Has input: Difference between revisions
m (→Child terms) |
mNo edit summary |
||
(29 intermediate revisions by 3 users not shown) | |||
Line 5: | Line 5: | ||
Identifies an entity affected (bound, transported, modified, consumed or destroyed) by the gene product's participation in a molecular function or biological process. | Identifies an entity affected (bound, transported, modified, consumed or destroyed) by the gene product's participation in a molecular function or biological process. | ||
== | ==Comment== | ||
[http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:has_participant#Comment '''More details on the limited use of has_input with biological process annotations'''] | |||
'''If you know that the target is bound by the annotated gene product then consider using this child relationship''' | |||
* [[Annotation_Extension_Relation:has_direct_input|has_direct_input]] | |||
For ''Molecular Function'' GO terms such as [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0004175 endopeptidase activity] use the relationship [http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:has_direct_input 'has_direct_input'] <span style="color:red">substrate</span> (possibly has_substrate if this relationship is made available). The substrate included in the annotation extension should be known to bind the protein annotated. | |||
The endopeptidase, in the example above, would also have the ''Biological Process'' GO term annotation (eg [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0006508 proteolysis] with the annotation extension relationship 'has_input' <span style="color:red">substrate</span>. | |||
For ''Molecular Function'' GO terms such as endopeptidase inhibitor activity use the relationship [http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:has_direct_input 'has_direct_input'] <span style="color:red">endopeptidase</span>, the protein included in the annotation extension should be known to bind the annotated inhibitor. | |||
'''If the annotation associated with the gene product is a regulation of ''Biological Process'' then consider using the child relationship''' | |||
* [http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:has_regulation_target 'has_regulation_target']<span style="color:red">target of biological process</span> | |||
eg: [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0045861 negative regulation of proteolysis] with the annotation extension relationship [http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:has_regulation_target 'has_regulation_target'] <span style="color:red">target of proteolysis</span>, with the substrate of the endopeptidase that is regulated by the inhibitor included in the annotation extension field | |||
If the annotation associated with the gene product is a regulation of | '''If the annotation associated with the gene product is a regulation of ''Molecular Function'' (eg if the gene product is an enzyme regulator) then consider using the child relationship''' | ||
* [http://wiki.geneontology.org/index.php/Annotation_Extension_Relation: | * [http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:has_input 'has_input'] <span style="color:red">endopeptidase</span> | ||
eg: [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0010951 negative regulation of endopeptidase activity], with the annotation relationship [http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:has_input 'has_input'] <span style="color:red">endopeptidase</span>, the endopeptidase that is inhibited by (in this case) the endopeptidase inhibitor is included in the annotation extension field | |||
<span style="color:blue">Therefore the endopeptidase inhibitor would have two ''Biological Process'' GO term annotations and one ''Molecular Function'' annotation eg:</span> | |||
* [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0045861 negative regulation of proteolysis] with the annotation extension relationship [http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:has_regulation_target 'has_regulation_target'] <span style="color:red">substrate</span>, with the substrate of the inhibited endopeptidase included in the annotation extension field | |||
* [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0010951 negative regulation of endopeptidase activity], with the annotation relationship [http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:has_input 'has_input'] <span style="color:red">endopeptidase</span>, with the endopeptidase that is inhibited in the annotation extension field | |||
* [http://www.ebi.ac.uk/QuickGO/GTerm?id=GO:0004866 endopeptidase inhibitor activity], with the annotation relationship [http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:has_direct_input 'has_direct_input'] <span style="color:red">endopeptidase</span>, with the endopeptidase included in the annotation extension known to bind the annotated inhibitor. | |||
{| class="wikitable" border="1" | |||
|- | |||
! Folded/unfolded | |||
! Gene Name (col 2) | |||
! GO ID (col 5) | |||
! Reference (col 6) | |||
! Evidence (col 7) | |||
! Annotation Extension (col 16) | |||
! Parent terms of new folded GO term | |||
|- | |||
| Unfolded | |||
| <span style="color:green">Endopeptidase A</span> | |||
| GO:0004175 <span style="color:green">endopeptidase activity</span> | |||
| PMID:1234567 | |||
| IDA | |||
| has_direct_input(<span style="color:green">substrate of endopeptidase A</span>) | |||
| | |||
|- | |||
| Folded | |||
| <span style="color:green">Endopeptidase A</span> | |||
| GO:0004175 <span style="color:green">endopeptidase activity</span> | |||
| PMID:1234567 | |||
| IDA | |||
| | |||
| <span style="color:red">No new GO term created</span> | |||
|} | |||
==Synonyms== | |||
has_target (EXACT) | |||
localizes (NARROW) | |||
==Child terms== | |||
If you know that the target is bound by the annotated gene product then consider using this child relationship | |||
* [[Annotation_Extension_Relation:has_direct_input|has_direct_input]] | |||
==Scope of use== | ==Scope of use== | ||
