Review annotations to 'integral to membrane' terms - Githubissues

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Review annotations to 'integral to membrane' terms #4187

Closed pgaudet closed 1 year ago

pgaudet commented 2 years ago

Hello,

The proposal has been made to obsolete membrane terms that describe protein topology, starting with 'integral to the membrane' terms, see https://github.com/geneontology/go-ontology/issues/23424

There are 3200 EXP annotations, see https://docs.google.com/spreadsheets/d/1wo9rjPeNi5yYwmzJnoq3SvHpu2VPxygIwoF3A0J3nyE/edit#gid=0

Counts by group and by term are shown below. If you agree with the REPLACED BY term as described in the ontolgy ticket (https://github.com/geneontology/go-ontology/issues/23424), and that your annotation tool handles automatic replacement, there is no action needed. Otherwise, please update your annotations.

Term ID | Term label | group | count | obsolete + replace by -- | -- | -- | -- | -- GO:0016021 | integral component of membrane | AgBase | 9 | membrane GO:0005887 | integral component of plasma membrane | AgBase | 7 | plasma membrane GO:0031307 | integral component of mitochondrial outer membrane | AgBase | 1 | mitochondrial outer membrane GO:0032592 | integral component of mitochondrial membrane | AgBase | 1 | mitochondrial membrane GO:0005887 | integral component of plasma membrane | ARUK-UCL | 5 | plasma membrane GO:0016021 | integral component of membrane | ARUK-UCL | 1 | membrane GO:0016021 | integral component of membrane | AspGD | 1 | membrane GO:0005887 | integral component of plasma membrane | BHF-UCL | 39 | plasma membrane GO:0016021 | integral component of membrane | BHF-UCL | 22 | membrane GO:0030176 | integral component of endoplasmic reticulum membrane | BHF-UCL | 4 | endoplasmic reticulum membrane GO:0031305 | integral component of mitochondrial inner membrane | BHF-UCL | 3 | mitochondrial inner membrane GO:0005779 | integral component of peroxisomal membrane | BHF-UCL | 2 | peroxisomal membrane GO:0031307 | integral component of mitochondrial outer membrane | BHF-UCL | 2 | mitochondrial outer membrane GO:0099055 | integral component of postsynaptic membrane | BHF-UCL | 2 | postsynaptic membrane GO:0099060 | integral component of postsynaptic specialization membrane | BHF-UCL | 2 | postsynaptic specialization membrane GO:0031301 | integral component of organelle membrane | BHF-UCL | 1 | organelle membrane GO:0032592 | integral component of mitochondrial membrane | BHF-UCL | 1 | mitochondrial membrane GO:0071458 | integral component of cytoplasmic side of endoplasmic reticulum membrane | BHF-UCL | 1 | cytoplasmic side of endoplasmic reticulum membrane GO:0071556 | integral component of lumenal side of endoplasmic reticulum membrane | BHF-UCL | 1 | lumenal side of endoplasmic reticulum membrane GO:0016021 | integral component of membrane | CACAO | 4 | membrane GO:0031303 | integral component of endosome membrane | CACAO | 4 | endosome membrane GO:0031307 | integral component of mitochondrial outer membrane | CACAO | 2 | mitochondrial outer membrane GO:0045203 | integral component of cell outer membrane | CACAO | 1 | cell outer membrane GO:0005887 | integral component of plasma membrane | CAFA | 8 | plasma membrane GO:0016021 | integral component of membrane | CAFA | 5 | membrane GO:0016021 | integral component of membrane | CGD | 6 | membrane GO:0005887 | integral component of plasma membrane | CGD | 4 | plasma membrane GO:0016021 | integral component of membrane | ComplexPortal | 20 | membrane GO:0005887 | integral component of plasma membrane | ComplexPortal | 18 | plasma membrane GO:0031305 | integral component of mitochondrial inner membrane | ComplexPortal | 9 | mitochondrial inner membrane GO:0030176 | integral component of endoplasmic reticulum membrane | ComplexPortal | 6 | endoplasmic reticulum membrane GO:0032592 | integral component of mitochondrial membrane | ComplexPortal | 3 | mitochondrial membrane GO:0031307 | integral component of mitochondrial outer membrane | ComplexPortal | 2 | mitochondrial outer membrane GO:0030173 | integral