October 2010 - tdwg-phylo - lists.tdwg.org

Re: [Tdwg-phylo] Publishing a tree in RDF
by Chris Baron 24 Oct '10

24 Oct '10

Yes, Triplify was the inspiration to the web2py plugin. Also, I've been working on a phylogentic tree editor called tred. http://code.google.com/p/tred/ Its still a little rough, but usable/stable. Realizing that many Biologists do not have their data in a relational database one could upload their newick, nexus, etc to tred, edit the tree then export to CDAO. I'd be happy to add functionality to tred for this purpose if people will use it. On Wed, Oct 20, 2010 at 5:00 AM, <tdwg-phylo-request(a)lists.tdwg.org> wrote: > Send tdwg-phylo mailing list submissions to > tdwg-phylo(a)lists.tdwg.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.tdwg.org/mailman/listinfo/tdwg-phylo > or, via email, send a message with subject or body 'help' to > tdwg-phylo-request(a)lists.tdwg.org > > You can reach the person managing the list at > tdwg-phylo-owner(a)lists.tdwg.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of tdwg-phylo digest..." > > > Today's Topics: > > 1. Re: Publishing a tree in RDF (Hilmar Lapp) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 19 Oct 2010 17:27:21 -0400 > From: Hilmar Lapp <hlapp(a)nescent.org> > Subject: Re: [Tdwg-phylo] Publishing a tree in RDF > To: Chris Baron <topher.baron(a)gmail.com> > Cc: "tdwg-phylo(a)lists.tdwg.org" <tdwg-phylo(a)lists.tdwg.org> > Message-ID: <FE252B2A-D7C2-4873-B5B0-4695D382CABE(a)nescent.org> > Content-Type: text/plain; charset="us-ascii" > > Hi Chris - you probably know the Triplify project? http://triplify.org/ > > -hilmar > > On Oct 19, 2010, at 1:03 PM, Chris Baron wrote: > > > I've written a plugin to transform relational database data into > > RDF : http://www.web2py.com/semantic > > > > If anyone keeps their data in a relational database, this would be > > useful. > > > > On Tue, Oct 19, 2010 at 11:58 AM, Arlin Stoltzfus <arlin(a)umd.edu> > > wrote: > > Chris-- > > > > It sounds like you have the skills and interest to do this. Our > > first goal is very modest: just assess what's possible given > > currently available tools. I only know about one so far, which > > will translate a file into CDAO with the option to add it to a > > triple store. A web server interface is here: > > > > http://www.cs.nmsu.edu/~cdaostore/phylows.php<http://www.cs.nmsu.edu/%7Ecdaostore/phylows.php> > > > > If you know about other tools, that would be great. > > > > The next step (weeks from now) would be to look ahead to the future > > and identify gaps. If you are interested, all you need to do is to > > sign up for TDWG twiki access (if you don't have it already) and > > start working. > > > > Arlin > > > > On Oct 19, 2010, at 12:33 PM, Chris Baron wrote: > > > >> Hi, > >> > >> My name is Chris Baron - a software developer, computer science > >> graduate student interested in linked data, working in BioSync at > >> the Field Museum on tree visualization. I have a few ideas on how > >> to publish trees in RDF (have even created a tool to do so) and > >> would like to speak to Biologists about how their data exists at > >> publication so I can form a proper solution. > >> > >> > >> > >> On Tue, Oct 19, 2010 at 5:00 AM, <tdwg-phylo- > >> request(a)lists.tdwg.org> wrote: > >> Send tdwg-phylo mailing list submissions to > >> tdwg-phylo(a)lists.tdwg.org > >> > >> To subscribe or unsubscribe via