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From: Rutger V. <rut...@gm...> - 2010-05-25 12:35:59
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http://iphylo.blogspot.com/2010/05/treebase-ii-makes-me-pull-my-hair-out.html -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: Jon A. <jon...@du...> - 2010-05-25 14:32:44
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If you all tell me what should rewrite to what, I can turn on the mojo and make it happen. We've got apache on the front end, so mod_rewrite is available. -Jon On May 25, 2010, at 8:35 AM, Rutger Vos wrote: > http://iphylo.blogspot.com/2010/05/treebase-ii-makes-me-pull-my-hair-out.html > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com > > ------------------------------------------------------------------------------ > > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
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From: Rutger V. <rut...@gm...> - 2010-05-25 14:38:28
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On Tue, May 25, 2010 at 3:32 PM, Jon Auman <jon...@du...> wrote: > If you all tell me what should rewrite to what, I can turn on the mojo and > make it happen. We've got apache on the front end, so mod_rewrite is > available. Bill probably still has the documentation for the URL API from version 1. If he can dig that up we should be able to rewrite a significant portion of those URLs to become PhyloWS URLs. This won't address his complaint about the old taxon IDs being gone though. -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: Jon A. <jon...@du...> - 2010-05-25 14:53:30
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We could : 1) keep the old site up and running and redirect all '/cgi-bin/foo' requests to the old server (seems backward) 2) Fix the 404 page to send users to the search page or custom 404 page (we should do this irregardless) 3) Create a lookup table that maps legacy taxonIDs to new ones. Seems like a one time thing, cause all new studies will not have legacy ID, right? 4) do #2 and not worry about the rest Just me 2 cents worth. Jon On May 25, 2010, at 10:38 AM, Rutger Vos wrote: > On Tue, May 25, 2010 at 3:32 PM, Jon Auman <jon...@du...> wrote: >> If you all tell me what should rewrite to what, I can turn on the mojo and >> make it happen. We've got apache on the front end, so mod_rewrite is >> available. > > Bill probably still has the documentation for the URL API from version > 1. If he can dig that up we should be able to rewrite a significant > portion of those URLs to become PhyloWS URLs. This won't address his > complaint about the old taxon IDs being gone though. > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com ------------------------------------------------------- Jon Auman Systems Administrator National Evolutionary Synthesis Center Duke University http:www.nescent.org jon...@ne... ------------------------------------------------------ |
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From: William P. <wil...@ya...> - 2010-05-25 15:42:48
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On May 25, 2010, at 7:53 AM, Jon Auman wrote: > We could : > 1) keep the old site up and running and redirect all '/cgi-bin/foo' requests to the old server (seems backward) > 2) Fix the 404 page to send users to the search page or custom 404 page (we should do this irregardless) > 3) Create a lookup table that maps legacy taxonIDs to new ones. Seems like a one time thing, cause all new studies will not have legacy ID, right? > 4) do #2 and not worry about the rest The legacy APIs are described here: http://treebase.peabody.yale.edu/treebase/urlapi.html -- In the case of uBio, they used the "Link by Taxon Name" -- so that would be an easy rewrite. However, they have already said that they will be rewriting their outlinks to comply with our /phylows/. So it's hardly worth changing for them. -- In the case of NCBI, they used the "Link by Taxon ID Number" method, so the problem there is that we don't have a /phylows/find/taxon/ that uses TB1 legacy ids (which are stored in the tb1legacyid field in the taxonlabel table). So to make us compatible with NCBI, we'd need to write additional API code. Note that NCBI's outlinks are based on a very very old dump to them (e.g. back when TreeBASE had only 15,000 names, instead of the 100,000+ names that it has now). It would be vastly better if we get NCBI to change their outlinks over to /phylows/ and use NCBI taxids instead of legacy TB1 ids. Perhaps we should create a /phylows/ query that asks "give list of all NCBI taxids" (e.g. find all taxa with ncbi taxid > 0 that relate to at least one taxonlabel in TreeBASE), so that NCBI can dynamically update their outlinks rather than relying on periodic dumps. bp |
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From: Hilmar L. <hl...@ne...> - 2010-05-25 15:41:23
