Gene Ontology: Ontology Comparison Report
Files used:
- file 1 (old): go-2011-09-03.obo; date: 02:09:2011 15:07; CVS revision: 1.2232
- file 2 (new): go-2011-09-10.obo; date: 09:09:2011 11:25; CVS revision: 1.2244
New terms
Obsoletions
ID | name | namespace |
---|---|---|
GO:0035557 | intracellular signal transduction involved in cell surface receptor linked signaling
This term was made obsolete because the syntax of the term is incorrect. |
biological_process |
GO:0035558 | phosphatidylinositol 3-kinase cascade involved in insulin receptor signaling
Consider: GO:0038028 This term was made obsolete because the syntax of the term is incorrect. |
biological_process |
GO:0035559 | MAPKKK cascade involved in epidermal growth factor receptor signaling
Consider: GO:0038029 This term was made obsolete because the syntax of the term is incorrect. |
biological_process |
GO:0090412 | positive regulation of transcription from RNA polymerase II promoter involved in fatty acid biosynthetic process | biological_process |
GO:0090413 | negative regulation of transcription from RNA polymerase II promoter involved in fatty acid biosynthetic process | biological_process |
Term merges
Old ID | Old name | Merged into | Merged term name |
---|---|---|---|
GO:0034404 | nucleobase, nucleoside and nucleotide biosynthetic process | GO:0034654 | nucleobase-containing biosynthetic process |
GO:0034656 | nucleobase, nucleoside and nucleotide catabolic process | GO:0034655 | nucleobase-containing catabolic process |
GO:0055086 | nucleobase, nucleoside and nucleotide metabolic process | GO:0006139 | nucleobase-containing compound metabolic process |
Term changes
File 1 (02:09:2011 15:07, 1.2232) | File 2 (09:09:2011 11:25, 1.2244) |
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GO:0003179 : heart valve morphogenesis | |
---|---|
synonym "heart valve remodeling" NARROW [GOC:vk, GOC:yaf] "heart valve remodelling" NARROW [GOC:vk, GOC:yaf] |
GO:0004733 : pyridoxamine-phosphate oxidase activity | |
---|---|
relationship part_of GO:0042823 |
GO:0006139 : nucleobase-containing compound metabolic process | |
---|---|
name |
name nucleobase-containing compound metabolic process alt_id GO:0055086 synonym "nucleobase, nucleoside and nucleotide metabolic process" NARROW [] "nucleobase, nucleoside and nucleotide metabolism" NARROW [] "nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] xref Reactome:REACT_100770 "Metabolism of nucleotides, Plasmodium falciparum" Reactome:REACT_105851 "Metabolism of nucleotides, Schizosaccharomyces pombe" Reactome:REACT_107755 "Metabolism of nucleotides, Mycobacterium tuberculosis" Reactome:REACT_107894 "Metabolism of nucleotides, Rattus norvegicus" Reactome:REACT_1698 "Metabolism of nucleotides, Homo sapiens" Reactome:REACT_28046 "Metabolism of nucleotides, Drosophila melanogaster" Reactome:REACT_29205 "Metabolism of nucleotides, Dictyostelium discoideum" Reactome:REACT_29767 "Metabolism of nucleotides, Saccharomyces cerevisiae" Reactome:REACT_33967 "Metabolism of nucleotides, Mus musculus" Reactome:REACT_77113 "Metabolism of nucleotides, Taeniopygia guttata" Reactome:REACT_78257 "Metabolism of nucleotides, Staphylococcus aureus N315" Reactome:REACT_82673 "Metabolism of nucleotides, Caenorhabditis elegans" Reactome:REACT_82902 "Metabolism of nucleotides, Canis familiaris" Reactome:REACT_82978 "Metabolism of nucleotides, Escherichia coli" Reactome:REACT_83845 "Metabolism of nucleotides, Bos taurus" Reactome:REACT_86759 "Metabolism of nucleotides, Oryza sativa" Reactome:REACT_90371 "Metabolism of nucleotides, Sus scrofa" Reactome:REACT_90903 "Metabolism of nucleotides, Gallus gallus" Reactome:REACT_96600 "Metabolism of nucleotides, Danio rerio" Reactome:REACT_97332 "Metabolism of nucleotides, Arabidopsis thaliana" Reactome:REACT_99343 "Metabolism of nucleotides, Xenopus tropicalis" is_a GO:0044281 |
GO:0006753 : nucleoside phosphate metabolic process | |
---|---|
is_a |
is_a GO:0006139 |
GO:0006913 : nucleocytoplasmic transport | |
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comment Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane, and is not traversed. |
GO:0007219 : Notch signaling pathway | |
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def |
def The series of molecular signals initiated by binding of the receptor Notch to an extracellular ligand. |
GO:0007227 : signal transduction downstream of smoothened | |
---|---|
is_a |
is_a GO:0035556 |
GO:0008101 : decapentaplegic signaling pathway | |
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name def synonym |
name decapentaplegic signaling pathway def The series of molecular signals generated as a consequence of the signal decapentaplegic binding to one of its physiological receptors. synonym "decapentaplegic receptor signaling pathway" RELATED [GOC:bf, GOC:sart, GOC:signaling] "decapentaplegic receptor signalling pathway" RELATED [] "dpp receptor signaling pathway" RELATED [] "dpp receptor signalling pathway" RELATED [] "dpp signaling pathway" RELATED [GOC:bf] |
