Better message for publications with no annotations

kimrutherford commented 6 years ago

All annotation pages have the text "Annotations from this publication:" after the details, even if there are no annotations. eg. https://www.pombase.org/reference/PMID:27677791

Change to something better like: "This publication has no annotations in PomBase because ..."

Reasons for no annotations:

not curatable
no annotations in the paper
not curated yet

anything else?

Note to self: we need to pass the "canto_triage_status" from Chado to the web code so the web code knows if the paper is Curatable.

mah11 commented 6 years ago

If it has to "know" the triage status anyway, maybe the pub page should use a couple of them to indicate some of the reasons for no annotations. Specifically, I suggest

methods paper
review

because each covers a fairly big chunk of the total uncuratable pubs (762 and 1126 respectively), and users might be interested in knowing if a particular paper is in one of those categories.

ValWood commented 6 years ago

I started to type the same somewhere in another window a while ago....but got side-tracked...

I think we should avoid "not curatable"

For papers which are identified as "curatable" but not yet curated we should have a message that the paper has not yet been curated....

mah11 commented 6 years ago

Yeah, different words will sound nicer than "not curatable". But I'm inclined to lump most of the subtypes of "uncuratable publications" rather than list every triage category.

Message ideas:

This publication has no annotations in PomBase because ...

it is a review.
it is a methods paper.
curators have found no annotatable gene-specific data in it.
it hasn't been curated yet. (Please contact us if you want to contribute annotations for this paper.)

kimrutherford commented 6 years ago

Note to self: we need to pass the "canto_triage_status" from Chado to the web code so the web code knows if the paper is Curatable.

I've done that now so any changes to the messages on the publication papers should be straight forward.

mah11 commented 6 years ago

Notes from call:

ignore untriaged pubs; they don't even get a page
any annotation (Canto, tab-delimited files, contig files, etc.) takes precedence over the "no annotations" options
"it hasn't been curated yet" = anything triaged curatable, but without approved session
"... found no annotatable ..." = (uncuratable BUT NOT (review OR methods)) AND (approved session with no annotations)

ValWood commented 6 years ago

super ;)

kimrutherford commented 6 years ago

ignore untriaged pubs; they don't even get a page

Currently untriaged publication do get pages on the main site. I'll fix that.

kimrutherford commented 6 years ago

Currently untriaged publication do get pages on the main site. I'll fix that.

I've fixed that for tomorrow night's load.

While testing, I found a publication in Chado that doesn't appear to have been through Canto: https://www.pombase.org/reference/PMID:17287513 It also doesn't seem to be a pombe paper. Very odd. I'll investigate how it ended up in Chado.

ValWood commented 6 years ago

presumably a typo chromosome1.contig:FT valproic acid; db_xref=PMID:17287513; date=20100917" chromosome1.contig:FT valproic acid; db_xref=PMID:17287513; date=20100917" chromosome2.contig:FT valproic acid; db_xref=PMID:17287513; date=20100917"

kimrutherford commented 6 years ago

presumably a typo chromosome1.contig:FT valproic acid; db_xref=PMID:17287513; date=20100917"

PMID:17287531 is in Chado too and also has some annotation for apm1.

ValWood commented 6 years ago

Valproic acid affects membrane trafficking and cell-wall integrity in fission yeast. Miyatake M, Kuno T, Kita A, Katsura K, Takegawa K, Uno S, Nabata T, Sugiura R. Genetics. 2007 Apr;175(4):1695-705. Epub 2007 Feb 7. PMID: 17287531

will fix

kimrutherford commented 6 years ago

The publication pages now show sensible messages when there is no annotation.

pombase / website

Better message for publications with no annotations #627