- id: GO_REF:0000001
  title: OBSOLETE GO Consortium unpublished data
  description: No abstract available.
  authors: GO Curators
  is_obsolete: true
  year: 1998
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  description: |-
    InterPro (http://www.ebi.ac.uk/interpro/) is an integrated resource from the EBI of protein families, domains and sites which are combined from a number 
    of different protein signature databases, including CATH-Gene3D, CDD, HAMAP, NCBIfam, Panther, Pfam, PIRSF, PRINTS, ProSite, SMART, and SUPERFAMILY. Signatures describing the same protein 
    family or domain are grouped into unique InterPro entries. When appropriate, the InterPro team maps InterPro entries to  GO terms (Molecular Function, Biological Process and/or Cellular Component). 
    InterPro runs InterProScan on the entire set of UniProt proteins. InterPro hits are assigned the corresponding GO annotations by the GOA pipeline. The mapping file is available at http://current.geneontology.org/ontology/external2go/interpro2go.
  comments:
    - Note that some groups filter GO annotations based on InterPro-to-GO transitive assignment, e.g. to remove annotations redundant with manual curation.
  alt_id:
    - GO_REF:0000007
    - GO_REF:0000014
    - GO_REF:0000016
    - GO_REF:0000017
  authors: GO Central Curators, 2024
  external_accession:
    - MGI:2152098
    - J:72247
    - ZFIN:ZDB-PUB-020724-1
    - FB:FBrf0174215
    - dictyBase_REF:10157
    - SGD_REF:S000124036
  is_obsolete: false
  year: 2001
- id: GO_REF:0000003
  title: Gene Ontology annotation based on Enzyme Commission mapping
  description: |-
    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: GO Central Curators, 2024
  external_accession:
    - ZFIN:ZDB-PUB-031118-3
    - SGD_REF:S000124037
  citation: PMID:31688925
  is_obsolete: false
  year: 2001
- id: GO_REF:0000004
  title: Gene Ontology annotation based on UniProtKB keyword mapping
  description: |-
    Transitive assignments using UniProtKB keywords. The UniProtKB keyword
    controlled vocabulary has been created and used by the UniProt Knowledgebase
    (UniProtKB) to supply 10 different categories of information to UniProtKB entries.
    Further information on the UniProtKB keyword resource can be found at
    http://www.uniprot.org/docs/keywlist.

    Further information on the UniProt annotation methods is available at
    https://www.uniprot.org/help/manual_curation and
    https://www.uniprot.org/help/automatic_annotation.

    When a UniProtKB keyword describes a concept that is within the scope of the Gene
    Ontology, it is investigated to determine whether it is appropriate to map the
    keyword to an equivalent term in GO. The mapping between UniProtKB keywords and
    GO terms is carried out manually. Definitions and hierarchies of the terms in the
    two resources are compared and the mapping generated will reflect the most correct
    correspondence. The translation table between GO terms and UniProtKB keywords is
    maintained by the UniProt-GOA team and available at
    http://www.geneontology.org/external2go/uniprotkb_kw2go.
  comments:
    - Formerly GOA:spkw.
  alt_id:
    - GO_REF:0000009
    - GO_REF:0000013
  authors: GOA Curators
  external_accession:
    - MGI:1354194
    - J:60000
    - ZFIN:ZDB-PUB-020723-1
    - SGD_REF:S000124038
  is_obsolete: false
  year: 2000
- id: GO_REF:0000006
  title: OBSOLETE Gene Ontology annotation by the MGI curatorial staff, Mouse Locus
    Catalog
  description: |-
    For annotations documented via this citation, curators used the information in
    the Mouse Locus Catalog in MGI to assign GO terms. The GO terms were assigned
    based on MLC textual descriptions of genes that could not be traced to the primary
    literature. Details of this strategy can be found in Hill et al, Genomics (2001)
    74:121-128.
  authors: Mouse Genome Informatics Scientific Curators
  citation: PMID:11374909
  external_accession:
    - MGI:2152097
    - J:72246
  is_obsolete: true
  year: 2001
- id: GO_REF:0000008
  title: Gene Ontology annotation by the MGI curatorial staff, curated orthology
  description: |-
    The sequence conservation that permits the establishment of orthology between
    mouse and rat or mouse and human genes is a strong predictor of the conservation
    of function for the gene product across these species. Therefore, in instances
    where a mouse gene product has not been functionally characterized, but its human
    or rat orthologs have, Mouse Genome Informatics (MGI) curators append the GO terms
    associated with the orthologous gene(s) to the mouse gene. Only those GO terms
    assigned by experimental determination to the ortholog of the mouse gene will
    be adopted by MGI. GO terms that are assigned to the ortholog of the mouse gene
    computationally (i.e. IEA), will not be transferred to the mouse ortholog. The
    evidence code represented by this citation is Inferred by Sequence Orthology (ISO).
  authors: Mouse Genome Informatics Scientific Curators
  external_accession:
    - MGI:2154458
    - J:73065
  is_obsolete: false
  year: 2001
- id: GO_REF:0000010
  title: OBSOLETE Gene Ontology annotation by the MGI curatorial staff, mouse gene
    nomenclature
  description: |-
    For annotations documented via this citation, curators designed queries based
    on their knowledge of mouse gene nomenclature to group genes that shared common
    molecular functions, biological processes or cellular components. GO annotations
    were assigned to these genes in groups. Details of this strategy can be found
    in Hill et al., Genomics (2001) 74:121-128.
  authors: Mouse Genome Informatics Scientific Curators
  citation: PMID:11374909
  external_accession:
    - MGI:1347124
    - J:56000
  is_obsolete: true
  year: 1999
- id: GO_REF:0000011
  title: Hidden Markov Models (TIGR)
  description: |-
    A Hidden Markov Model (HMM) is a statistical representation of patterns found
    in a data set. When using HMMs with proteins, the HMM is a statistical model of
    the patterns of the amino acids found in a multiple alignment of a set of proteins
    called the "seed". Seed proteins are chosen based on sequence similarity to each
    other. Seed members can be chosen with different levels of relationship to each
    other. They can be members of a superfamily (ex. ABC transporter, ATP-binding
    proteins), they can all share the same exact specific function (ex. biotin synthase)
    or they could share another type of relationship of intermediate specificity (ex.
    subfamily, domain). New proteins can be scored against the model generated from
    the seed according to how closely the patterns of amino acids in the new proteins
    match those in the seed. There are two scores assigned to the HMM which allow
    annotators to judge how well any new protein scores to the model. Proteins scoring
    above the "trusted cutoff" score can be assumed to be part of the group defined
    by the seed. Proteins scoring below the "noise cutoff" score can be assumed to
    NOT be a part of the group. Proteins scoring between the trusted and noise cutoffs
    may be part of the group but may not. One of the important features of HMMs is
    that they are built from a multiple alignment of protein sequences, not a pairwise
    alignment. This is significant, since shared similarity between many proteins
    is much more likely to indicate shared functional relationship than sequence similarity
    between just two proteins. The usefulness of an HMM is directly related to the
    amount of care that is taken in chosing the seed members, building a good multiple
    alignment of the seed members, assessing the level of specificity of the model,
    and choosing the cutoff scores correctly. In order to properly assess what functional
    relevance an above-trusted scoring HMM match has to a query, one must carefully
    determine what the functional scope of the HMM is. If the HMM models proteins
    that all share the same function then it is likely possible to assign a specific
    function to high-scoring match proteins based on the HMM. If the HMM models proteins
    that have a wide variety of functions, then it will not be possible to assign
    a specific function to the query based on the HMM match, however, depending on
    the nature of the HMM in question, it may be possible to assign a more general
    (family or subfamily level) function. In order to determine the functional scope
    of an HMM, one must carefully read the documentation associated with the HMM.
    The annotator must also consider whether the function attributed to the proteins
    in the HMM makes sense for the query based on what is known about the organism
    in which the query protein resides and in light of any other information that
    might be available about the query protein. After carefully considering all of
    these issues the annotator makes an annotation.
  authors: Michelle Gwinn, TIGR Curators
  is_obsolete: false
  year: 2003
- id: GO_REF:0000012
  title: Pairwise alignment (TIGR)
  description: |-
    Pairwise alignments are generated by taking two sequences and aligning them so
    that the maximum number of amino acids in each protein match, or are similar to,
    each other. Tools such as BLAST work by comparing a protein-of-interest individually
    with every protein in a database of known protein sequences and retaining only
    those matches with a high probability of being significant. Basic BLAST generates
    local alignments between proteins for regions of high similarity. Other pairwise
    alignment tools attempt to generate global (full-length) protein alignments. A
    tool called Blast_Extend_repraze (BER, http://ber.sourceforge.net) has some benefits
    over basic BLAST. Input into the BER tool includes the underlying DNA sequence
    for each protein as well as 300 nucleotides upstream and downstream of the predicted
    boundaries of the protein coding sequence. This allows annotators to see the DNA
    sequence that underlies the query protein as part of the alignment. In addition,
    the BER tool is able to look for continuation of regions of similarity through
    frameshifts and in-frame stop codons.  If such regions are found the alignment
    is continued. BER searches are done in a two-step process: step one is a BLAST
    search against a non-redundant protein database, significant BLAST hits are stored
    in a mini-database for each query protein; step two is a modified Smith-Waterman
    alignment between the query and the proteins in its mini-database. In order to
    assess whether a given BER alignment is good enough to assert that the query shares
    the function of the match protein, one must look at a several factors. First of
    all, the match protein must itself be experimentally characterized in order to
    avoid transitive annotation errors. In addition, any residues or secondary structures
    known to be important for function in the match protein must be conserved in the
    query. The alignment should be visually inspected to look for any areas of lesser
    quality that might indicate the two proteins do not share the same function. Although
    it is impossible to set cutoff values for percent identity and length of match
    that will apply for every alignment, there are some guidelines. In general at
    least 40% identity that extends over the full lengths of both proteins is required
    in order to even consider functional equivalence. However, this percentage is
    highly dependent on the length and complexity of the proteins. 40% identity between
    two proteins 500 amino acids long is much more significant that 40% identity between
    two proteins that are only 100 amino acids long. Therefore, the annotator's experience
    and knowledge of what is considered significant for the organism and protein family
    in question is very important. Some sets of proteins are much more highly conserved
    than others and therefore tolerances for percent identity may have to be adjusted.
    Finally, the alignment must be considered in the context of what else is known
    about the query protein and the organism as a whole.
  authors: Michelle Gwinn, TIGR Curators
  is_obsolete: false
  year: 2003
- id: GO_REF:0000015
  title: Use of the ND evidence code for Gene Ontology (GO) terms
  description: |-
    Direct annotations to any of the three root terms 'molecular function; GO:0003674',
    'biological process; GO:0008150' or 'cellular component; GO:0005575' indicate
    that curators have found no data supporting an annotation to a more specific term,
    either in the literature and/or by sequence similarity for this gene or protein
    as of the date of the annotation.
  authors: GO Curators
  external_accession:
    - ECO:0000307
    - AspGD_REF:ASPL0000111607
    - CGD_REF:CAL0125086
    - dictyBase_REF:2
    - dictyBase_REF:9851
    - FB:FBrf0159398
    - MGI:MGI:2156816
    - RGD:1598407
    - SGD_REF:S000069584
    - TAIR:Communication:1345790
    - ZFIN:ZDB-PUB-031118-1
    - GO_REF:nd
  is_obsolete: false
  year: 2002
- id: GO_REF:0000018
  title: OBSOLETE dictyBase 'Inferred from Electronic Annotation (BLAST method)'
  description: |-
    Gene Ontology (GO) annotations with the evidence code 'Inferred from Electronic
    Annotation' (IEA) are assigned automatically to gene products in dictyBase. All
    Dictyostelium protein sequences are analyzed by BLAST against GO gene association
    sequence files, identifying proteins in other organisms that align with Dictyostelium
    proteins with an E value less than or equal to e-50. GO annotations that have
    been manually assigned to these proteins from other species are then imported
    and attached to the corresponding gene product in dictyBase. The proteins from
    which the annotations are derived are displayed in the 'Evidence' column on the
    Gene Ontology evidence and references page.
  authors: DictyBase Curators
  external_accession:
    - dictyBase_REF:10158
  is_obsolete: true
  year: 2005
- id: GO_REF:0000019
  title: OBSOLETE Automatic transfer of experimentally verified manual GO annotation
    data to orthologs using Ensembl Compara
  description: |-
    GO terms from a source species are projected on to one or more target species
    based on gene orthology obtained from the Ensembl Compara system. Only one to
    one and apparent one to one orthologies are used for a restricted range of species.
    Only GO annotations with a manual experimental evidence type of IDA, IEP, IGI,
    IMP or IPI are projected. Projected GO annotations using this technique will receive
    the evidence code, inferred from electronic annotation, 'IEA'. The Ensembl protein
    identifier of the annotation source is indicated in the 'With' column of the GOA
    association file.
  authors: Ensembl Curators, GOA Curators
  is_obsolete: true
  year: 2006
- id: GO_REF:0000020
  title: OBSOLETE Electronic Gene Ontology annotations created by transferring manual
    GO annotations between orthologous microbial proteins
  description: |-
    GO terms are manually assigned to each HAMAP family rule. High-quality Automated
    and Manual Annotation of microbial Proteins (HAMAP) family rules are a collection
    of orthologous microbial protein families, from bacteria, archaea and plastids,
    generated manually by expert curators. The assigned GO terms are then transferred
    to all the proteins that belong to each HAMAP family. Only GO terms from the molecular
    function and biological process ontologies are assigned. GO annotations using
    this technique will receive the evidence code Inferred from Electronic Annotation
    (IEA). These annotations are updated monthly by HAMAP and are available for download
    on both GO and GOA EBI ftp sites. To report an annotation error or inconsistency,
    or for further information, please contact the GO Consortium at help@geneontology.org
    or submit a comment the SourceForge Annotation Issues tracker
    (http://sourceforge.net/projects/geneontology/). HAMAP is a project based at the Swiss
    Institute of Bioinformatics (Gattiker et al. 2003, Comp. Biol and Chem. 27: 49-58).
    For further information, please see http://www.expasy.org/sprot/hamap/.
  authors: Swiss Institute of Bioinformatics (SIB) Curators, GOA Curators
  is_obsolete: true
  year: 2006
- id: GO_REF:0000021
  title: Improving the representation of central nervous system development in the
    biological process ontology
  description: |-
    Current genetic and molecular studies in many model organisms are aimed at understanding
    formation and development of the nervous system. Up until this point, the GO has
    had a very shallow representation of processes pertaining to the nervous system.
    In June 2006, curators from MGI and ZFIN met with researchers studying central
    nervous system development to improve the representation of these processes in
    GO. In particular, emphasis was placed on three areas that are being addressed
    actively in current research: forebrain development, hindbrain development and
    neural tube development. This collaboration resulted in the addition of over 500
    terms that reflect the development of the forebrain, the hindbrain, and the neural
    tube from the perspective of biological process and anatomical structure.
  authors: Judith Blake (1, 2), William Bug (3), Rex Chisholm (1, 4), Jennifer Clark (1,
    5), Erika Feltrin (6), Jacqueline Finger (2), David Hill (1, 2), Midori Harris
    (1, 5), Terry Hayamizu (2), Doug Howe (9), Maryanne Martone (7), Kathleen Millen
    (8), Francis Sele (4) (1. The Gene Ontology Consortium, 2. Mouse Genome Informatics,
    Bar Harbor, ME, 3. Drexel University, Philadelphia, PA, 4. Northwestern University,
    Chicago, IL, 5. EMBL-EBI, Hinxton, Cambridgeshire, UK, 6. The University of Padua,
    Padua, Italy, 7. The University of California at San Diego, San Diego, CA, 8.
    The University of Chicago, Chicago, IL, 9. The Zebrafish Information Network,
    University of Oregon, Eugene, OR)
  is_obsolete: false
  year: 2006
- id: GO_REF:0000022
  title: Improving the representation of immunology in the biological process Ontology
  description: |-
    GO terms describing processes, functions, and cellular components related to the
    immune system have existed in the GO from its beginning and been used extensively
    in the annotation of gene products. However, particularly in the biological process
    ontology, the initial set of terms relating to immunology failed to cover the
    breadth of known immunological processes, and in many cases diverged from current
    usage and understanding in their names, definitions, and ontological placement.
    As part of a larger effort to improve the representation of immunology in the
    GO, a GO Content Meeting was held November 15-16, 2005, at The Institute for Genomic
    Research, to discuss improvements to representation of immunology in the biological
    process ontology of the GO. As a result of the meeting, a number of high level
    terms for immunological processes were created, an overall structure for immunologically
    related terms was established, and certain existing terms were renamed or redefined
    as well to bring them in line with current usage.
  authors: Alison Deckhut Augustine (1), Alan Collmer (2), Judith A. Blake (3, 4), Candace
    W. Collmer (2, 3), Shane C. Burgess (5), Lindsay Grey Cowell (6), Jennifer I.
    Clark (3, 7), Bernard de Bono (7), Russell T. Collins (8), Alexander D. Diehl
    (3, 4), Michelle Gwinn Giglio (3, 9), Jamie A. Lee (10), Linda Hannick (3, 9),
    Jane Lomax (3, 7), Midori A. Harris (3, 7), Christopher J. Mungall (3, 11), David
    P. Hill (3, 4), Richard H. Scheuermann (10), Amelia Ireland (3, 7), Alessandro
    Sette (12) (1. NIAID, 2. Cornell University, 3. The GO Consortium, 4. Mouse Genome
    Informatics, 5. Mississippi State University, 6. Duke University, 7. EMBL-EBI,
    8. University of Cambridge, 9. The Institute for Genomic Research, 10. U.T. Southwestern
    Medical Center, 11. HHMI, 12. La Jolla Institute for Allergy and Immunology)
  is_obsolete: false
  year: 2005
- id: GO_REF:0000023
  title: Gene Ontology annotation based on UniProtKB Subcellular Location vocabulary
    mapping
  description: |-
    Transitive assignment of GO terms based on the UniProtKB Subcellular Location
    vocabulary. UniProtKB Subcellular Location is a controlled vocabulary used to
    supply subcellular location information to UniProtKB entries in the SUBCELLULAR
    LOCATION lines. Terms from this vocabulary are annotated manually to UniProtKB/Swiss-Prot
    entries but  are automatically assigned to UniProtKB/TrEMBL entries from the underlying
    nucleic acid databases and/or by the UniProt automatic annotation program.

