Handling redundant information

[pgaudet]

Handling redundant information: Chris slides Montreal meeting Oct 2018: https://docs.google.com/presentation/d/1TzXfwR3ahQYL2MKp6yL5oO13CEUYL-WexzUyjV1OcSA/edit#slide=id.p2

• Define redundant information: (annotation group) New tools should have features that allow us to do queries to assess redundancy
• In AmiGO, we should be able to improve the display by removing redundant information. That information may be useful for certain purposes, so we should provide it in files. We could also provide the 'core set' ('stringent set') in some version of files. There are tickets that explains the strategy that will be taken for this: see https://github.com/geneontology/amigo/issues/43 and https://github.com/geneontology/amigo/issues/440
• Action item: Rules for flagging redundant annotations need to be documented - Chris
• Discussion points: Is redundant, non-experimental annotation ever useful?
• Are there any use cases where people have used these annotations for some type of Analysis?
• Some pipelines (InterPro2GO, SPKW, PAINT, F-P links), sometimes provide data that is already captured experimentally, and some groups would like the redundancy reduced.
• Should all GOC members be handling redundancy in the same way?
• If redundant, non-experimental annotations are present and are going to be removed, at what point in the pipeline should they be filtered, e.g. annotation file production by GOC, annotation file processing by MODs, website display?
• Action Item: need to have a consistent policy for isoform annotation, examine how groups do it, discuss and document for ourselves and for our users
• If we filter annotations files, should we then also provide two annotation files for users, one complete and one filtered?
• Action Item: EXP clobbers IEA, definitely for UI (what about in pipeline? Filter them out? Not comfortable with this for now.)
• Action Item: QA - aim to get rid of NAS/TAS annotation where possible
• Action Item: Share the rules so that there’s a chance for consistency of display
• Doubled up IBA+EXP annotations (from Karen Christie)
• Issue with GOC inference file (i) incorrect aspect reported
• Examples (different types of redundancy):
• TAS http://amigo.geneontology.org/amigo/gene_product/UniProtKB:P05177 (13 annotations to the same activity and 10 to the same component by TAS)
• Exact duplicates by GOC function-process pipeline
• Identical annotation by different groups (rare)

[pgaudet]

Proposal is here: https://docs.google.com/document/d/1ihIYZD_so8Gb06x6KE2GZZdJQ_ve0riy/edit

Discussed on today's QC call with @kltm @vanaukenk and @ValWood

Needs to be prioritized.

[pgaudet]

@lpalbou Can you give us feedback on the proposal ? https://docs.google.com/document/d/1ihIYZD_so8Gb06x6KE2GZZdJQ_ve0riy/edit