Line 50: | Line 95: | ||
==== Specifying the chemical that was applied and induced a 'response to chemicals' ==== | ==== Specifying the chemical that was applied and induced a 'response to chemicals' ==== | ||
GOC policy is not to use the annotation extension field to capture the input to the process (eg a chemical/protein), instead new GO terms are requested (using Term Genie). | |||
Line 185: | Line 223: | ||
==== Specifying the gene which is a target of a transcription factor ==== | ==== Specifying the gene which is a target of a transcription factor ==== | ||
'''gene transcription targets''' | '''gene transcription targets''' <span style="color:red">'''This example is still under discussion.''' </span> | ||
Statement example: | Statement example: | ||
Line 206: | Line 244: | ||
| PMID:xxx | | PMID:xxx | ||
| IDA | | IDA | ||
| | | has_regulation_target(UNIPROT:Qxxx <span style="color:green">Polo2</span>) | ||
| | | | ||
|- | |- | ||
Line 222: | Line 260: | ||
| PMID:xxx | | PMID:xxx | ||
| IDA | | IDA | ||
| | | has_direct_input(UNIPROT:Qxxx <span style="color:green">Polo2</span>) (could include a feature ID to specify the specific motif eg a SO ID or Ensembl ID for the gene ID) | ||
| | | | ||
|- | |- | ||
Line 249: | Line 287: | ||
| Unfolded | | Unfolded | ||
| Pxxx <span style="color:green">transcription factor A</span> | | Pxxx <span style="color:green">transcription factor A</span> | ||
| | | GO:0001228 <span style="color:green">RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription</span> | ||
| PMID:xxx | | PMID:xxx | ||
| IDA | | IDA | ||
Line 257: | Line 295: | ||
| Folded | | Folded | ||
| Pxxx <span style="color:green">transcription factor A</span> | | Pxxx <span style="color:green">transcription factor A</span> | ||
| GO | | New GO term <span style="color:green">RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription of Polo2</span> | ||
| PMID:xxx | | PMID:xxx | ||
| IDA | | IDA | ||
Line 271: | Line 309: | ||
[[Category:relations]] | [[Category:relations]] | ||
[[Category:annotation extension]] | [[Category:annotation extension]] | ||
[[Category: GO-CAM Relations]] |
Revision as of 11:53, 13 April 2019
Back to Annotation usage examples for each annotation extension relation
Definition
Identifies an entity affected (bound, transported, modified, consumed or destroyed) by the gene product's participation in a molecular function or biological process.
Comment
More details on the limited use of has_input with biological process annotations
If you know that the target is bound by the annotated gene product then consider using this child relationship
For Molecular Function GO terms such as endopeptidase activity use the relationship 'has_direct_input' substrate (possibly has_substrate if this relationship is made available). The substrate included in the annotation extension should be known to bind the protein annotated.
The endopeptidase, in the example above, would also have the Biological Process GO term annotation (eg proteolysis with the annotation extension relationship 'has_input' substrate.
For Molecular Function GO terms such as endopeptidase inhibitor activity use the relationship 'has_direct_input' endopeptidase, the protein included in the annotation extension should be known to bind the annotated inhibitor.
If the annotation associated with the gene product is a regulation of Biological Process then consider using the child relationship
- 'has_regulation_target'target of biological process
eg: negative regulation of proteolysis with the annotation extension relationship 'has_regulation_target' target of proteolysis, with the substrate of the endopeptidase that is regulated by the inhibitor included in the annotation extension field
If the annotation associated with the gene product is a regulation of Molecular Function (eg if the gene product is an enzyme regulator) then consider using the child relationship
- 'has_input' endopeptidase
eg: negative regulation of endopeptidase activity, with the annotation relationship 'has_input' endopeptidase, the endopeptidase that is inhibited by (in this case) the endopeptidase inhibitor is included in the annotation extension field
Therefore the endopeptidase inhibitor would have two Biological Process GO term annotations and one Molecular Function annotation eg:
- negative regulation of proteolysis with the annotation extension relationship 'has_regulation_target' substrate, with the substrate of the inhibited endopeptidase included in the annotation extension field
- negative regulation of endopeptidase activity, with the annotation relationship 'has_input' endopeptidase, with the endopeptidase that is inhibited in the annotation extension field
- endopeptidase inhibitor activity, with the annotation relationship 'has_direct_input' endopeptidase, with the endopeptidase included in the annotation extension known to bind the annotated inhibitor.
Folded/unfolded | Gene Name (col 2) | GO ID (col 5) | Reference (col 6) | Evidence (col 7) | Annotation Extension (col 16) | Parent terms of new folded GO term |
---|---|---|---|---|---|---|
Unfolded | Endopeptidase A | GO:0004175 endopeptidase activity | PMID:1234567 | IDA | has_direct_input(substrate of endopeptidase A) | |
Folded | Endopeptidase A | GO:0004175 endopeptidase activity | PMID:1234567 | IDA | No new GO term created |
Synonyms
has_target (EXACT)
localizes (NARROW)
Child terms
If you know that the target is bound by the annotated gene product then consider using this child relationship
Scope of use
Domain
BFO:0000007 ! process (Biological Process or Molecular Function)
Range
ENTITY_UNION:0000005 ! chemical, gene product, or complex
Annotation Extension Usage Examples
Enhancing Molecular Function and Biological Process Annotations
Specifying the chemical that was applied and induced a 'response to chemicals'
GOC policy is not to use the annotation extension field to capture the input to the process (eg a chemical/protein), instead new GO terms are requested (using Term Genie).
