Protein Binding clean up
Phase I of Protein Binding Clean-up: Removing gene product-specific binding terms.
Reasoning:
These terms identify specific GO terms that describe binding to a gene product as opposed to a family of proteins. As a gene product is described, it should be possible for the curator to determine what identifier should be included in the 'with' field.
Ones that have a relationship with a receptor activity have been excluded, as they are required for full description of a signalling pathway in GO.
Future requests for terms that describe a type of protein binding will be considered with regards to the above ontology development guidance.
Attention has been paid to ensure that when these terms are obsoleted, a parent term is available that can capture the functional family the interactor belongs to. If a suitable, information-rich protein binding parent is not available, one has been suggested below.
This first set of obsoletion suggestions has targeted terms which have a low number of manual annotations, therefore it is not intended to be complete, and it is likely more GO terms, matching the above requirements will be identified in future.
GO terms that are recommended for obsoletion (supplied with number of manual direct annotations and replacement term suggested):
1 GO:0017033 DNA topoisomerase I binding
Action needed: only parent is enzyme binding, create a new parent term 'DNA topoisomerase binding' to capture annotations where the interactor is topoisomerase I and II?
1 GO:0031006 filamin-A binding Use instead: GO:0031005 filamin binding
2 GO:0051419 nebulin binding Use instead: [GO:0008092-http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0008092] cytoskeletal protein binding
GO:0051420; nebulette binding Use instead: [GO:0008092-http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0008092] cytoskeletal protein binding
6 GO:0048273 mitogen-activated protein kinase p38 binding Use instead: GO:0051019 mitogen-activated protein kinase binding
6 GO:0048186 inhibin beta-A binding Use instead: GO:0034711 inhibin binding
0 GO:0034712 inhibin alpha binding Use instead: GO:0034711 inhibin binding
11 GO:0048187 inhibin beta-B binding Use instead: GO:0034711 inhibin binding
GO:0048154 S100 beta binding
Action needed: Create a term to describe S-100 protein binding, a family of low molecular weight protein found in vertebrates
2 GO:0002163 alpha-dystroglycan binding
3 GO:0002166 beta-dystroglycan binding
1 GO:0002162 dystroglycan binding
Action Needed: Currently GO:0005515 is the parent for these two terms. Should we create dystrophin-associated glycoprotein binding term, as a child of glycoprotein binding, which could also include the sarcoglycan, syntrophin protein interactors?)
1 GO:0031682 G-protein gamma-subunit binding
16 GO:0031681 G-protein beta-subunit binding
25 GO:0001965 G-protein alpha-subunit binding
Action Needed:-should there be the term: 'guanine nucleotide-binding protein binding' to group these? Currently all annotations would be then made to the protein binding parent.
8 GO:0051577 MyoD binding Use instead: GO:0043426 MRF binding
3 GO:0048184 follistatin binding
Action Needed: Only replacement parent is 'protein binding' However, shouldn't it be a child of glycoprotein binding? Is this information-rich enough, esp as v. Few annotations – one ISS, a NAS and IPI exist from AgBase and UniProtKB.
1 GO:0050430 syntaxin-6 binding Use instead: GO:0019905 syntaxin binding
2 GO:0080115 myosin XI tail binding - Use instead:GO:0017022 myosin binding
2 GO:0051535 syntaxin-5 binding Use instead: GO:0019905 syntaxin binding
1 GO:0034989 GTP-Ral binding Use instead: GO:0017160 Ral GTPase binding
9 GO:0051393 alpha-actinin binding Use instead: GO:0042805 actinin binding
1 GO:0032031 myosin I head/neck binding Use instead:GO:0017022 myosin binding
2 GO:0070855 myosin VI head/neck binding Use instead: GO:0017022 myosin binding
3 GO:0051372 nonmuscle alpha-actinin binding. Use instead: GO:0042805 actinin binding
3 GO:0048187 inhibin beta-B binding. Use instead: GO:0034711 inhibin binding
1 GO:0016030 metarhodopsin binding Use instead: [GO:0002046-http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0002046] opsin binding
2 GO:0030349 syntaxin-13 binding. Use instead: GO:0019905 syntaxin binding
5 GO:0034187 apolipoprotein E binding Use instead: GO:0034185 apolipoprotein binding
5 GO:0034186 apolipoprotein A-I binding Use instead: GO:0034185 apolipoprotein binding
5 GO:0072568 protein kinase C delta binding Use instead: GO:0005080 protein kinase C binding
4 GO:0030347 syntaxin-2 binding Use instead: GO:0019905 syntaxin binding
3 GO:0097024 protein kinase C alpha binding Use instead: GO:0005080 protein kinase C binding
3 GO:0051370 ZASP binding Use instead: GO:0008092 cytoskeletal protein binding
1 GO:0032028 myosin head/neck binding -Use instead: GO:0017022 myosin binding
1 GO:0051374 FATZ 1 binding Use instead: GO:0051373 FATZ binding
8 GO:0042808 neuronal Cdc2-like kinase binding Use instead: GO:0019901 protein kinase binding
11 GO:0048602 fibroblast growth factor 1 binding
8 GO:0048603 fibroblast growth factor 2 binding
4 GO:0048604 fibroblast growth factor 3 binding
0 GO:0048605 fibroblast growth factor 4 binding
0 GO:0048606 fibroblast growth factor 5 binding
0 GO:0048607 fibroblast growth factor 6 binding
Use instead: GO:0017134 fibroblast growth factor binding
8 GO:0048603 fibroblast growth factor 2 binding Use instead: GO:0017134 fibroblast growth factor binding
9 GO:0031014 troponin T binding
12 GO:0030172 troponin C binding
13 GO:0031013 troponin I binding
Action Needed: Create new parent grouping term: 'troponin binding' that would capture Troponin C/T/I binding?
2 GO:0051406 beta-actinin binding Use instead: GO:0042805 actinin binding
2 GO:0043106 GTP cyclohydrolase I binding
Action Needed: Current parent is 'enzyme binding'. Make a GTP cyclohydrolase binding parent term to reduce information loss?
7 GO:0048404 neurotrophin-3 binding Use instead: GO:0043121 neurotrophin binding
4 GO:0032145 succinate-semialdehyde dehydrogenase binding Action Needed:Create a more granular term than current parent 'enzyme binding', such as aldehyde dehydrogenase binding?
1 GO:0043238 laminin-2 binding Use instead:GO:0043236 laminin binding
8 GO:0048403 brain-derived neurotrophic factor binding Use instead: GO:0043121 neurotrophin binding
4 GO:0048405 neurotrophin-4/5 binding Use instead: GO:0043121 neurotrophin binding