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

1. How GO annotation errors/ inconsistencies/ ommissions can affect analysis. https://github.com/geneontology/go-annotation/issues/1869 encourage people to think about annotation depth (cytoplasmic translation) Slim numbers *should* be realtively stable now (ontology wise), and only affected by annotation increases and decreases I think I might be able to illustrate how errors affect analyses...

How errors /inconsistencies/ ommissions are identified.

• Blocking of very general high-level GO terms to increase specificity

Other rules?

• Annotation reviews from ontology development work examples

- 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) - 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

https://github.com/geneontology/go-annotation/issues?q=is%3Aissue+is%3Aopen+label%3A%22annotation+review%22

Review existing pages under Quality Control

http://wiki.geneontology.org/index.php/Category:Quality_Control