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From: Rutger V. <rut...@gm...> - 2012-02-21 16:02:47
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Hi Bill, I'm not getting a trace for uBio IDs. Under what conditions is this happening? Rutger On Tue, Feb 21, 2012 at 5:00 PM, William Piel <wil...@ya...> wrote: > > On Feb 21, 2012, at 6:30 AM, Rutger Vos wrote: > > what do you think of this new, simplified search > box: http://treebase-dev.nescent.org/treebase-web/search/taxonSearch.html > > > I like it. > > NCBI IDs and TreeBASE taxon IDs work, but not UBio IDs (they generate a > trace). > > The comma-separated terms works nicely -- so perhaps there's no need, then, > for the all / any radio button? i.e. if there are multiple items that are > comma separated, inevitably these must be viewed as an "Any" search, as an > "All" search always would result in nothing. > > I've done most of the prep work to have the same box for matrix, tree and > study searching so that end users just type their search terms and we try to > be clever in expanding those into the context-appropriate search predicates. > > > What if you preserve the popup list for what to search on, but the default > item is "guess" or "all" ? > > bp > > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
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From: William P. <wil...@ya...> - 2012-02-21 16:00:09
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On Feb 21, 2012, at 6:30 AM, Rutger Vos wrote: > what do you think of this new, simplified search box: http://treebase-dev.nescent.org/treebase-web/search/taxonSearch.html I like it. NCBI IDs and TreeBASE taxon IDs work, but not UBio IDs (they generate a trace). The comma-separated terms works nicely -- so perhaps there's no need, then, for the all / any radio button? i.e. if there are multiple items that are comma separated, inevitably these must be viewed as an "Any" search, as an "All" search always would result in nothing. > I've done most of the prep work to have the same box for matrix, tree and study searching so that end users just type their search terms and we try to be clever in expanding those into the context-appropriate search predicates. What if you preserve the popup list for what to search on, but the default item is "guess" or "all" ? bp |
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From: Rutger V. <rut...@gm...> - 2012-02-21 11:30:59
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Hi all, what do you think of this new, simplified search box: http://treebase-dev.nescent.org/treebase-web/search/taxonSearch.html I've done most of the prep work to have the same box for matrix, tree and study searching so that end users just type their search terms and we try to be clever in expanding those into the context-appropriate search predicates. Rutger -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
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From: Hilmar L. <hl...@ne...> - 2012-02-21 04:34:17
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I agree this would be quite useful. At present all PhyloWS query attributes map directly to attributes of the data. Querying presence of absence of would be a departure from that. I think ideally I'd like to see this supported through CDAO terms. Whether a tree has branch lengths or not is a piece of semantic metadata about the tree. A tree with branch lengths could be declared as an Instance of the subclass of trees that also have branch lengths. -hilmar On Feb 20, 2012, at 8:41 PM, Carl Boettiger wrote: > Hi Treebase developers, > > How difficult would it be to include the ability to restrict phylows API queries to only trees having branch length data? Can this be done already? If not, is it a straight forward modification? I would find this very useful (and would reduce my load on the server, since otherwise I have to do pull down each tree and check if it has this data...) > > Many thanks, > > Carl > > On Fri, Feb 17, 2012 at 10:32 AM, Rutger Vos <rut...@gm...> wrote: > Hi all, > > I've made some recent enhancements to the search facilities: > > - there was a bug in searching by tree quality, this has now been corrected > > - we can now search by doi, it is an option in the pull down menu on the study search page, and has also been added to the PhyloWS API: > > http://purl.org/phylo/treebase/dev/phylows/study/find?query=prism.doi="10.1016/j.ympev.2009.03.021" > > - I also added buttons to the twitter account and the mendeley group. > > Maybe we can push these things to production? > > Rutger > > -- > Dr. Rutger A. Vos > Bioinformaticist > NCB Naturalis > Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands > Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands > http://rutgervos.blogspot.com > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > > > -- > Carl Boettiger > UC Davis > http://www.carlboettiger.info/ > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d_______________________________________________ > 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: Carl B. <cbo...@gm...> - 2012-02-21 01:41:40