    Further information on these two different annotation methods is available at
    http://www.uniprot.org/faq/45 and
    http://www.uniprot.org/program/automatic_annotation.

    When a UniProtKB Subcellular Location term describes a concept that is within
    the scope of the Gene Ontology, it is investigated to determine whether it is
    appropriate to map the term to an equivalent term in GO. The mapping between UniProtKB
    Subcellular Location terms and GO terms is carried out manually. Definitions and
    hierarchies of the terms in the two resources are compared and the mapping generated
    will reflect the most correct correspondence. The translation table between GO
    terms and UniProtKB Subcellular Location term is maintained by the UniProt-GOA
    team and available at http://www.geneontology.org/external2go/spsl2go.
  authors: GOA Curators, UniProt Curators
  external_accession:
    - SGD_REF:S000125578
  is_obsolete: true
  year: 2007
- id: GO_REF:0000024
  title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
    by curator judgment of sequence similarity
  description: |-
    Method for transferring manual annotations to an entry based on a curator's judgment
    of its similarity to a putative ortholog that has annotations that are supported
    with experimental evidence. Annotations are created when a curator judges that
    the sequence of a protein shows high similarity to another protein that has annotation(s)
    supported by experimental evidence (and therefore display one of the evidence
    codes EXP, IDA, IGI, IMP, IPI or IEP). Annotations resulting from the transfer
    of GO terms display the 'ISS' evidence code and include an accession for the protein
    from which the annotation was projected in the 'with' field (column 8). This field
    can contain either a UniProtKB accession or an IPI (International Protein Index)
    identifier. Only annotations with an experimental evidence code and which do not
    have the 'NOT' qualifier are transferred. Putative orthologs are chosen using
    information combined from a variety of complementary sources. Potential orthologs
    are initially identified using sequence similarity search programs such as BLAST.
    Orthology relationships are then verified manually using a combination of resources
    including sequence analysis tools, phylogenetic and comparative genomics databases
    such as Ensembl Compara, INPARANOID and OrthoMCL, as well as other specialised
    databases such as species-specific collections (e.g. HGNC's HCOP). In all cases
    curators check each alignment and use their experience to assess whether similarity
    is considered to be strong enough to infer that the two proteins have a common
    function so that they can confidently project an annotation. While there is no
    fixed cut-off point in percentage sequence similarity, generally proteins which
    have greater than 30% identity that covers greater than 80% of the length of both
    proteins are examined further. For mammalian proteins this cut-off tends to be
    higher, with an average of 80% identity over 90% of the length of both proteins.
    Strict orthologs are desirable but not essential. In general, when there is evidence
    of multiple paralogs for a single species, annotations using less specific GO
    terms are transferred to the paralogs, however, annotations using more specific
    GO terms may be transferred to the most similar paralog in each species, this
    decision is taken on a case by case basis and may be influenced by statements
    by researchers in the field. Further detailed information on this procedure, including
    how ISS annotations are made to protein isoforms, can be found at:
    https://wiki.geneontology.org/Inferred_from_Sequence_or_structural_Similarity_(ISS).
  authors: AgBase, BHF-UCL, Parkinson's UK-UCL, dictyBase, HGNC, Roslin Institute,
    FlyBase and UniProtKB Curators
  external_accession:
    - dictyBase_REF:9
    - J:342587
    - FB:FBrf0255270
    - SGD_REF:S000250423
    - ZFIN:ZDB-PUB-110105-1
    - ZFIN:ZDB-PUB-040216-1
    - ZFIN:ZDB-PUB-071010-1
  is_obsolete: false
  year: 2011
- id: GO_REF:0000025
  title: DEPRECATED Operon structure as IGC evidence
  description: |-
    Genes in prokaryotic organisms are often arranged in operons. Genes in an operon
    are all transcribed into one mRNA. Generally the genes in the operons code for
    proteins that all have related functions. For example, they may be the steps in
    a biochemical pathway, or they may be the subunits of a protein complex. Often
    the genes in operons shared between organisms are syntenic; that is, the same
    genes are in the same order in the operon in different species. When assessing
    sequence-comparison-based evidence during the process of manual annotation of
    a genome, it is often the case that some of the genes in the operon will have
    strong sequence-based evidence while others will have weak evidence. If seen alone,
    not in the presence of an operon, the weak evidence in question may not be sufficient
    to make a functional annotation. However, in the presence of an operon in which
    there is strong evidence for some of the genes, the very presence of the gene
    in the operon is a strong indication that the gene shares in the process carried
    out by the operon. If the putative function is one expected to exist for the process
    in question and particularly if that function has been observed in the same operon
    in another species, then the annotation should be made. This type of evidence
    is inferred from the context of the gene in an operon, and therefore the evidence
    code is IGC "inferred from genomic context."
  authors: Michelle Gwinn, TIGR Curators
  is_obsolete: true
  year: 2007
- id: GO_REF:0000026
  title: OBSOLETE Improving the representation of muscle biology in the biological
    process and cellular component ontologies
  description: |-
    A meeting focused on the biology of skeletal and smooth muscle has been held on
    24-25 July 2007 at the University of Padua, Italy, as a collaboration with the
    GO consortium and CRIBI Biotechnology Center. The aims of this effort were to
    provide a comprehensive representation of muscle biology in the biological process
    and cellular component ontologies and to improve the organization of muscle-specific
    terms to better describe the current knowledge of biological mechanisms in muscle
    tissue. Thus, the collaboration brought together experts in several areas of muscle
    biology and physiology who carried out a thorough review of the existing GO muscle
    terms as these terms were largely created by non-muscle experts using older definitions.
    In particular, several areas are being addressed actively in current research:
    the biological processes of muscle contraction, muscle plasticity, muscle development,
    and muscle regeneration; and the sarcoplasmic reticulum and membrane delimited
    compartments. This work resulted in the addition of 159 new terms and in the modification
    of 57 terms to bring them in line with current usage. Funding for the meeting
    was provided by Italian Telethon Foundation.
  authors: Jennifer Deegan nee Clark (1, 5), Alexander D. Diehl (1,7), Elisabeth Ehler (2),
    Georgine Faulkner (3), Erika Feltrin (4), Jennifer Fordham (2), Midori Harris
    (1, 5), Ralph Knoell (6) David Hill (1, 7), Paolo Laveder (8), Alessandra Nori
    (8), Carlo Reggiani (8), Vincenzo Sorrentino (9), Giorgio Valle (4), Pompeo Volpe
    (8) (1. The Gene Ontology Consortium, 2. King's College, London, UK, 3. ICGEB,
    Trieste, Italy, 4. CRIBI - University of Padua, Padua, Italy 5. EMBL-EBI, Hinxton,
    Cambridgeshire, UK, 6. University of Goettingen, Goettingen, Germany 7. Mouse
    Genome Informatics, Bar Harbor, ME, 8. University of Padua, Padua, Italy, 9. University
    of Siena, Siena, Italy)
  citation: PMID:19178689
  is_obsolete: true
  year: 2007
- id: GO_REF:0000027
  title: BLAST search criteria for ISS assignment in PAMGO_GAT
  description: |-
    This GO reference describes the criteria used in assigning the evidence code of
    ISS via BLAST searches to annotate gene products from PAMGO_GAT. Standard BLASTP
    from NCBI was used (http://www.ncbi.nih.gov/blast) to query the non-redundant
    (NR) database. Hits are considered to be significant if the E-value is at or less
    than 10^-4. All other parameters are default according to http://www.ncbi.nih.gov/blast.
  authors: PAMGO_GAT Curators
  year: 2007
  is_obsolete: false
- id: GO_REF:0000028
  title: DEPRECATED Criteria for IDA, IEP, ISS, IGC, RCA, and IEA assignment in PAMGO_MGG
  description: |-
    This GO reference describes the criteria used in assigning the evidence codes
    of IDA (ECO:0000314), IEP (ECO:0000270), ISS (ECO:0000250), IGC (ECO_0000317),
    RCA (ECO:0000245) and IEA (ECO:0000501) to annotate gene products from PAMGO_MGG.
    Standard BLASTP from NCBI was used (http://www.ncbi.nih.gov/blast) to iteratively
    search reciprocal best hits and thus identify orthologs between predicted proteins
    of Magnaporthe grisea and GO proteins from multiple organisms with published association
    to GO terms. The alignments were manually reviewed for those hits with e-value
    equal to zero and with 80% or better coverage of both query and subject sequences,
    and for those hits with e<=10^-20, pid >=35 and sequence coverage >=80%. Furthermore,
    experimental or reviewed data from literature and other sources were incorporated
    into the GO annotation. IDA was assigned to an annotation if normal function of
    its gene was determined through transfections into a cell line and overexpression.
    IEP was assigned to an annotation if according to microarray experiments, its
    gene was upregulated in a biological process and the fold change was equal to
    or bigger than 10, or if according to Massively Parallel Signature Sequencing
    (MPSS), its gene was upregulated only in a certain biological process and the
    fold change was equal to or bigger than 10. ISS was assigned to an annotation
    if the entry at the With_column was experimentally characterized and the pairwise
    alignments were manually reviewed. IGC was assigned to an annotation if it based
    on comparison and analysis of gene location and structure, clustering of genes,
    and phylogenetic reconstruction of these genes. RCA was assigned to an annotation
    if it based on integrated computational analysis of whole genome microarray data,
    and matches to InterPro, pfam, and COG etc. IEA was assigned to an annotation
    if its function assignment based on computational work, and no manual review was
    done.
  authors: PAMGO_MGG Curators
  is_obsolete: true
  year: 2008
- id: GO_REF:0000029
  title: OBSOLETE Gene Ontology annotation based on information extracted from curated
    UniProtKB entries
  description: |-
    Active 2001-2007.

