QCQA call 2018-03-20
Agenda
GOC NYC May 2018
What do we want to report on? Review Cambridge meeting minutes: https://docs.google.com/document/d/1Y9_Mvqes3op36TPHgfaS7K5FHnGZLgUApghIFYyUKR8/edit
How GO annotation errors/ inconsistencies/ ommissions can affect analysis
- Encourage people to think about annotation depth (cytoplasmic translation)
- Slim numbers *should* now be relatively stable now (ontology wise), and only affected by annotation increases and decreases ( I might be able to illustrate how errors affect analyses...)
How errors /inconsistencies/ ommissions are identified
- Rules
- i) Blocking of very general high-level GO terms to increase specificity
- ii) Taxon constraints
- iii) Other rules?
- Annotation reviews from ontology development work
- examples
- identifies
- Specificity in the ontology changed to annotation+ extension
- general curator error
- Matrix and slimming (assessing annotation at the organism level)
https://www.slideshare.net/ValerieWood/copy-of-biocuration-2017 https://drive.google.com/drive/folders/0B0YtE_BqXTzQbkdFZmwzV1M2TjA
- Removal of incorrect IEA mappings (SPKW and InterPro)
- identifies
- general curation errors ontology fixes (tru path violations and missing parent)
- Adding new taxon restriction (not currently working?)
- other
Summarize major causes of errors: a) experimental readout b) annotating a cargo or target to a process c) ignoring author intent d) New biological insights https://github.com/geneontology/go-annotation/issues/1806 e) A phenotype not specific for a process etc
Why we should prioritise error fixing - should be considered critical like fixing bugs in software - small errors can uncover large issues (fix many problems simultaneously across multiple species) - prevents future propagation, via PAINt, Ensembl, InterPro mappings
What next?
- Removing redundancy?
https://github.com/geneontology/go-annotation/issues/1544 https://github.com/geneontology/go-annotation/issues/1674 https://github.com/geneontology/amigo/issues/43 https://github.com/geneontology/amigo/issues/295 https://github.com/geneontology/amigo/issues/440 this is related to QC. When the redundancy is removed its easier to spot errors
- Really need a way to identify unsupported ISS annotation (there is no alerting when the primary annotation is removed)
- some terms are really not ideal for annotation transfer
examples transporter specificity (changes frequently between species) drug related terms response to terms add examples....
Rules for protein complexes in 'with' column
https://github.com/geneontology/go-ontology/issues/15421
Progress on annotation reviews
Documentation for annotation reviews
Requesting an annotation review tool?
Review existing pages under Quality Control
http://wiki.geneontology.org/index.php/Category:Quality_Control