GO:0008293 : torso signaling pathway | |
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def |
def The series of molecular signals generated as a consequence of the transmembrane receptor tyrosine kinase torso binding to its physiological ligand. |
GO:0008615 : pyridoxine biosynthetic process | |
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xref |
GO:0008655 : pyrimidine-containing compound salvage | |
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is_a |
is_a GO:0034654 |
GO:0009034 : tryptophanase activity | |
---|---|
xref UniPathway:UPA00332 |
GO:0009112 : nucleobase metabolic process | |
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is_a |
is_a GO:0006139 |
GO:0009116 : nucleoside metabolic process | |
---|---|
is_a |
is_a GO:0006139 |
GO:0009163 : nucleoside biosynthetic process | |
---|---|
is_a |
is_a GO:0034654 |
GO:0009164 : nucleoside catabolic process | |
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is_a |
is_a GO:0034655 |
GO:0009165 : nucleotide biosynthetic process | |
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is_a |
is_a GO:0034654 |
GO:0009166 : nucleotide catabolic process | |
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is_a |
is_a GO:0034655 |
GO:0009443 : pyridoxal 5'-phosphate salvage | |
---|---|
is_a |
GO:0010144 : pyridoxal phosphate biosynthetic process from pyridoxamine | |
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is_a |
is_a GO:0009443 |
GO:0010678 : negative regulation of cellular carbohydrate metabolic process by negative regulation of transcription, DNA-dependent | |
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name |
name negative regulation of cellular carbohydrate metabolic process by negative regulation of transcription, DNA-dependent synonym "negative regulation of cellular carbohydrate metabolic process by repression of transcription" EXACT [GOC:bf, GOC:vw] intersection_of GO:0065007 negatively_regulates GO:0006351 negatively_regulates GO:0044262 |
GO:0015931 : nucleobase-containing compound transport | |
---|---|
name |
name nucleobase-containing compound transport synonym "nucleobase, nucleoside, nucleotide and nucleic acid transport" RELATED [GOC:dph, GOC:tb] |
GO:0015932 : nucleobase-containing compound transmembrane transporter activity | |
---|---|
name |
name nucleobase-containing compound transmembrane transporter activity synonym "nucleobase, nucleoside, nucleotide and nucleic acid transmembrane transporter activity" RELATED [GOC:dph, GOC:tb] |
GO:0015949 : nucleobase-containing compound interconversion | |
---|---|
name is_a |
name nucleobase-containing compound interconversion synonym "nucleobase, nucleoside and nucleotide interconversion" RELATED [GOC:dph, GOC:tb] is_a GO:0006139 |
GO:0017137 : Rab GTPase binding | |
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is_a |
GO:0019205 : nucleobase-containing compound kinase activity | |
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name |
name nucleobase-containing compound kinase activity synonym "nucleobase, nucleoside, nucleotide kinase activity" RELATED [GOC:dph, GOC:tb] |
GO:0019219 : regulation of nucleobase-containing compound metabolic process | |
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name |
name regulation of nucleobase-containing compound metabolic process synonym "regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] |
GO:0019221 : cytokine-mediated signaling pathway | |
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def |
def Any series of molecular signals generated as a consequence of a cytokine binding to a cell surface receptor. |
GO:0023035 : CD40 signaling pathway | |
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def |
def Any series of molecular signals generated as a consequence of the receptor CD40 binding to one of its physiological ligands. |
GO:0032239 : regulation of nucleobase-containing compound transport | |
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name |
name regulation of nucleobase-containing compound transport synonym "regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport" RELATED [GOC:dph, GOC:tb] |
GO:0032240 : negative regulation of nucleobase-containing compound transport | |
---|---|
name |
name negative regulation of nucleobase-containing compound transport synonym "negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport" RELATED [GOC:dph, GOC:tb] |
GO:0032241 : positive regulation of nucleobase-containing compound transport | |
---|---|
name |
name positive regulation of nucleobase-containing compound transport synonym "positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid transport" RELATED [GOC:dph, GOC:tb] |
GO:0033626 : positive regulation of integrin activation by cell surface receptor linked signal transduction | |
---|---|
name |
