Annotation Extension Relation:has output

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The purpose of annotation extensions is described in the main Annotation_Extension documentation page.

Usage guidelines

What to capture with the has_output relation

  • has output is used to specify the specific molecular output produced as a result of a Molecular Function.
  • The entity captured must have a unique, resolvable database identifier. As with annotation objects, gene identifiers may be used as a stand-in for a gene product, e.g. an mRNA or a protein. Curators may also use more specific gene product identifiers, e.g. RNACentral, PRO, Complex Portal, in extensions.
    • Specific protein isoforms or post-translationally modified proteins may be captured as outputs.
  • Note that more than one output may be captured for an annotation: this means that there are multiple products for a reaction. However if an enzyme has different substrates which are converted to different products, this should be captured as an independent annotation or independent annotation extensions for an annotation.
  • For Molecular Functions, outputs include:
    • Specific substrates for enzymes (includes modified forms of proteins)
  • Use of has output is encouraged when the product of the reaction is more specific than what the GO term describes. A use case is to specify the exact protein product of a molecular function, e.g. the specific modified form of a protein produced by a protein kinase activity.
  • In standard annotations, different annotations are not linked, so the BP annotation that corresponds to a MF should also have an extension if appropriate.
  • The output should represent the biologically meaningful output. Curators need to be careful in distinguishing the conclusion from an experiment from the assay conditions.

What not to capture

  • It is not necessary to capture the output if it is already represented by the GO term label or definition. For example for GO:0004396 hexokinase activity, has output(CHEBI:61567 D-hexose 6-phosphate) is redundant with the definition of the term and does not need to be captured.
  • Currency substrates that are general to a class of reactions and that do not provide information about substrate specificity; for example for a kinase activity, 'ADP' should not be added as an output in an annotation extension.
  • Products that are already present in the GO term definition should not be captured as output; for example for a kinase activity, ADP should not be added as an annotation extension.

Scope of use

Domain

Domain refers to the GO terms that can be further specified with the relation.

Range

Range describes the types of entities that can be used with the relation.

Most common ontology branches where output is specified

Usage examples for the has_output extension

1. Specifying the product of a catalytic activity

Human DGKA phosphorylates 1-O-palmityl-2-acetyl-sn-glycerol, producing 1-palmityl-2-acetyl-sn-glycero-3-phosphate(2−), PMID:22627129

Annotation for DGKA - input & output
Gene product UniProtKB:P23743 DGKA
GP2term relation enables
GO term GO:0004143 diacylglycerol kinase activity, has output(CHEBI:78385 1-palmityl-2-acetyl-sn-glycero-3-phosphate(2−))
Evidence IDA
Reference PMID:22627129

Note that this reaction has both an input and an output; if this data is available, both the input and the output are captured in the same annotation:

Annotation for DGKA
Gene product UniProtKB:P23743 DGKA
GP2term relation enables
GO term GO:0004143 diacylglycerol kinase activity, has input(CHEBI:75936 1-O-palmityl-2-acetyl-sn-glycerol), has output(CHEBI:78385 1-palmityl-2-acetyl-sn-glycero-3-phosphate(2−))
Evidence IDA
Reference PMID:22627129

2. Specifying the product of a biosynthetic process

Streptomyces coelicolor SCO5223 synthesizes the antibiotic albaflavenone 18234666

Annotation for SCO5223
Gene product UniProtKB:Q9K498 SCO5223
GP2term relation enables
GO term GO:0042181 ketone biosynthetic process, has output(CHEBI:51460 albaflavenone)
Evidence IMP
Reference PMID:18234666

3. Specifying the product of a protein-containing complex assembly process

Yeast IRC25 mediates proteasome core complex assembly [https://pubmed.ncbi.nlm.nih.gov/17707236/ PMID:17707236

Annotation for IRC25
Gene product UniProtKB:Q07951 IRC25
GP2term relation involved_in
GO term GO:0051131 chaperone-mediated protein complex assembly, has output(GO:0005839 proteasome core complex)
Evidence IMP
Reference PMID:17707236

Cross-reference to Relations Ontology (RO) term

RO:0002234 has output

Review Status

Last reviewed: 2021-10-07


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