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Hi Treebase developers, How difficult would it be to include the ability to restrict phylows API queries to only trees having branch length data? Can this be done already? If not, is it a straight forward modification? I would find this very useful (and would reduce my load on the server, since otherwise I have to do pull down each tree and check if it has this data...) Many thanks, Carl On Fri, Feb 17, 2012 at 10:32 AM, Rutger Vos <rut...@gm...> wrote: > Hi all, > > I've made some recent enhancements to the search facilities: > > - there was a bug in searching by tree quality, this has now been corrected > > - we can now search by doi, it is an option in the pull down menu on the > study search page, and has also been added to the PhyloWS API: > > http://purl.org/phylo/treebase/dev/phylows/study/find?query=prism.doi= > "10.1016/j.ympev.2009.03.021" > > - I also added buttons to the twitter account and the mendeley group. > > Maybe we can push these things to production? > > Rutger > > -- > Dr. Rutger A. Vos > Bioinformaticist > NCB Naturalis > Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the > Netherlands > Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands > http://rutgervos.blogspot.com > > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- Carl Boettiger UC Davis http://www.carlboettiger.info/ |
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From: Mattison W. <mat...@ne...> - 2012-02-20 16:19:49
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Rev 1073 has been pushed to production. Regards, Mattison On Fri, Feb 17, 2012 at 1:32 PM, Rutger Vos <rut...@gm...> wrote: > Hi all, > > I've made some recent enhancements to the search facilities: > > - there was a bug in searching by tree quality, this has now been corrected > > - we can now search by doi, it is an option in the pull down menu on the > study search page, and has also been added to the PhyloWS API: > > http://purl.org/phylo/treebase/dev/phylows/study/find?query=prism.doi="10.1016/j.ympev.2009.03.021" > > - I also added buttons to the twitter account and the mendeley group. > > Maybe we can push these things to production? > > Rutger > > -- > Dr. Rutger A. Vos > Bioinformaticist > NCB Naturalis > Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the > Netherlands > Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands > http://rutgervos.blogspot.com > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > -- Mattison Ward NESCent at Duke University 2024 W. Main Street, Suite A200 Durham, NC 27705-4667 919-668-4585 (desk) 919-668-4551 (alternate) 919-668-9198 (fax) |
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From: Hilmar L. <hl...@ne...> - 2012-02-17 23:54:59
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On Feb 17, 2012, at 1:32 PM, Rutger Vos wrote: > - there was a bug in searching by tree quality, this has now been corrected How is tree quality defined? I'm puzzled this is even there (I thought it wasn't) so perhaps I'm misunderstanding. Are you saying you can search for all trees that are "good", or "bad"? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Carl B. <cbo...@gm...> - 2012-02-17 18:48:48
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On Fri, Feb 17, 2012 at 10:32 AM, Rutger Vos <rut...@gm...> wrote: > Hi all, > > I've made some recent enhancements to the search facilities: > > - there was a bug in searching by tree quality, this has now been corrected > > - we can now search by doi, it is an option in the pull down menu on the > study search page, and has also been added to the PhyloWS API: Many thanks Rutger, this is great news! > > http://purl.org/phylo/treebase/dev/phylows/study/find?query=prism.doi="10.1016/j.ympev.2009.03.021" > > - I also added buttons to the twitter account and the mendeley group. > > Maybe we can push these things to production? > > Rutger > > -- > Dr. Rutger A. Vos > Bioinformaticist > NCB Naturalis > Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the > Netherlands > Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands > http://rutgervos.blogspot.com > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > -- Carl Boettiger UC Davis http://www.carlboettiger.info/ |
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From: Rutger V. <rut...@gm...> - 2012-02-17 18:33:05
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Hi all, I've made some recent enhancements to the search facilities: - there was a bug in searching by tree quality, this has now been corrected - we can now search by doi, it is an option in the pull down menu on the study search page, and has also been added to the PhyloWS API: http://purl.org/phylo/treebase/dev/phylows/study/find?query=prism.doi= "10.1016/j.ympev.2009.03.021" - I also added buttons to the twitter account and the mendeley group. Maybe we can push these things to production? Rutger -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
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From: Karen C. <kar...@gm...> - 2012-02-16 18:22:39