name positive regulation of integrin activation by cell surface receptor linked signal transduction synonym "cell surface receptor linked signal transduction leading to integrin activation" EXACT [GOC:bf, GOC:signaling] is_a GO:0033625 |
GO:0034654 : nucleobase-containing biosynthetic process | |
---|---|
name synonym |
name nucleobase-containing biosynthetic process alt_id GO:0034404 synonym "nucleobase, nucleoside and nucleotide anabolism" NARROW [] "nucleobase, nucleoside and nucleotide biosynthesis" NARROW [] "nucleobase, nucleoside and nucleotide biosynthetic process" NARROW [] "nucleobase, nucleoside and nucleotide formation" NARROW [] "nucleobase, nucleoside and nucleotide synthesis" NARROW [] "nucleobase, nucleoside, nucleotide and nucleic acid synthesis" NARROW [] is_a GO:0044283 |
GO:0034655 : nucleobase-containing catabolic process | |
---|---|
name |
name nucleobase-containing catabolic process alt_id GO:0034656 synonym "nucleobase, nucleoside and nucleotide breakdown" NARROW [] "nucleobase, nucleoside and nucleotide catabolic process" NARROW [] "nucleobase, nucleoside and nucleotide catabolism" NARROW [] "nucleobase, nucleoside and nucleotide degradation" NARROW [] "nucleobase, nucleoside, nucleotide and nucleic acid catabolic process" RELATED [GOC:dph, GOC:tb] is_a GO:0044282 |
GO:0035557 : intracellular signal transduction involved in cell surface receptor linked signaling | |
---|---|
def is_a relationship |
def OBSOLETE. The process in which a signal is passed on from a receptor at the cell surface to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. comment This term was made obsolete because the syntax of the term is incorrect. is_obsolete true |
GO:0035558 : phosphatidylinositol 3-kinase cascade involved in insulin receptor signaling | |
---|---|
def is_a relationship |
def OBSOLETE. The process in which a signal is passed from the insulin receptor to components of the phosphatidylinositol 3-kinase (PI3K) cascade, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. comment This term was made obsolete because the syntax of the term is incorrect. is_obsolete true consider GO:0038028 |
GO:0035559 : MAPKKK cascade involved in epidermal growth factor receptor signaling | |
---|---|
def is_a relationship |
def OBSOLETE. The process in which a signal is passed from the epidermal growth factor receptor (EGFR) to components of the MAPKKK cascade, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell. comment This term was made obsolete because the syntax of the term is incorrect. is_obsolete true consider GO:0038029 |
GO:0038027 : apolipoprotein A-I-mediated signaling pathway | |
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def |
def Any series of molecular signals initiated by the binding of apolipoprotein A-I to a cell surface receptor. |
GO:0042819 : vitamin B6 biosynthetic process | |
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synonym "pyridoxine-5'-phosphate biosynthesis" RELATED [GOC:yaf, UniPathway:UPA00244] |
GO:0042823 : pyridoxal phosphate biosynthetic process | |
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xref MetaCyc:PWY0-845 |
GO:0043101 : purine-containing compound salvage | |
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is_a |
is_a GO:0034654 |
GO:0043281 : regulation of cysteine-type endopeptidase activity involved in apoptotic process | |
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name def is_a |
name regulation of cysteine-type endopeptidase activity involved in apoptotic process def Any process that modulates the activity of a cysteine-type endopeptidase involved in apoptosis. synonym "regulation of caspase activity" BROAD [] is_a GO:2000116 intersection_of GO:2000116 part_of GO:0006915 relationship part_of GO:0006915 |
GO:0045500 : sevenless signaling pathway | |
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def |
def The series of molecular signals generated as a consequence of the receptor sevenless binding to one of its physiological ligands. |
GO:0045934 : negative regulation of nucleobase-containing compound metabolic process | |
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name |
name negative regulation of nucleobase-containing compound metabolic process synonym "negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] |
GO:0045935 : positive regulation of nucleobase-containing compound metabolic process | |
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name |
name positive regulation of nucleobase-containing compound metabolic process synonym "positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] |
GO:0046112 : nucleobase biosynthetic process | |
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is_a |
is_a GO:0034654 |
GO:0046113 : nucleobase catabolic process | |
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is_a |
is_a GO:0034655 |
GO:0055085 : transmembrane transport | |
