SIG: Annotation harmonization (BioC 2019 BoF proposal) #22
Description
There seems to be sufficient and widespread interest for this:
https://twitter.com/KMS_Meltzy/status/1118613260138369024 (note epic Twitter thread)
As it happens, this also showcases some of the great strengths of Bioconductor, which has been dealing with this chaos for the past 20 (25?) years or so. Perhaps it is also worth discussing MeSH terms and so forth. There is always an annotation session, but this would be different -- a focus on harmonizing existing literature and data using best practices and the BioC infrastructure.
It seems like @lwaldron ought to have veto power over this, having done more than most to present, expose, and improve the underlying BioC and HGNC[helper] infrastructures, but there are many other (perhaps lesser known) resources that arose in the discussion. Enough, perhaps, to justify a BoF this year and a full-length workshop next year?
For what it's worth, I can provide some historical background on mitochondrial genome annotation; the lack of much visible infrastructure in BioC for dealing with mitochondrial references and variants motivated me to write the MTseeker package. Compared to Levi's efforts and those of others, mine is quite germinal; yet it is already sufficient for my group (and perhaps others) to begin leveraging the vast publicly available MT resources of SRA in the BioC sphere.
This appears to be a recurrent problem among people who get serious about systematic reviews of genome information, clinical trials, immunology, and so forth, thus a popular enough topic.