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pombase / website

PomBase website v2
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unresolved external link? for expression profiling etc (see also issues/1821) #629

Closed ValWood closed 2 years ago

ValWood commented 6 years ago

/controlled_curation="term=external_link, deletion mutant expression profiling; db_xref=ArrayExpress:E-MTAB-2543"

kimrutherford commented 6 years ago

What do I need to do here?

ValWood commented 6 years ago

not urgent, but

any controlled_curation="term=external_link

should be displayed in the External link section as

Type: Expression Name: deletion mutant expression profiling Link: ArrayExpress:E-MTAB-2543 =https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2543/samples/?full=true

I think? @Antonialock ?

Antonialock commented 6 years ago

You asked me to hold off this ticket last summer but raise the priority if it is needed now:

https://github.com/pombase/curation/issues/550

ValWood commented 6 years ago

I flagged this one as "waiting for feedback" until pombase/curation#550 is done

kimrutherford commented 2 years ago

Am I missing something or could we add /db_xref="ArrayExpress:E-MTAB-2543" or /db_xref="EMD:2542" to the gene annotation? We can then configure things so those prefixes generate entries in the External links section. Like we do for /db_xref="SPD:51/51C03".

ValWood commented 2 years ago

I think that is the plan, but we don't want to do it in Artemis.

following back though pombase/curation#550 there is a spreadsheet https://docs.google.com/spreadsheets/d/1unk_qLm1C41DB_82Qtu7xbe6D5rx3w566vaxgFnVN9E/edit#gid=0

we planned to put these in the external references section, but they could appear on the publication pages too.

We can look at this on an upcoming call. Probably not this week.

ValWood commented 2 years ago

pombase/curation#550 is done forwards to https://github.com/pombase/website/issues/1821

ValWood commented 2 years ago

PMID:29235477 Links need adding to external links spreadsheet:

Mal3 pdb https://www.rcsb.org/structure/5MJS (Should the the pdb linking should happen automatically eventually?) Electron Microscopy Data Bank https://www.ebi.ac.uk/emdb/EMD-3522

These links could also be included on the publication page using: https://github.com/pombase/website/issues/1802

ValWood commented 2 years ago

Decided not to do this.

Meta data and PuBMed IDs are not well curated (AE and GOA), make it difficult to automate links to external datasets. We can add external links on publication pages on a case-by case basis (see PMID:34296454).