GO REFs

This is a collection of references used by the GO Consortium. GO References (GO_REFs) are non-PMID references used by the GO Consortium and usually describe the method or project used to generate a specific set of annotations.

• [GO_REF:0000002] Gene Ontology annotation through association of InterPro records with GO terms.
• [GO_REF:0000003] Gene Ontology annotation based on Enzyme Commission mapping
• [GO_REF:0000004] Gene Ontology annotation based on UniProtKB keyword mapping.
• [GO_REF:0000008] Gene Ontology annotation by the MGI curatorial staff, curated orthology
• [GO_REF:0000011] Hidden Markov Models (TIGR)
• [GO_REF:0000012] Pairwise alignment (TIGR)
• [GO_REF:0000015] Use of the ND evidence code for Gene Ontology (GO) terms.
• [GO_REF:0000021] Improving the representation of central nervous system development in the biological process ontology
• [GO_REF:0000022] Improving the representation of immunology in the biological process Ontology
• [GO_REF:0000024] Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity.
• [GO_REF:0000025] Operon structure as IGC evidence
• [GO_REF:0000027] BLAST search criteria for ISS assignment in PAMGO_GAT
• [GO_REF:0000028] Criteria for IDA, IEP, ISS, IGC, RCA, and IEA assignment in PAMGO_MGG
• [GO_REF:0000033] Annotation inferences using phylogenetic trees
• [GO_REF:0000034] Phenoscape Skeletal Anatomy Jamboree
• [GO_REF:0000036] Manual annotations that require more than one source of functional data to support the assignment of the associated GO term
• [GO_REF:0000041] Gene Ontology annotation based on UniPathway vocabulary mapping.
• [GO_REF:0000043] Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
• [GO_REF:0000044] Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt.
• [GO_REF:0000047] Gene Ontology annotation based on absence of key sequence residues.
• [GO_REF:0000050] Manual transfer of GO annotation data to genes by curator judgment of sequence model
• [GO_REF:0000051] S. pombe keyword mapping
• [GO_REF:0000052] Gene Ontology annotation based on curation of immunofluorescence data
• [GO_REF:0000054] Gene Ontology annotation based on curation of intracellular localizations of expressed fusion proteins in living cells.
• [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 in the Gene Ontology
• [GO_REF:0000069] Representation of transmembrane transport of a chemical as biological process in the Gene Ontology
• [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 Gene Ontology
• [GO_REF:0000072] Representation of chemical homeostasis and cellular chemical homeostasisl as biological process in the Gene Ontology
• [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 the Gene Ontology
• [GO_REF:0000076] Representation of transport or vesicle-mediated transport from cell component to cell component as biological process in the Gene Ontology
• [GO_REF:0000078] Representation for the transport or vesicle-mediated transport of a chemical from and/or to a cell component as biological process in the Gene Ontology
• [GO_REF:0000079] Representation of assembly or disassembly of a cell component as biological process in the Gene Ontology
• [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 process in the Gene Ontology
• [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:0000090] Automatic creation of relationships between ontology branches 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 Ontology
• [GO_REF:0000093] Representation for the degradation to or via a chemical as biological process in the Gene Ontology
• [GO_REF:0000094] Representation of metazoan development as biological process in the Gene Ontology
• [GO_REF:0000095] Literature reference not indexed by PubMed
• [GO_REF:0000096] Automated transfer of experimentally-verified manual GO annotation data to mouse-rat orthologs.
• [GO_REF:0000097] Gene Ontology annotation based on personal communication to FlyBase
• [GO_REF:0000101] Automated transfer of experimentally-verified GO annotation data to close orthologs
• [GO_REF:0000104] Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features.
• [GO_REF:0000105] Gene Ontology annotation of transfer RNAs based on tRNAscan-SE analysis of the Drosophila melanogaster genome (2002).
• [GO_REF:0000107] Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara.
• [GO_REF:0000108] Automatic assignment of GO terms using logical inference, based on on inter-ontology links.
• [GO_REF:0000109] Gene Ontology annotation based on curation of genome-wide subcellular localisation of proteins using fluorescent protein tagging in Trypanosoma brucei
• [GO_REF:0000110] Gene Ontology annotation of Drosophila melanogaster nuclear genes encoding proteins targeted to the mitochondrion.
• [GO_REF:0000111] Gene Ontology annotations Inferred by Curator (IC) using at least one Inferred by Sequence Similarity (ISS) annotation to support the inference
• [GO_REF:0000113] Gene Ontology annotation of human sequence-specific DNA binding transcription factors (DbTFs) based on the TFClass database
• [GO_REF:0000114] Manual transfer of experimentally-verified manual GO annotation data to homologous complexes by curator judgment of sequence, composition and function similarity
• [GO_REF:0000115] Automatic Gene Ontology annotation of non-coding RNA sequences through association of Rfam records with GO terms
• [GO_REF:0000116] Automatic Gene Ontology annotation based on Rhea mapping.
• [GO_REF:0000117] Electronic Gene Ontology annotations created by ARBA machine learning models
• [GO_REF:0000118] TreeGrafter-generated GO annotations
• [GO_REF:0000119] Automated transfer of experimentally-verified manual GO annotation data to mouse-human orthologs.
• [GO_REF:0000120] Combined Automated Annotation using Multiple IEA Methods.