    Method by which GO terms were manually assigned to UniProt KnowledgeBase accessions,
    using either a NAS or TAS evidence code, by applying information extracted from
    the corresponding publicly-available, manually curated UniProtKB entry. Such GO
    annotations were submitted by the GOA-UniProt group from 2001, but this annotation
    practice was discontinued in 2007.
  authors: GOA-UniProt Curators
  is_obsolete: true
  year: 2007
- id: GO_REF:0000030
  title: OBSOLETE Portable Annotation Rules
  description: |-
    The JCVI is developing a collection of mixed-evidence annotation rules, under
    the working name BrainGrab/RuleBase (BGRB). A rule has two parts. The first is
    the set of conditions that must be met for the rule to fire. The second is the
    set actions to be taken for rules that have fired. BGRB rules are designed to
    serve as proxies for the annotators that create them. They have very high fidelity
    but may have low coverage. Types of evidence used in combination include HMM hits
    and BLAST matches, hits to neighboring genes, pathway reconstruction reports from
    the Genome Properties system, and species taxonomy. BLAST matches are described
    by a number of separate parameters for raw score, percent sequence identity, and
    coverage of total sequence length by the match region. These parameters are customized
    for each protein family in order to achieve high fidelity in automated annotation
    systems. The flexible syntax makes it possible to use existing protein family
    classifiers, such as Pfam and TIGRFAMs HMMs, in new ways. It is especially useful
    in assigning GO terms to proteins such as SelD (selenide, water dikinase) that
    have different roles in different contexts.
  authors: Daniel Haft, JCVI
  year: 2008
  is_obsolete: true
- id: GO_REF:0000031
  title: OBSOLETE NIAID Cell Ontology Workshop
  description: |-
    The NIAID sponsored a Cell Ontology Workshop, May 13-14, 2008, in Bethesda, focusing
    on improving representation of immune cell types in the Cell Ontology. The participants
    in the workshop worked together to extend the current ontology in the area of
    immune cell types and to provide the necessary information for the upcoming restructuring
    of the Cell Ontology in single-inheritance form with genus-differentia definitions.
  authors: Alexander D. Diehl, Alison Deckhut Augustine, Judith A. Blake, Lindsay G. Cowell,
    Elizabeth S. Gold, Timothy A. Gondre-Lewis, Anna Maria Masci, Terrence F. Meehan,
    Penelope A. Morel, Anastasia Nijnik, Bjoern Peters, Bali Pulendran, Richard H.
    Scheuermann, Q. Alison Yao, Martin S. Zand, Christopher J. Mungall
  url: http://www.bioontology.org/wiki/index.php/NIAID_Cell_Ontology_Workshop_May_2008
  year: 2008
  is_obsolete: true
- id: GO_REF:0000032
  title: OBSOLETE Inference of Biological Process annotations from inter-ontology
    links
  description: |-
    We use the GOBO library to propagate annotations from Molecular Function to Biological
    Process. This results in both increased numbers of annotations, and increased
    consistency between curators.

    Duplicate of GO_REF:0000108.
  authors: Christopher J. Mungall, Tanya Z. Berardini, David P. Hill
  is_obsolete: true
  url: http://wiki.geneontology.org/index.php/GAF_Inference
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  description: |-
    The Phylogenetic ANnotation using Gene Ontology (PAN-GO) method annotates evolutionary
    trees from the PANTHER database with GO terms describing molecular function, biological
    process and cellular component. The GO terms are manually selected by a curator
    and used to annotate ancestral genes in the phylogenetic tree using the evidence
    code IBA (Inferred from Biological Ancestor). All supporting annotations must
    be based on experimental data from the scientific literature. The PAN-GO annotations
    are fully traceable from the data in the 'with/from' column of the annotation,
    which provides the PANTHER node ID (PTN) from which the annotation is derived,
    as well as all descendants sequences that support the annotation of the ancestral
    node.

    The full method is described in PMID:21873635.
  authors: Marc Feuermann, Huaiyu Mi, Pascale Gaudet, Dustin Ebert, Anushya Muruganujan,
    Paul Thomas
  external_accession:
    - SGD_REF:S000185201
    - TAIR:Communication:501741973
    - MGI:MGI:4459044
    - J:161428
    - ZFIN:ZDB-PUB-110330-1
    - FB:FBrf0258542
  is_obsolete: false
  url: https://wiki.geneontology.org/Phylogenetic_Annotation_Project
  year: 2010
- id: GO_REF:0000034
  title: Phenoscape Skeletal Anatomy Jamboree
  description: |-
    Skeletal cell terms and relationships were added and revised at the Skeletal Anatomy
    Jamboree held by Phenoscape (NSF grant BDI-0641025) and hosted by the National
    Evolutionary Synthesis Center (NESCent), April 9-10, 2010.
  authors: Brian K. Hall (Dalhousie University), Matthew Vickaryous (Ontario Veterinary College,
    University of Guelph), David Blackburn, University of Kansas; Wasila Dahdul, University
    of South Dakota and NESCent; Alexander Diehl, Mouse Genome Informatics (MGI);
    Melissa Haendel, Oregon Health Sciences University; John G. Lundberg, Department
    of Ichthyology, Academy of Natural Sciences, Philadelphia; Paula Mabee, Department
    of Biology, University of South Dakota; Martin Ringwald, Mouse Genome Informatics
    (MGI); Erik Segerdell, Oregon Health Sciences University; Ceri Van Slyke, Zebrafish
    Information Network (ZFIN); Monte Westerfield, Zebrafish Information Network (ZFIN)
    and Institute of Neuroscience, University of Oregon
  year: 2010
- id: GO_REF:0000035
  title: OBSOLETE Automatic transfer of experimentally verified manual GO annotation
    data to plant orthologs using Ensembl Compara
  description: |-
    GO terms from a source species are projected onto one or more target species based
    on gene orthology obtained from the Ensembl Compara system. One to one, one to
    many and many to many orthologies are used but annotations are only projected
    between orthologs that have at least a 40% peptide identity to each other. Only
    GO annotations with an evidence type of IDA, IEP, IGI, IMP or IPI are projected,
    no annotations with a 'NOT' qualifier are projected and annotations to the GO:0005515
    protein binding term are not projected. Projected GO annotations using this technique
    will receive the evidence code Inferred from Electronic Annotation (IEA). The
    model organism database identifier of the annotation source will be indicated
    in the 'With' column of the GOA association file.

    Duplicate of GO_REF:0000107.
  authors: Ensembl, GRAMENE, GOA Curators
  is_obsolete: true
  year: 2011
- id: GO_REF:0000036
  title: Manual annotations that require more than one source of functional data to
    support the assignment of the associated GO term (IC)
  description: |-
    The Gene Ontology Consortium uses the IC (Inferred by Curator) evidence code when
    an annotation cannot be supported by any direct evidence, but can be inferred
    by GO annotations that have been annotated to the same gene/gene product identifier
    in conjunction with the curator's knowledge of biology (supporting GO annotations
    must not be IC-evidenced). In many cases an IC-evidenced annotation simply applies
    the same reference that was used in the supporting GO annotation.  The use of
    IC evidence code in an annotation with reference GO_REF:0000036 signifies a curator
    inferred the GO term based on evidence from multiple sources of evidence/GO annotations.
    The 'with/from' field in these annotations will therefore supply more than one
    GO identifier, obtained from the set of supporting GO annotations assigned to
    the same gene/gene product identifier which cite publicly-available references.
  authors: GO Annotation working group
  external_accession:
    - SGD_REF:S000147045
    - J:342596
    - ZFIN:ZDB-PUB-031118-2
  year: 2011
- id: GO_REF:0000037
  title: OBSOLETE Gene Ontology annotation based on manual assignment of UniProtKB
    keywords in UniProtKB/Swiss-Prot entries
  description: |-
    Transitive assignments using UniProtKB keywords. The UniProtKB keyword controlled
    vocabulary has been created and used by the UniProt Knowledgebase (UniProtKB)
    to supply 10 different categories of information to UniProtKB entries. Further
    information on the UniProtKB keyword resource can be found at
    http://www.uniprot.org/docs/keywlist. UniProtKB keywords are manually applied to
    UniProtKB/Swiss-Prot entries by UniProt curators. Further information on the
    UniProtKB manual annotation process is available at http://www.uniprot.org/faq/45.

    When a UniProtKB keyword describes a concept that is within the scope of the Gene
    Ontology, it is investigated to determine whether it is appropriate to map the
    keyword to an equivalent term in GO. The mapping between UniProtKB keywords and
    GO terms is carried out manually. Definitions and hierarchies of the terms in
    the two resources are compared and the mapping generated will reflect the most
    correct correspondence. The translation table between GO terms and UniProtKB keywords
    is maintained by the UniProt-GOA team and available at
    http://www.geneontology.org/external2go/uniprotkb_kw2go.

    Duplicate of GO_REF:0000043.
  authors: UniProt-GOA
  is_obsolete: true
  year: 2011
  evidence_codes:
    - ECO:0000501
- id: GO_REF:0000038
  title: OBSOLETE Gene Ontology annotation based on automatic assignment of UniProtKB
    keywords in UniProtKB/TrEMBL entries
  description: |-
    Transitive assignments using UniProtKB keywords. The UniProtKB keyword controlled
    vocabulary has been created and used by the UniProt Knowledgebase (UniProtKB)
    to supply 10 different categories of information to UniProtKB entries. Further
    information on the UniProtKB keyword resource can be found at
    http://www.uniprot.org/docs/keywlist. UniProtKB keywords are automatically assigned
    to UniProtKB/TrEMBL entries from the underlying nucleic acid databases and/or by
    the UniProt automatic annotation program. Further information on the prediction
    systems applied by UniProt is available here:
    http://www.uniprot.org/program/automatic_annotation.

