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From: William P. <wil...@ya...> - 2012-04-25 06:17:47
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On Apr 24, 2012, at 9:17 PM, Carl Boettiger wrote: > Hi list, > > I'm curious what license, if any, covers the treebase data? Dryad is very clear about all their data being public domain / CC0, but it's not obvious to me from the treebase website. > > Thanks > > Carl Our "story" so far is that in the spectrum of Art vs. Ideas, TreeBASE stores ideas. Even if the original published tree was an "artwork" with respect to the journal, in TreeBASE the nodes and edges are decomposed into tables, and when re-serialized you can't be sure that it will look like the original artwork. So in that sense we are storing the concepts or ideas, not the art -- and therefore while some of these objects may be patented, we don't think they should be copyrightable. Hence copyright simply does not apply to the data, only to the codebase. While citations and abstracts are often considered art (and we also store those), I think our redistribution of them is considered "fair use". bp |
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From: Carl B. <cbo...@gm...> - 2012-04-24 18:17:31
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Hi list, I'm curious what license, if any, covers the treebase data? Dryad is very clear about all their data being public domain / CC0, but it's not obvious to me from the treebase website. Thanks Carl -- Carl Boettiger UC Davis http://www.carlboettiger.info/ |
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From: Hilmar L. <hl...@ne...> - 2012-04-23 13:48:27
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Great, thanks Bill! -hilmar On Apr 23, 2012, at 3:01 AM, William Piel wrote: > > On Apr 22, 2012, at 4:47 PM, Hilmar Lapp wrote: > >> Databib still seems to be missing TreeBASE. The catalog is community-curated and community-editable, so someone from TreeBASE will need to request the entry. Or was this considered as not worth doing? >> >> -hilmar > > I've just submitted something. > > bp > > > > > Title > TreeBASE > URL > http://www.treebase.org > Authority > Phyloinformatics Research Foundation, Inc. > Subjects > Evolution (Biology) > Phylogeny > DNA data banks > Genetics > Nucleotide sequence > Morphology > Animal behavior > Amino acid sequence > Cladistic analysis > Phylogeography > Description > TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes; morphological or behavioral matrices;amino acid or nucleotide sequences) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. > Access > open > Start Date > 1994 > Location > USA > Reuse > Open- http://www.treebase.org/treebase-web/urlAPI.html > Deposit > Accepts data from researchers- > http://www.treebase.org/treebase-web/submitTutorial.html > Type > disciplinary > > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: William P. <wil...@ya...> - 2012-04-23 07:02:45
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On Apr 22, 2012, at 4:47 PM, Hilmar Lapp wrote: > Databib still seems to be missing TreeBASE. The catalog is community-curated and community-editable, so someone from TreeBASE will need to request the entry. Or was this considered as not worth doing? > > -hilmar I've just submitted something. bp Title TreeBASE URL http://www.treebase.org Authority Phyloinformatics Research Foundation, Inc. Subjects Evolution (Biology) Phylogeny DNA data banks Genetics Nucleotide sequence Morphology Animal behavior Amino acid sequence Cladistic analysis Phylogeography Description TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes; morphological or behavioral matrices;amino acid or nucleotide sequences) representing all biotic taxa. Data in TreeBASE are exposed to the public if they are used in a publication that is in press or published in a peer-reviewed scientific journal, book, conference proceedings, or thesis. Access open Start Date 1994 Location USA Reuse Open- http://www.treebase.org/treebase-web/urlAPI.html Deposit Accepts data from researchers- http://www.treebase.org/treebase-web/submitTutorial.html Type disciplinary |
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From: Mattison W. <mat...@ne...> - 2012-04-20 17:54:08
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I believe the new treebase development server is ready for business running on the new (virtual) hardware with tomcat6. I have submitted files and clicked through the interface, but don't know if I have touched everything. Please give it a try and let me know if you find any problems. Go to http://tbdev.nescent.org/treebase-web/search/studySearch.html If you go to http://tbdev.nescent.org, it will redirect you to the old treebase-dev server. Regards, Mattison On Wed, Apr 18, 2012 at 11:40 AM, William Piel <wil...@ya...