FYI - I've moved this discussion back to the issue that started this thread:
https://issues.jalview.org/browse/JAL-2755 On 25/09/2018 12:18, James Procter wrote: > > Awesome - thanks Andy ! > > Looking forward to the shiny new unified endpoint :) ... j. > > > On 25/09/2018 12:14, Andy Yates wrote: >> Hi Jim and Jalview developers >> >> To clarify a few things here that I hope will help your decision process >> >> - The medium term idea is to provide Ensembl/EG data through a single >> unified interface. We are planning to finish this work on merging the two >> REST servers into one URL by Q1 2019 (release 96). We don't envisage >> developer having to change anything on their side (though the websites will >> not be merging) >> >> - There is a pan Ensembl (including EG) id lookup redirect for the website >> from http://www.ensemblgenomes.org/id/{id} e.g. >> http://www.ensemblgenomes.org/id/ENSG00000139618 and >> http://www.ensemblgenomes.org/id/AT3G52430 redirect to their respective >> website >> >> - ES-Ensembl is unlikely to be a production system until 2020 so holding on >> for that may not be the right thing to do >> >> Finally I believe the logic you have about UniProt holding division-specific >> identifiers is for URL reconstruction. We can provide ID redirection, as >> shown above, but any genome location links need to the which site it's >> hosted on. >> >> Hope this helps, >> >> Andy >> >>> On 25 Sep 2018, at 10:14, James Procter <[email protected]> wrote: >>> >>> Hi Andy (cc-ed the public jalview-dev list for posterity) >>> We are wrestling with Jalview's Ensembl abstraction and wondering whether >>> the struggle is worth it. We currently provide two Ensembl 'data sources' >>> - Ensembl and EnsemblGenomes - and are also having to do some additional >>> work to resolve the EnsemblFungi/etc Division based cross-references that >>> Uniprot serve. >>> >From a UX perspective it is (IMHO) preferable to have a single 'Ensembl' >>> >datasource for resolution of any identifier, but because there are >>> >separate endpoints, under the hood we still need to distinguish >>> >identifiers for divisions held at EnsemblGenomes. >>> I seem to remember you mentioning that there was a plan that once >>> ES-Ensembl was up and running, EnsemblGenomes would probably disappear (or >>> just proxy to the same endpoint as Ensembl). Is that still going to be the >>> case ? If yes, and it is going to happen in the next year, then that might >>> help us decide the most appropriate technical solution here. >>> >>> Jim. >>> >>> PS. It just occured to me that the only reason Uniprot holds >>> division-specific Ensembl identifiers is that it allows the Uniprot web >>> site to provide web-links to the different division front-ends. I guess >>> that reason is good enough for Jalview to do the same - but the multiple >>> end-point discussion still stands ;) >>> -- >>> ------------------------------------------------------------------- >>> Dr JB Procter, Jalview Coordinator, The Barton Group >>> Division of Computational Biology, School of Life Sciences >>> University of Dundee, Dundee DD1 5EH, UK. >>> +44 1382 388734 | >>> www.jalview.org | www.compbio.dundee.ac.uk >>> >>> >>> >>> >>> The University of Dundee is a registered Scottish Charity, No: SC015096 > > -- > ------------------------------------------------------------------- > Dr JB Procter, Jalview Coordinator, The Barton Group > Division of Computational Biology, School of Life Sciences > University of Dundee, Dundee DD1 5EH, UK. > +44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk > > > The University of Dundee is a registered Scottish Charity, No: SC015096 > > > _______________________________________________ > Jalview-dev mailing list > [email protected] > http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev -- ------------------------------------------------------------------- Dr JB Procter, Jalview Coordinator, The Barton Group Division of Computational Biology, School of Life Sciences University of Dundee, Dundee DD1 5EH, UK. +44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk
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