    When a UniProtKB keyword describes a concept that is within the scope of the Gene
    Ontology, it is investigated to determine whether it is appropriate to map the
    keyword to an equivalent term in GO. The mapping between UniProtKB keywords and
    GO terms is carried out manually. Definitions and hierarchies of the terms in
    the two resources are compared and the mapping generated will reflect the most
    correct correspondence. The translation table between GO terms and UniProtKB keywords
    is maintained by the UniProt-GOA team and available at
    http://www.geneontology.org/external2go/uniprotkb_kw2go.

    Duplicate of GO_REF:0000043.
  authors: UniProt-GOA
  is_obsolete: true
  year: 2011
- id: GO_REF:0000039
  title: OBSOLETE Gene Ontology annotation based on the manual assignment of UniProtKB
    Subcellular Location terms in UniProtKB/Swiss-Prot entries
  description: |-
    Transitive assignment of GO terms based on the UniProtKB Subcellular Location
    vocabulary. UniProtKB Subcellular Location is a controlled vocabulary used to
    supply subcellular location information to UniProtKB entries in the SUBCELLULAR
    LOCATION lines. Terms from this vocabulary are annotated manually to UniProtKB/Swiss-Prot
    entries. Further information on the UniProtKB manual annotation method is available
    at http://www.uniprot.org/faq/45.

    When a UniProtKB Subcellular Location term describes a concept that is within
    the scope of the Gene Ontology, it is investigated to determine whether it is
    appropriate to map the term to an equivalent term in GO. The mapping between UniProtKB
    Subcellular Location terms and GO terms is carried out manually. Definitions and
    hierarchies of the terms in the two resources are compared and the mapping generated
    will reflect the most correct correspondence. The translation table between GO
    terms and UniProtKB Subcellular Location terms is maintained by the UniProt-GOA
    team and available at http://www.geneontology.org/external2go/spsl2go.
  authors: UniProt-GOA
  is_obsolete: true
  year: 2011
- id: GO_REF:0000040
  title: OBSOLETE Gene Ontology annotation based on the automatic assignment of UniProtKB
    Subcellular Location terms in UniProtKB/TrEMBL entries
  description: |-
    Transitive assignment of GO terms based on the UniProtKB Subcellular Location
    vocabulary. UniProtKB Subcellular Location is a controlled vocabulary used to
    supply subcellular location information to UniProtKB entries in the SUBCELLULAR
    LOCATION lines. Terms from this vocabulary are applied automatically to UniProtKB/TrEMBL
    entries from the underlying nucleic acid databases and/or by the UniProt automatic
    annotation program. Further information on the UniProtKB automatic annotation
    program is available at http://www.uniprot.org/faq/45.

    When a UniProtKB Subcellular Location term describes a concept that is within
    the scope of the Gene Ontology, it is investigated to determine whether it is
    appropriate to map the term to an equivalent term in GO. The mapping between UniProtKB
    Subcellular Location terms and GO terms is carried out manually. Definitions and
    hierarchies of the terms in the two resources are compared and the mapping generated
    will reflect the most correct correspondence. The translation table between GO
    terms and UniProtKB Subcellular Location terms is maintained by the UniProt-GOA
    team and available at http://www.geneontology.org/external2go/spsl2go.
  authors: UniProt-GOA
  is_obsolete: true
  year: 2011
- id: GO_REF:0000041
  title: Gene Ontology annotation based on UniPathway vocabulary mapping
  description: |-
    Transitive assignment of GO terms based on the UniPathway pathway vocabulary.
    UniPathway is not maintained anymore. It was a manually curated resource of enzyme-catalyzed and spontaneous
    chemical reactions that provided a hierarchical representation of metabolic pathways. The last release of UniPathway 
    was in March 2015 and is archived at NCBO: 
    https://bioportal.bioontology.org/ontologies/UPA.
  authors: UniProt-GOA
  external_accession:
    - ZFIN:ZDB-PUB-130131-1
    - J:342601
    - SGD_REF:S000150560
  year: 2012
- id: GO_REF:0000042
  title: OBSOLETE Gene Ontology annotation through association of InterPro records
    with GO terms, accompanied by conservative changes to GO terms applied by UniProt
  description: |-
    Transitive assignment of GO terms based on InterPro classification. For any database
    entry (representing a protein or protein-coding gene) that has been annotated
    with one or more InterPro domains, The corresponding GO terms are obtained from
    a translation table of InterPro entries to GO terms (interpro2go) generated manually
    by the InterPro team at EBI. The mapping file is available at
    http://www.geneontology.org/external2go/interpro2go.

    Please note that the GO term in the annotation assigned with this GO reference
    has been changed from that originally applied by the InterPro2GO mapping. This
    change has been carried out by the UniProt group to ensure the GO annotation obeys
    the GO Consortium’s ontology structure and taxonomic constraints. Further information
    on the rules used by UniProt to transform specific incorrect IEA annotations is
    available at http://www.ebi.ac.uk/QuickGO/AnnotationPostProcessing.html.

    Duplicate of GO_REF:0000002.
  authors: UniProt-GOA
  is_obsolete: true
  year: 2012
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  description: |-
    Gene Ontology annotation of virus proteins based on UniProtKB/Swiss-Prot keyword mapping. 
    The UniProtKB keyword resource can be found at https://www.uniprot.org/keywords/. 
    UniProtKB keywords are assigned to UniProtKB/Swiss-Prot entries by UniProt curators 
    as part of the UniProtKB manual curation process. UniProtKB keywords are also automatically 
    assigned to UniProtKB/TrEMBL entries from sequence databases and/or by the UniProt automatic 
    annotation program. When a UniProtKB keyword describes a concept that is within the scope of 
    the Gene Ontology, a mapping is manually made to the corresponding GO term. The translation 
    table between GO terms and UniProtKB keywords is maintained by the EBI GOA team and available at 
    http://www.geneontology.org/external2go/uniprotkb_kw2go. 
    Note that this pipeline was formally run for all species, but is now restricted to viruses (NCBITaxon:10239).
  authors: UniProt-GOA
  year: 2012
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  description: |-
    Transitive assignment of GO terms based on the UniProtKB/Swiss-Prot Subcellular
    Location vocabulary. UniProtKB Subcellular Location is a controlled vocabulary
    used to supply subcellular location information to UniProtKB entries in the SUBCELLULAR
    LOCATION lines. Terms from this vocabulary are annotated manually to UniProtKB/Swiss-Prot
    entries but are automatically assigned to UniProtKB/TrEMBL entries from the underlying
    nucleic acid databases and/or by the UniProt automatic annotation program. Further
    information on these two different annotation methods is available
    https://www.uniprot.org/help/keywords.
    When a UniProtKB Subcellular Location term describes a concept that is within
    the scope of the Gene Ontology, a mapping is made to the corresponding
    GO term. The translation table between GO terms and UniProtKB Subcellular Location
    term is maintained by the EBI GOA team and available at
    http://current.geneontology.org/ontology/external2go/uniprotkb_sl2go.
  authors: UniProt-GOA
  external_accession:
    - TAIR:AnalysisReference:501756971
    - TAIR:AnalysisReference:50175724
    - J:342604
    - ZFIN:ZDB-PUB-120306-4
    - SGD_REF:S000250403
  year: 2012
- id: GO_REF:0000045
  title: OBSOLETE Gene Ontology annotation based on UniProtKB/TrEMBL entries keyword
    mapping, accompanied by conservative changes to GO terms applied by UniProt
  description: |-
    Transitive assignments using UniProtKB/TrEMBL keywords. The UniProtKB keyword
    controlled vocabulary has been created and used by the UniProt Knowledgebase (UniProtKB)
    to supply 10 different categories of information to UniProtKB/TrEMBL entries entries.
    Further information on the UniProtKB keyword resource can be found at
    http://www.uniprot.org/docs/keywlist.

    UniProtKB keywords are assigned to UniProtKB/UniProtKB entries by UniProt curators
    as part of the UniProtKB manual curation process. In contrast however, UniProtKB
    keywords are automatically assigned to UniProtKB/TrEMBL entries from the underlying
    nucleic acid databases and/or by the UniProt automatic annotation program.

    Further information on the two different UniProt annotation methods is available
    at http://www.uniprot.org/faq/45 and http://www.uniprot.org/program/automatic_annotation.

    When a UniProtKB keyword describes a concept that is within the scope of the Gene
    Ontology, it is investigated to determine whether it is appropriate to map the
    keyword to an equivalent term in GO. The translation table between GO terms and
    UniProtKB keywords is maintained by the UniProt-GOA team and available at
    http://www.geneontology.org/external2go/uniprotkb_kw2go.

    Please note that the GO term in the annotation assigned with this GO reference
    has been changed from that originally applied by the UniProtKB keywords 2GO mapping.
    This change has been carried out by the UniProt group to ensure the GO annotation
    obeys the GO Consortium’s ontology structure and taxonomic constraints. Further
    information on the rules used by UniProt to transform specific incorrect IEA annotations
    is available at http://www.ebi.ac.uk/QuickGO/AnnotationPostProcessing.html.

    Duplicate of GO_REF:0000004.
  authors: UniProt-GOA
  is_obsolete: true
  year: 2012
- id: GO_REF:0000046
  title: OBSOLETE Gene Ontology annotation based on UniProtKB/TrEMBL Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  description: |-
    Transitive assignment of GO terms based on the UniProtKB/TrEMBL Subcellular Location
    vocabulary. UniProtKB Subcellular Location is a controlled vocabulary used to
    supply subcellular location information to UniProtKB entries in the SUBCELLULAR
    LOCATION lines. Terms from this vocabulary are annotated manually to UniProtKB/Swiss-Prot
    entries but are automatically assigned to UniProtKB/TrEMBL entries from the underlying
    nucleic acid databases and/or by the UniProt automatic annotation program.

    Further information on these two different annotation methods is available at
    http://www.uniprot.org/faq/45 and http://www.uniprot.org/program/automatic_annotation.

    The translation table between GO terms and UniProtKB Subcellular Location term
    is maintained by the UniProt-GOA team and available at
    http://www.geneontology.org/external2go/spsl2go.

    Please note that the GO term in the annotation assigned with this GO reference
    has been changed from that originally applied by the UniProtKB Subcellular Location2GO
    mapping. This change has been carried out by the UniProt group to ensure the GO
    annotation obeys the GO Consortium’s ontology structure and taxonomic constraints.
    Further information on the rules used by UniProt to transform specific incorrect
    IEA annotations is available at http://www.ebi.ac.uk/QuickGO/AnnotationPostProcessing.html.

    Duplicate of GO_REF:0000023.
  authors: UniProt-GOA
  is_obsolete: true
  year: 2012
- id: GO_REF:0000047
  title: Gene Ontology annotation based on absence of key sequence residues
  description: |-
    This describes a method for supplying a NOT-qualified, IKR-evidenced GO annotation
    to a gene product, when general sequence homology considerations would suggest
    a function or location, or a role in a biological process, but where a curator
    has determined that the absence of key sequence residues, known to be required
    for an expected activity or location, indicating the gene product is unlikely
    to be able to carry out the implied activity, involvement in a process or cellular
    component location. This reference should only be used used when an IKR-evidenced
    annotation is made based on curator judgement from manually reviewing the sequence
    of the gene product and where no publication can be found to support the curators
    conclusion. It is preferable to cite a peer-reviewed publication (such as a PubMed
    identifier) for IKR-evidenced annotations whenever possible. Curators will have
    carefully reviewed the sequence of the annotated protein, and established that
    the key residues known to be required for an expected activity or location are
    not present. Inclusion of an identifier in the 'with/from' field, that highlights
    to the user the lacking residues(e.g. an alignment, domain or rule identifier)
    is absolutely required when annotating to IKR with this GO_REF. Documentation
    on the GOC website provides more details on the
    <a href="http://www.geneontology.org/GO.evidence.shtml#ikr">correct use of the
    IKR evidence code</a>.
  authors: GO Curators
  external_accession:
    - FB:FBrf0254415
  year: 2012
- id: GO_REF:0000048
  title: OBSOLETE TIGR's Eukaryotic Manual Gene Ontology Assignment Method
  description: |-
    This describes TIGR curators' interpretation of a combination of evidence. Our
    internal software tools present us with a great deal of evidence based on domains,
    sequence similarities, signal sequences, paralogous proteins, etc. The curator
    interprets the body of evidence to make a decision about a GO assignment when
    an external reference is not available. The curator places one or more accessions
    that informed the decision in the "with" field.
  authors: TIGR Arabidopsis annotation team
  external_accession:
    - TAIR:Communication:501714663
  is_obsolete: true
  year: 2005
- id: GO_REF:0000049
  title: OBSOLETE Automatic transfer of experimentally verified manual GO annotation
    data to fungal orthologs using Ensembl Compara
  description: |-
    GO terms from a source species are projected onto one or more target species based
    on gene orthology obtained from the Ensembl Compara system. One to one, one to
    many and many to many orthologies are used but annotations are only projected
    between orthologs that have at least a 40% peptide identity to each other. Only
    GO annotations with an evidence type of IDA, IEP, IGI, IMP or IPI are projected,
    no annotations with a 'NOT' qualifier are projected and annotations to the GO:0005515
    protein binding term are not projected. Projected GO annotations using this technique
    will receive the evidence code Inferred from Electronic Annotation (IEA). The
    model organism database identifier of the annotation source will be indicated
    in the 'With' column of the GOA association file.

