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 protein binding (GO:0005515) 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
SYD-2 positive regulation of ATP-dependent microtubule motor activity, plus-end-directed (GO:2000582) IMP has_regulation_target (UNC-104)
SYD-2 positive regulation of ATP-dependent microtubule motor activity, plus-end-directed (GO:2000582) IMP directly_activates (UNC-104)
SYD-2 regulation of microtubule motor activity (GO:2000574) IMP regulates_o_enabled_by (UNC-104) occurs_in (neuron WBbt:0003679)
UNC-104 anterograde synaptic vesicle transport (GO:0048490) IDA
UNC-104 anterograde axonal transport (GO:0008089) IDA Didn't chose anterograde synaptic vesicle transport as not what I want to transport. new term? "anterograde synaptic vesicle protein transport vesicle transport" (note definition of "synaptic vesicle protein transport vesicle ; GO:0097547" vs " synaptic vesicle ; GO:0008021) or "anterograde axon cargo transport "
SYD-2 regulation of microtubule-based movement (GO:0060632) IGI UNC-104
SYD-2 positive regulation of anterograde synaptic vesicle transport (GO:1903744) IMP occurs_in (neuron WBbt:0003679)
SYD-2 NEW TERM: positive regulation of anterograde transport or positive regulation of anterograde axon cargo transport IMP has_regulation_target (UNC-104)
SYD-2 protein localization (GO:0008104) IMP has_input (UNC-104) occurs_in (neuron WBbt:0003679)
SYD-2 protein localization to axon (GO:0099612) IMP has_direct_input (UNC-104)
UNC-104 axo-dendritic transport (GO:0008088) IDA occurs_in (neuron WBbt:0003679)
DLC-1 axo-dendritic transport (GO:0008088) IDA occurs_in (neuron WBbt:0003679)
UNC-116 axo-dendritic transport (GO:0008088) IDA occurs_in (neuron WBbt:0003679)
UNC-104 axon (GO:0030424) IMP happens_during (larval development)
SYB-1 synapse (GO:0045202) IDA
  • Other comments: "Not inclined to annotate the regulation of clustering as it is not entirely clear what these clusters are - "These results provide evidence that UNC-104 cluster are dynamic membranous structures to which motors can accumulate (from suppl ""possibly serving as an active motor pool) and eventually move along the neurite. Interestingly, clusters are not solely stationary motor deposits, as we also occasionally observe whole clusters moving"")"