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dictyBase / Migration

Entrypoint for dictybase overhaul project
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Searching dictyBase for data from External Resources #44

Open rjdodson opened 9 years ago

rjdodson commented 9 years ago

Hello:

Currently, it is not possible to search for information displayed on the gene page from External Resources, eg. Uniprot accession numbers and EC numbers. It is also not possible to search and retrieve information for a pubmed id.

The need to search for and retrieve data based on these would be useful to us as curators, and I could imagine it might be useful for our users as well. While this is not urgent or absolutely necessary, it would be useful to be able to do so, depending on how difficult or time-consuming it is to provide this capability.

Let me know if you have any questions, Thanks, Bob

pfey03 commented 7 years ago

I would emphasise, it's the external sources we have MAPPINGs for and therefore LINK to. Since those are stored in database should be able to be searchable in the future.

cybersiddhu commented 7 years ago

You mean you like to do this http://dictybase.org/publication/pubmed/28346441 with pubmed For uniprot we could do similar.

rjdodson commented 7 years ago

Just as an example, from the gene page glpD. The external resources section has links to UniProtKB:P34114 and EC:24.1.1. From the gene page, both of these links work just fine and take me to the external link for each of these. If I search for "P34114" from the search bar on the main page, the search correctly links to the gene page for glpD. (So maybe this has changed since I submitted this ticket). However, if I search for "2.4.1.1" or "EC:2.4.1.1", the result does not link back to the gene page for glpD, it just pulls up results from our Web pages, eg. Annual Conference, dictyNews, etc. Would be great if we or one of our users could retrieve a gene page in our database based on an EC number search.

With regard to pubmed IDs, yes, if I search with "28346441" I get no results. Searches for other pubmeds might pull up webpages as mentioned above for the EC number search. For example, if I search with "9405107", I pull up 1 result from a webpage. But note if I search with "9405107" in Stock Center search, the result is a link to the 3 strains linked to this pubmed id.

I guess my point is, I would love to be able to take a pubmed accession, search with it in the main search box from the home page, and be able to retrieve everything in dictyBase associated with that accession: strains, phenotypes, literature references, etc. instead of searching in multiple search windows for each specific result. That may be asking too much for right now, but maybe is a good goal for the future.

Let me know if you have further questions. Thanks Sidd

pfey03 commented 7 years ago

There will be such different search in the future! As I see it, all info stored locally in dictyBase will be searchable with Faceted Search. PMIDs are stored, so these definitely will be searchable. With EC numbers I'm not sure, if just a link to external resource, these are not stored in database?

@cybersiddhu, let me know if this thinking is correct.