.45 03/18/2011)
README
48424843JCVI Locus Name
Gene Symbol
H
SO_2953
sample list
IMP(5) ISS(5253) TAS(48) ND(6813)
Silicibacter pomeroyi
gene_association.jcvi_Spomeroyi (1.41 03/18/2011)
README
4252SPO_3786
sample list
IDA(2) ISS(6618) TAS(117) NAS(2) IC(15) ND(3974)
Cholera spirillum - Vibrio cholerae
gene_association.jcvi_Vcholerae (1.48 03/18/2011)
README
38583885JCVI Locus Name
Gene Symbol
holB
VC_2015
sample list
IDA(6) IMP(11) IGI(28) ISS(4266) ND(5078)
Mouse - Mus musculus
MGI
gene_association.mgi
README
24765MGI_ID
Gene Symbol
Gene_Symbol (old)
P2ry12
MGI:1918089
P2Y12
sample list
EXP(341) IDA(52246) IPI(16827) IMP(43918) IGI(9169) IEP(1539) ISS(1793) ISO(123961) ISA(4699) ISM(25) RCA(306) TAS(2915) NAS(644) IC(544) ND(17584) IEA(74920)
Default URL template: http://www.informatics.jax.org/searches/accession_report.cgi?id=
Yeast - Schizosaccharomyces pombe
PomBase
gene_association.pombase (11/25/2011)
README
5399Systematic Name
Gene Name
Gene Synonym
SPCC191.07
cyc1
sample list
EXP(784) IDA(7502) IPI(2745) IMP(4759) IGI(838) IEP(27) ISS(1459) ISO(5187) ISM(1547) TAS(396) NAS(733) IC(1774) ND(2221) IEA(3382)
Default URL template: http://www.pombase.org/gene/
Pseudomonas - Pseudomonas aeruginosa PAO1
PseudoCAP
gene_association.pseudocap
1538PA#
Gene Name
Alt. Gene Name (opt.)
fliD
PA1094
hook-associated protein
sample list
EXP(48) IDA(950) IPI(42) IMP(1225) IGI(66) IEP(13) ISS(1256) ISO(14) ISA(10) IGC(49) TAS(11) NAS(18) IEA(14)
Default URL template: http://www.pseudomonas.com/AnnotationByPAU.asp?PA=
Rat - Rattus norvegicus
RGD
gene_association.rgd
README
21201RGD_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(316) IDA(30460) IPI(7839) IMP(9724) IGI(329) IEP(10548) ISS(24089) ISO(207102) TAS(3451) NAS(633) IC(215) ND(6597) IEA(130636)
Default URL template: http://rgd.mcw.edu/tools/genes/genes_view.cgi?id=
Yeast - Saccharomyces cerevisiae
SGD
gene_association.sgd
README
64397166SGD_ID
Gene Name
Systematic ORF Name
YJL166W
S000003702
COR5
QCR8
sample list
IDA(17237) IPI(2587) IMP(13788) IGI(5286) IEP(36) ISS(1142) ISO(7) ISA(316) ISM(446) TAS(366) NAS(75) IC(1422) ND(3672) IEA(51039)
Default URL template: http://www.yeastgenome.org/locus/
Common wallcress - Arabidopsis thaliana
TAIR
gene_association.tair
README
32973TAIR Accession
Gene Name
Gene Alias
AT4G31210
AT4G31210.1
LOCUS:2128101
F8F16.30
F8F16_30
sample list
IDA(35780) IPI(17542) IMP(15281) IGI(3683) IEP(4941) ISS(6798) ISM(37756) RCA(3) TAS(6745) NAS(749) IC(212) ND(21984) IEA(37723)
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
1426022246Protein Name
Gene Name
Gene Symbol
casy-1
B0034.3
cdh-11
WBGENE00000403
sample list
EXP(6) IDA(7321) IPI(3924) IMP(9079) IGI(4603) IEP(171) ISS(1847) ISO(1) ISM(9) TAS(181) NAS(182) IC(112) ND(407) IEA(64972)
Default URL template: http://www.wormbase.org/db/gene/gene?name=
Zebrafish - Danio rerio
ZFIN
gene_association.zfin
README
2448822409ZFIN_ID
Gene Symbol
ZDB-GENE-030131-6506
mobkl1b
sample list
IDA(3791) IPI(901) IMP(16226) IGI(4849) IEP(154) ISS(6303) ISO(10) TAS(46) NAS(129) IC(83) ND(6420) IEA(127799)
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.
 


Help Resources

For background and description of GO Term Mapper, please see the:



References

For background and description of GO-TermFinder, please see Boyle et al, Bioinformatics (2004)


Citation

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:



Please send comments or questions to gotools@genomics.princeton.edu
.