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== Review Status == | == Review Status == | ||
Last reviewed: 2021- | Last reviewed: 2021-10-07 | ||
Back to [http://wiki.geneontology.org/index.php/Annotation_Extension Annotation_Extension] | Back to [http://wiki.geneontology.org/index.php/Annotation_Extension Annotation_Extension] |
Revision as of 11:36, 7 October 2021
The purpose of annotation extensions is described in the main Annotation_Extension documentation page.
Usage guidelines
What to capture with the has_input relation
- has_input is used to specify the specific molecular target of a Molecular Function or a Biological Process. Targets correspond to specific substrates for enzymes, interactors for binding and adaptor activities, gene for transcription factors. Is also used to describe inputs of Biological Processes that have a high degree of molecular specificity, e.g. to specify the target gene for 'regulation of transcription'.
- Use of this relation is particularly encouraged when the molecular target of the Molecular Function or Biological Process is more specific than what the GO term describes. A common use case is to specify the exact protein target of an MF, e.g. the target of a protein kinase activity.
- More than one input may be captured for an annotation; this means that there are multiple substrates for a single reaction. However, if an enzyme can act on different substrates, or if a transcription factor has multiple targets, this should be captured as independent annotations or independent annotation extensions for an annotation.
- In standard annotations, different annotations are not linked, so the BP annotation that corresponds to a MF should also have an extension if appropriate.
What not to capture
- It not necessary to capture the input if it already represented by the GO term label or definition. For example for GO:0004396 hexokinase activity, has input(CHEBI:4194 D-hexose) 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, ATP should not be added as an input in an annotation extension.
- Chemical analogs and other assay conditions should not be captured. The input should represent the biologically meaningful input.
- Co-factors should not be captured as inputs.
- x-dependent activities : for example, calcium-dependent protein kinase: do not capture has_input 'calcium', since this is not the molecule that is being acted on.
- Sequence Ontology terms
Scope of use
Domain
Domain refers to the GO terms that can be further specified with the relation.
- BFO:0000007 process, which corresponds to GO Biological Process and Molecular Function
Range
Range describes the types of entities that can be used with the relation.
- Chemical entity: CHEBI:24431 - chemical entity
- Gene or Gene product (includes transcript, ncRNAs and protein): UniProt and MOD IDs
- Protein-containing complex: GO:0032991 - protein-containing complex
Most common ontology branches where input is specified
- Molecular function:
- Biological process:
Distinction between 'has input' and 'with/from'
- with/from is intended to capture the sequence supporting the evidence; while the input represents the physiological input represented by the experiment.
- for example, for an IPI experiment where a mouse protein is tested for its ability to bind a protein using a human protein ortholog in the assay, the annotation would be mouse protein A - protein binding - with:human protein B - has input: mouse protein B
Usage examples for the has_input extension
1. Specifying the substrate (chemical) of a catalytic activity
Human DGKA phosphorylates 1-O-palmityl-2-acetyl-sn-glycerol, PMID:22627129
Annotation for DGKA - input & output | |
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) |
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 protein target of a catalytic activity
Human CDC7 phosphorylates MCM2, PMID:15668232
Annotation for CDC7 | |
Gene product | UniProtKB:O00311 CDC7 |
GP2term relation | enables |
GO term | GO:0004672 protein kinase activity, has input(UniProtKB:P49736 MCM2) |
Evidence | IMP |
Reference | PMID:15668232 |
3. Specifying the gene target of a DNA binding transcription factor
Human NKX6-3 regulates transcription of BAK1, PMID:26314965
Annotation for NKX6-3 | |
Gene product | UniProtKB:A6NJ46 NKX6-3 |
GP2term relation | enables |
GO term | GO:0001228 DNA-binding transcription activator activity, RNA polymerase II-specific, has input(UniProtKB:Q16611, BAK1) |
Evidence | IDA |
Reference | PMID:26314965 |
The corresponding Biological Process can be annotated with its input:
Annotation for NKX6-3 | |
Gene product | UniProtKB:A6NJ46 NKX6-3 |
GP2term relation | enables |
GO term | GO:0045944 positive regulation of transcription by RNA polymerase II, has input(UniProtKB:Q16611, BAK1) |
Evidence | IDA |
Reference | PMID:26314965 |
4. Specifying an interaction partner
Human DNM1L binds RAB29, PMID:25767741
Annotation for DNM1L | |
Gene product | UniProtKB:O00429 DNM1L |
GP2term relation | enables |
GO term | GO:0031267 small GTPase binding, has input(UniProtKB:O14966, RAB29) |
Evidence | IDA |
Reference | PMID:25767741 |
5. Specifying the target(s) of a macromolecule adaptor
Human TJP2 is a molecular adaptor for tight junction proteins F11R and AFDN, PMID:23885123
Annotation for TJP2 | |
Gene product | UniProtKB:Q9UDY2 TJP2 |
GP2term relation | enables |
GO term | GO:0030674 protein-macromolecule adaptor activity, has input(UniProtKB:Q9Y624, F11R), has input(UniProtKB:P55196, AFDN) |
Evidence | IDA |
Reference | PMID:23885123 |
6. Specifying the input of a catabolic process
TO COMPLETE
Cross-reference to Relations Ontology (RO) term
Review Status
Last reviewed: 2021-10-07
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