>wrote: > Hi Mattison, > > On Apr 18, 2012, at 11:31 AM, Mattison Ward wrote: > > Hi Bill and Harry. > > I have the new VMs for treebase and treebase-dev. > > As I start to set them up, I have a few questions: > > The current release version of Mesquite is 2.75 build 564 (the version > used now is 2.01). Do you want me to try the 2.75 version. > > > I believe that the Mesquite we use has custom code changes that do not > allow for easily upgrading to a new version. But I will cc: to TreeBASE Dev > for others, like Rutger, to chime in. > > I am planning to use tomcat 6 unless you object. > > > I have no view on this -- but others may. > > I have started testing at http://tbdev.nescent.org/treebase-web/ > > Do you use the staging environment? It is worthwhile to set up a staging > environment on the new server? > > > We used to use it to test the Dryad-TreeBASE handshaking because > demo-Dryad pointed to it, and the database was not refreshed from > production every evening (this persistence making it easier to test new > data added from Dryad). But I don't think we really use it much anymore. > Dev and Production are probably sufficient, but again, I'll let others > chime in. > > regards, > > Bill > > > > > > > > -- 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: Rutger V. <rut...@gm...> - 2012-04-18 15:49:45
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Yes, you can't simply upgrade mesquite, unfortunately. On Wed, Apr 18, 2012 at 5:40 PM, William Piel <wil...@ya...> wrote: > Hi Mattison, > > On Apr 18, 2012, at 11:31 AM, Mattison Ward wrote: > > Hi Bill and Harry. > > I have the new VMs for treebase and treebase-dev. > > As I start to set them up, I have a few questions: > > The current release version of Mesquite is 2.75 build 564 (the version used > now is 2.01). Do you want me to try the 2.75 version. > > > I believe that the Mesquite we use has custom code changes that do not allow > for easily upgrading to a new version. But I will cc: to TreeBASE Dev for > others, like Rutger, to chime in. > > I am planning to use tomcat 6 unless you object. > > > I have no view on this -- but others may. > > I have started testing at http://tbdev.nescent.org/treebase-web/ > > Do you use the staging environment? It is worthwhile to set up a staging > environment on the new server? > > > We used to use it to test the Dryad-TreeBASE handshaking because demo-Dryad > pointed to it, and the database was not refreshed from production every > evening (this persistence making it easier to test new data added from > Dryad). But I don't think we really use it much anymore. Dev and Production > are probably sufficient, but again, I'll let others chime in. > > regards, > > Bill > > > > > > > > > ------------------------------------------------------------------------------ > Better than sec? Nothing is better than sec when it comes to > monitoring Big Data applications. Try Boundary one-second > resolution app monitoring today. Free. > http://p.sf.net/sfu/Boundary-dev2dev > _______________________________________________ > 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...> - 2012-04-18 15:40:23
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Hi Mattison, On Apr 18, 2012, at 11:31 AM, Mattison Ward wrote: > Hi Bill and Harry. > > I have the new VMs for treebase and treebase-dev. > > As I start to set them up, I have a few questions: > > The current release version of Mesquite is 2.75 build 564 (the version used now is 2.01). Do you want me to try the 2.75 version. I believe that the Mesquite we use has custom code changes that do not allow for easily upgrading to a new version. But I will cc: to TreeBASE Dev for others, like Rutger, to chime in. > I am planning to use tomcat 6 unless you object. I have no view on this -- but others may. > I have started testing at http://tbdev.nescent.org/treebase-web/ > > Do you use the staging environment? It is worthwhile to set up a staging environment on the new server? We used to use it to test the Dryad-TreeBASE handshaking because demo-Dryad pointed to it, and the database was not refreshed from production every evening (this persistence making it easier to test new data added from Dryad). But I don't think we really use it much anymore. Dev and Production are probably sufficient, but again, I'll let others chime in. regards, Bill |
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From: Rutger V. <rut...@gm...> - 2012-03-27 05:54:05
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If it was me it must have been ages ago cause I don't remember. Their metadata is basically correct - maybe someone else did it? Bill? On Tue, Mar 27, 2012 at 5:41 AM, Hilmar Lapp <hl...@ne...> wrote: > Rutger, was that your doing, or did they pick it up themselves? Either way, > it's great it's now listed! > > -hilmar > > Sent with a tap. > > Begin forwarded message: > > From: "ProgrammableWeb via RT" <he...@tr...> > Date: March 26, 2012 6:00:18 PM EDT > Subject: [treebase-help #13297] Your API has been published on > ProgrammableWeb > Reply-To: he...@tr... > > > The TreeBASE API is now live on ProgrammableWeb. You can view it here: > > http://www.programmableweb.com/api/treebase > > Thanks for sharing it with our community. Let us know if there's anything we > can do to help. > > Best regards, > The ProgrammableWeb Team > > > ------------------------------------------------------------------------------ > This SF email is sponsosred by: > Try Windows Azure free for 90 days Click Here > http://p.sf.net/sfu/sfd2d-msazure > _______________________________________________ > 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: Hilmar L. <hl...@ne...> - 2012-03-27 03:42:06
