Difference between revisions of "FlyBase:Gene Ontology (GO) Annotation"
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Revision as of 17:30, 12 March 2021
G.3. Classification of Gene Products using Gene Ontology (GO) terms
FlyBase uses Gene Ontology (GO) controlled vocabulary (CV) terms for cellular component, biological process and molecular function to describe properties of gene products. Although GO terms are intended to describe the properties of gene products, FlyBase currently assigns GO terms to genes rather than protein or RNA.
FlyBase is one of the founding members of the Gene Ontology (GO) Consortium and follows the general guidelines for GO annotation as described in the GO documentation.
Also, see the related video tutorial Finding related genes in FlyBase: The Gene Ontology.
G.3.1. FlyBase GO data
GO data is displayed in the Gene Ontology: Function, Process, and Cellular component section of individual Gene Reports.
In addition, the current release of GO data for all Drosophila melanogaster FlyBase genes can be found in the tab delimited text file gene_association.fb.
From FB2020_06 a new version of the gene association file (GAF2.2) - gene_association_v2.2.fb, is available for download. This will become the default release version by FB2021_01. In this version, column 4 has an expanded range of values (gene product to term relations, gp2term rel) which are mandatory. NOT is pipe-separated from the gp2term rel e.g. NOT|enables
The following provides a brief description of the columns in the gene_association.fb file.
Gene Association file columns
- 1. DB The database contributing the gene_association file
- FB File: always "FB" for gene_association.fb.
- 2. DB_Object_ID A unique identifier in the database for the item being annotated.
- FB File: This is always the primary FlyBase identifier number for a Drosophila gene.
- Example: FBgn0000490
- 3. DB_Object_Symbol
- A (unique and valid) symbol to which the DB_Object_ID is matched.
- FB File: This is always the valid gene symbol for a Drosophila gene.
- Example: dpp
- 4. Qualifier
- For each GO annotation, one of the following as qualifier(s):
- 'acts_upstream_of', 'acts_upstream_of_negative_effect',
- 'acts_upstream_of_positive_effect', 'colocalizes_with',
- 'contributes_to', 'enables', 'involved_in', 'is_active_in', 'located_in', 'part_of'.
- May also contain the 'NOT' qualifier, separated by a pipe (|).
- 5. GO ID
- The unique GO identifier for the GO term attributed to the DB_Object_ID.
- Example: GO:0005160
- 6. DB:Reference
- The unique identifier for the reference to which the GO annotation is attributed.
- FB File: Each FlyBase reference including published literature,
- conference abstracts, personal communications, sequence records and
- computer files has a unique 7 digit identifier (an FBrf). Where this
- reference is a published paper with a PubMed identifier, the PubMed ID
- is also listed in column 6, separated from the FBrf with a pipe (|).
- Example: FB:FBrf0136863|PMID:11432817
- 7. Evidence
- The evidence code for the GO annotation; one of IMP, IGI, IPI, ISS, IDA, IEP, IEA, TAS, NAS, ND, IC, RCA, HDA, HMP, HGI, HEP, IBA
- 8. With (or) From
- FB File: This column contains the identifier for annotations where the
- evidence code is IGI, IPI, ISS, IEA or IC. For IGI the database gene
- symbol and identifier is listed. For ISS and IPI the identifier can be a gene
- symbol and identifier, or a sequence (protein or nucleic acid)
- identifier. For IC, the GO identifier of the term used as the basis of
- a curator inference is given. With statements for IC are not currently
- displayed in gene_association.fb, but they will be displayed in the
- next release of the FlyBase gene_association file.
- IGI example: FLYBASE:rpr; FB:FBgn0011706
- ISS example: UniProt:P35569
- ISS example: EMBL:AF064523
- ISS example: SGD_LOCUS:COP1; SGD:S0002304
- IC example: GO:0045298
- 9. Aspect
- Which ontology the GO term belongs to: Function (F), Process (P) or Component (C).
- Example: P
- 10. DB_Object_Name
- FB File: The full name of the FlyBase gene.
- Example: decapentaplegic
- Where a FlyBase gene has no full name (eg Pten), this field is left blank.
- 11. DB_Object_Synonym
- Alternative names by which the database object is known.
- FB File: Multiple synonyms of a FlyBase gene are separated by a pipe (|).
- Example: M(2)LS1|shortvein|Dm-DPP|dpp|Dpp|DPP|CG9885|
- 12. DB_Object_Type
- The type of object being annotated. Always a gene for FlyBase data.
- FB file: always "gene" for gene_association.fb.
- 13. taxon
- The taxonomic identifier of the species encoding the gene product
- Example: taxon:7227
- 14. Date
- The date of last annotation update, in the format 'YYYYMMDD'. At
- present this date is the same for all annotations and corresponds to
- the date of the latest FlyBase update; we are in the process of
- changing our system so that dates more accurately reflect the date the
- annotation is made.
