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.

The following provides a brief description of the columns in the gene_association.fb file.

The Gene Association file (GAF) version used by FlyBase is GAF2.2. The documentation provided by the GOC can be found here

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 gene product to term relations are used:

'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'.

This column may also contain the 'NOT' qualifier, separated by a pipe (|) from the gene product to term relation, which makes the annotation statement a negation.

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.

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|

DPP-C|ho|M(2)23AB|blk|l(2)22Fa|l(2)k17036|Tg|TGF&bgr;

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.

16. Annotation Extension

Aannotation extension add contextual information to standard annotations, generally in the form of a relation qualifying the way the GO term is link to the extension and an ID from an ontology e.g. part_of(GO:0008286) or has_input(FB:FBgn0262407).

Pipes (|) and commas (,) used in column 8 and 16 have these meanings:

A pipe (|) specifies an independent statement (OR) and is equivalent to making separate annotations. A comma (,) specifies a connected statement (AND) and indicates that all conditions are required to infer the annotated GO term.

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.

G.3.2. Evidence

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.

G.3.2.1. GO Evidence Codes

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.3.2.2. 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 or for non-coding RNAs, RNA sequence families that are mapped to GO terms provided by Rfam.

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.

IC 'from'

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.3.3. 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.3.4. Use of negation

NOT is a qualifier used to indicate that a gene or it product doesn't do something that it would be assumed to do.

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.

e.g. if a protein has sequence similarity to galactosyltransferases, but has been shown experimentally not to have the galactosyltransferase activity, it can be annotated with NOT galactosyltransferase activity (GO:0008378).

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).

In FlyBase, annotations where negation is used are excluded from searches.

NOT can be used to document conflicting claims in the literature (i.e. this paper says this enzyme is a galactosyltransferase and this paper shows that this enzyme does not possess this activity) and curators cannot use other means (i.e. other supporting evidence) to resolve the conflict.

NOT may be used with terms from any of the three GO ontologies (cellular component, biological process, molecular function).

G.3.5. Topic-specific GO annoation guidelines

Guidelines used by FlyBase curators in GO curation.

Signaling Pathway Curation Manual

Guide to annotation of piRNA processing factors to the most specific GO term

FlyBase:Gene Ontology (GO) Annotation

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