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Rutger, was that your doing, or did they pick it up themselves? Either way, it's great it's now listed! -hilmar Sent with a tap. Begin forwarded message: > From: "ProgrammableWeb via RT" <he...@tr...> > Date: March 26, 2012 6:00:18 PM EDT > Subject: [treebase-help #13297] Your API has been published on ProgrammableWeb > Reply-To: he...@tr... > > The TreeBASE API is now live on ProgrammableWeb. You can view it here: > > http://www.programmableweb.com/api/treebase > > Thanks for sharing it with our community. Let us know if there's anything we > can do to help. > > Best regards, > The ProgrammableWeb Team > |
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From: Rutger V. <rut...@gm...> - 2012-03-01 09:47:20
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Hi Bill, all, I've noticed that Bill has made some edits to the shared tb2_doc dropbox folder (members of this folder are Harry, Bill and I - please indicate if you want access as well). Does this mean we are moving forward on a TreeBASE manuscript? If so, I guess we need to decide some things: * where do we want to send it? Systbiol would be nice, but perhaps we should ask if they're interested. Or are we shopping this around elsewhere? * who's the corresponding author (Bill, I'm guessing)? * can we come up with a "to do" list of things to make this into a ready submision? Rutger On Tue, Jan 26, 2010 at 12:19 AM, Hilmar Lapp <hl...@ne...> wrote: > > On Jan 25, 2010, at 9:01 AM, William Piel wrote: > >> >> Yeah, that's what I had in mind. A "manual" to PhyloWS using TreeBASE API >> as the first implementation of it. > > > That would indeed be a good example for a manual, but I think pretty > strongly that PhyloWS needs to go into an evolutionary data interoperability > story combining PhyloWS with NeXML and relevant ontologies (such as CDAO). > > -hilmar > > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > -- 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...> - 2012-02-22 19:00:19
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I fixed it. On Tue, Feb 21, 2012 at 10:35 PM, William Piel <wil...@ya...> wrote: > 2481730 -- 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 21:35:16
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On Feb 21, 2012, at 11:02 AM, Rutger Vos wrote: > Hi Bill, > > I'm not getting a trace for uBio IDs. Under what conditions is this happening? > > Rutger If I enter "2481730" (uBio namebank ID for Homo sapiens) I get the (below) result. Perhaps it's just for that number? bp Uncaught Exception Encountered java.lang.NullPointerException at org.cipres.treebase.web.controllers.TaxonSearchController.doIdentifierSearch(TaxonSearchController.java:273) at org.cipres.treebase.web.controllers.TaxonSearchController.doCQLQuery(TaxonSearchController.java:159) at org.cipres.treebase.web.controllers.TaxonSearchController.doCQLQuery(TaxonSearchController.java:101) at org.cipres.treebase.web.controllers.TaxonSearchController.handleQueryRequest(TaxonSearchController.java:409) at org.cipres.treebase.web.controllers.SearchController.showForm(SearchController.java:589) at org.springframework.web.servlet.mvc.SimpleFormController.showForm(SimpleFormController.java:175) at org.springframework.web.servlet.mvc.AbstractFormController.showNewForm(AbstractFormController.java:338) at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:278) at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153) at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48) at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858) at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792) at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476) at org.springframework.web.servlet.FrameworkServlet.doGet(FrameworkServlet.java:431) at javax.servlet.http.HttpServlet.service(HttpServlet.java:627) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164) at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141) at org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:90) at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:406) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:70) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119) at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107) at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191) at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274) at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148) at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:185) at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:159) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:215) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188) at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213) at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117) at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108) at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174) at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:837) at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:640) at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1286) at java.lang.Thread.run(Thread.java:636) Cookies: __utmz=[5099126.1325874733.106.3.utmcsr] __utmc=[5099126] __utmb=[5099126.5.10.1329859997] __utma=[5099126.226138284.1305666484.1329839287.1329859997.128] JSESSIONID=[FCCFCFD207DE05FC97C1ABC65F9D7AAC] __utma=[53240375.1924499357.1236724314.1323364793.1327431391.169] __qca=[P0-99604753-1323893020687] __utmz=[53240375.1319935395.167.45.utmccn] |