    Duplicate of GO_REF:0000107.
  authors: Ensembl Genomes
  is_obsolete: true
  year: 2012
- id: GO_REF:0000050
  title: Manual transfer of GO annotation data to genes by curator judgment of sequence
    model
  description: |-
    Transitive assignment of GO terms to a gene based on a curator's judgment of its
    match to a sequence model,such as a Pfam or InterPro entry, that has manually
    curated GO annotations, mappings to GO terms, or a description from which GO terms
    can be inferred. A statistical model of a sequence or group of sequences is used
    to make a prediction about the function of a protein or RNA. Annotations are created
    when a curator evaluates the results, using criteria that include excluding false
    positives and ensuring that the annotation is accurate for all matches. Statistical
    scores (such as e values and cutoff scores) and the functional specificity of
    the model may also be (but are not always) considered. Annotations resulting from
    the transfer of GO terms use the 'ISM' evidence code and include an accession
    for the model from which the annotation was projected in the 'with' field (column
    8).
  authors: PomBase Curators
  external_accession:
    - FB:FBrf0231277
  year: 2012
- id: GO_REF:0000051
  title: S. pombe keyword mapping
  description: |-
    Keywords derived from manually curated primary annotation, e.g. gene product descriptions,
    are mapped to GO terms. Annotations made by this method have the evidence code
    Non-traceable Author Statement (NAS), and are filtered from the PomBase annotation
    files wherever another annotation exists that is equally or more specific, and
    supported by experimental or manually evaluated comparative evidence (such as
    ISS and its subtypes). Formerly GOC:pombekw2GO.
  authors: PomBase Curators
  is_obsolete: false
  year: 2012
- id: GO_REF:0000052
  title: Gene Ontology annotation based on curation of immunofluorescence data
  description: |-
    GO Cellular Component terms are manually assigned by curators studying
    high resolution confocal microscopy images of immunohistochemically stained
    tissue. The methodology uses antibody-based proteomics which combines high-throughput
    generation of affinity-purified antibodies with protein profiling in a variety
    of cells and tissues. Further information on the annotation methods can be found
    at http://www.proteinatlas.org/about/assays+annotation

    Annotations are only
    exported to the GO Consortium if the localizations are supported by literature,
    according to the following validation grading:

    Supportive - Subcellular localization
    supported by literature.

    1) One/multiple localizations supported by literature.
    2) Multiple localizations partly supported (at least one) by literature.
    3) One/multiple
    localizations in cytoplasm (i.e. Golgi, mitochondria, ER etc) with literature
    supporting cytoplasmic localization.

    Prior to February 2013, all Human Protein
    Atlas annotations were referenced by PMID:18029348 (Barbe et al. 2008 Mol. Cell
    Proteomics. 7:499-508), a paper describing the protein localization pilot study
    and methodology used by the Human Protein Atlas. However, it has been decided
    that these annotations are more correctly described by a GO reference.

    Resource
    URL: http://www.proteinatlas.org

    Protein subcellular localization images can
    be viewed on the Human Protein Atlas website, e.g.
    http://www.proteinatlas.org/ENSG00000175899/summary#ifcelline
  authors: Human Protein Atlas
  year: 2013
- id: GO_REF:0000053
  title: OBSOLETE Automatic classification of GO using the ELK reasoner
  description: |-
    We use the <a href="http://code.google.com/p/elk-reasoner/">ELK reasoner</a> as
    part of an ontology development and release pipeline to automatically construct
    and check a large portion of the GO graph. The editors version of the GO
    (gene_ontology_write.obo) contains additional metadata, including provenance of
    graph links. Every week, the GO pipeline executes a process which first removes
    all links tagged as "is_inferred". The reasoner then generates a list of inferred
    links which are automatically added to the ontology with the "is_inferred" tag
    set. The pipeline generates a report describing which links have changed as a
    part of this process.
  authors: GO Ontology Editors
  year: 2013
  is_obsolete: true
- id: GO_REF:0000054
  title: Gene Ontology annotation based on curation of intracellular localizations
    of expressed fusion proteins in living cells
  description: |-
    LIFEdb is a database that was created to manage the experimental data
    produced by the German Cancer Research Institute (DKFZ) and its collaborators,
    from work on cDNAs contained in the German cDNA Consortium collection.

    A novel cloning technology was used to rapidly generate N- and C-terminal green fluorescent
    protein fusions of cDNAs to examine the intracellular localizations of expressed
    fusion proteins in living cells. GO Cellular Component terms are manually assigned
    by curators studying fluorescence microscope images of cells labelled with GFP-fused
    cDNAs. Protein coding regions of novel full length cDNAs are tagged with the
    coding sequence of the green fluorescent protein, the fusion proteins are then
    expressed and analyzed for their subcellular localization.

    Prior to February 2013, all LIFEdb annotations were referenced by PMID: 11256614 (Simpson et al.
    2000 EMBO Rep. 1:287-292), a paper describing the protein subcellular localization
    pilot study and methodology used by LIFEdb. However, it has been decided that
    these annotations are more correctly described by a GO reference.