component of Golgi membrane | ComplexPortal | 1 | Golgi membrane GO:0031166 | integral component of vacuolar membrane | ComplexPortal | 1 | vacuolar membrane GO:1905103 | integral component of lysosomal membrane | ComplexPortal | 1 | lysosomal membrane GO:0005887 | integral component of plasma membrane | dictyBase | 7 | plasma membrane GO:0016021 | integral component of membrane | dictyBase | 3 | membrane GO:0030176 | integral component of endoplasmic reticulum membrane | dictyBase | 2 | endoplasmic reticulum membrane GO:0005887 | integral component of plasma membrane | EcoCyc | 155 | plasma membrane GO:0016021 | integral component of membrane | EcoCyc | 21 | membrane GO:0045203 | integral component of cell outer membrane | EcoCyc | 17 | cell outer membrane GO:0071575 | integral component of external side of plasma membrane | EcoCyc | 11 | external side of plasma membrane GO:1990914 | integral component of periplasmic side of plasma membrane | EcoCyc | 1 | periplasmic side of plasma membrane GO:0005887 | integral component of plasma membrane | EcoliWiki | 33 | plasma membrane GO:0016021 | integral component of membrane | EcoliWiki | 29 | membrane GO:0045203 | integral component of cell outer membrane | EcoliWiki | 4 | cell outer membrane GO:0071575 | integral component of external side of plasma membrane | EcoliWiki | 1 | external side of plasma membrane GO:0005887 | integral component of plasma membrane | FlyBase | 131 | plasma membrane GO:0016021 | integral component of membrane | FlyBase | 53 | membrane GO:0030176 | integral component of endoplasmic reticulum membrane | FlyBase | 10 | endoplasmic reticulum membrane GO:0030173 | integral component of Golgi membrane | FlyBase | 5 | Golgi membrane GO:0090740 | integral component of pigment granule membrane | FlyBase | 2 | pigment granule membrane GO:0005639 | integral component of nuclear inner membrane | FlyBase | 1 | nuclear inner membrane GO:0030285 | integral component of synaptic vesicle membrane | FlyBase | 1 | synaptic vesicle membrane GO:0031301 | integral component of organelle membrane | FlyBase | 1 | organelle membrane GO:0031303 | integral component of endosome membrane | FlyBase | 1 | endosome membrane GO:0031305 | integral component of mitochondrial inner membrane | FlyBase | 1 | mitochondrial inner membrane GO:0031309 | integral component of nuclear outer membrane | FlyBase | 1 | nuclear outer membrane GO:0099055 | integral component of postsynaptic membrane | FlyBase | 1 | postsynaptic membrane GO:0099056 | integral component of presynaptic membrane | FlyBase | 1 | presynaptic membrane GO:0099061 | integral component of postsynaptic density membrane | FlyBase | 1 | postsynaptic density membrane GO:1905103 | integral component of lysosomal membrane | FlyBase | 1 | lysosomal membrane GO:0016021 | integral component of membrane | GeneDB | 33 | membrane GO:0005887 | integral component of plasma membrane | GeneDB | 9 | plasma membrane GO:0030176 | integral component of endoplasmic reticulum membrane | GeneDB | 4 | endoplasmic reticulum membrane GO:0031307 | integral component of mitochondrial outer membrane | GeneDB | 3 | mitochondrial outer membrane GO:0030173 | integral component of Golgi membrane | GeneDB | 1 | Golgi membrane GO:0031305 | integral component of mitochondrial inner membrane | GeneDB | 1 | mitochondrial inner membrane GO:0031353 | integral component of plastid inner membrane | GeneDB | 1 | plastid inner membrane GO:0031355 | integral component of plastid outer membrane | GeneDB | 1 | plastid outer membrane GO:0016021 | integral component of membrane | GO_Central | 2 | membrane GO:0005887 | integral component of plasma membrane | GO_Central | 1 | plasma membrane GO:0030176 | integral component of endoplasmic reticulum membrane | GO_Central | 1 | endoplasmic reticulum membrane GO:0016021 | integral component of membrane | HGNC-UCL | 11 | membrane GO:0005887 | integral component of plasma membrane | HGNC-UCL | 10 | plasma membrane GO:0030176 | integral component of endoplasmic reticulum membrane | HGNC-UCL | 1 | endoplasmic reticulum membrane GO:0005639 | integral component of nuclear inner membrane | JaponicusDB | 3 | nuclear inner membrane GO:0005887 | integral component of plasma membrane | MGI | 82 | plasma membrane GO:0016021 | integral component of membrane | MGI | 65 | membrane GO:0030176 | integral component of endoplasmic reticulum membrane | MGI | 5 | endoplasmic reticulum membrane GO:0005639 | integral component of nuclear inner membrane | MGI | 3 | nuclear inner membrane GO:0005779 | integral component of peroxisomal membrane | MGI | 1 | peroxisomal membrane GO:0030285 | integral component of synaptic vesicle membrane | MGI | 1 | synaptic vesicle membrane GO:0031301 | integral component of organelle membrane | MGI | 1 | organelle membrane GO:0031307 | integral component of mitochondrial outer membrane | MGI | 1 | mitochondrial outer membrane GO:0032592 | integral component of mitochondrial membrane | MGI | 1 | mitochondrial membrane GO:0099061 | integral component of postsynaptic density membrane | MGI | 1 | postsynaptic density membrane GO:0005887 | integral component of plasma membrane | MTBBASE | 101 | plasma membrane GO:0016021 | integral component of membrane | MTBBASE | 1 | membrane GO:0016021 | integral component of membrane | ParkinsonsUK-UCL | 3 | membrane GO:0005887 | integral component of plasma membrane | ParkinsonsUK-UCL | 2 | plasma membrane GO:0030176 | integral component of endoplasmic reticulum membrane | ParkinsonsUK-UCL | 1 | endoplasmic reticulum membrane GO:0031307 | integral component of mitochondrial outer membrane | ParkinsonsUK-UCL | 1 | mitochondrial outer membrane GO:0097637 | integral component of autophagosome membrane | ParkinsonsUK-UCL | 1 | autophagosome membrane GO:1905103 | integral component of lysosomal membrane | ParkinsonsUK-UCL | 1 | lysosomal membrane GO:0005887 | integral component of plasma membrane | PomBase | 10 | plasma membrane GO:0016021 | integral component of membrane | PomBase | 9 | membrane GO:0005639 | integral component of nuclear inner membrane | PomBase | 3 | nuclear inner membrane GO:0071627 | integral component of fungal-type vacuolar membrane | PomBase | 3 | fungal-type vacuolar membrane GO:0030176 | integral component of endoplasmic reticulum membrane | PomBase | 2 | endoplasmic reticulum membrane GO:0031307 | integral component of mitochondrial outer membrane | PomBase | 2 | mitochondrial outer membrane GO:0030173 | integral component of Golgi membrane | PomBase | 1 | Golgi membrane GO:0031305 | integral component of mitochondrial inner membrane | PomBase | 1 | mitochondrial inner membrane GO:0031309 | integral component of nuclear outer membrane | PomBase | 1 | nuclear outer membrane GO:0016021 | integral component of membrane | PseudoCAP | 5 | membrane GO:0016021 | integral component of membrane | RGD | 49 | membrane GO:0005887 | integral component of plasma membrane | RGD | 22 | plasma membrane GO:0031307 | integral component of mitochondrial outer membrane | RGD | 3 | mitochondrial outer membrane GO:0030176 | integral component of endoplasmic reticulum membrane | RGD | 2 | endoplasmic reticulum membrane GO:0031305 | integral component of mitochondrial inner membrane | RGD | 2 | mitochondrial inner membrane GO:0005639 | integral component of nuclear inner membrane | RGD | 1 | nuclear inner membrane GO:0030173 | integral component of Golgi membrane | RGD | 1 | Golgi membrane GO:0030176 | integral component of endoplasmic reticulum membrane | SGD | 53 | endoplasmic reticulum membrane GO:0016021 | integral component of membrane | SGD | 44 | membrane GO:0031305 | integral component of mitochondrial inner membrane | SGD | 28 | mitochondrial inner membrane GO:0005887 | integral component of plasma membrane | SGD | 26 | plasma membrane GO:0031307 | integral component of mitochondrial outer membrane | SGD | 25 | mitochondrial outer membrane GO:0030173 | integral component of Golgi membrane | SGD | 21 | Golgi membrane GO:0005779 | integral component of peroxisomal membrane | SGD | 11 | peroxisomal membrane GO:0032592 | integral component of mitochondrial membrane | SGD | 8 | mitochondrial membrane GO:0071627 | integral