krassowski commented 5 years ago

[x] prepare changelog
[x] calculate and import ActveDriver lists
[x] consider collapsing glycosites subtypes in filters
[x] copy the logo graphics for glycosylation motifs to the production server
[x] export data for download and update the download files
[x] add the changelog to the website

krassowski commented 4 years ago

(Draft) changelog notes

I will keep updating the notes below

PTM sites

Glycosylation sites (N-, O-, S-, C-) were added based on the UniProt (May 2019)
Other types of PTM sites were updated using the UniProt data
The origin database is now stored and displayed for each PTM site to help users in further investigation, including scrutinizing the evidence quality and citing the original reporters. It can be accessed by hovering over the site in the SequenceView:

Mutations

Inherited/Clinical/ClinVar

Clinical mutations from ClinVar were updated using May 2019 release (20190520)
ClinVar mutations are now stringently filtered to only include clinically relevant, non-somatic mutations. Specifically:
- mutations with germline, parental, maternal, biparental, etc origin are included; de novo mutations are also included
- mutations with a somatic origin, or missing the origin information are excluded (see here for the blacklist)
- only mutations associated with a disease, or conferring sensitivity (but not resistance) are included (details here)
ClinVar mutations include more metadata:
- gold stars which describe the quality of evidence are now displayed (one per underlying variation)
- links to both the dbSNP entry (e.g. https://www.ncbi.nlm.nih.gov/snp/rs755131800) and the variation entries in ClinVar database (VCV record, e.g. https://www.ncbi.nlm.nih.gov/clinvar/variation/548576/) are now provided

Genes

Gene information, including identifiers mapping to external databases, were updated using the UCSC Genome Browser distributed tables of RefSeq database and the UniProt database.

Sequence view

conservation track showing phyloP scores (based on the 100way track from UCSC Genome Browser) was added. The per-aminoacid scores were calculated as an average of the codon scores.

Active genes

ActiveDriver results for ClinVar are now computed on the pathogenic/likely pathogenic/drug response subset of mutations

Pathways

Reactome and Gene Ontology pathways were updated using the gprofiler distributed lists
top pathways were calculated ActivePathways

Technical

BerkeleyDB was replaced with LightningDB offering higher performance for bulk mutations queries