The purpose of annotation extensions is described in the main Annotation_Extension documentation page.
What to capture with the has_output relation
has outputis 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 products of enzymatic reactions (includes modified forms of proteins)
- Use of
has outputis 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 refers to the GO terms that can be further specified with the relation.
Range describes the types of entities that can be used with the relation.
- CHEBI:24431 chemical entity
- GO:0032991 protein-containing complex
- Gene or Gene product (includes transcript, ncRNAs, protein and modified gene products): UniProt, MOD IDs, RNACentral, PRO (Protein Ontology)
Most common ontology branches where output is specified
- Molecular function:
- Biological process:
Usage examples for the has_output extension
1. Specifying the product of a catalytic activity
|Annotation for DGKA - input & output|
|Gene product||UniProtKB:P23743 DGKA|
|GO term||GO:0004143 diacylglycerol kinase activity, has output(CHEBI:78385 1-palmityl-2-acetyl-sn-glycero-3-phosphate(2−))|
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|
|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−))|
2. Specifying the product of a biosynthetic process
|Annotation for SCO5223|
|Gene product||UniProtKB:Q9K498 SCO5223|
|GO term||GO:0042181 ketone biosynthetic process, has output(CHEBI:51460 albaflavenone)|
3. Specifying the product of a protein-containing complex assembly process
|Annotation for IRC25|
|Gene product||UniProtKB:Q07951 IRC25|
|GO term||GO:0051131 chaperone-mediated protein complex assembly, has output(GO:0005839 proteasome core complex)|
Cross-reference to Relations Ontology (RO) term
Last reviewed: 2021-10-07