the World Wide Web, visit > >> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo > >> or, via email, send a message with subject or body 'help' to > >> tdwg-phylo-request(a)lists.tdwg.org > >> > >> You can reach the person managing the list at > >> tdwg-phylo-owner(a)lists.tdwg.org > >> > >> When replying, please edit your Subject line so it is more specific > >> than "Re: Contents of tdwg-phylo digest..." > >> > >> > >> Today's Topics: > >> > >> 1. publishing trees in CDAO as linked open data? (Arlin Stoltzfus) > >> > >> > >> ---------------------------------------------------------------------- > >> > >> Message: 1 > >> Date: Mon, 18 Oct 2010 12:32:39 -0400 > >> From: Arlin Stoltzfus <arlin(a)umd.edu> > >> Subject: [Tdwg-phylo] publishing trees in CDAO as linked open data? > >> To: CDAO list <cdao-discuss(a)lists.sourceforge.net>, Phylogenetics > >> Standards Interest Group <tdwg-phylo(a)lists.tdwg.org> > >> Message-ID: <BAAFA68C-2622-409A-B530-1CABADC36016(a)umd.edu> > >> Content-Type: text/plain; charset="US-ASCII"; format=flowed; > >> delsp=yes > >> > >> Dear all-- > >> > >> At the Biodiversity Information Standards (TDWG) meeting last > >> month, a > >> sub-group of the phylogenetic standards working group started a > >> project to assess "current best practices for publishing trees > >> electronically". At present, probably the best way to publish a > >> tree > >> is to use the TreeBASE submission process, which makes it possible to > >> upload a NEXUS file and create associations of OTUs with taxon IDs, > >> and of data rows with accessions, and so on. But there are also some > >> other possibilities. The preliminary report is being assembled here: > >> > >> http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/LinkingTrees2010 > >> > >> Our plan is (over the next 6 weeks) to get feedback on this > >> preliminary report, then analyze the results and prepare a more > >> extensive report for publication. > >> > >> One possibility that we haven't examined yet is to publish a tree > >> electronically by rendering it in RDF in the language of CDAO > >> (Comparative Data Analysis Ontology) and then contributing it to the > >> Linked-Open-Data cloud in some way. > >> > >> Does anyone out there want to explore this idea and contribute the > >> results to the TDWG project? If so, please let me know. > >> > >> Arlin > >> ------- > >> Arlin Stoltzfus (arlin(a)umd.edu) > >> Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST > >> IBBR, 9600 Gudelsky Drive, Rockville, MD > >> tel: 240 314 6208; web: www.molevol.org > >> > >> > >> > >> ------------------------------ > >> > >> _______________________________________________ > >> tdwg-phylo mailing list > >> tdwg-phylo(a)lists.tdwg.org > >> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo > >> > >> > >> End of tdwg-phylo Digest, Vol 2, Issue 3 > >> **************************************** > >> > >> > >> > >> -- > >> Chris Baron > >> <ATT00001.txt> > > > > > > ------- > > Arlin Stoltzfus (arlin(a)umd.edu) > > Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST > > IBBR, 9600 Gudelsky Drive, Rockville, MD > > tel: 240 314 6208; web: www.molevol.org > > > > > > > > > > -- > > Chris Baron > > _______________________________________________ > > tdwg-phylo mailing list > > tdwg-phylo(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-phylo > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > >