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Over the next 3 weeks NESCent will be putting together our application as a mentoring organization to the 2012 Google Summer of Code: http://www.google-melange.com/gsoc/homepage/google/gsoc2012 This is a call for all prospective mentors, primary and secondary, to step forward. Our primary admin for this year is me, Karen Cranston, but I am thrilled to announce that Jim Proctor (Jalview) will be joining me as secondary admin. Participating as an organization is competitive, with an acceptance rate of 30-35%. The most important component of an organization application are the Project Ideas. These project ideas are contributed by you, our mentors. Ideally, our list of potential projects is diverse, with different degrees of difficulty, from different participating open-source projects, using different programming languages. This year, we are making a special effort to attract more women as mentors and as applicants to the program. If you have an idea of how a student could contribute to your open-source project, or would you like to serve as a mentor or help someone else as a secondary mentor, contact us at phy...@ne... so that we can add you to our (private) mentors mailing list (if you aren't already on the list). Then, add your project idea and information about yourself to the informatics wiki (*): http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2012 We will send further guidance on drafting project ideas, but for now you can see examples on pages from previous years (click on "Ideas"): http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2011 http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2010 http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2009 http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2008 http://informatics.nescent.org/wiki/Phyloinformatics_Summer_of_Code_2007 If you are new to Summer of Code and wonder what it takes or what it is like to be a mentor, don't hesitate to ask questions or to contact previous mentors (see URLs above for past projects). Being a mentor does require time (see http://goo.gl/iluTd), but our past mentors have almost unanimously found it a fun and rewarding experience. The student contributes code to your project, and has the potential to stay on as a developer beyond the end of the Summer of Code. The organizational application is due March 9. In order to include a project idea in our submission, it must be in reasonable shape by the morning of March 9. If we are then accepted, ideas can be refined (or added) between March 17-25. See http://goo.gl/Jzeq5 for a full timeline of the whole program. Feel free to forward this call to colleagues or other relevant mailing lists. Cheers, and we look forward to hearing from you! Karen Cranston Jim Proctor (*) To edit content on the NESCent Informatics wiki, you have to login. If you don't already have an account, you can create one using OpenID or your Google account. When you edit the Project Ideas section, you will see a template you can use as the basis for an idea. -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Karen Cranston, PhD Training Coordinator and Informatics Project Manager nescent.org ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -- ~~~~~~~~~~~~~~~~~~~~~~~ kar...@gm... ~~~~~~~~~~~~~~~~~~~~~~~ |
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From: Hilmar L. <hl...@ne...> - 2012-02-16 14:33:00
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On Feb 16, 2012, at 9:07 AM, William Piel <wil...@ya...> wrote: > Deposit restrictions: Deposits accepted subject to acquisitions policy; phylogenetic data accepted in NEXUS format; some metadata accetped in tab-separated text format I wouldn't put the current format requirements there (because they may - and in fact hopefully will - change in the near future). And shouldn't this include that data must be associated with a publication, since that's not really up for debate? > Access restrictions: Data that accompany a peer-reviewed scientific publication that is "in press" or published are available as Open Access. Add explicitly that data are embargoed until publication of the associated article? Also, your formulation suggests that there are also data that don't accompany a publication. Are there indeed? (I thought not.) > > Licence agreement: The phylogenetic data are considered digitally encoded concepts or ideas, not art, and therefore the data are not subject to copyright. Does that mean CC0 or something else? Can we be explicit here? -hilmar Sent with a tap. |
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From: Rutger V. <rut...@gm...> - 2012-02-16 14:16:46
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> > Subject area(s): phylogenetics, evolution, bioinformatics, phyloinformatics > MorphoBank also mentions "cladistics". Maybe do that as well? And what about language evolution? -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
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From: William P. <wil...@ya...> - 2012-02-16 14:08:00