    Resource URL: http://www.dkfz.de/en/mga/Groups/LIFEdb-Database.html

    Protein subcellular localization images can be viewed on the LIFEdb website,
    http://www.dkfz.de/gpcf/lifedb.php
  authors: LIFEdb
  year: 2013
- id: GO_REF:0000055
  title: OBSOLETE Gene Ontology Cellular Component annotation based on cellular fractionation
  description: |-
    Assignment of GO Cellular Component terms based on experimental evidence of cellular
    localization from Differential Detergent Fractionation (DDF). Cellular proteins
    are differentially fractionated and detected using mass spectrometry. Subcellular
    localization is based upon identification of proteins in different fractions and
    analysis of their predicted transmembrane domains. Proteins are assigned GO CC
    based upon a manually reviewed DDF2GO mapping file.
  authors: AgBase Biocurators
  year: 2013
  is_obsolete: true
- id: GO_REF:0000056
  title: OBSOLETE Taxon constraints to detect inconsistencies in annotation and ontology
    structure
  description: |-
    GO is intended to cover the full range of species, therefore GO terms are defined
    to be taxon neutral, avoiding reliance on taxon information for full definition
    of the given process, function, or component. For certain terms, however, there
    is obvious implicit taxon specificity, such that the term should only be used
    to categorize gene products from particular species. Taxon specificity of GO terms
    is captured using relationships such as "only_in_taxon" and "never_in_taxon".
    All taxon constraints are inherited by sub-types and parts of the GO term they
    are applied to. Taxon constraints are used to prevent inappropriate annotations
    from being made by curators as well as to identify pre-existing annotations that
    violate the taxon constraints. Errors in annotations are automatically detected
    by looking for inconsistencies between the taxonomic origin of the annotated gene
    products and the implicit taxon specificity of the GO terms. The inconsistencies
    are passed on to curators for correction, in some cases the constraints need to
    be tightened or relaxed or the structure of the ontology needs to be adjusted.
    The taxon constraints are further described in this publication: Deegan, Dimmer
    and Mungall. BMC Bionformatics (2010) Formalization of taxon-based constraints
    to detect inconsistencies in annotaiton and ontology development. (PMID:20973947).
  authors: The GO Consortium
  year: 2013
  is_obsolete: true
- id: GO_REF:0000058
  title: Representation of regulation in the Gene Ontology (biological process)
  description: |-
    We have created a standard template for the definition of classes for the regulation
    of a biological process. This includes the definitions for positive and negative
    regulation. The equivalence axiom templates are "GO:0065007 and 'regulates' some
    X" (regulation), "GO:0065007 and 'negatively_regulates' some X" (negative regulation),
    and "GO:0065007 and 'positively_regulates' some X" (positive regulation), where
    X is a biological process.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000059
  title: Representation of regulation in the Gene Ontology (molecular function)
  description: |-
    We have created a standard template for the definition of classes for the regulation
    of a molecular function. This includes the definitions for positive and negative
    regulation. The equivalence axiom templates are "GO:0065007 and 'regulates' some
    X" (regulation), "GO:0065007 and 'negatively_regulates' some X" (negative regulation),
    and "GO:0065007 and 'positively_regulates' some X" (positive regulation), where
    X is a molecular function.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000060
  title: Representation of processes involved in other process in the Gene Ontology
  description: |-
    We have created a standard template for classes describing processes involved
    in other processes. The underlying equivalence axiom template is "P and 'part_of'
    some W", where P and W are biological processes.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000061
  title: Representation of a molecular function involved in a biological process in
    the Gene Ontology
  description: |-
    We have created a standard template for classes describing molecular function
    involved in other biological processes. The underlying equivalence axiom template
    is "P and 'part_of' some W", where P is a molecular function and W is a biological
    processes.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000062
  title: Representation of processes occurring in parts of the cell in the Gene Ontology
  description: |-
    We have created a standard template for classes describing processes occurring
    in parts of the cell. The underlying equivalence axiom template is "P and 'occurs
    in' some C", where P is a biological process and C is a cellular component.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000063
  title: Representation of processes regulated by other regulating processes in the
    Gene Ontology
  description: |-
    We have created a standard template for classes describing processes regulated
    by other regulating processes. The underlying equivalence axiom template is "R
    and 'results_in' some P", where R is a biological process and P is a regulation
    of biological process subclass.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000064
  title: Representation of cell components as part of other cell components in the
    Gene Ontology
  description: |-
    We have created a standard template for classes describing cell components as
    part of other cell components. The underlying equivalence axiom template is "P
    and 'part_of' some W", where P and W are cell components.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000065
  title: Representation of transport of a chemical entity as a biological process
    in the Gene Ontology
  description: |-
    We have created a standard template for classes describing transport of a chemical
    entity (ChEBI) as a biological process. The underlying equivalence axiom template
    is "GO:0006810 and 'transports or maintains localization of' some X", where X
    is a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI has been
    described in the following publication: PMID:23895341.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000066
  title: Representation of transport of a chemical entity as molecular function in
    the Gene Ontology
  description: |-
    We have created a standard template for classes describing the transport of a
    chemical entity (ChEBI) as a molecular function. The underlying equivalence axiom
    template is "GO:0005215 and 'transports or maintains localization of' some X",
    where X is a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI
    has been described in the following publication: PMID:23895341.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000067
  title: Representation of binding to a chemical entity as molecular function in the
    Gene Ontology
  description: |-
    We have created a standard template for classes describing the binding to a chemical
    entity (ChEBI) as a molecular function. The underlying equivalence axiom template
    is "GO:0005488 and 'has input' some X", where X is a chemical entity (CHEBI:24431).
    The approach to combine GO and ChEBI has been described in the following publication:
    PMID:23895341.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000068
  title: Representation of metabolic triad (metabolism, catabolism, biosynthesis)
    as biological process in the Gene Ontology
  description: |-
    We have created a standard template for classes each describing the metabolism,
    catabolism, or biosynthesis of a chemical entity (ChEBI) as a process. The underlying
    equivalence axiom templates are "GO:0008152 and 'has participant' some X" (metabolism),
    "GO:0009056 and 'has input' some X" (catabolism), "GO:0009058 and 'has output'
    some X" and (biosynthesis),  where X is a chemical entity (CHEBI:24431). The approach
    to combine GO and ChEBI has been described in the following publication: PMID:23895341.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000069
  title: Representation of transmembrane transport of a chemical as biological process
    in the Gene Ontology
  description: |-
    We have created a standard template for classes describing the transmembrane transport
    of a chemical entity (ChEBI) as a biological process. The underlying equivalence
    axiom template is "GO:0055085 and 'transports or maintains localization of' some
    X", where X is a chemical entity (CHEBI:24431). The approach to combine GO and
    ChEBI has been described in the following publication: PMID:23895341.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000070
  title: Representation of transmembrane transporter activity as molecular function
    in the Gene Ontology
  description: |-
    We have created a standard template for classes describing the transmembrane transporter
    activity a chemical entity (ChEBI) as molecular function. This includes variants
    for secondary active transmembrane transporter activity (GO:0015291), uptake transmembrane
    transporter activity (GO:0015563), and ATPase activity, coupled to transmembrane
    movement of substances (GO:0042626). The underlying equivalence axiom template
    is "G and 'transports or maintains localization of' some X",  where the genus
    G is either GO:0022857 (transmembrane transporter activity), GO:0015291, GO:0015563,
    or GO:0042626 depending on the variant. The variable X is a chemical entity (CHEBI:24431).
    The approach to combine GO and ChEBI has been described in the following publication:
    PMID:23895341.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000071
  title: Representation of response to and cellular response to a chemical as biological
    process in the Gene Ontology
  description: |-
    We have created a standard template for classes describing the response to and
    cellular response to a chemical entity (ChEBI) as a biological process. The underlying
    equivalence axiom templates are "GO:0050896 and 'has input' some X" (response
    to) and "GO:0070887 and 'has input' some X" (cellular response to), where X is
    a chemical entity (CHEBI:24431). The approach to combine GO and ChEBI has been
    described in the following publication: PMID:23895341.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000072
  title: Representation of chemical homeostasis and cellular chemical homeostasisl
    as biological process in the Gene Ontology
  description: |-
    We have created a standard template for classes describing the homeostasis and
    cellular homeostasis for a chemical entity (ChEBI) as a biological process. The
    underlying equivalence axiom templates are "GO:0048878 and 'regulates level of'
    some X" (homeostasis) and "GO:0055082 and 'regulates level of' some X" (cellular
    homeostasis), where X is a chemical entity (CHEBI:24431). The approach to combine
    GO and ChEBI has been described in the following publication: PMID:23895341.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000073
  title: Representation of import of a chemical as biological process in the Gene
    Ontology
  description: |-
    We have created a standard template for classes describing the import of a chemical
    entity (ChEBI) as a biological process. The underlying equivalence axiom template
    is "GO:0006810 and 'imports' some X", where X is a chemical entity (CHEBI:24431).
    The approach to combine GO and ChEBI has been described in the following publication:
    PMID:23895341.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000074
  title: Representation of export of a chemical as biological process in the Gene
    Ontology
  description: |-
    We have created a standard template for classes describing the export of a chemical
    entity (ChEBI) as a biological process. The underlying equivalence axiom template
    is "GO:0006810 and 'exports' some X", where X is a chemical entity (CHEBI:24431).
    The approach to combine GO and ChEBI has been described in the following publication:
    PMID:23895341.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000075
  title: Representation of transport of a chemical into a cellular component as biological
    process in the Gene Ontology
  description: |-
    We have created a standard template for classes describing the transport of a
    chemical entity (ChEBI) into a cellular component as a biological process. The
    underlying equivalence axiom template is "GO:0006810 and 'has_target_end_location'
    some T and 'imports' some S", where T is a cellular component and S is a chemical
    entity (CHEBI:24431). The approach to combine GO and ChEBI has been described
    in the following publication: PMID:23895341.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000076
  title: Representation of transport or vesicle-mediated transport from cell component
    to cell component as biological process in the Gene Ontology
  description: |-
    We have created a standard template for classes describing the transport or vesicle-mediated
    transport from cellular component to cellular component as a biological process.
    The underlying equivalence axiom templates are "GO:0006810 and 'has_target_start_location'
    some F and 'has_target_end_location' some T" (transport) and "GO:0016192 and
    'has_target_start_location' some F and 'has_target_end_location' some T" (vesicle-mediated
    transport), where F and T are a cellular components.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000077
  title: OBSOLETE Representation of transport of a cellular component as biological
    process in the Gene Ontology
  description: |-
    We have created a standard template for classes describing the transport or vesicle-mediated
    transport of a cellular component as a biological process. The underlying equivalence
    axiom templates are "GO:0006810 and 'transports or maintains localization of'
    some C" (transport) and "GO:0016192 and 'transports or maintains localization
    of' some C" (vesicle-mediated transport), where C is a cellular component.
  authors: GO Ontology Editors
  year: 2013
  is_obsolete: true
- id: GO_REF:0000078
  title: 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
  description: |-
    We have created a standard template for classes describing the transport or vesicle-mediated
    transport of a chemical entity (ChEBI) from and/or to a cellular component as
    a biological process. The underlying equivalence axiom templates are "GO:0006810
    and 'transports or maintains localization of' some X [ and 'has_target_start_location'
    some F] [ and 'has_target_end_location' some T]" (transport) and "GO:0016192 and
    'transports or maintains localization of' some X [ and 'has_target_start_location'
    some F] [ and 'has_target_end_location' some T]" (vesicle-mediated transport),
    where F and T are cellular components and X is a chemical entity (CHEBI:24431).
    The approach to combine GO and ChEBI has been described in the following publication:
    PMID:23895341.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000079
  title: Representation of assembly or disassembly of a cell component as biological
    process in the Gene Ontology
  description: |-
    We have created a standard template for classes describing the assembly or disassembly
    of a cellular component as a biological process. The underlying equivalence axiom
    templates are "GO:0022607 and 'results_in_assembly_of' some C" (assembly) and
    "GO:0022411 and 'results_in_disassembly_of' some C" (disassembly), where C is
    a cellular component.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000080
  title: Representation of plant development as biological process in the Gene Ontology
  description: |-
    We have created a standard template for classes describing the development of
    a plant structure as a biological process. The underlying equivalence axiom template
    is "'anatomical structure development' and 'results in development of' some P",
    where P is a plant anatomical entity (PO:0025131).
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000081
  title: Representation of plant formation as biological process in the Gene Ontology
  description: |-
    We have created a standard template for classes describing the formation of a
    plant structure as a biological process. The underlying equivalence axiom template
    is "'anatomical structure formation involved in morphogenesis' and 'results in
    formation of' some P", where P is a plant anatomical entity (PO:0025131).
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000082
  title: OBSOLETE Representation of plant maturation as biological process in the
    Gene Ontology
  description: |-
    We have created a standard template for classes describing the maturation of a
    plant structure as a biological process. The underlying equivalence axiom template
    is "'developmental maturation' and 'results in developmental progression of' some
    P", where P is a plant anatomical entity (PO:0025131).
  authors: GO Ontology Editors
  is_obsolete: true
  year: 2013
- id: GO_REF:0000083
  title: Representation of plant morphogenesis as biological process in the Gene Ontology
  description: |-
    We have created a standard template for classes describing the morphogenesis of
    a plant structure as a biological process. The underlying equivalence axiom template
    is "'anatomical structure morphogenesis' and 'results in morphogenesis of' some
    P", where P is a plant anatomical entity (PO:0025131).
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000084
  title: Representation of plant structural organization as biological process in
    the Gene Ontology
  description: |-
    We have created a standard template for classes describing the structural organization
    of a plant structure as a biological process. The underlying equivalence axiom
    template is "'anatomical structure arrangement' and 'results in structural organization
    of' some P", where P is a plant anatomical entity (PO:0025131).
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000085
  title: Representation of cell apoptotic process as biological process in the Gene
    Ontology
  description: |-
    We have created a standard template for classes describing the apoptotic process
    for a cell type as a biological process. The underlying equivalence axiom template
    is "'apoptotic process' and 'occurs in' some C", where C is a native cell (CL:0000003).
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000086
  title: Representation of cell differentiation as biological process in the Gene
    Ontology
  description: |-
    We have created a standard template for classes describing the differentiation
    process for a cell type as a biological process. The underlying equivalence axiom
    template is "GO:0030154 and 'results in acquisition of features of' some C", where
    C is a native cell (CL:0000003).
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000087
  title: Representation of protein localization and establishment of protein localization
    as biological process in the Gene Ontology
  description: |-
    We have created a standard template for classes describing the protein localization
    and establishment of protein localization to a cellular component as a biological
    process. The underlying equivalence axiom templates are "GO:0008104 and
    'has_target_end_location' some C" (protein localization) and "GO:0045184 and
    'has_target_end_location' some C" (establishment of protein localization), where C
    is cellular component.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000088
  title: Representation of protein complex by molecular function in the Gene Ontology
  description: |-
    We have created a standard template for classes defining a protein complex by
    a molecular function as a cellular component. The underlying equivalence axiom
    template is "GO:0043234 and 'capable_of' some ?A", where A is a molecular function.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000089
  title: Representation of single-organism and multi-organism biological processes
    in the Gene Ontology
  description: |-
    We have created a standard template for classes describing the single-organism
    and multi-organism biological processes. The underlying equivalence axiom templates
    are "P and 'bearer_of' some PATO:0002487" (single-organism) and "P and 'bearer_of'
    some PATO:0002486" (multi-organism), where P is a biological process.
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000090
  title: Automatic creation of relationships between ontology branches in the Gene
    Ontology
  description: |-
    We have created a rule-based approach to create relations between the branches
    of the Gene Ontology. The approach uses the equivalence axioms and a given pattern
    to create non-subClassOf relationships between the three different branches of
    the Gene Ontology (biological process, molecular function, cellular component).
    Currently, there are the following rules: "'transporter activity' and
    'transports_or_maintains_localization_of' some X' -part_of-> "transport and
    'transports_or_maintains_localization_of' some X"; "'transmembrane transporter activity'
    and 'transports_or_maintains_localization_of' some X -part_of-> 'transmembrane transport'
    and 'transports_or_maintains_localization_of' some X"
  authors: GO Ontology Editors
  year: 2013
- id: GO_REF:0000091
  title: Representation of cell migration as biological processes in the Gene Ontology
  description: |-
    We have created a standard template for classes describing the cell migration
    process for a cell type as a biological process. The underlying equivalence axiom
    template is "'cell migration' and 'alters_location_of' some C", where C is a native
    cell (CL:0000004).
  authors: GO Ontology Editors
  year: 2014
- id: GO_REF:0000092
  title: Representation for the biosynthesis from or via a chemical as biological
    process in the Gene Ontology
  description: |-
    We have created a standard template for classes describing the biosynthesis of
    a chemical entity from or via an other chemical entity as biological processes.
    The underlying equivalence axiom templates are "GO:0009058 and 'has output' some
    T and 'has input' some F" (biosynthesis from) and "GO:0009058 and 'has output'
    some T and 'has intermediate' some I" (biosynthesis via), where T,F, and I are
    chemical entities (CHEBI:24431). The approach to combine GO and ChEBI has been
    described in the following publication: PMID:23895341.
  authors: GO Ontology Editors
  year: 2014
- id: GO_REF:0000093
  title: Representation for the degradation to or via a chemical as biological process
    in the Gene Ontology
  description: |-
    We have created a standard template for classes describing the degradation of
    a chemical entity to or via an other chemical entity as biological processes.
    The underlying equivalence axiom templates are "GO:0009056 and 'has input' some
    S and 'has output' some T" (catabolism to) and "GO:0009056 and 'has input' some
    S and 'has intermediate' some I" (catabolism via), where S,T, and I are chemical
    entities (CHEBI:24431). The approach to combine GO and ChEBI has been described
    in the following publication: PMID:23895341.
  authors: GO Ontology Editors
  year: 2014
- id: GO_REF:0000094
  title: Representation of metazoan development as biological process in the Gene
    Ontology
  description: |-
    We have created a standard template for classes describing the development of
    a metazoan structure as a biological process. The underlying equivalence axiom
    template is "'anatomical structure development' and 'results in development of'
    some E", where E is a anatomical entity (UBERON:0001062).
  authors: GO Ontology Editors
  year: 2014
- id: GO_REF:0000095
  title: Literature reference not indexed by PubMed
  description: This article is not referenced in PubMed. Please see contributing data
    resource for details.
  authors: Mouse Genome Informatics Scientific Curators and FlyBase
  year: 2014
- id: GO_REF:0000096
  title: Automated transfer of experimentally-verified manual GO annotation data to 
    mouse-rat orthologs
  description: |-
    The Alliance of Genome Resources (https://www.alliancegenome.org/) has procedures in 
    place to establish orthology relationships between genes. The experimentally-based 
    annotations (IDA, IMP IPI, IGI, and EXP) annotated by Rat Genome Database (RGD) and 
    The Mouse Genome Database (MGD) are used to provide annotations to the respective 
    mouse and rat orthologs, and given the ISO evidence code and an entry in the "With 
    (or) From" field to indicate the orthologous entity.
  authors: The Gene Ontology Consortium
  external_accession:
    - J:155856
  year: 2014
- id: GO_REF:0000097
  title: Gene Ontology annotation based on personal communication to FlyBase
  description: |-
    FlyBase occasionally makes GO annotations based on information that has been sent
    to us directly by researchers as a personal communication to FlyBase. In each
    case, the full details of the communication including any associated data and
    analyses are recorded in a FlyBase publication (FBrf) available from our website
    (http://flybase.org).
  authors: FlyBase
  year: 2014
- id: GO_REF:0000098
  title: OBSOLETE Gene Ontology annotation based on research conference abstracts
  description: |-
    Prior to 2008, FlyBase made GO annotations based on information in abstracts for
    research conferences, primarily the Annual Drosophila Research Conference and
    the European Drosophila Research Conference. We no longer curate conference abstracts
    and we are gradually replacing all abstract-based GO annotation with annotation
    based on experimental data in primary research papers.
  authors: FlyBase
  is_obsolete: true
  year: 2014
- id: GO_REF:0000099
  title: OBSOLETE Gene Ontology annotation based on DNA/RNA sequence records
  description: |-
    Prior to 2005, FlyBase made GO annotations based on information in DNA/RNA sequence
    records in GenBank/EMBL/DDBJ. We no longer add GO annotations based on sequence
    records and gradually replacing these GO annotations as other sources of evidence
    become available.
  authors: FlyBase
  is_obsolete: true
  year: 2014
- id: GO_REF:0000100
  title: OBSOLETE Gene Ontology annotation by SEA-PHAGE biocurators
  description: |-
    This GO reference describes the criteria used by biocurators of the SEA-PHAGE
    consortium for the annotation of predicted gene products from newly sequenced
    bacteriophage genomes in the SEA-PHAGE phagesdb.org and other databases and in
    the GenBank records periodically released to NCBI for these genomes. In particular,
    this GO reference describes the criteria used to assign evidence codes ISS, ISA,
    ISO, ISM, IGC and ND. To assign ISS, ISA, ISO and ISM evidence codes, SEA-PHAGE
    biocurators use a varied array of bioinformatics tools to establish homology and
    conservation of sequence and structure functional determinants with proteins from
    multiple organisms with published association to experimental GO terms and lacking
    NOT qualifiers. These proteins are referenced in the WITH field of the annotation
    using their xref database accession. The primary tools for homology search in
    ISS, ISA, ISO and ISM assignments are BLASTP and HHpred, using a maximum e-value
    of 10^-7 for BLASTP and a minimum probability of 0.9 for HHpred, and manual inspection
    of alignments in both cases. For ISS and ISA assignments, BLASTP alignments are
    required to have at least 75% coverage and 30% identity. For ISO assignments,
    orthology is further validated using reciprocal BLASTP with the identified hit.
    For HHpred results, ISS or ISM annotations are made only if the source for the
    original GO annotation explicitly defines a matched domain function, or if more
    than half of the domains of the query protein are identified in the matching protein.
    All ISS, ISA, ISO and ISM assignments entail the manual verification of the source
    for the GO term in the matching protein sequence and critical curator assessment
    of the likelihood of preservation of function, process or component in the context
    of bacteriophage biology. IGC codes are assigned on the basis of suggestive evidence
    for function based on synteny, as inferred from whole-genome comparative analyses
    of multiple bacteriophage genomes using primarily the Phamerator software platform,
    and with special emphasis on the bacteriophage virion structure and assembly genes.
    When extensive review of published literature on putative homologs reveals no
    experimental evidence of function, component or process for a particular gene
    product, it is assigned an ND evidence code and annotated to the root term for
    Cellular Component, Molecular Function and Biological Process. As part of the
    review process for assignment of ISS, ISA, ISO, IGC and ISM evidence codes, SEA-PHAGE
    curators are required to analyze the reference literature for identified matches
    and shall perform GO annotations with appropriate evidence codes if these were
    not available.
  authors: Ivan Erill, SEA-PHAGE Biocurators
  is_obsolete: true
  year: 2014
- id: GO_REF:0000101
  title: Automated transfer of experimentally-verified GO annotation data to close
    orthologs
  description: |-
    This reference is used to describe functional annotations transferred from one
    or more reference ("source") organisms to a newly annotated ("target") organism
    on the basis of ortholog cluster membership. In detail, predicted (e.g. by AUGUSTUS,
    see doi:10.1186/1471-2105-7-62) or transferred (e.g. via RATT, see doi:10:1093/nar/gkg1268)
    gene models in the target genome are translated and processed by OrthoMCL 1.4
    together with reference protein sequences to produce clusters of gene products
    derived from orthologous genes. For each cluster, GO terms are automatically transferred
    from source products to the target gene products if they are experimentally verified
    (IDA (ECO:0000314), IMP (ECO:0000315), IPI (ECO:0000353), IGI (ECO:0000316), (EXP
    ECO:0000269). They are tagged with the ISO evidence code and the "with/from" is
    populated with the source feature references (e.g. "GeneDB:LmjF.28.0960"). OrthoMCL
    runs are done using the parameterization suggested in the OrthoMCL algorithm document
    (blastall -F 'm S' -e 1e-5).
  authors: Sascha Steinbiss, GeneDB Curators
  year: 2015
- id: GO_REF:0000102
  title: OBSOLETE Representation of cellular component binding as molecular functions
    in the Gene Ontology
  description: |-
    We have created a standard template for classes cellular component binding as
    a molecular function. The underlying equivalence axiom template is "'binding'
    and 'has input' some C", where C is a cellular component (GO:0005575).
  authors: GO Ontology Editors
  is_obsolete: true
  year: 2015
- id: GO_REF:0000103
  title: OBSOLETE Representation of cellular component organization as biological
    process in the Gene Ontology
  description: |-
    We have created a standard template for classes cellular component organization
    as a biological process. The underlying equivalence axiom template is "'cellular
    component organization' and 'results_in_organization_of' some C", where C is a
    cellular component (GO:0005575).
  authors: GO Ontology Editors
  is_obsolete: true
  year: 2015
- id: GO_REF:0000104
  title: Electronic Gene Ontology annotations created by transferring manual GO annotations
    between related proteins based on shared sequence features
  description: |-
    GO terms are manually assigned to each rule in UniRule. These rules are prepared
    manually by UniProt curators based on the annotations present in reviewed UniProtKB/Swiss-Prot
    records that share sequence features, sequence similarity and taxonomy. The assigned
    GO terms are then transferred to all unreviewed UniProtKB/TrEMBL proteins that
    meet the conditions given in the UniRule rule. GO annotations using this technique
    receive the evidence code Inferred from Electronic Annotation (IEA; ECO:0000501).
    These annotations are updated regularly by UniProt and are available for download
    on both the GO and GOA EBI ftp sites. To report an annotation error or inconsistency,
    or for further information, please contact the UniProt Automated Annotation team
    at automated_annotation@ebi.ac.uk. UniRule is a collaboration between the European
    Bioinformatics Institute (EMBL-EBI), the Swiss Institute of Bioinformatics (SIB),
    and the Protein Information Resource at Georgetown University (PIR). For further
    information, please see UniProt: a hub for protein information Nucleic Acids Res.
    2015, 43, D204, doi: 10.1093/nar/gku989 or www.uniprot.org.
  authors: UniProt Curators
  external_accession:
    - ZFIN:ZDB-PUB-170525-1
    - J:342612
    - SGD_REF:S000181514
  year: 2015
- id: GO_REF:0000105
  title: Gene Ontology annotation of transfer RNAs based on tRNAscan-SE analysis of
    the Drosophila melanogaster genome (2002)
  description: |-
    Gene Ontology annotation based on predicted cytoplasmic tRNAs using tRNAscan-SE
    analysis (doi: 10.1093/nar/25.5.0955) of the Drosophila melanogaster genome (2002).
    Annotations have been reviewed by FlyBase (2015) and found to be consistent when
    compared with the most recent tRNAscan-SE analysis of the genome
    (http://gtrnadb.ucsc.edu/genomes/eukaryota/Dmela6/).
  authors: FlyBase
  external_accession:
    - FB:FBrf0145624
  year: 2016
- id: GO_REF:0000106
  title: OBSOLETE Gene Ontology annotation based on protein sequence records
  description: |-
    Between 1986 and 2005 GO annotations were made by FlyBase curators based on information
    in UniProtKB/Swiss-Prot protein sequence records. We no longer add GO annotations
    based on sequence records and are gradually replacing these GO annotations as
    other sources of evidence become available.
  authors: FlyBase
  is_obsolete: true
  year: 2016
- id: GO_REF:0000107
  title: Automatic transfer of experimentally verified manual GO annotation data to
    orthologs using Ensembl Compara
  description: |-
    GO terms from a source species are projected onto one or more target species based
    on gene orthology obtained from Ensembl Compara. One-to-one, one-to-many and many-to-many
    orthology relations and anntations are transferred between orthologs that have
    at least a 40% peptide identity to each other. Only GO annotations with evidence
    codes ECO:0000314 (IDA), ECO:0000270 (IEP), ECO:0000316 (IGI), ECO:0000315 (IMP),
    and ECO:0000353 (IPI), or their descendants, are transferred; annotations with
    a 'NOT' qualifier are not transferred, and neither are annotations to GO:0005515
    (protein binding). Annotations that are transferred using this method receive
    the evidence code ECO:0000265 (sequence orthology evidence used in automatic assertion),
    which maps up to the GO Inferred from Electronic Annotation (IEA) evidence code.  The
    model organism database identifier of the annotation source will be indicated
    in the 'With' column of the GOA association file.
  authors: GOA Curators
  external_accession:
    - J:342605
  year: 2016
- id: GO_REF:0000108
  title: Automatic assignment of GO terms using logical inference, based on on inter-ontology
    links
  description: |-
    GO terms are automatically assigned based on inter-ontology links to generate
    inferred annotations. 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.
  authors: GOA Curators
  external_accession:
    - J:346132
    - SGD_REF:S000204515
  year: 2016
- id: GO_REF:0000109
  title: Gene Ontology annotation based on curation of genome-wide subcellular localisation
    of proteins using fluorescent protein tagging in Trypanosoma brucei
  description: |-
    Trypanosomes are exquisitely structured cells in which protein localisation can
    be extremely informative for likely function. TrypTag is a project using expression
    of N- and C-terminal mNeonGreen fusion proteins from the endogenous loci to determine
    the subcellular localisation of every gene in the Trypanosoma brucei genome. GO
    Cellular Component terms are manually assigned by curators studying fluorescence
    microscope images of the resulting cells labelled with mNeonGreen fusion proteins.
    As trypanosomes are a pathogenic basal eukaryote, this will indicate likely function
    of both highly conserved eukaryote genes and parasite-specific genes. Resource
    URL: http://www.tryptag.org Protein subcellular localisation images can be viewed
    on the Tryptag website, e.g. http://www.tryptag.org?id=Tb927.8.1550
  authors: TrypTag
  year: 2016
- id: GO_REF:0000110
  title: Gene Ontology annotation of Drosophila melanogaster nuclear genes encoding
    proteins targeted to the mitochondrion
  description: |-
    Gene Ontology annotation of Drosophila melanogaster nuclear genes encoding proteins
    targeted to the mitochondrion based on analysis by MitoDrome (http://mitodrome.ba.itb.cnr.it/)
    by comparison of human mitochondrial proteins available in SWISSPROT vs. the Drosophila
    genome, ESTs and cDNA sequences available in the FlyBase database (PMID:12520013).
  authors: FlyBase
  external_accession:
    - FB:FBrf0159903
  year: 2003
- id: GO_REF:0000111
  title: Gene Ontology annotations Inferred by Curator (IC) using at least one Inferred
    by Sequence Similarity (ISS) annotation to support the inference
  description: |-
    The Gene Ontology Consortium uses the IC (Inferred by Curator; ECO:0000305) 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:0000111 indicates that a curator inferred
    the GO term based on at least one supporting annotation with an 'Inferred from
    Sequence Similarity' (ISS; ECO:0000250) evidence code.  Note that additional supporting
    annotations may be experimentally evidenced. When using GO_REF:0000111, the 'with/from'
    field must contain all GO identifiers used as supporting annotations.
  authors: TBD
  external_accession:
    - FB:FBrf0233689
    - J:342606
  year: 2016
- id: GO_REF:0000112
  title: OBSOLETE Gene Ontology annotation by CACAO biocurators
  description: |-
    This GO reference describes the criteria used by biocurators participating in
    the Community Assessment of Community Annotation with Ontologies (CACAO) to annotate
    gene products from genomes of interest through the use of computational methods
    to establish and manually validate function or homology to gene products. In particular,
    this GO reference describes the criteria used to make annotations based on evidence
    codes ISS, ISA, ISO, ISM and IGC. To perform ISS-, ISA-, and ISO-based annotations
    on a gene product, CACAO biocurators use sequence- and structure-based search
    algorithms (e.g. BLASTP, HHPred) to establish homology, conservation of sequence
    and structure functional determinants between the target gene product and gene
    products from other organisms with published GO annotations supported by experimental
    codes and lacking NOT qualifiers. These gene products are referenced in the WITH
    field of the annotation using their xref database accession. ISM-based annotations
    make use of published computational methods (e.g. TMHMM, SignalP) to predict gene
    product structure, localization or function. IGC-based annotations are made on
    the basis of suggestive evidence for function based on synteny. Parameters and
    criteria for use of all computational methods (e.g. e-value) are listed and versioned
    in the publicly available CACAO documentation (http://gowiki.tamu.edu/). Annotations
    made by CACAO biocurators are reviewed by CACAO team instructors before their
    release.
  authors: Ivan Erill, James Hu, Community Assessment of Community Annotation with
    Ontologies
  is_obsolete: true
  year: 2017
- id: GO_REF:0000113
  title: Gene Ontology annotation of human sequence-specific DNA binding transcription
    factors (DbTFs) based on the TFClass database
  description: |-
    The TFClass (http://tfclass.bioinf.med.uni-goettingen.de/index.jsf) database provides
    a comprehensive classification of mammalian DNA binding transcription factors
    (DbTFs) based on their DNA binding domains (DBDs) (PMID:29087517). TFClass classifies
    mammalian DbTFs by a five-level classification in which the four highest levels
    represent groups defined by structural and sequence similarities (superclass,
    class, family, subfamily, and genera) (more details at
    http://www.edgar-wingender.de/TFClass_schema.html). This classification is based on
    the combination of background knowledge of the molecular structural features of DBDs
    (PMID:9340487, PMID:23427989) and phylogenetic trees constructed via multiple sequence
    alignment with hierarchical clustering of manually validated DBDs and/or full-length
    protein sequences retrieved from UniProt (PMID:23427989, PMID:23180794, PMID:23427989).