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comment Transmembrane transport requires transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. |
GO:0070120 : ciliary neurotrophic factor-mediated signaling pathway | |
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def |
def A series of molecular signals generated as a consequence of a ciliary neurotrophic factor binding to a cell surface receptor. |
GO:0071847 : TNFSF11-mediated signaling pathway | |
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GO:0090097 : regulation of decapentaplegic signaling pathway | |
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name def |
name regulation of decapentaplegic signaling pathway def Any process that modulates the frequency, rate, or extent of the decapentaplegic signaling pathway. The decapentaplegic signaling pathway is the series of molecular signals generated as a consequence of the signal decapentaplegic binding to one of its physiological receptors. synonym "regulation of decapentaplegic receptor signaling pathway" EXACT [GOC:bf] |
GO:0090098 : positive regulation of decapentaplegic signaling pathway | |
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name def |
name positive regulation of decapentaplegic signaling pathway def Any process that increases the frequency, rate, or extent of the decapentaplegic signaling pathway. The decapentaplegic signaling pathway is the series of molecular signals generated as a consequence of the signal decapentaplegic binding to one of its physiological receptors. synonym "positive regulation of decapentaplegic receptor signaling pathway" EXACT [GOC:bf] |
GO:0090099 : negative regulation of decapentaplegic signaling pathway | |
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name def |
name negative regulation of decapentaplegic signaling pathway def Any process that decreases the frequency, rate, or extent of the decapentaplegic signaling pathway. The decapentaplegic signaling pathway is the series of molecular signals generated as a consequence of the signal decapentaplegic binding to one of its physiological receptors. synonym "negative regulation of decapentaplegic receptor signaling pathway" EXACT [GOC:bf] |
GO:0090412 : positive regulation of transcription from RNA polymerase II promoter involved in fatty acid biosynthetic process | |
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is_a intersection_of relationship |
is_obsolete true |
GO:0090413 : negative regulation of transcription from RNA polymerase II promoter involved in fatty acid biosynthetic process | |
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is_a intersection_of relationship |
is_obsolete true |
GO:0097103 : endothelial stalk cell fate specification | |
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GO:2000001 : regulation of DNA damage checkpoint | |
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subset |
GO:2000002 : negative regulation of DNA damage checkpoint | |
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subset |
GO:2000003 : positive regulation of DNA damage checkpoint | |
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subset |
GO:2000015 : regulation of determination of dorsal identity | |
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subset |
GO:2000016 : negative regulation of determination of dorsal identity | |
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subset |
GO:2000017 : positive regulation of determination of dorsal identity | |
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subset |
GO:2000018 : regulation of male gonad development | |
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subset |
GO:2000019 : negative regulation of male gonad development | |
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subset |
GO:2000020 : positive regulation of male gonad development | |
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subset |
GO:2000531 : regulation of fatty acid biosynthetic process by regulation of transcription from RNA polymerase II promoter | |
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name def synonym intersection_of relationship |
name regulation of fatty acid biosynthetic process by regulation of transcription from RNA polymerase II promoter def Any process that modulates the frequency, rate or extent of the biosynthesis of fatty acids, by modulating the frequency, rate or extent of transcription from an RNA polymerase II promoter. is_a GO:0042304 |
File Stats
Ontology | Old file | New file | Change |
---|---|---|---|
molecular function |
9062 9062 (100.0%) defined |
9063 9063 (100.0%) defined |
+1 |
cellular component |
2895 2895 (100.0%) defined |
2896 2896 (100.0%) defined |
+1 |
biological process |
21387 21387 (100.0%) defined |
21396 21396 (100.0%) defined |
+9 |
Obsolete | 1575 (4.5% of total) |
1580 (4.5% of total) |
+5 (+0.3%) |
Totals |
33344 33344 (100.0%) defined 34919 inc. obsoletes |
33355 33355 (100.0%) defined 34935 inc. obsoletes |
+16 (0.0%) |