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From: Roderic P. <r....@bi...> - 2012-02-21 19:04:59
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I guess I'd (ideally) show a preview of the trees, or at least a link for each that will return a list of those trees. I don't think people get the metaphor that the results of a query carry across tabs. You could use a facetted-browser type display (e.g., a list of the left hand side of studies, taxa, trees, etc. that match a particular query (with numbers of each item that match that query), people will grok this. In my phyloinformatics course people had no idea what was going on. The mantra should be "don't make me think!" http://www.amazon.co.uk/Dont-Make-Me-Think-Usability/dp/0321344758 Regards Rod On 21 Feb 2012, at 17:46, Rutger Vos wrote: >> Nice to have a generic search box, now if we could just get rid of the >> "projection metaphor" because it is as confusing as hell! > > I guess we don't present it well by calling it a projection, but > people will obviously want to do things like "get me the trees for > taxon X". What would be the right way to present this? > >> Oh, and why doesn't TreeBASE support searching by higher taxa? This is easy >> to do, and seems an obvious feature to have... > > Yes. > >> On 21 Feb 2012, at 17:18, Rutger Vos wrote: >> >> The only thing that people may not expect is the tokenization based on comma >> rather than whitespace, because it's different from what Google does (which >> is what everyone is used to). >> >> >> Except it isn't precisely what google does, because it weighs >> occurrences of words near each other higher, so that typing 'Homo >> sapiens' (no quotes) won't just return a bucket of pages that have the >> words 'Homo' and 'sapiens' anywhere in them. And maybe we don't want >> people to have to write 'Homo sapiens' (with quotes) every time they >> search for a species - which will be always once they find out we >> don't do higher taxa. >> >> On Feb 21, 2012, at 11:57 AM, Rutger Vos wrote: >> >> >> When it encounters an integer, it assumes it could be any of these >> predicates: >> >> >> - 'tb.identifier.ncbi', >> >> - 'tb.identifier.ubio', >> >> - 'tb.identifier.taxon', >> >> - 'tb.identifier.taxon.tb1' >> >> >> For things that look like TreeBASE id's (e.g. /^[A-Z][a-z]*\d+$/): >> >> >> - 'tb.identifier.taxon', >> >> - 'tb.identifier.taxon.tb1' >> >> >> Words: >> >> >> - 'tb.title.taxon', >> >> - 'tb.title.taxonLabel', >> >> - 'tb.title.taxonVariant' >> >> >> What users type in the search box is split on commas. In an earlier >> >> iteration I made it split on (quoted) words/white space - but that >> >> messes up what is probably the 80% use case of people entering "Genus >> >> species" (without quotes). >> >> >> If you now type "Homo sapiens, 9606" (without quotes), you will get >> >> hits that have 9606 as any identifier, and hits for Homo sapiens, >> >> including Homo sapiens neanderthalensis. By clicking on the advanced >> >> search button, users might be able to figure out (and influence) what >> >> exactly is searched on. Maybe we could have a screen cast that >> >> explains the search logic? >> >> >> On Tue, Feb 21, 2012 at 5:30 PM, Hilmar Lapp <hl...@ne...> wrote: >> >> Nice! I didn't try it extensively. What does it recognize and/or >> >> specifically search? >> >> >> -hilmar >> >> >> On Feb 21, 2012, at 6:30 AM, Rutger Vos wrote: >> >> >> 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 >> >> ------------------------------------------------------------------------------ >> >> 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 : >> >> =========================================================== >> >> >> >> >> >> >> >> -- >> >> 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 >> >> >> -- >> >> =========================================================== >> >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> >> =========================================================== >> >> >> >> >> >> >> >> -- >> 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 >> >> ------------------------------------------------------------------------------ >> 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 >> >> >> --------------------------------------------------------- >> 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 > --------------------------------------------------------- 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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From: Rutger V. <rut...@gm...> - 2012-02-21 17:46:54