    The NTNU curation team has evaluated each family and assigned a molecular function
    annotation, GO:0000981 (DNA-binding transcription factor activity, RNA polymerase
    II-specific), and a cellular component annotation GO:0000790 (nuclear chromatin),
    as appropriate. The superclass/class/family or subfamily ID is specified in the
    "With/From" field. The annotations are supported by the evidence code ECO:0005556
    (multiple sequence alignment evidence used in manual assertion).
  authors: Marcio Luis Acencio (1), George Georghiou (2), Sandra Orchard (2), Liv Thommensen
    (1), Martin Kuiper (1) and Astrid Lægreid (1). (1) Norwegian University of Science
    and Technology (NTNU), Trondheim, Norway; (2) European Bioinformatics Institute
    (EBI), Hinxton, Cambridgeshire, United Kingdom
  year: 2018
- id: GO_REF:0000114
  title: Manual transfer of experimentally-verified manual GO annotation data to homologous
    complexes by curator judgment of sequence, composition and function similarity
  description: |-
    Method for transferring manual annotations to an entry based on a curator's judgment
    of its similarity to a putative homolog that has annotations that are supported
    with experimental evidence. Annotations are created when a curator judges that
    the sequence, composition and function of a complex shows high similarity to another
    complex that has annotation(s) supported by experimental evidence (and therefore
    display one of the evidence codes ECO:0000353 [IPI] or ECO:0005543). Annotations
    resulting from the transfer of GO terms display the ECO:0005610, ECO:0005544 or
    ECO:0005546 evidence codes and include an accession for the complex from which
    the annotation was projected in the 'with/from' field (column 8). This field MUST
    contain a Complex Portal accession identifier. Putative homologs are chosen using
    information combined from a variety of complementary sources. Potential homologs
    are initially identified using sequence similarity search programs such as BLAST.
    Homologous relationships are then verified manually using a combination of resources
    including sequence analysis tools, phylogenetic and comparative genomics databases
    such as Ensembl Compara, INPARANOID and OrthoMCL, as well as other specialised
    databases such as species-specific collections (e.g. HGNC's HCOP). In all cases
    curators check the alignments for each complex component and use their experience
    to assess whether similarity is considered to be strong enough to infer that the
    two proteins have a common function so that they can confidently project an annotation.
    While there is no fixed cut-off point in percentage sequence similarity, generally
    proteins which have greater than 70% identity that covers greater than 90% of
    the length of both proteins are examined further. Whilst we expect subunit composition
    to be conserved between closely related species, this is not an absolute rule
    and orthologous complexes may differ if a subunit cannot be traced in one species
    or is experimentally shown not to be present. When there is evidence of multiple
    paralogs for a single species, multiple variants of the complex can be inferred.
  authors: Birgit Meldal and Sandra Orchard (1). (1) European Bioinformatics Institute
    (EBI), Hinxton, Cambridgeshire, United Kingdom
  external_accession:
    - J:342607
    - SGD_REF:S000250427
  year: 2018
- id: GO_REF:0000115
  title: Automatic Gene Ontology annotation of non-coding RNA sequences through association
    of Rfam records with GO terms
  description: |-
    Rfam (http://rfam.org, PMID:29112718) is a database of non-coding RNA families
    which are manually annotated with GO terms by Rfam curators. RNAcentral (http://rnacentral.org,
    PMID:27794554) maintains a comprehensive collection of non-coding RNA sequences
    that are regularly annotated with Rfam families using the Infernal software (PMID:24008419).
    When a non-coding RNA sequence is matched to one or more Rfam families by sequence
    similarity, the GO terms associated with the Rfam family are transitively assigned
    to the non-coding RNA sequence. Annotations resulting from the transfer of GO
    terms are assigned the ECO:0000256 evidence code (match to sequence model evidence
    used in automatic assertion) and include RNAcentral and Rfam accessions. The annotations
    are available on the GOA and EMBL-EBI FTP sites. 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.
  authors: RNAcentral (1). (1) European Bioinformatics Institute (EMBL-EBI), Hinxton,
    Cambridgeshire, United Kingdom
  external_accession:
    - FB:FBrf0253064
    - SGD_REF:S000246363
  year: 2018
- id: GO_REF:0000116
  title: Automatic Gene Ontology annotation based on Rhea mapping
  description: |-
    Rhea (https://www.rhea-db.org/, PMID:30272209) is an expert-curated knowledgebase
    of chemical and transport reactions of biological interest - and the standard
    for enzyme and transporter annotation in UniProtKB (PMID:31688925). Rhea uses
    the chemical dictionary ChEBI (Chemical Entities of Biological Interest) to describe
    reaction participants and their chemical transformations in a computationally
    tractable manner. GO terms corresponding to Rhea reactions are assigned a Rhea
    database cross-reference. The corresponding GO term is automatically applied to
    all UniProt entries annotated with a Rhea reaction. The mapping file is available
    at: http://current.geneontology.org/ontology/external2go/rhea2go.
  authors: GO Central Curators, GOA Curators, Rhea Curators
  external_accession:
    - J:342608
    - ZFIN:ZDB-PUB-221108-20
    - SGD_REF:S000309092
  citation: PMID:30272209
  year: 2020
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  description: |-
    Association-Rule-Based Annotator (ARBA) predicts Gene Ontology (GO) terms among
    other types of functional annotation such as Protein Description (DE), Keywords
    (KW), Enzyme Commission numbers (EC), subcellular LOcation (LO), etc. For all
    annotation types, reviewed UniProtKB/Swiss-Prot records having manual annotations
    as reference data are used to perform the machine learning phase and generate
    prediction models. For GO terms, ARBA has an additional feature to augment reference
    data using the relations between GO terms in the GO graph. The data augmentation
    is based on adding more general annotations into records containing manual GO
    terms, which will result in richer reference data. The predicted GO terms are
    then propagated to all unreviewed UniProtKB/TrEMBL proteins that meet the conditions
    of ARBA models. GO annotations using this technique receive the evidence code
    Inferred from Electronic Annotation (IEA; ECO:0000501). Links: ARBA documentation
    at UniProt (https://www.uniprot.org/help/arba), Blog on ARBA
    (http://insideuniprot.blogspot.com/2020/09/association-rule-based-annotator-arba.html).
  authors: UniProt
  external_accession:
    - J:342609
    - ZFIN:ZDB-PUB-221108-21
    - SGD_REF:S000315490
  year: 2021
- id: GO_REF:0000118
  title: TreeGrafter-generated GO annotations
  description: |-
    TreeGrafter is a software tool for annotating protein sequences using pre-annotated
    PANTHER phylogenetic trees. TreeGrafter takes an input query protein sequence,
    finds the best matching homologous family, and then grafts it to the best location
    in the tree. It then annotates the query sequence by propagating annotations from
    the appropriate ancestral node(s) in the reference tree, which were manually annotated
    using the PAN-GO method (see GOREF_0000033). This method is integrated into InterProScan,
    which produces annotations to millions of genes across tens of thousands of organisms.

