search

japonicusdb / japonicus-config

Configuration for JaponicusDB
0 stars 1 forks source link

add NOT Scomber. japonicus to Canto publication loading #1

Closed ValWood closed 1 year ago

ValWood commented 3 years ago

add NOT Scomber. japonicus to Canto publication loading

ValWood commented 3 years ago

Do we want Canto stuff on the Canto tracker with a japonicus label?

ValWood commented 3 years ago

Obviously only for future. existing ones can easily be filtered as "wrong organism".

ValWood commented 3 years ago

and "Sicyopterus japonicus" "Stichopus japonicus" "Synagrops japonicus" "styrax macrocarpus" "Styrax japonicus" "Stichopus japonicus" "Sea cucumber" "Semanotus japonicus"

kimrutherford commented 3 years ago

Do we want Canto stuff on the Canto tracker with a japonicus label?

Let's keep it separate unless there's a Canto bug that need fixing.

kimrutherford commented 3 years ago

I did some testing with those filters added. And I also changed "Schizosaccharomyces japonicus" to ("Schizosaccharomyces" AND "japonicus") which picks up a few extra papers.

How does this look?: https://pubmed.ncbi.nlm.nih.gov/?term=(("Schizosaccharomyces"+AND+"japonicus")+OR+"S.+japonicus")+NOT+"Scomber+japonicus"+NOT+"sicyopterus+japonicus"+NOT+"stichopus+japonicus"+NOT+"synagrops+japonicus"+NOT+"styrax+macrocarpus"+NOT+"styrax+japonicus"+NOT+"stichopus+japonicus"+NOT+"sea+cucumber"+NOT+"semanotus+japonicus"

There are still a few false positives.

One of the extra papers is: https://pubmed.ncbi.nlm.nih.gov/26263485/ Which wasn't picked up by our initial query using "Schizosaccharomyces japonicus" because of a typo in the abstract:

  Recent work on another member of the same genus, Schisozaccharomyces japonicus, suggests that ...

Whoops.

ValWood commented 3 years ago

Whoops indeed!

False positive are inevitable, and this isn't a big deal because the number of papers makes triage easy anyway. I get many FP for pombe.

So if Snezka agrees that all the papers are in this list we con continue with this search string. I can't imagine this string would miss any future papers and if it did they can be added manually.

I am sure we are missing some pombe ones. Sometimes people forget to mention the organism in the title, abstract or keywords (more often than you would imagine!)

ValWood commented 3 years ago

I think we can close this?

kimrutherford commented 3 years ago

I haven't made a script to do this nightly yet.

kimrutherford commented 1 year ago

I haven't made a script to do this nightly yet.

Done! It didn't need a script, just a cron entry.