hattrill
commented
1 month ago The new refs should point towards this webpage: https://geneontology.org/GO_REF/XXXXXX e.g. https://geneontology.org/GO_REF/0000002 which is pulling from: https://github.com/geneontology/go-site/blob/master/metadata/gorefs.yaml
These are the references that need fixing: # U FBrf0232077 T personal communication to FlyBase a Sawford T. t 2016- u Automatic assignment of GO terms using logical inference, based on on inter-ontology links. R https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-0000108.md L English G GO terms are automatically assigned based on inter-ontology links to generate inferred annotations (e.g. the link between the function term GO:0016301 (kinase activity) can be used to infer the process term GO:0016310 (phosphorylation)). Annotations from Molecular Function to Biological Process can be propagated, as well as between Biological Process and Cellular Component. Annotations that are created using this inference method receive either the evidence code ECO:0000366 (evidence based on logical inference from automatic annotation used in automatic assertion) or ECO:0000364 (evidence based on logical inference from manual annotation used in automatic assertion), depending on whether the source annotation has a manual or automatic evidence code. Both of these codes map up to the GO Inferred from Electronic Annotation (IEA) evidence code. The annotations are attributed to GOC because Gene Ontology Consortium (http://www.geneontology.org/) editors define the links, the pipeline that these annotations are taken from is run by GOA (http://www.ebi.ac.uk/GOA). # U FBrf0253064 T personal communication to FlyBase a RNAcentral t 2018- u Automatic Gene Ontology annotation of non-coding RNA sequences through association of Rfam records with GO terms. R https://github.com/geneontology/go-site/tree/master/metadata/gorefs#goref0000115 L English G The mapping between Rfam families and GO terms is available at http://www.geneontology.org/external2go/rfam2go, and the Infernal software can be downloaded at http://eddylab.org/infernal. To report an annotation error or inconsistency, or for further information, please visit the RNAcentral website at http://rnacentral.org. This reference corresponds to annotations made to GO_REF:0000115 # U FBrf0233689 T FlyBase analysis a FlyBase Curators t 2016- u Assigning Gene Ontology (GO) terms Inferred by Curator (IC) using at least one Inferred by Sequence Similarity (ISS) annotation to support the inference. R https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-0000111.md L English G The Gene Ontology Consortium uses the IC (Inferred by Curator) evidence code when assignment of a GO term cannot be supported by direct experimental or sequence-based evidence, but can, based on a curator's biological knowledge, be reasonably inferred from existing GO annotations to the same gene/gene product. Use of the IC evidence code with GO_REF:00001111 indicates that a curator inferred the GO term based on at least one supporting annotation with an 'Inferred from Sequence Similarity' (ISS) evidence code. When using GO_REF:0000111, the 'with/from' field must contain all GO identifiers used as supporting annotations. # U FBrf0258542 T personal communication to FlyBase a GO Reference Genome Project t 2011- u Phylogenetic annotation using the Gene Ontology. R https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-0000033.md L English G Phylogenetic ANnotation using Gene Ontology (PAN-GO) was formally known as Phylogenetic Annotation and INference Tool (PAINT). # U FBrf0254415 T FlyBase analysis a GO curators t 2012- u Gene Ontology annotation based on absence of key sequence residues. R https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-0000047.md L English # U FBrf0255270 T personal communication to FlyBase a Gene Ontology Curators t 2002- u Gene Ontology Curators, (2002-). Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity. R https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-0000024.md L English G This reference corresponds to annotations made to GO_REF:0000024. # U FBrf0231277 T FlyBase analysis a FlyBase Curators t 2011- u Manual transfer of GO annotation data to genes by curator judgment of sequence model. R https://github.com/geneontology/go-site/blob/master/metadata/gorefs/goref-0000050.md L English *G This reference corresponds to GO_REF:0000050. #
GO_REFs url has chnaged. Update FBrfs that point to old page