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On Feb 16, 2012, at 5:52 AM, Rutger Vos wrote: > Hi all, > > we need to decide what to put in DataCite's incomplete entry for TreeBASE (http://datacite.org/repolist) that Hilmar brought to our attention. > > Rutger Here's a suggestion. bp Repository: TreeBASE Website: http://www.treebase.org Subject area(s): phylogenetics, evolution, bioinformatics, phyloinformatics Funding model: NSF, NESCent Deposit restrictions: Deposits accepted subject to acquisitions policy; phylogenetic data accepted in NEXUS format; some metadata accetped in tab-separated text format Access restrictions: Data that accompany a peer-reviewed scientific publication that is "in press" or published are available as Open Access. Licence agreement: The phylogenetic data are considered digitally encoded concepts or ideas, not art, and therefore the data are not subject to copyright. Country: USA; the Netherlands Identifier/s: UUIDs Abbreviation: TreeBASE Notes: Phylogenetic trees, cladograms, phylograms, DNA and Protein alignments, morphological character matrices |
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From: Rutger V. <rut...@gm...> - 2012-02-16 10:52:35
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Hi all, we need to decide what to put in DataCite's incomplete entry for TreeBASE ( http://datacite.org/repolist) that Hilmar brought to our attention. Rutger ---------- Forwarded message ---------- From: datasets <dat...@bl...> Date: Thu, Feb 16, 2012 at 10:02 AM Subject: RE: [Contact the Managing Agent] TreeBASE entry incomplete To: rv...@tr... Dear Rutger, Many thanks for getting in touch. The table is actually a collaborative document held outside of DataCite, but if you could send me the updated and completed information, I can put these into the table for you. Best regards, Rachael. -----Original Message----- From: web...@da... [mailto:web...@da...] On Behalf Of rv...@tr... Sent: 15 February 2012 17:34 To: Fra...@ti...; Jan...@ti...; datasets Subject: [Contact the Managing Agent] TreeBASE entry incomplete Rutger Vos (rv...@tr...) sent a message using the contact form at http://datacite.org/contact. Dear sir or madam, the entry for TreeBASE is incomplete. How would we go about updating this information? Best regards, Rutger Vos -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
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From: William P. <wil...@ya...> - 2012-02-10 23:57:43
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On Feb 10, 2012, at 1:05 AM, Hilmar Lapp wrote: > Can anyone give me a quick estimate of how many tip nodes all published trees in TreeBASE amount to? SELECT count(*) FROM study JOIN phylotree USING (study_id) JOIN phylotreenode USING (phylotree_id) WHERE studystatus_id = 3 AND child_id IS NULL; Number of tip nodes on all published trees = 480,596 SELECT count(*) FROM ( SELECT DISTINCT ptn.name FROM study JOIN phylotree USING (study_id) JOIN phylotreenode ptn USING (phylotree_id) WHERE studystatus_id = 3 AND child_id IS NULL ) cnt; Size of the set of all distinct taxon labels on tips of all published trees = 189,012 SELECT count(*) FROM ( SELECT DISTINCT taxon_id FROM study JOIN phylotree USING (study_id) JOIN phylotreenode USING (phylotree_id) JOIN taxonlabel USING (taxonlabel_id) JOIN taxonvariant USING (taxonvariant_id) WHERE studystatus_id = 3 AND child_id IS NULL ) cnt Number of distinct "taxa" that map to all published trees = 83,742 |
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From: Hilmar L. <hl...@ne...> - 2012-02-10 18:26:44
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Thanks Carl, this is great! The context of my question is actually the 2012 iEvoBio challenge. You'll know when you see the website with the Challenge call go up. In short, we were going to suggest (all or a subset of) TreeBASE as one possible dataset, and I was wondering whether it would meet the criteria. -hilmar On Feb 10, 2012, at 1:21 PM, Carl Boettiger wrote: > whoops, different conventions on trees, Nnode is internal nodes only so that should have been x$Nnode+1. > > tips <- unlist(sapply(all_treebase, function(x) (x$Nnode+1)))) > sum(tips) > 116319 > > mean(tips) > [1] 43.43503 > > max(tips) > [1] 794 > > histogram > <image.png> > > > On Fri, Feb 10, 2012 at 9:55 AM, Carl Boettiger <cbo...@gm...> wrote: > From a slightly dated cache in R treebase, I get: > > > sum(unlist(sapply(all_treebase, function(x) (x$Nnode-1)/2))) > 55481 > > that's probably way under, since it's a few months behind and some trees get dropped by treebase if the server times out, probably need a better way to handle those things. Others can probably give a much better number. > > Carl > > > On Thu, Feb 9, 2012 at 10:05 PM, Hilmar Lapp <hl...@ne...> wrote: > Can anyone give me a quick estimate of how many tip nodes all published trees in TreeBASE amount to? > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > > > -- > Carl Boettiger > UC Davis > http://www.carlboettiger.info/ > > > > > -- > Carl Boettiger > UC Davis > http://www.carlboettiger.info/ > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Carl B. <cbo...@gm...> - 2012-02-10 17:56:03
