glygener / glygen-issues

Repository for public GlyGen tickets
GNU General Public License v3.0
0 stars 0 forks source link

Create new triples connecting enzyme EC number and reaction ID #1443

Open rykahsay opened 2 months ago

rykahsay commented 2 months ago

Triples like this (this is for Rhea but I also want the same for Reactome reaction IDs):

<http://rdf.rhea-db.org/69607> <https://sparql.glyge.org/ontology/hasEnzyme> <http://purl.uniprot.org/enzyme/2.3.1.308> .

image

pkay47 commented 1 month ago

This is available in 2024_04 datasets: https://ftp.ebi.ac.uk/pub/contrib/glygen/current_release/

bash-4.4$ zgrep hasEnzyme uniprot-proteome-homo-sapiens.nt.gz | grep 69607 http://rdf.rhea-db.org/69607 https://sparql.glygen.org/ontology/hasEnzyme http://purl.uniprot.org/enzyme/2.3.1.308 .

bash-4.4$ zgrep -c hasEnzyme uniprot-proteome* uniprot-proteome-arabidopsis-thaliana.nt.gz:1250 uniprot-proteome-dictyostelium-discoideum.nt.gz:636 uniprot-proteome-drosophila-melanogaster.nt.gz:692 uniprot-proteome-gallus-gallus.nt.gz:984 uniprot-proteome-hepatitis-c-virus-1a.nt.gz:3 uniprot-proteome-hepatitis-c-virus-1b.nt.gz:3 uniprot-proteome-homo-sapiens.nt.gz:1632 uniprot-proteome-mus-musculus.nt.gz:1606 uniprot-proteome-rattus-norvegicus.nt.gz:1390 uniprot-proteome-saccharomyces-cerevisiae.nt.gz:868 uniprot-proteome-sars-coronavirus.nt.gz:5 uniprot-proteome-sars-cov-2.nt.gz:5 uniprot-proteome-sus-scrofa.nt.gz:1094

pkay47 commented 1 month ago

@rykahsay please take a look