Cellular response to drug
Statement from paper: incubation of cells with low concentrations of phenformin and depletion of Ppm1E increased AMPK phosphorylation
So one of the annotations would be:
DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Evidence (Col 7) | Extension (Col 16) |
---|---|---|---|---|---|
Q8WY54 | PPM1E | GO:0035690 cellular response to drug | PMID:20801214 | IDA | has_input(CHEBI:6801 metformin) |
Specifying the protein which is a target of a Biological Process
Proteolysis targets
Statement from paper: MICA shedding by tumor cells was inhibited by silencing of the related ADAM10 and ADAM17 proteases.
No direct binding of MICA to ADAM10 and ADAM17 was shown therefore the relationship 'has_direct_input' was not applied.
So one of the annotations would be:
DB (Col 2) | Object (Col 3) | GO ID (Col 5) | Reference (Col 6) | Evidence (Col 7) | Extension (Col 16) |
---|---|---|---|---|---|
O14672 | ADAM10 | GO:0006509 membrane protein ectodomain proteolysis | PMID:18676862 | IMP | has_input(UNIPROT:Q29983 MICA) |
Using examples (from above) to demonstrate Folding_and_Unfolding using the relationship has_input
Specifying the protein which is a target of a Biological Process
Proteolysis targets
Statement from paper: MICA shedding by tumor cells was inhibited by silencing of the related ADAM10 and ADAM17 proteases
Folded/unfolded | Gene Name (col 2) | GO ID (col 5) | Reference (col 6) | Evidence (col 7) | Annotation Extension (col 16) | Parent terms of new folded GO term |
---|---|---|---|---|---|---|
Unfolded | O14672 ADAM10 | GO:0006509 membrane protein ectodomain proteolysis | PMID:18676862 | IMP | has_input(UNIPROT:Q29983 MICA) | |
Folded | O14672 ADAM10 | GO:0006509 membrane protein ectodomain proteolysis | PMID:18676862 | IMP | No new GO term created |
OWL class expression: GO:0006509 membrane protein ecodomain proteolysis AND has_input SOME UNIPROT:Q29983 MICA
No new term will be created in this example because this is outside of the scope of GO, although tools using GO could use the relationship to create the following:
Folded/unfolded | Gene Name (col 2) | GO ID (col 5) | Reference (col 6) | Evidence (col 7) | Annotation Extension (col 16) | Parent terms of new folded GO term |
---|---|---|---|---|---|---|
Unfolded | O14672 ADAM10 | GO:0006509 membrane protein ectodomain proteolysis | PMID:18676862 | IMP | has_input(UNIPROT:Q29983 MICA) | |
Folded | O14672 ADAM10 | New GO term membrane protein ectodomain proteolysis of MICA | PMID:18676862 | IMP | GO:0006509 membrane protein ectodomain proteolysis |
OWL class expression: GO:0006509 membrane protein ecodomain proteolysis AND has_input SOME UNIPROT:Q29983 MICA
Specifying the gene which is a target of a transcription factor
gene transcription targets This example is still under discussion.
Statement example:
DNA binding transcription factor A binds the promoter of Polo2 and increases transcription of Polo2
Folded/unfolded | Gene Name (col 2) | GO ID (col 5) | Reference (col 6) | Evidence (col 7) | Annotation Extension (col 16) | Parent terms of new folded GO term |
---|---|---|---|---|---|---|
Unfolded | Pxxx transcription factor A | GO:0001228 RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription | PMID:xxx | IDA | has_regulation_target(UNIPROT:Qxxx Polo2) | |
Folded | Pxxx transcription factor A | GO:0001228 RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription | PMID:xxx | IDA | No new GO term created | |
Unfolded | Pxxx transcription factor A | GO:0044212 transcription regulatory region DNA binding | PMID:xxx | IDA | has_direct_input(UNIPROT:Qxxx Polo2) (could include a feature ID to specify the specific motif eg a SO ID or Ensembl ID for the gene ID) | |
Folded | Pxxx transcription factor A | GO:0044212 transcription regulatory region DNA binding | PMID:xxx | IDA | No new GO term created |
No new term will be created in this example because this is outside of the scope of GO, although tools using GO could use the relationship to create the following:
Folded/unfolded | Gene Name (col 2) | GO ID (col 5) | Reference (col 6) | Evidence (col 7) | Annotation Extension (col 16) | Parent terms of new folded GO term |
---|---|---|---|---|---|---|
Unfolded | Pxxx transcription factor A | GO:0001228 RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription | PMID:xxx | IDA | has_input(UNIPROT:Qxxx Polo2) | |
Folded | Pxxx transcription factor A | New GO term RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription of Polo2 | PMID:xxx | IDA | GO:0001228 RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription |
Back to Annotation usage examples for each annotation extension relation