Difference between revisions of "Talk:2010 GO camp binding documentation issues"

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[[User:Siegele|Siegele]] 21:54, 29 June 2010 (UTC)
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[[User:Siegele|Siegele]] 00:30, 1 July 2010 (UTC)
  
As many terms in the Molecular Function ontology implicitly or explicitly imply the binding of a chemical or protein, it is unnecessary to co-annotate a gene product to a term from the binding node of GO to describe the binding of substrates or products that are already adequately captured in the definition of the Molecular Function term.
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As many terms in the Molecular Function ontology implicitly or explicitly imply the binding of a chemical or protein, it is unnecessary to co-annotate a gene product to a term from the binding node of GO to describe the binding of substrates or products that are already adequately captured in the definition of the Molecular Function term. For instance, an enzyme MUST bind all of the substrates and products of the reaction it catalyzes. Similarly, a transporter MUST bind the molecules it transports. Therefore, as binding is implied, curators should avoid making redundant annotations. 
  
For instance, an enzyme MUST bind all of the substrates and products of the reaction it catalyzes. Similarly, a transporter MUST bind the molecules it transports. Therefore, as binding is implied, curators should avoid making redundant annotations.
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There will be some cases, however, where it is appropriate to annotate a binding relationship. For example, published experiments may show that a gene product binds a non-hydrolyzable ATP analog, without demonstrating that it has ATPase activity. In such a case, it would be appropriate to annotate to GO:0005524 ATP binding using an IDA evidence code.
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The GO is committed to ‘annotating to the experiment’. Therefore the curator should try to capture the specifics as much as feasible: use the binding term if the experiment shows binding, but not catalysis/transport; don’t use the binding term if the experiment does show catalysis/transport.
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The curator may come across Molecular Function terms where the definition doesn't adequately describe the specific substrate/target being bound, and where the request of a more specific Molecular Function would be considered inappropriate.  In such cases, the identity of the substrate/target being bound can be captured in the [‘with’ column (8) or] annotation extension column (16) using identifiers from other ontologies or databases.  Small molecule substrate/targets should be identified with accessions from [http://www.ebi.ac.uk/chebi/ ChEBI], and protein substrate/targets can be identified with accessions from UniProtKB (others?).  Substrate/target information should be entered in [column 8 or] column 16 in the form CheBI:xxxx or UniProtKB:xxxxx.  Multiple entries should be separated by pipes (add example). Keep in bind that [column 8 or] the annotation extension column (16) should be used '''only''' for direct interactions and '''only''' when the binding relationship is not already included in the GO term and/or definition.
  
There will be some cases, however, where it is appropriate to annotate a binding relationship. For example, published experiments may show that a gene product binds a non-hydrolyzable ATP analog, without demonstrating that it has ATPase activity. In such a case, it would be appropriate to annotate to GO:0005524 ATP binding using an IDA evidence code.
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Annotations to protein binding terms should be maximally informative. Child terms that describe a particular class of protein binding (e.g. GO:0030971 ‘receptor tyrosine kinase binding’) should be used in preference to the parent term 'protein binding'; GO:0005515.  Where possible the precise identity of the interacting protein should be captured in [the ‘with’ field or] the annotation extension column (16) of an annotation.  The IPI evidence code should be used for annotation of ‘’’all’’’ protein-protein interactions rather than IDA. 
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Future ontology development efforts should be relied upon to improve the searching capability of any user who is specifically interested in gene products carrying out a certain type of substrate/product binding.  Ongoing relevant ontology development of 'has_part' relationships will provide links to implied substrate binding (Chris and Jane are developing 'has_part' relationships to implying substrate binding).  [something missing here] existing GO to follow this new format eg Transcription factor activity has_part DNA binding. Curators can request new 'has_part' relationships (and terms) if these do not exist.
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* Not sure where to put the following statement:
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Curators should use their judgment to decide whether the interaction is physiologically relevant and capture information relevant to the in vivo situation, not artificial substrates.
  
The GO is committed to ‘annotating to the experiment’. Therefore the curator should try to capture the specifics as much as feasible: use the binding term if the experiment shows binding, but not catalysis or transport; don’t use the binding term if the experiment shows catalysis or transport.
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* Note:  The [http://geneontology.org/GO.evidence.shtml#ipi “Guide to GO Evidence Codes”] still makes the following recommendation. This needs to be updated.
  