11 21

Re: [Tdwg-phylo] Publishing trees in RDF
by Chris Baron 22 Oct '10

22 Oct '10

Are there any ideas for getting phylogentic data into CDAO format ? Its probably a bad idea to choose one existing viewer, add the functionality, and ask everyone to use it. Apologies for the proposition. I'll suggest a web based tool that takes phylogenetic data in a common format ( Newick, Nexus, etc ), asks a few questions ( i.e. - what do the labels, lengths correspond to? ), and fills in some of the basic CDAO elements using this data. If the user wants to describe their tree in more detail, the tool will provide methods for filling in any/all of the CDAO fields. On Fri, Oct 22, 2010 at 12:06 PM, <tdwg-phylo-request(a)lists.tdwg.org> wrote: > Send tdwg-phylo mailing list submissions to > tdwg-phylo(a)lists.tdwg.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.tdwg.org/mailman/listinfo/tdwg-phylo > or, via email, send a message with subject or body 'help' to > tdwg-phylo-request(a)lists.tdwg.org > > You can reach the person managing the list at > tdwg-phylo-owner(a)lists.tdwg.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of tdwg-phylo digest..." > > > Today's Topics: > > 1. Re: Publishing a trees in RDF (Arlin Stoltzfus) > 2. Re: Publishing a trees in RDF (Kidd, David M) > 3. Re: Publishing a trees in RDF (Roderic Page) > 4. Re: Publishing a trees in RDF (Arlin Stoltzfus) > 5. Re: Publishing a trees in RDF (William Piel) > 6. Re: Publishing a trees in RDF (Hilmar Lapp) > 7. Re: Publishing a trees in RDF (Richard Ree) > 8. Re: Publishing a trees in RDF (Nico Cellinese) > 9. Re: Publishing a trees in RDF (Hilmar Lapp) > 10. Re: Publishing a trees in RDF (Arlin Stoltzfus) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 22 Oct 2010 10:29:31 -0400 > From: Arlin Stoltzfus <arlin(a)umd.edu> > Subject: Re: [Tdwg-phylo] Publishing a trees in RDF > To: "tdwg-phylo(a)lists.tdwg.org Interest Group" > <tdwg-phylo(a)lists.tdwg.org> > Message-ID: <35E60BB1-E806-4AAC-A916-6F4439F48980(a)umd.edu> > Content-Type: text/plain; charset="US-ASCII"; format=flowed; delsp=yes > > QED. The technology is out there. IMHO, the continual propagation of > new tree-viewers by developers, and the sense of users that there is > no tree viewer that satisfies their needs, is (in the medium-term and > long-term) a cultural-organizational-educational problem and not at > all a technical problem. > > If this is true, then in order to solve the real problem, we need to > think about things like changes in funding structure, standards > development, and modes of user engagement, not new graphics libraries > that do just the right thing with only a few commands. > > Arlin > > On Oct 21, 2010, at 12:57 PM, Christian M Zmasek wrote: > > > Hi, Dave and Rutger: > > > > My own tree viewer "Archaeopteryx" provides such an overview when > > zoomed > > in, plus some other features described as "missing" in most current > > tools. > > > > See: http://www.phylosoft.org/archaeopteryx/ > > > > Example: http://www.phylosoft.org/archaeopteryx/examples/mollusca.html > > > > Archaeopteryx also provides other useful features (at least for > > comparative genomics use cases). For example, the ability to infer > > internal taxonomies (if all external nodes have _some_ taxonomic > > information associated with them; standalone version only; via uniprot > > taxonomy database). > > > > Please let me know if you'd like to know more or have suggestions for > > improvement (although keep in mind that this Archaeopteryx is just a > > peculiar hobby of mine). > > > > Christian > > > > > > > > On 10/21/2010 3:39 AM, Rutger Vos wrote: > >> Hi Dave, > >> > >>> The ability to browse large trees seems to be a particular > >>> limitation of existing tools (I'd love to be corrected if I am > >>> wrong). Having a tree larger than the widget, as in Phylowidget, > >>> is one approach, however, an overview window would be nice to > >>> orientate your view in relation to the entire tree. I have also > >>> been considering displaying only a subset of nodes and then having > >>> 'expand', 'contract' and 'pan' (by expanding and contracting) > >>> functions for navagation. The ability to display node subsets is > >>> probably more important for networks than trees as reticulation > >>> will often result in visual occlusion. > >> > >> Rod Page has coded a web widget (I believe all javascript) that has a > >> small preview window for the whole tree and a larger "zoomed in" > >> view. > >> "TreeJuxtaposer" is a java app(let?) that allows you to contract and > >> expand selections of nodes/clades. I think these come closest to what > >> you are talking about, though neither operates on networks. > >> > >> Cheers, > >> > >> Rutger > >> > > > > _______________________________________________ > > tdwg-phylo mailing list > > tdwg-phylo(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-phylo > > ------- > Arlin Stoltzfus (arlin(a)umd.edu) > Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST > IBBR, 9600 Gudelsky Drive, Rockville, MD > tel: 240 314 6208; web: www.molevol.org > > > > ------------------------------ > > Message: 2 > Date: Fri, 22 Oct 2010 15:55:35 +0100 > From: "Kidd, David M" <d.kidd(a)imperial.ac.uk> > Subject: Re: [Tdwg-phylo] Publishing a trees in RDF > To: "tdwg-phylo(a)lists.tdwg.org" <tdwg-phylo(a)lists.tdwg.org> > Message-ID: > <F5AF129F0DF96748BF87616878EA92934EAE05B214(a)ICEXM5.ic.