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Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Rename or merge GO:0015563 uptake transmembrane transporter activity and children #14372

Closed pgaudet closed 6 years ago

pgaudet commented 6 years ago

Following up on #14322

GO ID Term Action
GO:0015563 uptake transmembrane transporter activity Merge into GO:0022857 transmembrane transporter activity (No annotations, no InterPro mappings)
GO:0005274 allantoin uptake transmembrane transporter activity    Renamed 'allantoin:proton symporter activity' to match the definition; Check annotations https://github.com/geneontology/go-annotation/issues/1692
GO:0080138 borate uptake transmembrane transporter activity  merge into GO:0046715 borate transmembrane transporter activity (since protein annotated by TAIR @tberardini - annotated to both terms)
GO:0015088 copper uptake transmembrane transporter activity merge into GO:0005375 copper ion transmembrane transporter activity - EXP annotations: SGD:S000006328; SGD:S000004403; SGD:S000001218; TAIR TAIR:locus:2049113; CGD UniProtKB:Q59NP1; TAIR TAIR:locus:2133965; SGD SGD:S000000855; RGD RGD:620059; MGI MGI:MGI:1333843; FlyBase FB:FBgn0062413; FlyBase FB:FBgn0062412; EcoCyc UniProtKB:P0A8H3; CGD CGD:CAL0000196962
GO:0015639 ferrous iron uptake transmembrane transporter activity merge into GO:0015093 ferrous iron transmembrane transporter activity - single EXP annotation P49281 (Swiss-Prot)
GO:0015659 formate uptake transmembrane transporter activity merge into GO:0015499 formate transmembrane transporter activity Single annotation Slc26a6 MGI
GO:0015092 high-affinity ferric iron uptake transmembrane transporter activity  Renamed high-affinity ferric iron transmembrane transporter activity - Removed x-reference to http://www.tcdb.org/search/result.php?tc=9.A.10.1.1 as this entry does not mention iron transport - No annotations
GO:0061840 high-affinity ferrous iron uptake transmembrane transporter activity  Renamed remove uptake - Single annotation Pombase fip1, also annotated to BP iron import
GO:0000006 high-affinity zinc uptake transmembrane transporter activity  Renamed remove uptake - 3 EXP annotations ZRT1 SGD:S000003224, Zrt1 PomBase:SPBC16D10.06, ZnuB UniProtKB:P39832 EcoCyc
GO:0015318 inorganic solute uptake transmembrane transporter activity TO DO: request to obsolete  There were no objection to obsoletion; however I found the ChEBI term 'inorganic molecular entity' that seemed a better description. Renamed term. // Add DO NOT ANNOTATE flag
GO:1901549 malonic acid uptake transmembrane transporter activity merge into GO:1901239 malonate(1-) transmembrane transporter activity - Single annotation Pombase mae1
GO:0015638 microcin uptake transporter activity   Rename microcin transmembrane transporter activity & fix definition - Single annotation sbmA P0AFY6 EcoCyc
GO:0015513 nitrite uptake transmembrane transporter activity  Renamed high-affinity secondary active nitrite transmembrane transporter activity based on existing parent (secondary active) and annotations (to proteins named high-affinity transporter) & Fixed logical definition - EXP annotations to 8 proteins: AspGD:ASPL0000073089 (AspGD), AspGD:ASPL0000056693 (AspGD), AspGD:ASPL0000060467(AspGD), AspGD:ASPL0000056693 (AspGD), UniProtKB:Q5AST3 (AspGD), UniProtKB:P22152 (AspGD), UniProtKB:G5EB18 (AspGD), UniProtKB:P10903 (EcoCyc), UniProtKB:P0AC26 (EcoCyc).
GO:0015558 p-aminobenzoyl-glutamate uptake transmembrane transporter activity  Merge parent GO:0015569 p-aminobenzoyl-glutamate transmembrane transporter activity (no annotation) into GO:0015558 Single annotation P46133 EcoCyc - See https://github.com/geneontology/go-annotation/issues/1672, renamed secondary active p-aminobenzoyl-glutamate transmembrane transporter activity, added missing parent and updated definition
GO:0015544 phenyl propionate uptake uniporter activity  No annotations, rename phenyl propionate uniporter activity
GO:0015388 potassium uptake transmembrane transporter activity  Merge into GO:0015079 potassium ion transmembrane transporter activity - 4 EXP annotations: PomBase:SPAC3F10.02c, UniProtKB:P0AFZ7 EcoCyc, UniProtKB:P23849 (CACAO + EcoCyc). Consider annotating to the BP GO:1990573 potassium ion import across plasma membrane
GO:0015541 secondary active cyanate uptake transmembrane transporter activity  No annotations. Renamed remove uptake
GO:0015636 short-chain fatty acid uptake transporter activity  1 EXP annotation Q8IVM8 Swiss-Prot Merge parent GO:0015635 short-chain fatty acid transporter activity (No annotations) into GO:0015636 & rename TM transporter activity
GO:0015344 siderophore uptake transmembrane transporter activity  TO DO Merge into parent GO:0015343 siderophore transmembrane transporter activity 15 EXP annotations: SGD:S000000791 SGD, PseudoCAP:PA2466 PseudoCAP, PseudoCAP:PA0931 PseudoCAP, PseudoCAP:PA4156 PseudoCAP, PseudoCAP:PA2688 PseudoCAP, PseudoCAP:PA4675 PseudoCAP, PseudoCAP:PA1912 PseudoCAP, UniProtKB:Q9HVC0 PseudoCAP, UniProtKB:Q9I527 PseudoCAP, UniProtKB:Q9HWM5 PseudoCAP, UniProtKB:Q9I116 PseudoCAP, UniProtKB:Q9I2J2 PseudoCAP, UniProtKB:Q05098 PseudoCAP, UniProtKB:P06972 EcoCyc, #UniProtKB:P07821 EcoCyc
GO:0015654 tellurite uptake transmembrane transporter activity  Merge parent GO:0015118 (No annotations) into GO:0015654 - 2 EXP annotations: P32705 and P0AFJ7 (both EcoCyc)
GO:0015403 thiamine uptake transmembrane transporter activity   Merge into parent GO:0015234 thiamine transmembrane transporter activity (8 EXP) 3 EXP MGI:MGI:1931307 (BHF), MGI:MGI:1928761 (BHF), and UniProtKB:O60779 (GOA)

When appropriate, changed definitions as recommended here: http://wiki.geneontology.org/index.php/Transporter_terms_standard_definitions#Other_standard_definitions

ValWood commented 6 years ago

Fine with the merge. Anything with uptake has a process describing import.

pgaudet commented 6 years ago

Obsoletion notice sent Dear all,

The proposal has been made to obsolete 'GO:0015318 inorganic solute uptake transmembrane transporter activity’

The reason for obsoletion is that is a grouping term that does not correspond to any ChEBI class, so that it currently has no children. Moreover, 'inorganic solute’ is probably not that useful as a grouping class for transporters. Please add any comments to the issue: https://github.com/geneontology/go-ontology/issues/14372

We are opening a comment period for this proposed obsoletion. We’d like to proceed and obsolete this term on Nov 6, 2017. Unless objections are received by Nov 6,2017, we will assume that you agree to this change.

Thanks, Pascale

pgaudet commented 6 years ago

There were no objection to obsoletion; however I found the ChEBI term 'inorganic molecular entity' that seemed a better description. Renamed term. // Added DO NOT ANNOTATE flag