- Example: 20040821
- 15. Assigned_by
- The source of the GO annotation.
- FB File: One of either FB or UniProtKB.
The latest version of this data is also available for download here from the Gene Ontology consortium site. The accompanying README document includes a detailed description of the file format, FlyBase GO annotation policy and sources used for FlyBase GO annotations.
Note that the GO data available from FlyBase will not necessarily be identical to that found on the GO website. GO validate the data FlyBase submits and remove lines of data that are no longer valid e.g. when a GO term becomes obsolete.
QueryBuilder can be used to identify all the genes associated with a particular GO term. The AmiGO and QuickGO browsing tools can be used to find GO terms of interest. See video tutorial Finding related genes in FlyBase: The Gene Ontology.
Evidence for a GO term consists of an evidence code that describes the type of analysis carried out together with, in some cases, a reference to another database object in that supports the evidence (see with/from Supporting Evidence below).
Evidence codes The Gene Ontology Evidence Codes contains comprehensive descriptions of the evidence codes used in GO annotation. FlyBase uses the following evidence codes when assigning GO data:
- inferred from experiment (EXP)
- inferred from mutant phenotype (IMP)
- inferred from genetic interaction (IGI)
- inferred from direct assay (IDA)
- inferred from physical interaction (IPI)
- inferred from expression pattern (IEP)
- inferred from high throughput experiment (HTP)
- inferred from high throughput mutant phenotype (HMP)
- inferred from high throughput genetic interaction (HGI)
- inferred from high throughput direct assay (HDA)
- inferred from expression pattern (HEP)
- inferred from sequence or structural similarity (ISS)
- inferred from sequence orthology (ISO)
- inferred from sequence alignment (ISA)
- inferred from biological aspect of ancestor (IBA)
- inferred from electronic annotation (IEA)
- inferred from reviewed computational analysis (RCA)
- traceable author statement (TAS)
- non-traceable author statement (NAS)
- inferred by curator (IC)
- no biological data available (ND)
G.3.2.1. Use of evidence codes
Consistent with the aims of the GO reference genome project, FlyBase prefers to assign GO terms based on experimental evidence codes (IMP, IGI, IDA, IPI, IEP). Infrequently, GO annotations will be associated with genes frim high throughput (HTP) experiments. The HTP experiments are only annotated when the satisfy a number of rules, to ensure that there are minimal false positives propagated by GO annotation. These experimental annotations are marked by the evidence codes HTP, HDA, HMP, HGI and HEP, so that they can be distinguished from low-throughput, hypothesis-driven experiments.
Evidence codes based on computer predictions (IEA, RCA), author statements (NAS, TAS) and curator inference (IC) will continue to be used in the absence of experimental data for the same or a more specific GO term. However, we aim to remove GO data with these codes when experimental evidence for the term is curated.
The evidence code ND (no biological data available) is used in combination with the root GO terms "molecular_function ; GO:0003674", "biological_process ; GO:0008150" or "cellular_component ; GO:0008372". In FlyBase the use of any of these three GO terms, attributed to reference FBrf0159398 and supported by the ND evidence code, signifies that a curator has examined the available literature and sequence for this gene and that, as of the date of the annotation to the term, there is no information supporting an annotation to a specific GO term.
with/from Supporting Evidence Some evidence codes (IGI, IPI, ISS, IEA, IC) are used in conjunction 'with' supporting data in the form of a reference to another database object. These objects are identified by their database abbreviation followed by a colon and the unique identifier for the object in that database. A list of current database abbreviations can be found in the GO.xrf_abbs file. See the GO Annotation Guide for more details.
ISS and IEA 'with'
FlyBase captures GO data based on similarity to other gene products that are known to have that attribute. Since October 1st 2006, it has been mandatory for ISS annotations to include an identifier for the sequence used to make the annotation; earlier FlyBase ISS annotations that do not include identifiers will be updated gradually. In line with current guidelines for reference genomes, curators now check that the similar sequence can be annotated to the GO term with experimental evidence (IDA, IMP, IGI, IPI, IEP) before making an ISS annotation. This policy was adopted to avoid circular similarity-based annotations. Consequently, GO terms are not curated based multiple sequence alignments if none of the sequences in the alignment have been experimentally verified. Annotations made before October 2006 have not necessarily been checked in this way.
The combined evidence appears on the gene report in the format:
inferred from sequence or structural similarity with FLYBASE:Max; FB:FBgn0017578
In this case we have give two identifiers (symbol and gene ID) for the same sequence; identifiers for the same sequence are separated by a semi-colon. If more than one sequence is used to make the annotation then the identifiers for the different sequences are separated by a comma. Note that this use of multiple identifiers is a different to that for IGI and IPI.