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> Nice to have a generic search box, now if we could just get rid of the > "projection metaphor" because it is as confusing as hell! I guess we don't present it well by calling it a projection, but people will obviously want to do things like "get me the trees for taxon X". What would be the right way to present this? > Oh, and why doesn't TreeBASE support searching by higher taxa? This is easy > to do, and seems an obvious feature to have... Yes. > On 21 Feb 2012, at 17:18, Rutger Vos wrote: > > The only thing that people may not expect is the tokenization based on comma > rather than whitespace, because it's different from what Google does (which > is what everyone is used to). > > > Except it isn't precisely what google does, because it weighs > occurrences of words near each other higher, so that typing 'Homo > sapiens' (no quotes) won't just return a bucket of pages that have the > words 'Homo' and 'sapiens' anywhere in them. And maybe we don't want > people to have to write 'Homo sapiens' (with quotes) every time they > search for a species - which will be always once they find out we > don't do higher taxa. > > On Feb 21, 2012, at 11:57 AM, Rutger Vos wrote: > > > When it encounters an integer, it assumes it could be any of these > predicates: > > > - 'tb.identifier.ncbi', > > - 'tb.identifier.ubio', > > - 'tb.identifier.taxon', > > - 'tb.identifier.taxon.tb1' > > > For things that look like TreeBASE id's (e.g. /^[A-Z][a-z]*\d+$/): > > > - 'tb.identifier.taxon', > > - 'tb.identifier.taxon.tb1' > > > Words: > > > - 'tb.title.taxon', > > - 'tb.title.taxonLabel', > > - 'tb.title.taxonVariant' > > > What users type in the search box is split on commas. In an earlier > > iteration I made it split on (quoted) words/white space - but that > > messes up what is probably the 80% use case of people entering "Genus > > species" (without quotes). > > > If you now type "Homo sapiens, 9606" (without quotes), you will get > > hits that have 9606 as any identifier, and hits for Homo sapiens, > > including Homo sapiens neanderthalensis. By clicking on the advanced > > search button, users might be able to figure out (and influence) what > > exactly is searched on. Maybe we could have a screen cast that > > explains the search logic? > > > On Tue, Feb 21, 2012 at 5:30 PM, Hilmar Lapp <hl...@ne...> wrote: > > Nice! I didn't try it extensively. What does it recognize and/or > > specifically search? > > > -hilmar > > > On Feb 21, 2012, at 6:30 AM, Rutger Vos wrote: > > > 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 > > ------------------------------------------------------------------------------ > > 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 : > > =========================================================== > > > > > > > > -- > > 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 > > > -- > > =========================================================== > > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > > =========================================================== > > > > > > > > -- > 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 > > ------------------------------------------------------------------------------ > 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 > > > --------------------------------------------------------- > 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...> - 2012-02-21 17:31:12
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Nice to have a generic search box, now if we could just get rid of the "projection metaphor" because it is as confusing as hell! Oh, and why doesn't TreeBASE support searching by higher taxa? This is easy to do, and seems an obvious feature to have... Regards Rod On 21 Feb 2012, at 17:18, Rutger Vos wrote: >> The only thing that people may not expect is the tokenization based on comma rather than whitespace, because it's different from what Google does (which is what everyone is used to). > > Except it isn't precisely what google does, because it weighs > occurrences of words near each other higher, so that typing 'Homo > sapiens' (no quotes) won't just return a bucket of pages that have the > words 'Homo' and 'sapiens' anywhere in them. And maybe we don't want > people to have to write 'Homo sapiens' (with quotes) every time they > search for a species - which will be always once they find out we > don't do higher taxa. > >> On Feb 21, 2012, at 11:57 AM, Rutger Vos wrote: >> >>> When it encounters an integer, it assumes it could be any of these predicates: >>> >>> - 'tb.identifier.ncbi', >>> - 'tb.identifier.ubio', >>> - 'tb.identifier.taxon', >>> - 'tb.identifier.taxon.tb1' >>> >>> For things that look like TreeBASE id's (e.g. /^[A-Z][a-z]*\d+$/): >>> >>> - 'tb.identifier.taxon', >>> - 'tb.identifier.taxon.tb1' >>> >>> Words: >>> >>> - 'tb.title.taxon', >>> - 'tb.title.taxonLabel', >>> - 'tb.title.taxonVariant' >>> >>> What users type in the search box is split on commas. In an earlier >>> iteration I made it split on (quoted) words/white space - but that >>> messes up what is probably the 80% use case of people entering "Genus >>> species" (without quotes). >>> >>> If you now type "Homo sapiens, 9606" (without quotes), you will get >>> hits that have 9606 as any identifier, and hits for Homo sapiens, >>> including Homo sapiens neanderthalensis. By clicking on the advanced >>> search button, users might be able to figure out (and influence) what >>> exactly is searched on. Maybe we could have a screen cast that >>> explains the search logic? >>> >>> On Tue, Feb 21, 2012 at 5:30 PM, Hilmar Lapp <hl...@ne...