From d1754fe2060a7d0fc925f52807e95eb11ada7e3f Mon Sep 17 00:00:00 2001 From: pgaudet Date: Thu, 2 May 2024 11:43:51 +0200 Subject: [PATCH 1/2] Update gorefs.yaml update GO_REF:0000003 --- metadata/gorefs.yaml | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/metadata/gorefs.yaml b/metadata/gorefs.yaml index 3bd6ca05..643fa6c3 100644 --- a/metadata/gorefs.yaml +++ b/metadata/gorefs.yaml @@ -35,12 +35,11 @@ - id: GO_REF:0000003 title: Gene Ontology annotation based on Enzyme Commission mapping description: |- - Transitive assignment using Enzyme Commission identifiers. This method is used - for any database entry, such as a protein record in UniProtKB or TrEMBL, that - has had an Enzyme Commission number assigned. The corresponding GO term is determined - using the EC cross-references in the GO molecular function ontology. Also see - Hill et al., Genomics (2001) 74:121-128. The mapping file is available at - http://www.geneontology.org/external2go/ec2go. + Enzyme Commission (EC) numbers (https://enzyme.expasy.org/) are manually curated into the description line of Swiss-Prot entries and added automatically to + TrEMBL entries. A mapping between EC numbers and GO Molecular Function terms is maintainted by GO editors. UniProt entries (Swiss-Prot and TrEMBL) that have been assigned an EC number + that has a GO mapping are automatically annotated with the correponding GO term. GO annotations using this method receive the evidence code + Inferred from Electronic Annotation (IEA). This method has been evaluated at up to 100% accurate (Camon et. al. 2005). The EC2GO mapping file is available at + http://current.geneontology.org/ontology/external2go/ec2go. alt_id: - GO_REF:0000005 authors: GOA curators, MGI curators From 759ba185fa99921247f31a0708b77c8d5fc332ba Mon Sep 17 00:00:00 2001 From: pgaudet Date: Thu, 2 May 2024 11:55:46 +0200 Subject: [PATCH 2/2] Update gorefs.yaml --- metadata/gorefs.yaml | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) diff --git a/metadata/gorefs.yaml b/metadata/gorefs.yaml index 643fa6c3..f381101d 100644 --- a/metadata/gorefs.yaml +++ b/metadata/gorefs.yaml @@ -35,20 +35,16 @@ - id: GO_REF:0000003 title: Gene Ontology annotation based on Enzyme Commission mapping description: |- - Enzyme Commission (EC) numbers (https://enzyme.expasy.org/) are manually curated into the description line of Swiss-Prot entries and added automatically to - TrEMBL entries. A mapping between EC numbers and GO Molecular Function terms is maintainted by GO editors. UniProt entries (Swiss-Prot and TrEMBL) that have been assigned an EC number - that has a GO mapping are automatically annotated with the correponding GO term. GO annotations using this method receive the evidence code + In UniProt, proteins with enzymatic activities have traditionally been annotated using reference vocabularies such as the hierarchical enzyme classification of the Enzyme Nomenclature Committee of the IUBMB + (often referred to as Enzyme Commission or EC numbers; https://enzyme.expasy.org/). EC numbers are manually curated in Swiss-Prot ('UniProt Reviewed') entries and added automatically to + TrEMBL ('UniProt Uneviewed') entries. A mapping between EC numbers and GO Molecular Function terms is maintainted by GO editors. UniProt entries assigned with an EC number + with a GO mapping are automatically annotated with the correponding GO term, as described in PMID:30395331. GO annotations using this method receive the evidence code Inferred from Electronic Annotation (IEA). This method has been evaluated at up to 100% accurate (Camon et. al. 2005). The EC2GO mapping file is available at http://current.geneontology.org/ontology/external2go/ec2go. alt_id: - GO_REF:0000005 - authors: GOA curators, MGI curators - citation: PMID:11374909 - external_accession: - - MGI:2152096 - - J:72245 - - ZFIN:ZDB-PUB-031118-3 - - SGD_REF:S000124037 + authors: GO Central curators + citation: PMID:31688925 is_obsolete: false year: 2001 - id: GO_REF:0000004