IEA annotations in FlyBase are based on the presence of InterPro protein domains that are mapped to GO terms provided by EMBL-EBI Gene Ontology Annotation InterPro2GO. GO annotations based on InterPro-to-GO transitive assignment undergo subsequent filtering to remove annotations redundant with manual curation.
IGI, HGI and IPI 'with'
For both IGI and IPI there is a special meaning and All annotations inferred from genetic interaction (IGI) include an identifier for the interacting gene. If the GO term is inferred based on multiple genes interacting simultaneously then all interacting genes are identified using 'with' (separated by commas). However, if the GO term is inferred from multiple pairwise interactions these are treated as separate pieces of experimental evidence and appear with separate evidence codes on the gene report.
For example, Bruce is annotated with the GO term 'programmed cell death' based on two different pairwise genetic interaction experiments; the evidence appears on the gene report as:
inferred from genetic interaction with FLYBASE:grim; FB:FBgn0015946 AND inferred from genetic interaction with FLYBASE:rpr; FB:FBgn0011706
Contrast this with, the following which would imply that all three genes had to interact together to provide evidence for the annotation:
inferred from genetic interaction with FLYBASE:grim; FB:FBgn0015946, FLYBASE:rpr; FB:FBgn0011706
Similar notation is used for IPI where the interacting gene product is identified using 'with'. Where several gene products interact simultaneously they are recorded in a single annotation (separated by commas after the evidence code). Pairwise physical interactions are recorded independently with using separate evidence codes.
Evidence inferred by curator (IC) is the case that includes 'from'. Curators use this code for those cases where an annotation is not supported by any evidence, but can be reasonably inferred by from other GO annotations, for which evidence is available. The object identified in the IC evidence is always a GO term identifier.
For example, a protein shown to have transcription factor activity in a direct assay could be annotated with the GO term 'general RNA polymerase II transcription factor' (GO:0016251). In the absence of any evidence for the cellular location of that protein, if would be reasonable for the the curator to infer that it is (at least sometimes) located in the nucleus. This would lead the the annotation, nucleus inferred by curator from GO:0016251; the annotation is attributed to the reference that contains evidence for transcription factor activity.
G.3.2.2. Use of Gene Product To Term Relations
Gene product to term relations are used to modify the interpretation of an annotation by adding contextual information. On the gene report page, qualifiers precede the GO term in the CV column. More information about using qualifiers is available in the GO Annotation Guide.
Gene product to term relations used in FlyBase
|gp2term relation||GO aspect||Meaning||Relations Ontology Mapping ID||Made available from release:|
|enables||molecular function||gene product directly performs this molecular function||RO:0002327||FB2020_06|
|contributes_to||molecular function||gene product is part of an indivisible molecular machine that performs this molecular function||RO:0002326||FB2020_06|
|involved_in||biological process||gene product directly participates in a particular biological program||RO:0002331||FB2020_06|
|acts_upstream_of||biological process||gene product takes part in a process that precedes a particular biological program||RO:0002263||FB2021_01|
|acts_upstream_of_positive_effect||biological process||gene product takes part in a process that precedes and up-regulates the activity of a particular biological program||RO:0004034||FB2021_01|
|acts_upstream_of_negative_effect||biological process||gene product takes part in a process that precedes and down-regulates the activity of a particular biological program||RO:0004035||FB2021_01|
|located_in||cellular component||gene product localizes to a particular cellular compartment (may be active or inactive in this component)||RO:0001025||FB2020_06|
|part_of||cellular component||gene product is a subunit of a protein-containing complex||BFO:0000050||FB2020_06|
|is_active_in||cellular component||gene product localizes to a particular cellular compartment and is active here||RO:0002432||FB2021_01|
|colocalizes_with||cellular component||gene product localization is proximal to a cellular component||RO:0002325||FB2020_06|
G.3.2.3. Use of negation
NOT may be used with terms from any of the three GO ontologies (cellular component, biological process, molecular function).
NOT is used to make an explicit note that the gene product is not associated with the GO term. This is particularly important in cases where associating a GO term with a gene product should be avoided (but might otherwise be made, especially by an automated method).
For example, if a protein has sequence similarity to an enzyme such as galactosyltransferase, but has been shown experimentally not to have the galactosyltransferase activity, it can be annotated as NOT galactosyltransferase activity (GO molecular function term: GO:0008378).
NOT can also be used when a cited reference explicitly says (e.g. "our favorite protein is not found in the nucleus"). Prefixing a GO term with the string NOT allows curators to state that a particular gene product is NOT associated with a particular GO term. This usage of NOT was introduced to allow curators to document conflicting claims in the literature.
Note that NOT is used when a GO term might otherwise be expected to apply to a gene product, but an experiment, sequence analysis, etc. proves otherwise; it is not generally used for negative or inconclusive experimental results.
Annotations where negation is used are excluded from searches.