> wrote: >>>> Nice! I didn't try it extensively. What does it recognize and/or >>>> specifically search? >>>> >>>> -hilmar >>>> >>>> On Feb 21, 2012, at 6:30 AM, Rutger Vos wrote: >>>> >>>> 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 >>>> ------------------------------------------------------------------------------ >>>> 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 : >>>> =========================================================== >>>> >>>> >>>> >>> >>> >>> >>> -- >>> 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 >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> =========================================================== >> >> >> > > > > -- > 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 > > ------------------------------------------------------------------------------ > 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 > --------------------------------------------------------- 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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From: Hilmar L. <hl...@ne...> - 2012-02-21 17:24:59
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Right. So ideally people can type in "homo sapiens" (w/o quotes) just as well as two identifiers separated by whitespace, and the system does the Right Thing in each case. You could see if your first two tokens are alphanumeric, and then try the whole thing as a (possibly qualified) species name. If you get zero results, you try them white-space tokenized and OR'ed. -hilmar On Feb 21, 2012, at 12:18 PM, Rutger Vos wrote: >> The only thing that people may not expect is the tokenization based on comma rather than whitespace, because it's different from what Google does (which is what everyone is used to). > > Except it isn't precisely what google does, because it weighs > occurrences of words near each other higher, so that typing 'Homo > sapiens' (no quotes) won't just return a bucket of pages that have the > words 'Homo' and 'sapiens' anywhere in them. And maybe we don't want > people to have to write 'Homo sapiens' (with quotes) every time they > search for a species - which will be always once they find out we > don't do higher taxa. > >> On Feb 21, 2012, at 11:57 AM, Rutger Vos wrote: >> >>> When it encounters an integer, it assumes it could be any of these predicates: >>> >>> - 'tb.identifier.ncbi', >>> - 'tb.identifier.ubio', >>> - 'tb.identifier.taxon', >>> - 'tb.identifier.taxon.tb1' >>> >>> For things that look like TreeBASE id's (e.g. /^[A-Z][a-z]*\d+$/): >>> >>> - 'tb.identifier.taxon', >>> - 'tb.identifier.taxon.tb1' >>> >>> Words: >>> >>> - 'tb.title.taxon', >>> - 'tb.title.taxonLabel', >>> - 'tb.title.taxonVariant' >>> >>> What users type in the search box is split on commas. In an earlier >>> iteration I made it split on (quoted) words/white space - but that >>> messes up what is probably the 80% use case of people entering "Genus >>> species" (without quotes). >>> >>> If you now type "Homo sapiens, 9606" (without quotes), you will get >>> hits that have 9606 as any identifier, and hits for Homo sapiens, >>> including Homo sapiens neanderthalensis. By clicking on the advanced >>> search button, users might be able to figure out (and influence) what >>> exactly is searched on. Maybe we could have a screen cast that >>> explains the search logic? >>> >>> On Tue, Feb 21, 2012 at 5:30 PM, Hilmar Lapp <hl...@ne...> wrote: >>>> Nice! I didn't try it extensively. What does it recognize and/or >>>> specifically search? >>>> >>>> -hilmar >>>> >>>> On Feb 21, 2012, at 6:30 AM, Rutger Vos wrote: >>>> >>>> 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 >>>> ------------------------------------------------------------------------------ >>>> 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 : >>>> =========================================================== >>>> >>>> >>>> >>> >>> >>> >>> -- >>> 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 >> >> -- >> =========================================================== >> : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >> =========================================================== >> >> >> > > > > -- > 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 -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2012-02-21 17:18:19
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> The only thing that people may not expect is the tokenization based on comma rather than whitespace, because it's different from what Google does (which is what everyone is used to). Except it isn't precisely what google does, because it weighs occurrences of words near each other higher, so that typing 'Homo sapiens' (no quotes) won't just return a bucket of pages that have the words 'Homo' and 'sapiens' anywhere in them. And maybe we don't want people to have to write 'Homo sapiens' (with quotes) every time they search for a species - which will be always once they find out we don't do higher taxa. > On Feb 21, 2012, at 11:57 AM, Rutger Vos wrote: > >> When it encounters an integer, it assumes it could be any of these predicates: >> >> - 'tb.identifier.ncbi', >> - 'tb.identifier.ubio', >> - 'tb.identifier.taxon', >> - 'tb.identifier.taxon.tb1' >> >> For things that look like TreeBASE id's (e.g. /^[A-Z][a-z]*\d+$/): >> >> - 'tb.identifier.taxon', >> - 'tb.identifier.taxon.tb1' >> >> Words: >> >> - 'tb.title.taxon', >> - 'tb.title.taxonLabel', >> - 'tb.title.taxonVariant' >> >> What users type in the search box is split on commas. In an earlier >> iteration I made it split on (quoted) words/white space - but that >> messes up what is probably the 80% use case of people entering "Genus >> species" (without quotes). >> >> If you now type "Homo sapiens, 9606" (without quotes), you will get >> hits that have 9606 as any identifier, and hits for Homo sapiens, >> including Homo sapiens neanderthalensis. By clicking on the advanced >> search button, users might be able to figure out (and influence) what >> exactly is searched on. Maybe we could have a screen cast that >> explains the search logic? >> >> On Tue, Feb 21, 2012 at 5:30 PM, Hilmar Lapp <hl...