Evidence for Inferences based on Ontology links

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Background on Inferences based on InterOntology Links

  • MF-BP links: Since MFs are part_of some BP, the ontology editors have been adding some links between F and P aspects to connect the two aspects and give some context to the function. A simple example is: kinase activity part_of phosphorylation. Part_of links have been put in place in the ontology file (gene_ontology_write.obo file) between the MF and BP terms. You can find some information in the wiki- http://wiki.geneontology.org/index.php/Function-Process_Use_Cases


  • BP-CC links: There are some processes that occur in certain subcellular locations and the location name is part of the BP term (vacoular acidification or mitochondrial translation for example). In these cases a link is placed in the ontology to link the BP term to the corresponding CC term. CC Inferences are then made using these links similar to the MF-BP links.

Evidence for these inferences

For the MF-BP inferences the original evidence code is retained for the inferred annotation as well. For example if the gp is annotated to Kinase activity with IDA, then phosphorylation is inferred by this script with IDA and so far we did not come across situations where that did not make sense.

However, for CC, inferences with the same evidence code as the BP annotation doesn't some times makes sense. If a gp is annotated to mitochondrial translation using IMP, it doesn't make sense to have CC annotation to mitochondria using IMP.

New Evidence code for these inferences

We are proposing a new evidence code for these inferences.

Inferred from biological knowledge encoded in Ontology by Computer (IOC)
or
Automatic Assertion based on biological knowledge encoded in the Ontology (AAO).
or
Inferred Electronically based on knowledge encoded in Ontology (IEO)
Providing the GOID in the With/from column from which the inter-ontology link was made would allow us to track the source of the annotation.

In ECO this would be a synonym of ECO:000322 and would map upto ECO:311 

ECO:0000311 imported information used in automatic assertion
   ECO:0000322 imported manually asserted information used in automatic assertion
   ECO:0000323 imported automatically asserted information used in automatic assertion

Definitions

  • ECO: 0000322 Evidence that was initially used in manual assertion by one person or group, which is imported by a second person or group and used in automatic assertion.
  • ECO: 0000323 Evidence that was initially used in automatic assertion by one person or group, which is imported by a second person or group and used in automatic assertion.

Open to other suggestions.

Questions:

  • What should the reference be if we decide to go with the new ev-code?
  • We should be consistent and extend the use of the new code to MF-BP inferences also?

Icing on the cake

Moving to this ev.code will also resolve the whole Assigned_by= RefGenome for PAINT annotations (was discussed in the UCL GOC meeting)

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