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GO_REF Refactor
Raw
gorefs.yaml
- 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title: OBSOLETE GO Consortium unpublished data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: >-
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.
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: DDB, FB, MGI, GOA, ZFIN curators
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: >-
Transitive assignment using Enzyme Commission identifiers. This method is used
for any database entry, such as a protein record in UniProtKB or TrEMBL, that
has had an Enzyme Commission number assigned. The corresponding GO term is determined
using the EC cross-references in the GO molecular function ontology. Also see
Hill et al., Genomics (2001) 74:121-128. The mapping file is available at http://www.geneontology.org/external2go/ec2go.
alt_id:
- GO_REF:0000005
authors: GOA curators, MGI curators
citation: PMID:11374909
external_accession:
- MGI:2152096
- J:72245
- ZFIN:ZDB-PUB-031118-3
- SGD_REF:S000124037
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: http://www.ebi.ac.uk/GOA/ISS_method.html.
authors: AgBase, BHF-UCL, Parkinson's UK-UCL, dictyBase, HGNC, Roslin Institute,
FlyBase and UniProtKB curators.
external_accession:
- dictyBase_REF:9
- J:73065
- J:104715
- FB:FBrf0255270
is_obsolete: false
year: 2011
- id: GO_REF:0000025
title: 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: false
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: 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: false
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:S000146947
- TAIR:Communication:501741973
- MGI:MGI:4459044
- 'J:161428 '
- ZFIN:ZDB-PUB-110330-1
- FB:FBrf0232076
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
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
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 a manually curated resource of enzyme-catalyzed and spontaneous
chemical reactions. It provides a hierarchical representation of metabolic pathways.
Descriptions of the pathway(s) that a particular protein is involved in are included
in UniProtKB records.
UniPathway data are cross-linked to existing pathway resources such as KEGG and
MetaCyc. Further information on the UniPathway resource is available at http://www.unipathway.org/obiwarehouse/unipathway.
When a UniPathway pathway 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 UniPathway 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 UniPathway
pathways is maintained by the UniPathway team and is available at http://www.grenoble.prabi.fr/dev/obiwarehouse/download/unipathway/public/unipathway2go.tsv.
authors: UniProt-GOA
external_accession:
- ZFIN:ZDB-PUB-130131-1
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: >-
Transitive assignments using UniProtKB/Swiss-Prot keywords. The UniProtKB keyword
controlled vocabulary contains 10 different categories of information to UniProtKB
entries. Further information on 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 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 https://www.uniprot.org/help/keywords.. 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.
authors: UniProt-GOA
external_accession:
- SGD_REF:S000148669
- J:60000
- TAIR:AnalysisReference:501756968
- TAIR:AnalysisReference:501756970
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 manually 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://www.geneontology.org/external2go/spsl2go.
authors: UniProt-GOA
external_accession:
- TAIR:AnalysisReference:501756971
- TAIR:AnalysisReference:50175724
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
close orthologs.
description: >-
Mouse Genome Database (MGD), The HUGO Gene Nomenclature Committee (HGNC), and
Rat Genome Database (RGD) have extensive procedures in place, overseen by expert
curation, to establish orthology relationships between their genes. The Experimentally
based annotations annotated by each group (IDA, IMP IPI, IGI, and EXP) are used
to provide annotations to the respective mouse and rat orthologs, and given the
ISO evidence code and an entry in the inferred_from field to indicate the orthologous
entity.
authors: Mouse Genome Informatics scientific curators
external_accession:
- J:164563
- J:155856
- RGD:1624291
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
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
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
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
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
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
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
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
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 inferred_from field to indicate
the orthologous entity.
authors: The Gene Ontology Consortium
year: 2023
external_accession:
- J:164563
is_obsolete: false
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