Clarify tax ID issues - Githubissues

kmartinez834 commented 1 year ago

Proteins use these tax IDs:

"tax_id","short_name","long_name","common_name","nt_file","is_reference","sort_order"
"9606","human","Homo sapiens","Human","uniprot-proteome-homo-sapiens.nt","yes","1"
"10090","mouse","Mus musculus","Mouse","uniprot-proteome-mus-musculus.nt","yes","2"
"10116","rat","Rattus norvegicus","Rat","uniprot-proteome-rattus-norvegicus.nt","yes","3"
"63746","hcv1a","Hepatitis C virus (isolate H)","HCV-H","uniprot-proteome-hepatitis-c-virus-1a.nt","yes","4"
"11116","hcv1b","Hepatitis C virus (isolate Japanese)","HCV-Japanese","uniprot-proteome-hepatitis-c-virus-1b.nt","yes","5"
"694009","sarscov1","Severe acute respiratory syndrome-related coronavirus","HCoV-SARS","uniprot-proteome-sars-coronavirus.nt","yes","6"
"2697049","sarscov2","Severe acute respiratory syndrome coronavirus 2","SARS-CoV-2","uniprot-proteome-sars-cov-2.nt","yes","7"
"7227","fruitfly","Drosophila melanogaster","Fruit fly","uniprot-proteome-drosophila-melanogaster.nt","yes","8"
"559292","yeast","Saccharomyces cerevisiae S288C","Yeast","uniprot-proteome-saccharomyces-cerevisiae.nt","yes","9"

Glycans use these tax IDs:

"tax_id","short_name","long_name","common_name","nt_file","is_reference","sort_order"
"9606","human","Homo sapiens","Human","uniprot-proteome-homo-sapiens.nt","yes","1"
"10090","mouse","Mus musculus","Mouse","uniprot-proteome-mus-musculus.nt","yes","2"
"10116","rat","Rattus norvegicus","Rat","uniprot-proteome-rattus-norvegicus.nt","yes","3"
"63746","hcv1a","Hepatitis C virus (isolate H)","HCV-H","uniprot-proteome-hepatitis-c-virus-1a.nt","yes","4"
"694009","sarscov1","Severe acute respiratory syndrome-related coronavirus","HCoV-SARS","uniprot-proteome-sars-coronavirus.nt","yes","6"
"2697049","sarscov2","Severe acute respiratory syndrome coronavirus 2","SARS-CoV-2","uniprot-proteome-sars-cov-2.nt","yes","7"
"7227","fruitfly","Drosophila melanogaster","Fruit fly","uniprot-proteome-drosophila-melanogaster.nt","yes","8"
"10114","","Rattus","rats","","no","1000"
"4932","","Saccharomyces cerevisiae","Yeast","","no","1000"
"11103","","Hepacivirus C","HCV","","no","1000"
"9823","","Sus scrofa","Pig","","no","1000"
"9825","","Sus scrofa domesticus","","","no","1000"
"44689","","Dictyostelium discoideum","","","no","1000"

Issues:

Clarify which "long_name" to use on front end and in BCO organism field --> NCBI, EBI, UniProt?
Can "common_name" be the same for two tax ids (ex. Yeast, Rat)?
Will glycans also have yeast (559292) annotation?
How to ensure glycan stats and searches will include both (applies to Rat, Pig, HCV)?

kmartinez834 commented 1 year ago

Items to discuss w/ @rykahsay on Monday:

How is proteoform species mapping occurring?
How does multiple genus/species/strain for one organism affect searching & filtering?
Homepage statistics & BCO filters --> could we use common names instead of scientific names so we can combine different tax id's for Rat, Yeast, etc.?

ReneRanzinger commented 1 year ago

From Group meeting on 9/20: for 2.2 we go with common name to collapse numbers for yeast and rat.

@jeet-vora will setup a dedicated meeting to come to a final decision moving forward (#717)

kmartinez834 commented 1 year ago

Note, collapsing common names leaves "11103","Hepacivirus C","HCV" glycans out of the homepage statistics because it would apply to both HCV isolates. Discuss how to handle this in meeting #717

kmartinez834 commented 2 months ago

Organism decisions documented here: GlyGen Organisms

glygener / glygen-issues

Clarify tax ID issues #680