    The full method is described in PMID:30032202.
  authors: Haiming Tang, Dustin Ebert, Matthias Blum, Robert Finn, Paul Thomas
  year: 2023
  is_obsolete: false
- id: GO_REF:0000119
  title: Automated transfer of experimentally-verified manual GO annotation data to 
    mouse-human orthologs
  description: |-
    The Alliance of Genome Resources (https://www.alliancegenome.org/) has procedures in 
    place to establish orthology relationships between genes. The experimentally-based 
    annotations (IDA, IMP IPI, IGI, and EXP) for human genes generated by the GOA pipeline 
    are used to provide annotations to the respective mouse orthologs, and given the ISO 
    evidence code and an entry in the "With (or) From" field to indicate the orthologous 
    entity.
  authors: The Gene Ontology Consortium
  year: 2023
  external_accession:
    - J:164563
  is_obsolete: false
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  description: |-
    An automated process that integrates identical annotations from multiple electronic pipelines,
    including UniRule(GO_REF:0000104), ARBA(GO_REF:0000117), InterPro2GO(GO_REF:0000002), 
    TreeGrafter2GO(GO_REF:0000118), RHEA2GO(GO_REF:0000116), KeyWord2GO(GO_REF:0000004), 
    SubCellular2GO(GO_REF:0000109), EC2GO(GO_REF:0000003), and EnsEMBL Compara(GO_REF:0000107). 
    This method reduces redundancy in automated GO annotations, offering a clearer and less 
    cluttered page view. The combined annotations use the ECO:0000501 evidence code, with the 
    sources of GO annotation assignments from individual IEA pipelines listed in the “with/from” field,
    separated by a pipe delimiter.
  authors: UniProt
  year: 2024
  is_obsolete: false
- id: GO_REF:0000121
  title: RGD ISO annotations to rat from other mammalian species
  description: |-
    RGD (https://rgd.mcw.edu/) imports high quality ortholog calls from the Human Gene 
    Nomenclature Committee's HCOP tool and the Alliance of Genome Resources for multiple mammalian species 
    and manually assigns orthologs between rat genes and those in other species where necessary based on 
    sequence similarity and synteny. Experimentally-based manual GO annotations (IDA, IMP IPI, IGI, and EXP) 
    from other RGD species are used to provide annotations to the respective rat orthologs. The resulting 
    annotations are given the ISO evidence code and an entry is made in the "With (or) From" field 
    to indicate the orthologous entity.
  authors: RGD
  year: 2025
  external_accession:
    - RGD:1624291
  is_obsolete: false
- id: GO_REF:0000122
  title: AtSubP analysis
  description: |-
    AtSubP predicts the subcellular localization of Arabidopsis protein sequences utilizing five diverse prediction modules,  
    aa composition, PSI-BLAST, & Position Spec. Scoring Matrix.
  authors: TAIR
  year: 2010
  external_accession:
    - TAIR:AnalysisReference:501780126
  is_obsolete: false
- id: GO_REF:0000123
  title: YeastPathways to GO-CAM conversion
  description: |-
    YeastPathways is a database of metabolic pathways and enzymes in the budding yeast Saccharomyces cerevisiae. YeastPathways content is manually curated and maintained by the curation team at the Saccharomyces Genome Database (SGD), the model organism database for budding yeast. Only genes involved in metabolic pathways and reactions are included in the set of 220 YeastPathways, but the YeastPathways also contained manual summaries of the pathways and a complete list of references used to construct each pathway. YeastPathways were built in from MetaCyc data in 2003 using the Pathways Tools software from Bioinformatics Research Group at SRI International, and in 2020 Yeast Pathways were converted from biopax3 to TTL files and loaded into Noctua, the curation tool from the Gene Ontology. YeastPathways are available at https://pathway.yeastgenome.org/ and as Noctua models.
    To create complete GO annotations for the individual enzymes in each pathway, the annotations logically constructed from the imported Noctua models were given the evidence code computational combinatorial evidence used in manual assertion (ECO:0000245), which corresponds to the GO evidence code RCA. This is further detailed in PMID:39530598.
  authors: SGD
  year: 2025
  is_obsolete: false
