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Find out if PRIDE data make into UniProt #536

Open jeet-vora opened 1 year ago

jeet-vora commented 1 year ago

@pkay47

Step 1 - Can you find out if data (Glycosylation, phosphorylation) from PRIDE or similar mass spec databases makes it into UniProt and is later shared with GlyGen? Can you look into it and prepare a short report/presentation?

Step 2 - To initiate cross-linking to PRIDE - GlyGen

pkay47 commented 1 year ago

There is xref to PRIDE, but no PTM info.

There are xrefs to 11 proteomics resources, https://www.uniprot.org/database?facets=category_exact%3AProteomic%20databases&query=%2A again, no ptm info.

Reading about tools/libraries like PRIDE Mod - https://www.ebi.ac.uk/pride/markdownpage/prideutilities#ms-data-core-api:_reading_any_proteomics_format

jeet-vora commented 1 year ago
pkay47 commented 5 months ago

Organisms having PRIDE xrefs

  1. homo-sapiens
  2. mus-musculus
  3. rattus-norvegicus
  4. sus-scrofa
  5. saccharomyces-cerevisiae
  6. arabidopsis-thaliana
  7. drosophila-melanogaster
pkay47 commented 5 months ago

image

pkay47 commented 5 months ago

PRIDE xref for P0DOY2 in uniprot-proteome-homo-sapiens.nt

http://purl.uniprot.org/uniprot/P0DOY2 http://www.w3.org/2000/01/rdf-schema#seeAlso http://purl.uniprot.org/pride/P0DOY2 . http://purl.uniprot.org/pride/P0DOY2 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://purl.uniprot.org/core/Resource .
http://purl.uniprot.org/pride/P0DOY2 http://purl.uniprot.org/core/database http://purl.uniprot.org/database/PRIDE .

pkay47 commented 5 months ago

PRIDE page can be linked using url template - https://www.ebi.ac.uk/pride/peptidome/peptidesearch?keyword=

eg: https://www.ebi.ac.uk/pride/peptidome/peptidesearch?keyword=P0DOY2

pkay47 commented 3 months ago

@jeet-vora please close issue if all PRIDE questions are covered

jeet-vora commented 2 months ago

@katewarner Can you ask Jie if there are PRIDE xrefs for other newly integrated organisms. Thanks

Organisms having PRIDE xrefs

  1. homo-sapiens
  2. mus-musculus
  3. rattus-norvegicus
  4. sus-scrofa
  5. saccharomyces-cerevisiae
  6. arabidopsis-thaliana
  7. drosophila-melanogaster
  8. sars-cov-2
katewarner commented 2 months ago

@jeet-vora

UniProt does provide pride xrefs to us for everything except sars-cov-2, which doesn't have pride xrefs in UniProt, and we created pride xrefs datasets for these species in the last release. I checked the bovine ebi download and they also contain pride xrefs, so we should have the new dataset in the 2.7 release.

[k.warner1@glygen-vm-dev ~]$ cd /data/shared/glygen/releases/data/v-2.6.1/reviewed/
[k.warner1@glygen-vm-dev reviewed]$ ls *_pride.csv
arabidopsis_protein_xref_pride.csv  human_protein_xref_pride.csv  pig_protein_xref_pride.csv  yeast_protein_xref_pride.csv
fruitfly_protein_xref_pride.csv     mouse_protein_xref_pride.csv  rat_protein_xref_pride.csv