@ne...> wrote: >>> Nice! I didn't try it extensively. What does it recognize and/or >>> specifically search? >>> >>> -hilmar >>> >>> On Feb 21, 2012, at 6:30 AM, Rutger Vos wrote: >>> >>> 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 >>> ------------------------------------------------------------------------------ >>> 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 : >>> =========================================================== >>> >>> >>> >> >> >> >> -- >> 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 > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > -- 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 17:10:28
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A screen cast would be nice, but given the below this is all straightforward and seems intuitive, so just having your explanation pop up when one clicks the question mark should do it. The only thing that people may not expect is the tokenization based on comma rather than whitespace, because it's different from what Google does (which is what everyone is used to). -hilmar On Feb 21, 2012, at 11:57 AM, Rutger Vos wrote: > When it encounters an integer, it assumes it could be any of these predicates: > > - 'tb.identifier.ncbi', > - 'tb.identifier.ubio', > - 'tb.identifier.taxon', > - 'tb.identifier.taxon.tb1' > > For things that look like TreeBASE id's (e.g. /^[A-Z][a-z]*\d+$/): > > - 'tb.identifier.taxon', > - 'tb.identifier.taxon.tb1' > > Words: > > - 'tb.title.taxon', > - 'tb.title.taxonLabel', > - 'tb.title.taxonVariant' > > What users type in the search box is split on commas. In an earlier > iteration I made it split on (quoted) words/white space - but that > messes up what is probably the 80% use case of people entering "Genus > species" (without quotes). > > If you now type "Homo sapiens, 9606" (without quotes), you will get > hits that have 9606 as any identifier, and hits for Homo sapiens, > including Homo sapiens neanderthalensis. By clicking on the advanced > search button, users might be able to figure out (and influence) what > exactly is searched on. Maybe we could have a screen cast that > explains the search logic? > > On Tue, Feb 21, 2012 at 5:30 PM, Hilmar Lapp <hl...@ne...> wrote: >> Nice! I didn't try it extensively. What does it recognize and/or >> specifically search? >> >> -hilmar >> >> On Feb 21, 2012, at 6:30 AM, Rutger Vos wrote: >> >> 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 >> ------------------------------------------------------------------------------ >> 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 : >> =========================================================== >> >> >> > > > > -- > 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 -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2012-02-21 17:05:09
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> Because the NEXUS files has that. Or is it recomputed? And if it is, it's not at runtime, right? I.e., for the purposes of the search system, they are columns of a database table, aren't they? Ah, I see what you mean. Those are indeed not computed at runtime. And we probably also can't do the branch lengths thing at runtime either. -- 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...> - 2012-02-21 16:57:47
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When it encounters an integer, it assumes it could be any of these predicates: - 'tb.identifier.ncbi', - 'tb.identifier.ubio', - 'tb.identifier.taxon', - 'tb.identifier.taxon.tb1' For things that look like TreeBASE id's (e.g. /^[A-Z][a-z]*\d+$/): - 'tb.identifier.taxon', - 'tb.identifier.taxon.tb1' Words: - 'tb.title.taxon', - 'tb.title.taxonLabel', - 'tb.title.taxonVariant' What users type in the search box is split on commas. In an earlier iteration I made it split on (quoted) words/white space - but that messes up what is probably the 80% use case of people entering "Genus species" (without quotes). If you now type "Homo sapiens, 9606" (without quotes), you will get hits that have 9606 as any identifier, and hits for Homo sapiens, including Homo sapiens neanderthalensis. By clicking on the advanced search button, users might be able to figure out (and influence) what exactly is searched on. Maybe we could have a screen cast that explains the search logic? On Tue, Feb 21, 2012 at 5:30 PM, Hilmar Lapp <hl...@ne...> wrote: > Nice! I didn't try it extensively. What does it recognize and/or > specifically search? > > -hilmar > > On Feb 21, 2012, at 6:30 AM, Rutger Vos wrote: > > 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 > ------------------------------------------------------------------------------ > 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 : > =========================================================== > > > -- 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 16:43:05