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I vote against putting effort into that. It would be perpetuating old URLs for no new ground being gained, and bypasses the proper mechanism, so really is a hack. Instead, we should construct a new LinkOut mapping file for NCBI and submit it to their ftp server at the appropriate location. That would be the clean and Right Way. -hilmar On May 25, 2010, at 8:53 AM, Jon Auman wrote: > We could : > 1) keep the old site up and running and redirect all '/cgi-bin/foo' > requests to the old server (seems backward) > 2) Fix the 404 page to send users to the search page or custom 404 > page (we should do this irregardless) > 3) Create a lookup table that maps legacy taxonIDs to new ones. > Seems like a one time thing, cause all new studies will not have > legacy ID, right? > 4) do #2 and not worry about the rest > > Just me 2 cents worth. > > Jon > > On May 25, 2010, at 10:38 AM, Rutger Vos wrote: > >> On Tue, May 25, 2010 at 3:32 PM, Jon Auman <jon...@du...> >> wrote: >>> If you all tell me what should rewrite to what, I can turn on the >>> mojo and >>> make it happen. We've got apache on the front end, so mod_rewrite is >>> available. >> >> Bill probably still has the documentation for the URL API from >> version >> 1. If he can dig that up we should be able to rewrite a significant >> portion of those URLs to become PhyloWS URLs. This won't address his >> complaint about the old taxon IDs being gone though. >> >> -- >> Dr. Rutger A. Vos >> School of Biological Sciences >> Philip Lyle Building, Level 4 >> University of Reading >> Reading >> RG6 6BX >> United Kingdom >> Tel: +44 (0) 118 378 7535 >> http://www.nexml.org >> http://rutgervos.blogspot.com > > ------------------------------------------------------- > Jon Auman > Systems Administrator > National Evolutionary Synthesis Center > Duke University > http:www.nescent.org > jon...@ne... > ------------------------------------------------------ > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: William P. <wil...@ya...> - 2010-05-26 00:01:26
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On May 25, 2010, at 8:41 AM, Hilmar Lapp wrote: > Instead, we should construct a new LinkOut mapping file for NCBI and submit it to their ftp server at the appropriate location. That would be the clean and Right Way. Ah... I didn't know the outlinks could be submitted that way. I was preparing the send off the (below) message to Scott Federhen. If this letter to him is still relevant, please make comments / edits. I'm thinking that I should remove the bit about returning a list of studies / matrices / trees because those links don't seem to work -- they are returning the taxon tab instead of jumping to the respective study / matrix/ tree tab. Bill ===================================================== On May 1, 2003, at 6:21 AM, Scott Federhen wrote: > Hi Bill: > > The TreeBase links went up in Entrez yesterday - > you can find all of them with: > > http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Taxonomy > search for "loprovtreebase[filter]" (no quotes) and hit 'Go' > switch from 'Summary' to 'LinkOut' and hit 'Display' Dear Scott, Thanks very much for posting NCBI's outlinks to TreeBASE over the last seven years. TreeBASE has now been redeveloped from the ground up. Among the new features, the following items are relevant to NCBI's outlinks: - TreeBASE has a new RESTful API based on the PhyloWS standard - Regrettably, TreeBASE has had to reissue new taxon id numbers. The old version was essentially just a distinct list of taxon labels. The new version is the result of a mapping between taxon labels in each study and a taxonomy, in which homonyms receive distinct IDs. Since our concept of what is a "taxon" has changed (from unique string to a vetted list) the ID numbers for these has also changed. - TreeBASE now tries to store the equivalent NCBi taxid for each taxon in TreeBASE. This means that Entrez can outlink to TreeBASE by using NCBI taxids rather than having to store any of TreeBASE's IDs. All that's needed is for NCBI to know which of its taxa are also in TreeBASE. I am attaching a list of all NCBI taxids that current map to data objects in TreeBASE. The PhyloWS format for creating an outlink to Homo sapiens in TreeBASE (using NCBI taxid 9606) is as follows: http://purl.org/phylo/treebase/phylows/taxon/find?query=tb.identifier.ncbi=9606&format=html or if it's safer to use %3D as a substitute for the equals sign: http://purl.org/phylo/treebase/phylows/taxon/find?query=tb.identifier.ncbi%3D9606&format=html If you want to return a list of studies, use the following: http://purl.org/phylo/treebase/phylows/taxon/find?query=tb.identifier.ncbi%3D9606&format=html&recordSchema=study If you want to return a list of matrices (i.e. alignments), use the following: http://purl.org/phylo/treebase/phylows/taxon/find?query=tb.identifier.ncbi%3D9606&format=html&recordSchema=matrix If you want to return a list of trees, use the following: http://purl.org/phylo/treebase/phylows/taxon/find?query=tb.identifier.ncbi%3D9606&format=html&recordSchema=tree I hope you're able to update your outlinks without too much trouble. I'd be happy to provide these data in a difference format, if it's helpful. regards, Bill |
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From: Hilmar L. <hl...@ne...> - 2010-05-26 04:32:38
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On May 25, 2010, at 6:01 PM, William Piel wrote: > If this letter to him is still relevant, please make comments / edits. I don't think it's still relevant. The instructions are here: http://bit.ly/NCBI_LinkOut We can email him once we have those two files set up and deposited. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2010-05-27 10:06:20
