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Planteome / planteome-annotation-data

This is a place to discuss issues around the Planteome annotation data and store useful scripts etc.
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4 Reference xref sources don't have URLs #10

Open elserj opened 6 years ago

elserj commented 6 years ago

These 4 reference (column 6 from GAF) sources do not have working URLs in AmiGO: GRIMS IRIC GRIN CIAT_project

The first 3 are in files added by @austinmeier and have stanzas in dbxrefs.yaml, but they should be of the form GRIMS:XXXXXX rather than just the text GRIMS. This is causing these to have no working URL. Possible solution since those don't appear to be publication references like a PMID (which is the preferred value for this column), is to create GRIMS_ref xrefs to some publication.

The CIAT_project does not have a xref at all, so we either need to find a publication to replace these with, or create an xref so that these at least work.

austinmeier commented 6 years ago

You've hit the nail on the head: I've done some digging on pubmed, and google scholar; there is no exact publication for these databases, but I can dig up something that should work.

For GRIMS and IRIC (essentially the same resource), I found a paper from 2005 about the IRRI germplasm management system : DOI: https://doi.org/10.1104/pp.105.063438. This was before they named it GRIMS, but I believe it to be the same thing.

Replace with "PMID:16219924"

For IRIC, I wonder if using a link to IRRI's annual reports would work? Perhaps just linking to the same publication as above?

For GRIN- I found a publication, but no actual PMID. Can we use DOI? DOI:10.17660/ActaHortic.2010.859.4

elserj commented 6 years ago

Up to you, I would say if the publication covers both, than use it. DOI are fine, just need to follow the example id as in here: https://github.com/Planteome/go-site-xrefs-fork/blob/master/metadata/db-xrefs.yaml#L566

Not sure on the IRRI annual reports, as I don't think there is a good xref in the db-xrefs.yaml file for it. You would have to add one if you wanted it to go there.

You want to change them in svn, or do you want me to?

austinmeier commented 6 years ago

If you have them readily accessible, go ahead and change them. I'll change the line in my GAF scripts, so all the next files I generate will be correct. If you want me to regenerate them, I can do that as well.

Thanks Justin