component of fungal-type vacuolar membrane | SGD | 5 | fungal-type vacuolar membrane GO:0005639 | integral component of nuclear inner membrane | SGD | 2 | nuclear inner membrane GO:0031166 | integral component of vacuolar membrane | SGD | 1 | vacuolar membrane GO:0031303 | integral component of endosome membrane | SGD | 1 | endosome membrane GO:0031309 | integral component of nuclear outer membrane | SGD | 1 | nuclear outer membrane GO:0071458 | integral component of cytoplasmic side of endoplasmic reticulum membrane | SGD | 1 | cytoplasmic side of endoplasmic reticulum membrane GO:0016021 | integral component of membrane | SGN | 5 | membrane GO:0099056 | integral component of presynaptic membrane | SynGO | 171 | presynaptic membrane GO:0099055 | integral component of postsynaptic membrane | SynGO | 134 | postsynaptic membrane GO:0099061 | integral component of postsynaptic density membrane | SynGO | 134 | postsynaptic density membrane GO:0030285 | integral component of synaptic vesicle membrane | SynGO | 97 | synaptic vesicle membrane GO:0099060 | integral component of postsynaptic specialization membrane | SynGO | 61 | postsynaptic specialization membrane GO:0099059 | integral component of presynaptic active zone membrane | SynGO | 43 | presynaptic active zone membrane GO:0099699 | integral component of synaptic membrane | SynGO | 15 | synaptic membrane GO:0099066 | integral component of neuronal dense core vesicle membrane | SynGO | 8 | neuronal dense core vesicle membrane GO:0030176 | integral component of endoplasmic reticulum membrane | SynGO | 5 | endoplasmic reticulum membrane GO:0032592 | integral component of mitochondrial membrane | SynGO | 3 | mitochondrial membrane GO:0099065 | integral component of spine apparatus membrane | SynGO | 2 | spine apparatus membrane GO:0099067 | integral component of presynaptic endosome membrane | SynGO | 1 | presynaptic endosome membrane GO:0099055 | integral component of postsynaptic membrane | SynGO-UCL | 4 | postsynaptic membrane GO:0099056 | integral component of presynaptic membrane | SynGO-UCL | 4 | presynaptic membrane GO:0005887 | integral component of plasma membrane | SynGO-UCL | 1 | plasma membrane GO:0030176 | integral component of endoplasmic reticulum membrane | SynGO-UCL | 1 | endoplasmic reticulum membrane GO:0031307 | integral component of mitochondrial outer membrane | TAIR | 13 | mitochondrial outer membrane GO:0016021 | integral component of membrane | TAIR | 11 | membrane GO:0031359 | integral component of chloroplast outer membrane | TAIR | 8 | chloroplast outer membrane GO:0005779 | integral component of peroxisomal membrane | TAIR | 5 | peroxisomal membrane GO:0030176 | integral component of endoplasmic reticulum membrane | TAIR | 5 | endoplasmic reticulum membrane GO:0005887 | integral component of plasma membrane | TAIR | 3 | plasma membrane GO:0030173 | integral component of Golgi membrane | TAIR | 2 | Golgi membrane GO:0031351 | integral component of plastid membrane | TAIR | 2 | plastid membrane GO:0031357 | integral component of chloroplast inner membrane | TAIR | 2 | chloroplast inner membrane GO:0031303 | integral component of endosome membrane | TAIR | 1 | endosome membrane GO:0031361 | integral component of thylakoid membrane | TAIR | 1 | thylakoid membrane GO:0032592 | integral component of mitochondrial membrane | TAIR | 1 | mitochondrial membrane GO:0005887 | integral component of plasma membrane | TIGR | 1 | plasma membrane GO:0016021 | integral component of membrane | TIGR | 1 | membrane GO:0030176 | integral component of endoplasmic reticulum membrane | TIGR | 1 | endoplasmic reticulum membrane GO:0005887 | integral component of plasma membrane | UniProt | 543 | plasma membrane GO:0016021 | integral component of membrane | UniProt | 213 | membrane GO:0030176 | integral component of endoplasmic reticulum membrane | UniProt | 92 | endoplasmic reticulum membrane GO:0031305 | integral component of mitochondrial inner membrane | UniProt | 32 | mitochondrial inner membrane GO:0030173 | integral component of Golgi membrane | UniProt | 27 | Golgi membrane