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Ok, so, about the searching thing. Here's what I think we could do: * we create a separate page, something like "meta search", or "simple search" or whatever * on that page is just a single search box, a la google * you stick in anything you like and press the button * with javascript, we then compose all phylows queries we currently support, i.e. match against taxon names, taxon IDs, study IDs, etc., * we fire those requests as AJAX calls * on the server side, we return the results structured as rss (but maybe translate them to JSON) * as the AJAX responses are coming in, we count the number of items in each result feed * we can then report how many hits there were on each supported query * and we can make expandable boxes to actually list those hits, or make the hit reports clickable to take you to our normal results pages It seems to me that this would be the easiest way to support this functionality. On Tue, May 25, 2010 at 1:35 PM, Rutger Vos <rut...@gm...> wrote: > http://iphylo.blogspot.com/2010/05/treebase-ii-makes-me-pull-my-hair-out.html > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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From: Hilmar L. <hl...@ne...> - 2010-05-27 13:15:13
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What you describe sounds similar in concept to NCBI's GQuery, so you might want to look at that: http://www.ncbi.nlm.nih.gov/gquery/ -hilmar On May 27, 2010, at 4:06 AM, Rutger Vos wrote: > Ok, so, about the searching thing. Here's what I think we could do: > > * we create a separate page, something like "meta search", or "simple > search" or whatever > > * on that page is just a single search box, a la google > > * you stick in anything you like and press the button > > * with javascript, we then compose all phylows queries we currently > support, i.e. match against taxon names, taxon IDs, study IDs, etc., > > * we fire those requests as AJAX calls > > * on the server side, we return the results structured as rss (but > maybe translate them to JSON) > > * as the AJAX responses are coming in, we count the number of items in > each result feed > > * we can then report how many hits there were on each supported query > > * and we can make expandable boxes to actually list those hits, or > make the hit reports clickable to take you to our normal results pages > > It seems to me that this would be the easiest way to support this > functionality. > > On Tue, May 25, 2010 at 1:35 PM, Rutger Vos <rut...@gm...> > wrote: >> http://iphylo.blogspot.com/2010/05/treebase-ii-makes-me-pull-my-hair-out.html >> >> -- >> Dr. Rutger A. Vos >> School of Biological Sciences >> Philip Lyle Building, Level 4 >> University of Reading >> Reading >> RG6 6BX >> United Kingdom >> Tel: +44 (0) 118 378 7535 >> http://www.nexml.org >> http://rutgervos.blogspot.com >> > > > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading > RG6 6BX > United Kingdom > Tel: +44 (0) 118 378 7535 > http://www.nexml.org > http://rutgervos.blogspot.com > > ------------------------------------------------------------------------------ > > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Xianhua L. <xl...@du...> - 2010-05-27 13:26:28
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My 2 cents. Please consider supporting pagination of searching results. Too many hits in the search results will overwhelm the browser and make it hang forever. Xianhua On May 27, 2010, at 9:15 AM, Hilmar Lapp wrote: > What you describe sounds similar in concept to NCBI's GQuery, so you > might want to look at that: > > http://www.ncbi.nlm.nih.gov/gquery/ > > -hilmar > > On May 27, 2010, at 4:06 AM, Rutger Vos wrote: > >> Ok, so, about the searching thing. Here's what I think we could do: >> >> * we create a separate page, something like "meta search", or "simple >> search" or whatever >> >> * on that page is just a single search box, a la google >> >> * you stick in anything you like and press the button >> >> * with javascript, we then compose all phylows queries we currently >> support, i.e. match against taxon names, taxon IDs, study IDs, etc., >> >> * we fire those requests as AJAX calls >> >> * on the server side, we return the results structured as rss (but >> maybe translate them to JSON) >> >> * as the AJAX responses are coming in, we count the number of items >> in >> each result feed >> >> * we can then report how many hits there were on each supported query >> >> * and we can make expandable boxes to actually list those hits, or >> make the hit reports clickable to take you to our normal results >> pages >> >> It seems to me that this would be the easiest way to support this >> functionality. >> >> On Tue, May 25, 2010 at 1:35 PM, Rutger Vos <rut...@gm...> >> wrote: >>> http://iphylo.blogspot.com/2010/05/treebase-ii-makes-me-pull-my-hair-out.html >>> >>> -- >>> Dr. Rutger A. Vos >>> School of Biological Sciences >>> Philip Lyle Building, Level 4 >>> University of Reading >>> Reading >>> RG6 6BX >>> United Kingdom >>> Tel: +44 (0) 118 378 7535 >>> http://www.nexml.org >>> http://rutgervos.blogspot.com >>> >> >> >> >> -- >> Dr. Rutger A. Vos >> School of Biological Sciences >> Philip Lyle Building, Level 4 >> University of Reading >> Reading >> RG6 6BX >> United Kingdom >> Tel: +44 (0) 118 378 7535 >> http://www.nexml.org >> http://rutgervos.blogspot.com >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> Treebase-devel mailing list >> Tre...@li... >> https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel |
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From: Rutger V. <rut...@gm...> - 2010-05-27 13:41:27
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On Thu, May 27, 2010 at 2:15 PM, Hilmar Lapp <hl...@ne...> wrote: > What you describe sounds similar in concept to NCBI's GQuery, so you might > want to look at that: > > http://www.ncbi.nlm.nih.gov/gquery/ It's no coincidence that it sounds similar. The OP was meant to replicate that functionality on a shoestring :-) -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading RG6 6BX United Kingdom Tel: +44 (0) 118 378 7535 http://www.nexml.org http://rutgervos.blogspot.com |
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