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On Feb 21, 2012, at 11:40 AM, Rutger Vos wrote: >> There's nothing wrong with computed metadata. It's just not something that >> TreeBASE does right now. > > It isn't? We let people search on ntax and nchar... Because the NEXUS files has that. Or is it recomputed? And if it is, it's not at runtime, right? I.e., for the purposes of the search system, they are columns of a database table, aren't they? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Rutger V. <rut...@gm...> - 2012-02-21 16:40:34
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> There's nothing wrong with computed metadata. It's just not something that > TreeBASE does right now. It isn't? We let people search on ntax and nchar... > On Feb 21, 2012, at 11:30 AM, Carl Boettiger wrote: > > Hi Hilmar, list, > > Good point, I see the importance of not departing from the standards. > > I wouldn't phrase this as an "absence of data", but rather as fundemental > metadata describing the kind of data provided -- i.e. is the data just a > topology, is it a phylogram where branch lengths describe mutational steps, > or is it a chronogram/ultrametric tree where branch lengths are calibrated > into units of time? (notably, knowing whether a tree was ultrametric/time > calibrated or if branch lengths were in units of mutational steps would be > very useful thing to know through the API). I'm not quite sure why this is > any less metadata while things like tb:kind.tree (i.e. Species Tree / gene > tree), or tb.quality, etc. > > > > -Carl > > On Mon, Feb 20, 2012 at 8:33 PM, Hilmar Lapp <hl...@ne...> wrote: >> >> 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 : >> =========================================================== >> >> >> > > > > -- > Carl Boettiger > UC Davis > http://www.carlboettiger.info/ > > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > ------------------------------------------------------------------------------ > 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: Hilmar L. <hl...@ne...> - 2012-02-21 16:38:36
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Ah sorry - re-reading the first sentence I wrote I'm not sure I was yet fully booted into the right mental state. What I meant was the difference between actual (entered or submitted by someone) metadata and computed metadata. Whether a tree has branch lengths would be computed. There's nothing wrong with computed metadata. It's just not something that TreeBASE does right now. -hilmar On Feb 21, 2012, at 11:30 AM, Carl Boettiger wrote: > Hi Hilmar, list, > > Good point, I see the importance of not departing from the standards. > > I wouldn't phrase this as an "absence of data", but rather as fundemental metadata describing the kind of data provided -- i.e. is the data just a topology, is it a phylogram where branch lengths describe mutational steps, or is it a chronogram/ultrametric tree where branch lengths are calibrated into units of time? (notably, knowing whether a tree was ultrametric/time calibrated or if branch lengths were in units of mutational steps would be very useful thing to know through the API). I'm not quite sure why this is any less metadata while things like tb:kind.tree (i.e. Species Tree / gene tree), or tb.quality, etc. > > > > -Carl > > On Mon, Feb 20, 2012 at 8:33 PM, Hilmar Lapp <hl...@ne...> wrote: > 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 : > =========================================================== > > > > > > > -- > Carl Boettiger > UC Davis > http://www.carlboettiger.info/ > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
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From: Hilmar L. <hl...@ne...> - 2012-02-21 16:30:58
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Nice! I didn't try it extensively. What does it recognize and/or specifically search? -hilmar On Feb 21, 2012, at 6:30 AM, Rutger Vos wrote: > 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 > ------------------------------------------------------------------------------ > 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 16:30:28
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Hi Hilmar, list, Good point, I see the importance of not departing from the standards. I wouldn't phrase this as an "absence of data", but rather as fundemental metadata describing the kind of data provided -- i.e. is the data just a topology, is it a phylogram where branch lengths describe mutational steps, or is it a chronogram/ultrametric tree where branch lengths are calibrated into units of time? (notably, knowing whether a tree was ultrametric/time calibrated or if branch lengths were in units of mutational steps would be very useful thing to know through the API). I'm not quite sure why this is any less metadata while things like tb:kind.tree (i.e. Species Tree / gene tree), or tb.quality, etc. -Carl On Mon, Feb 20, 2012 at 8:33 PM, Hilmar Lapp <hl...@ne...> wrote: > 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 : > =========================================================== > > > > -- Carl Boettiger UC Davis http://www.carlboettiger.info/ |
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