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>From a slightly dated cache in R treebase, I get: > sum(unlist(sapply(all_treebase, function(x) (x$Nnode-1)/2))) 55481 that's probably way under, since it's a few months behind and some trees get dropped by treebase if the server times out, probably need a better way to handle those things. Others can probably give a much better number. Carl On Thu, Feb 9, 2012 at 10:05 PM, Hilmar Lapp <hl...@ne...> wrote: > Can anyone give me a quick estimate of how many tip nodes all published > trees in TreeBASE amount to? > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > > ------------------------------------------------------------------------------ > Virtualization & Cloud Management Using Capacity Planning > Cloud computing makes use of virtualization - but cloud computing > also focuses on allowing computing to be delivered as a service. > http://www.accelacomm.com/jaw/sfnl/114/51521223/ > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > -- Carl Boettiger UC Davis http://www.carlboettiger.info/ |
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From: Hilmar L. <hl...@ne...> - 2012-02-10 06:06:34
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Can anyone give me a quick estimate of how many tip nodes all published trees in TreeBASE amount to? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2012-02-09 14:46:31
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Hi all, as an experiment, I built a widget that fetches images of taxa from recent submissions: http://dl.dropbox.com/u/4180059/treebase/imageFeed.html It uses iphylo.org/linkout and dbpedia.org to locate the images, so they're not as likely to be wrong. A downside is that there is quite a bit of fetching and joining of RDF records, so it's all a bit fragile. Nonetheless, might be fun to have something like this on the home page? Rutger -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
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From: Rutger V. <rut...@gm...> - 2012-02-07 19:28:56
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Ah, I stand corrected. Cool, I didn't realize. On Tue, Feb 7, 2012 at 7:39 PM, William Piel <wil...@ya...> wrote: > > On Feb 7, 2012, at 5:20 AM, Rutger Vos wrote: > > We don't store PubMed ids. > > > I think we do have a facility for that. > > e.g. go here: > > http://purl.org/phylo/treebase/phylows/study/TB2:S1163?format=html > > ... and scroll down to External Links -- see "PMID". > > But seldom do authors type this one in; and this predicate is not yet in > phylows. > > bp > > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > Treebase-devel mailing list > Tre...@li... > https://lists.sourceforge.net/lists/listinfo/treebase-devel > > -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
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From: William P. <wil...@ya...> - 2012-02-07 18:39:23
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On Feb 7, 2012, at 5:20 AM, Rutger Vos wrote: > We don't store PubMed ids. I think we do have a facility for that. e.g. go here: http://purl.org/phylo/treebase/phylows/study/TB2:S1163?format=html ... and scroll down to External Links -- see "PMID". But seldom do authors type this one in; and this predicate is not yet in phylows. bp |
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From: Hilmar L. <hl...@ne...> - 2012-02-07 17:24:47
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On Feb 7, 2012, at 5:21 AM, Roderic Page wrote: > A clean separation of data input from data output would go some way to curing TreeBASE's performance issues... Sigh. Also something we proposed in the just-declined ABI grant :-) -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2012-02-07 17:02:58
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Here's a taxon search, along similar lines: http://dl.dropbox.com/u/4180059/treebase/taxonSearch.html On Tue, Feb 7, 2012 at 11:21 AM, Roderic Page <r....@bi...> wrote: > As a follow on, tools like Elastic Search http://www.elasticsearch.org/could be used to provide some nice functionality independent of the current > web site design. For example, you could set up a tool that consumed > TreeBASE RSS to get the latest updates, pulled off the corresponding NEXML, > added that to a search index, and provide a nice interface sitting on top. > Apart from the initial harvesting there would be no more calls to the > current TreeBASE database, leaving it to handle the data uploads. > > A clean separation of data input from data output would go some way to > curing TreeBASE's performance issues... > > Regards > > Rod > > > On 7 Feb 2012, at 09:53, Rutger Vos wrote: > > Hi all, > > here's a prototype of a simplified search interface: > http://dl.dropbox.com/u/4180059/treebase/query.html > > It gives users the ability to just type any words, and the javascript > infers whether the terms are identifiers or something else. It then turns > the terms into a PhyloWS query and calls that. It would need some > configuration to use the right predicates for each search page, but it > would simplify things for users, and if power users want to see (and edit) > the underlying query they can still do so. > > Rutger > > -- > Dr. Rutger A. Vos > Bioinformaticist > NCB Naturalis > Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the > Netherlands > Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands > http://rutgervos.blogspot.com > > > --------------------------------------------------------- > Roderic Page > Professor of Taxonomy > Institute of Biodiversity, Animal Health and Comparative Medicine > College of Medical, Veterinary and Life Sciences > Graham Kerr Building > University of Glasgow > Glasgow G12 8QQ, UK > > Email: r....