Annotation Conf. Call 2016-03-22

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Bluejeans

Agenda

IC from ISS

  • From 2016-03-08 annotation call, we agreed that IC annotations from existing ISS annotations would be okay, but would require a new GO_REF to document the annotation practice.
    • Rebecca drafted the text of the new GO_REF:
 GO_REF:0000109
 title: Gene Ontology annotations Inferred by Curator (IC) using at least one Inferred by Sequence Similarity (ISS) annotation to 
 support the inference
 year: 2016
 The Gene Ontology Consortium uses the IC (Inferred by Curator) evidence code when assignment of a GO term cannot be supported by 
 direct experimental or sequence-based evidence, but can, based on a curator’s biological knowledge, be reasonably inferred from 
 existing GO annotations to the same gene/gene product.  Use of the IC evidence code with GO_REF:0000109 indicates that a curator 
 inferred the GO term based on at least one supporting annotation with an ‘Inferred from Sequence Similarity’ (ISS) evidence code.  
 Note that additional supporting annotations may be experimentally evidenced. When using GO_REF:0000109, the 'with/from' field must 
 contain all GO identifiers used as supporting annotations.
  • As well as a proposed update to the GO website documentation:
 In cases where the GO term is inferred from sequence similarity evidence, such IC-annotations will use reference GO_REF:0000105. When 
 using this reference, one or more supporting annotations will be ISS-evidenced; a supporting ISS-evidenced annotation may also be used 
 together with a experimentally-evidenced supporting annotation (e.g. IDA or IMP).
 GO_REF:0000105 can be used where the supporting ISS annotations are transferred from different species. For example, an IC-evidenced 
 GO term can be created for a human protein based on two different GO terms; one ISS'd from mouse to human, and one ISS'd from rat to 
 human.

Use of has_participant Annotation Extension Relation

  • Definition: Identifies an entity affected by the gene product's participation in a molecular function or biological process
  • has_participant documention on GO wiki
  • Okay to use this annotation extension relation when it is capturing legacy information?
    • In MGI we captured thousands of annotations where a term was associated with an anatomical structure before the method of using relations was in place. In these cases, we know that the structure somehow participates in the process, but we don't know exactly how. We would like to allow these annotations extensions to pass the checks.

http://amigo.geneontology.org/amigo/gene_product/MGI:MGI:1276112

  • Would it be possible to allow our legacy annotations, but have the rule that this relation should not be used for new manual annotations?

Annotation Consistency Exercise

Gene/Marker Name GO term Evidence Code With/From Annotation Extension Annotation Extension Annotation Extension Annotation Extension Comment
SYD-2 kinesin binding (GO:0019894) IPI UNC-104
UNC-104 protein binding (GO:0005515) IPI SYD-2
SYD-2 kinesin binding (GO:0019894) IDA has_input (UNC-104) occurs_in (dendrite GO:0030425) occurs_in (head neuron WBbt:0006751)
UNC-104 protein binding (GO:0005515) IPI SYD-2 occurs_in (dendrite GO:0030425) occurs_in (head neuron WBbt:0006751)
SYD-2 kinesin binding (GO:0019894) IDA has_direct_input (UNC-104)
SYD-2 kinesin binding (GO:0019894) IDA has_input (UNC-104) part_of (protein binding, bridging GO:0030674)
UNC-104 ATP-dependent microtubule motor activity, plus-end-directed (GO:0008574) IDA