GO:0031307 | integral component of mitochondrial outer membrane | UniProt | 20 | mitochondrial outer membrane GO:0005779 | integral component of peroxisomal membrane | UniProt | 18 | peroxisomal membrane GO:1905103 | integral component of lysosomal membrane | UniProt | 13 | lysosomal membrane GO:0031301 | integral component of organelle membrane | UniProt | 11 | organelle membrane GO:0071458 | integral component of cytoplasmic side of endoplasmic reticulum membrane | UniProt | 10 | cytoplasmic side of endoplasmic reticulum membrane GO:0030285 | integral component of synaptic vesicle membrane | UniProt | 9 | synaptic vesicle membrane GO:0032592 | integral component of mitochondrial membrane | UniProt | 8 | mitochondrial membrane GO:0071556 | integral component of lumenal side of endoplasmic reticulum membrane | UniProt | 5 | lumenal side of endoplasmic reticulum membrane GO:0031359 | integral component of chloroplast outer membrane | UniProt | 4 | chloroplast outer membrane GO:0005639 | integral component of nuclear inner membrane | UniProt | 2 | nuclear inner membrane GO:0031303 | integral component of endosome membrane | UniProt | 2 | endosome membrane GO:0031361 | integral component of thylakoid membrane | UniProt | 2 | thylakoid membrane GO:0099056 | integral component of presynaptic membrane | UniProt | 2 | presynaptic membrane GO:0031309 | integral component of nuclear outer membrane | UniProt | 1 | nuclear outer membrane GO:0031357 | integral component of chloroplast inner membrane | UniProt | 1 | chloroplast inner membrane GO:0097631 | integral component of omegasome membrane | UniProt | 1 | omegasome membrane GO:0097637 | integral component of autophagosome membrane | UniProt | 1 | autophagosome membrane GO:0099061 | integral component of postsynaptic density membrane | UniProt | 1 | postsynaptic density membrane GO:1990701 | integral component of endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane | UniProt | 1 | endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane GO:0005887 | integral component of plasma membrane | WB | 32 | plasma membrane GO:0016021 | integral component of membrane | WB | 4 | membrane GO:0030173 | integral component of Golgi membrane | WB | 4 | Golgi membrane GO:0030176 | integral component of endoplasmic reticulum membrane | WB | 3 | endoplasmic reticulum membrane GO:0005639 | integral component of nuclear inner membrane | WB | 1 | nuclear inner membrane GO:0031301 | integral component of organelle membrane | WB | 1 | organelle membrane GO:0031303 | integral component of endosome membrane | WB | 1 | endosome membrane GO:0031305 | integral component of mitochondrial inner membrane | WB | 1 | mitochondrial inner membrane GO:0005887 | integral component of plasma membrane | ZFIN | 23 | plasma membrane GO:0016021 | integral component of membrane | ZFIN | 10 | membrane GO:0099055 | integral component of postsynaptic membrane | ZFIN | 2 | postsynaptic membrane GO:0099056 | integral component of presynaptic membrane | ZFIN | 2 | presynaptic membrane

RLovering commented 2 years ago

Hi Pascale

have you discussed this with the SYNGO community?

Best

Ruth

pfey03 commented 2 years ago

Dicty is done updating

pgaudet commented 2 years ago

have you discussed this with the SYNGO community?

@RLovering I emailed Frank just now.

RLovering commented 2 years ago

I will leave the UCL annotations to be automatically moved to the more general term Thanks Ruth

ValWood commented 2 years ago

Agree to automated migration of PamBase annotations

pgaudet commented 2 years ago

Frank's answer (SynGO):

I suppose that's [the refactoring] understandable. However, for SynGO we won't refactor current ontologies and annotations anytime soon; some users need/use this information, so we'll continue making annotations against current terms and will rely on the mapping table to comply with this update.

I checked the table with replacement terms in the GitHub link you shared, everything looks fine for SynGO.

pgaudet commented 1 year ago

Terms are now obsoleted. Remaining annotations appear in error reports.