@bi... > Tel: +44 141 330 4778 > Fax: +44 141 330 2792 > AIM: rod...@ai... > Facebook: http://www.facebook.com/profile.php?id=1112517192 > Twitter: http://twitter.com/rdmpage > Blog: http://iphylo.blogspot.com > Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html > > -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
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From: Rutger V. <rut...@gm...> - 2012-02-07 12:16:09
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> A clean separation of data input from data output would go some way to > curing TreeBASE's performance issues... > Absolutely. Once a study has been deposited there is no reason at all to serve it up dynamically - the output side could (a purist might say: should) be completely static. > On 7 Feb 2012, at 09:53, Rutger Vos wrote: > > Hi all, > > here's a prototype of a simplified search interface: > http://dl.dropbox.com/u/4180059/treebase/query.html > > It gives users the ability to just type any words, and the javascript > infers whether the terms are identifiers or something else. It then turns > the terms into a PhyloWS query and calls that. It would need some > configuration to use the right predicates for each search page, but it > would simplify things for users, and if power users want to see (and edit) > the underlying query they can still do so. > > Rutger > > -- > Dr. Rutger A. Vos > Bioinformaticist > NCB Naturalis > Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the > Netherlands > Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands > http://rutgervos.blogspot.com > > > --------------------------------------------------------- > Roderic Page > Professor of Taxonomy > Institute of Biodiversity, Animal Health and Comparative Medicine > College of Medical, Veterinary and Life Sciences > Graham Kerr Building > University of Glasgow > Glasgow G12 8QQ, UK > > Email: r....@bi... > Tel: +44 141 330 4778 > Fax: +44 141 330 2792 > AIM: rod...@ai... > Facebook: http://www.facebook.com/profile.php?id=1112517192 > Twitter: http://twitter.com/rdmpage > Blog: http://iphylo.blogspot.com > Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html > > -- Dr. Rutger A. Vos Bioinformaticist NCB Naturalis Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands http://rutgervos.blogspot.com |
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From: Roderic P. <r....@bi...> - 2012-02-07 10:21:39
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As a follow on, tools like Elastic Search http://www.elasticsearch.org/ could be used to provide some nice functionality independent of the current web site design. For example, you could set up a tool that consumed TreeBASE RSS to get the latest updates, pulled off the corresponding NEXML, added that to a search index, and provide a nice interface sitting on top. Apart from the initial harvesting there would be no more calls to the current TreeBASE database, leaving it to handle the data uploads. A clean separation of data input from data output would go some way to curing TreeBASE's performance issues... Regards Rod On 7 Feb 2012, at 09:53, Rutger Vos wrote: > Hi all, > > here's a prototype of a simplified search interface: http://dl.dropbox.com/u/4180059/treebase/query.html > > It gives users the ability to just type any words, and the javascript infers whether the terms are identifiers or something else. It then turns the terms into a PhyloWS query and calls that. It would need some configuration to use the right predicates for each search page, but it would simplify things for users, and if power users want to see (and edit) the underlying query they can still do so. > > Rutger > > -- > Dr. Rutger A. Vos > Bioinformaticist > NCB Naturalis > Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the Netherlands > Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands > http://rutgervos.blogspot.com --------------------------------------------------------- Roderic Page Professor of Taxonomy Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary and Life Sciences Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK Email: r....@bi... Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rod...@ai... Facebook: http://www.facebook.com/profile.php?id=1112517192 Twitter: http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html |
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