The curator may come across Molecular Function terms where the definition doesn't adequately describe the specific substrate/target being bound, and where the request of a more specific Molecular Function would be considered inappropriate.  In such cases, the annotation extension column (column 16) can be used to capture this information using the accession from ChEBI (add link) for small molecules or from UniProtKB (others?) for proteins. Enter the substrate/target information in column 16 in the form ChEBI:xxxxx or UniProtKB:xxxxxx. Remember, use annotation extension column (16) only if this information is not already included in the GO term and/or definition.
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Usage of the With/From Column for IPI
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We strongly recommend making an entry in the with/from column when using this evidence code to include an identifier for the other protein or other macromolecule or other chemical involved in the interaction. When multiple entries are placed in the with/from field, they are separated by pipes. Consider using IDA when no identifier can be entered in the with/from column.

Revision as of 16:30, 30 June 2010

Siegele 00:30, 1 July 2010 (UTC)

As many terms in the Molecular Function ontology implicitly or explicitly imply the binding of a chemical or protein, it is unnecessary to co-annotate a gene product to a term from the binding node of GO to describe the binding of substrates or products that are already adequately captured in the definition of the Molecular Function term. For instance, an enzyme MUST bind all of the substrates and products of the reaction it catalyzes. Similarly, a transporter MUST bind the molecules it transports. Therefore, as binding is implied, curators should avoid making redundant annotations.

There will be some cases, however, where it is appropriate to annotate a binding relationship. For example, published experiments may show that a gene product binds a non-hydrolyzable ATP analog, without demonstrating that it has ATPase activity. In such a case, it would be appropriate to annotate to GO:0005524 ATP binding using an IDA evidence code.

The GO is committed to ‘annotating to the experiment’. Therefore the curator should try to capture the specifics as much as feasible: use the binding term if the experiment shows binding, but not catalysis/transport; don’t use the binding term if the experiment does show catalysis/transport.

The curator may come across Molecular Function terms where the definition doesn't adequately describe the specific substrate/target being bound, and where the request of a more specific Molecular Function would be considered inappropriate. In such cases, the identity of the substrate/target being bound can be captured in the [‘with’ column (8) or] annotation extension column (16) using identifiers from other ontologies or databases. Small molecule substrate/targets should be identified with accessions from ChEBI, and protein substrate/targets can be identified with accessions from UniProtKB (others?). Substrate/target information should be entered in [column 8 or] column 16 in the form CheBI:xxxx or UniProtKB:xxxxx. Multiple entries should be separated by pipes (add example). Keep in bind that [column 8 or] the annotation extension column (16) should be used only for direct interactions and only when the binding relationship is not already included in the GO term and/or definition.

Annotations to protein binding terms should be maximally informative. Child terms that describe a particular class of protein binding (e.g. GO:0030971 ‘receptor tyrosine kinase binding’) should be used in preference to the parent term 'protein binding'; GO:0005515. Where possible the precise identity of the interacting protein should be captured in [the ‘with’ field or] the annotation extension column (16) of an annotation. The IPI evidence code should be used for annotation of ‘’’all’’’ protein-protein interactions rather than IDA.

Future ontology development efforts should be relied upon to improve the searching capability of any user who is specifically interested in gene products carrying out a certain type of substrate/product binding. Ongoing relevant ontology development of 'has_part' relationships will provide links to implied substrate binding (Chris and Jane are developing 'has_part' relationships to implying substrate binding). [something missing here] existing GO to follow this new format eg Transcription factor activity has_part DNA binding. Curators can request new 'has_part' relationships (and terms) if these do not exist.


  • Not sure where to put the following statement:

Curators should use their judgment to decide whether the interaction is physiologically relevant and capture information relevant to the in vivo situation, not artificial substrates.

Usage of the With/From Column for IPI We strongly recommend making an entry in the with/from column when using this evidence code to include an identifier for the other protein or other macromolecule or other chemical involved in the interaction. When multiple entries are placed in the with/from field, they are separated by pipes. Consider using IDA when no identifier can be entered in the with/from column.