Obsolete GO REFs

• [GO_REF:0000001] OBSOLETE GO Consortium unpublished data
• [GO_REF:0000006] OBSOLETE Gene Ontology annotation by the MGI curatorial staff, Mouse Locus Catalog
• [GO_REF:0000010] OBSOLETE Gene Ontology annotation by the MGI curatorial staff, mouse gene nomenclature
• [GO_REF:0000018] OBSOLETE dictyBase 'Inferred from Electronic Annotation (BLAST method)'
• [GO_REF:0000019] OBSOLETE Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
• [GO_REF:0000020] OBSOLETE Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins
• [GO_REF:0000023] Gene Ontology annotation based on UniProtKB Subcellular Location vocabulary mapping.
• [GO_REF:0000026] OBSOLETE Improving the representation of muscle biology in the biological process and cellular component ontologies.
• [GO_REF:0000029] OBSOLETE Gene Ontology annotation based on information extracted from curated UniProtKB entries
• [GO_REF:0000030] OBSOLETE Portable Annotation Rules
• [GO_REF:0000031] OBSOLETE NIAID Cell Ontology Workshop
• [GO_REF:0000032] OBSOLETE Inference of Biological Process annotations from inter-ontology links
• [GO_REF:0000035] OBSOLETE Automatic transfer of experimentally verified manual GO annotation data to plant orthologs using Ensembl Compara
• [GO_REF:0000037] OBSOLETE Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries.
• [GO_REF:0000038] OBSOLETE Gene Ontology annotation based on automatic assignment of UniProtKB keywords in UniProtKB/TrEMBL entries.
• [GO_REF:0000039] OBSOLETE Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries.
• [GO_REF:0000040] OBSOLETE Gene Ontology annotation based on the automatic assignment of UniProtKB Subcellular Location terms in UniProtKB/TrEMBL entries.
• [GO_REF:0000042] OBSOLETE Gene Ontology annotation through association of InterPro records with GO terms, accompanied by conservative changes to GO terms applied by UniProt.
• [GO_REF:0000045] OBSOLETE Gene Ontology annotation based on UniProtKB/TrEMBL entries keyword mapping, accompanied by conservative changes to GO terms applied by UniProt.
• [GO_REF:0000046] OBSOLETE Gene Ontology annotation based on UniProtKB/TrEMBL Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt.
• [GO_REF:0000048] OBSOLETE TIGR's Eukaryotic Manual Gene Ontology Assignment Method
• [GO_REF:0000049] OBSOLETE Automatic transfer of experimentally verified manual GO annotation data to fungal orthologs using Ensembl Compara
• [GO_REF:0000053] OBSOLETE Automatic classification of GO using the ELK reasoner
• [GO_REF:0000055] OBSOLETE Gene Ontology Cellular Component annotation based on cellular fractionation.
• [GO_REF:0000056] OBSOLETE Taxon constraints to detect inconsistencies in annotation and ontology structure.
• [GO_REF:0000077] OBSOLETE Representation of transport of a cellular component as biological process in the Gene Ontology
• [GO_REF:0000082] OBSOLETE Representation of plant maturation as biological process in the Gene Ontology
• [GO_REF:0000098] OBSOLETE Gene Ontology annotation based on research conference abstracts
• [GO_REF:0000099] OBSOLETE Gene Ontology annotation based on DNA/RNA sequence records
• [GO_REF:0000100] OBSOLETE Gene Ontology annotation by SEA-PHAGE biocurators
• [GO_REF:0000102] OBSOLETE Representation of cellular component binding as molecular functions in the Gene Ontology
• [GO_REF:0000103] OBSOLETE Representation of cellular component organization as biological process in the Gene Ontology
• [GO_REF:0000106] OBSOLETE Gene Ontology annotation based on protein sequence records.
• [GO_REF:0000112] OBSOLETE Gene Ontology annotation by CACAO biocurators