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geneontology / go-ontology

Source ontology files for the Gene Ontology
http://geneontology.org/page/download-ontology
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Fix some GO_REFs #18662

Open pgaudet opened 4 years ago

pgaudet commented 4 years ago

Hello,

We have a bunch of GO_REFs that were created for TermGenie term creation, that essentially describe the branch under which the term is (see table below).

All terms with those GOREFs also have 'GOC:TermGenie', and as far as I can see, they also have a reference (PMID or wikipedia).

So, @ukemi , based on the statement you made In ticket #16895 David writes "I would like to see the definition xrefs reserved for stable publications that support the existence, placement and definition of a term." , all those can go, right ?

GOREF ID  Description
GO_REF:0000058 Representation of regulation in the Gene Ontology (biological process)
GO_REF:0000059 Representation of regulation in the Gene Ontology (molecular function)
GO_REF:0000060 Representation of processes involved in other process in the Gene Ontology
GO_REF:0000061 Representation of a molecular function involved in a biological process in the Gene Ontology
GO_REF:0000062 Representation of processes occurring in parts of the cell in the Gene Ontology
GO_REF:0000063 Representation of processes regulated by other regulating processes in the Gene Ontology
GO_REF:0000064 Representation of cell components as part of other cell components in the Gene Ontology
GO_REF:0000065 Representation of transport of a chemical entity as a biological process in the Gene Ontology
GO_REF:0000066 Representation of transport of a chemical entity as molecular function in the Gene Ontology
GO_REF:0000067 Representation of binding to a chemical entity as molecular function in the Gene Ontology
GO_REF:0000068 Representation of metabolic triad (metabolism, catabolism, biosynthesis) as biological process
GO_REF:0000069 Representation of transmembrane transport of a chemical as biological process in the Gene Ontol
GO_REF:0000070 Representation of transmembrane transporter activity as molecular function in the Gene Ontology
GO_REF:0000071 Representation of response to and cellular response to a chemical as biological process in the
GO_REF:0000072 Representation of chemical homeostasis and cellular chemical homeostasisl as biological process
GO_REF:0000073 Representation of import of a chemical as biological process in the Gene Ontology
GO_REF:0000074 Representation of export of a chemical as biological process in the Gene Ontology
GO_REF:0000075 Representation of transport of a chemical into a cellular component as biological process in th
GO_REF:0000076 Representation of transport or vesicle-mediated transport from cell component to cell component
GO_REF:0000078 Representation for the transport or vesicle-mediated transport of a chemical from and/or to a c
GO_REF:0000079 Representation of assembly or disassembly of a cell component as biological process in the Gene
GO_REF:0000080 Representation of plant development as biological process in the Gene Ontology
GO_REF:0000081 Representation of plant formation as biological process in the Gene Ontology
GO_REF:0000083 Representation of plant morphogenesis as biological process in the Gene Ontology
GO_REF:0000084 Representation of plant structural organization as biological process in the Gene Ontology
GO_REF:0000085 Representation of cell apoptotic process as biological process in the Gene Ontology
GO_REF:0000086 Representation of cell differentiation as biological process in the Gene Ontology
GO_REF:0000087 Representation of protein localization and establishment of protein localization as biological
GO_REF:0000088 Representation of protein complex by molecular function in the Gene Ontology
GO_REF:0000089 Representation of single-organism and multi-organism biological processes in the Gene Ontology
GO_REF:0000091 Representation of cell migration as biological processes in the Gene Ontology
GO_REF:0000092 Representation for the biosynthesis from or via a chemical as biological process in the Gene On
GO_REF:0000093 Representation for the degradation to or via a chemical as biological process in the Gene Ontol
GO_REF:0000094 Representation of metazoan development as biological process in the Gene Ontology

Thanks, Pascale

pgaudet commented 4 years ago

First PR: https://github.com/geneontology/go-ontology/pull/18656/commits/1d996a0f7807c9c3ce9c714689f91147106b678e

cmungall commented 3 years ago

these should be obsoleted and replaced_by individual dosdps