Has input: Difference between revisions
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===What to capture with the has_input relation=== | ===What to capture with the has_input relation=== | ||
* <code>has input</code> is used to specify the '''specific molecular target''' of a Molecular Function or a Biological Process. | * <code>has input</code> is used to specify the '''specific molecular target''' of a Molecular Function or a Biological Process. | ||
* 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 inputs. | |||
* For Molecular Functions, inputs include: | * For Molecular Functions, inputs include: | ||
** Specific substrates for enzymes | ** Specific substrates for enzymes | ||
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* For Biological Processes that have a high degree of molecular specificity inputs include: | * For Biological Processes that have a high degree of molecular specificity inputs include: | ||
** Target genes for 'regulation of transcription' or other 'regulation of gene expression' terms. | ** Target genes for 'regulation of transcription' or other 'regulation of gene expression' terms. | ||
* Use of <code>has input</code> is particularly encouraged when the 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 substrate of a protein kinase activity, or | * Use of <code>has input</code> is particularly encouraged when the 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 substrate of a protein kinase activity, or a more specific chemical entity acted upon by an MF that is not otherwise stated in the term definition. | ||
* Note that there does NOT need to be evidence for a direct physical interaction in order to capture an input. Direct physical interaction between an enabler and its input may be implied (e.g. an enzymatic activity assay) and does not necessarily need to be shown with a separate physical interaction assay (e.g. Y2H or co-IP). | |||
* 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 with independent annotation extensions for each. | * 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 with independent annotation extensions for each. | ||
* In standard annotations, different annotations are not linked, so the BP annotation that corresponds to an MF should also have an extension if appropriate. | * In standard annotations, different annotations are not linked, so the BP annotation that corresponds to an MF should also have an extension if appropriate. | ||
===What not to capture=== | ===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. | * 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 textual 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. | * 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. | * | ||
* Co-factors should not be captured as inputs. For example, many enzymes use metal ions such as magnesium, copper or zinc as cofactors. These inorganic ions should not be captured as inputs to the corresponding Molecular Function. Likewise, organic cofactors, or coenzymes, such as flavin mononucleotide or coenzyme Q should not be captured. | |||
* 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. | * 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 | * Sequence Ontology terms | ||
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* [https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:24431 CHEBI:24431 chemical entity] | * [https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:24431 CHEBI:24431 chemical entity] | ||
* [http://amigo.geneontology.org/amigo/term/GO:0032991 GO:0032991 protein-containing complex] | * [http://amigo.geneontology.org/amigo/term/GO:0032991 GO:0032991 protein-containing complex] | ||
* Gene or Gene product (includes | * Gene or Gene product (includes transcripts, ncRNAs, proteins, and modified gene products): UniProtKB, Model Organism Database, RNACentral, PRO (Protein Ontology) | ||
'''Most common ontology branches where input is specified''' | '''Most common ontology branches where input is specified''' | ||
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|- | |- | ||
| '''GP2term relation''' | | '''GP2term relation''' | ||
| | | involved in | ||
|- | |- | ||
| '''GO term''' | | '''GO term''' | ||
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== Review Status == | == Review Status == | ||
Last reviewed: 2021-10- | Last reviewed: 2021-10-19 | ||
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 15:52, 11 January 2022
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.- 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 inputs.
- For Molecular Functions, inputs include:
- Specific substrates for enzymes
- Interactors for binding and adaptor activities
- Target genes for transcription factors
- For Biological Processes that have a high degree of molecular specificity inputs include:
- Target genes for 'regulation of transcription' or other 'regulation of gene expression' terms.
- Use of
has input
is particularly encouraged when the 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 substrate of a protein kinase activity, or a more specific chemical entity acted upon by an MF that is not otherwise stated in the term definition. - Note that there does NOT need to be evidence for a direct physical interaction in order to capture an input. Direct physical interaction between an enabler and its input may be implied (e.g. an enzymatic activity assay) and does not necessarily need to be shown with a separate physical interaction assay (e.g. Y2H or co-IP).
- 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 with independent annotation extensions for each.
- In standard annotations, different annotations are not linked, so the BP annotation that corresponds to an 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 textual 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. For example, many enzymes use metal ions such as magnesium, copper or zinc as cofactors. These inorganic ions should not be captured as inputs to the corresponding Molecular Function. Likewise, organic cofactors, or coenzymes, such as flavin mononucleotide or coenzyme Q should not be captured.
- 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.
Range
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 transcripts, ncRNAs, proteins, and modified gene products): UniProtKB, Model Organism Database, RNACentral, PRO (Protein Ontology)
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:
IPI annotation example: 'input' versus 'with' | |
Gene product | mouse protein A |
GP2term relation | enables |
GO term | GO:0005515 protein binding, has input(mouse protein B) |
Evidence | IPI |
with/from | human 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 | involved in |
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
Human ACOT7 degrades palmitoyl-CoA, PMID:10578051
Annotation for ACOT7 | |
Gene product | UniProtKB:O00154 ACOT7 |
GP2term relation | enables |
GO term | GO:0036116 long-chain fatty-acyl-CoA catabolic process, has input(CHEBI:15525 palmitoyl-CoA) |
Evidence | IDA |
Reference | PMID:10578051 |
Cross-reference to Relations Ontology (RO) term
Review Status
Last reviewed: 2021-10-19
Back to Annotation_Extension