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > > Thank you Rutger, Christian, Cindy, Hilmar and Arlin, > > Whatever the technological maturity of tools, there remains the hurdle of > finding the viewers, assessing their functionality and assessing whether a > task can be completed with the available tools given a time-scale and skill > set. I have just started to put together a comparison site describing > functionality and where the same trees can be viewed in the different > viewers. > > Sorry for interrupting the RDF flow - it has been very interesting to > follow. > > - Dave > > > David M. Kidd > > Research Associate > Center for Population Biology > Silwood Park Campus > Imperial College London > 0207 594 2470 > > > -----Original Message----- > From: tdwg-phylo-bounces(a)lists.tdwg.org [mailto: > tdwg-phylo-bounces(a)lists.tdwg.org] On Behalf Of Arlin Stoltzfus > Sent: 22 October 2010 15:30 > To: tdwg-phylo(a)lists.tdwg.org Interest Group > Subject: Re: [Tdwg-phylo] Publishing a trees in RDF > > QED. The technology is out there. IMHO, the continual propagation of new > tree-viewers by developers, and the sense of users that there is no tree > viewer that satisfies their needs, is (in the medium-term and > long-term) a cultural-organizational-educational problem and not at all a > technical problem. > > If this is true, then in order to solve the real problem, we need to think > about things like changes in funding structure, standards development, and > modes of user engagement, not new graphics libraries that do just the right > thing with only a few commands. > > Arlin > > On Oct 21, 2010, at 12:57 PM, Christian M Zmasek wrote: > > > Hi, Dave and Rutger: > > > > My own tree viewer "Archaeopteryx" provides such an overview when > > zoomed > > in, plus some other features described as "missing" in most current > > tools. > > > > See: http://www.phylosoft.org/archaeopteryx/ > > > > Example: http://www.phylosoft.org/archaeopteryx/examples/mollusca.html > > > > Archaeopteryx also provides other useful features (at least for > > comparative genomics use cases). For example, the ability to infer > > internal taxonomies (if all external nodes have _some_ taxonomic > > information associated with them; standalone version only; via uniprot > > taxonomy database). > > > > Please let me know if you'd like to know more or have suggestions for > > improvement (although keep in mind that this Archaeopteryx is just a > > peculiar hobby of mine). > > > > Christian > > > > > > > > On 10/21/2010 3:39 AM, Rutger Vos wrote: > >> Hi Dave, > >> > >>> The ability to browse large trees seems to be a particular > >>> limitation of existing tools (I'd love to be corrected if I am > >>> wrong). Having a tree larger than the widget, as in Phylowidget, > >>> is one approach, however, an overview window would be nice to > >>> orientate your view in relation to the entire tree. I have also > >>> been considering displaying only a subset of nodes and then having > >>> 'expand', 'contract' and 'pan' (by expanding and contracting) > >>> functions for navagation. The ability to display node subsets is > >>> probably more important for networks than trees as reticulation > >>> will often result in visual occlusion. > >> > >> Rod Page has coded a web widget (I believe all javascript) that has a > >> small preview window for the whole tree and a larger "zoomed in" > >> view. > >> "TreeJuxtaposer" is a java app(let?) that allows you to contract and > >> expand selections of nodes/clades. I think these come closest to what > >> you are talking about, though neither operates on networks. > >> > >> Cheers, > >> > >> Rutger > >> > > > > _______________________________________________ > > tdwg-phylo mailing list > > tdwg-phylo(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-phylo > > ------- > Arlin Stoltzfus (arlin(a)umd.edu) > Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST > IBBR, 9600 Gudelsky Drive, Rockville, MD > tel: 240 314 6208; web: www.molevol.org > > _______________________________________________ > tdwg-phylo mailing list > tdwg-phylo(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-phylo > > > ------------------------------ > > Message: 3 > Date: Fri, 22 Oct 2010 16:00:14 +0100 > From: Roderic Page <r.page(a)bio.gla.ac.uk> > Subject: Re: [Tdwg-phylo] Publishing a trees in RDF > To: "tdwg-phylo(a)lists.tdwg.org Interest Group" > <tdwg-phylo(a)lists.tdwg.org> > Message-ID: <C924C5F0-1B8A-4754-A8CC-80C344675835(a)bio.gla.ac.uk> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > There are other issues here as well. Technology advances rapidly, and > what once seemed a good choice may rapidly become dated. Without > wishing to start a flame war, I think Java applets are dead (sorry > Phylowidget), Flash is fading away (thank you Steve), and increasingly > we will see lightweight SVG and Canvas-based browsers, non-web based > browsers that exploit specific hardware (iPad anyone), and Google- > Earth based browsers. > > I doubt one-size-fits all will work. Standards themselves won't > address this issue, and I personally doubt RDF is where we want to be > focussing efforts anyway. A decent JSON format for trees and > associated metadata would be much more palatable for developers. It's > worth remembering that the great success of Newick (and Nexus) was > largely due to the ease of parsing. > > Regards > > Rod > > On 22 Oct 2010, at 15:29, Arlin Stoltzfus wrote: > > > QED. The technology is out there. IMHO, the continual propagation of > > new tree-viewers by developers, and the sense of users that there is > > no tree viewer that satisfies their needs, is (in the medium-term and > > long-term) a cultural-organizational-educational problem and not at > > all a technical problem. > > > > If this is true, then in order to solve the real problem, we need to > > think about things like changes in funding structure, standards > > development, and modes of user engagement, not new graphics libraries > > that do just the right thing with only a few commands. > > > > Arlin > > > > On Oct 21, 2010, at 12:57 PM, Christian M Zmasek wrote: > > > >> Hi, Dave and Rutger: > >> > >> My own tree viewer "Archaeopteryx" provides such an overview when > >> zoomed > >> in, plus some other features described as "missing" in most current > >> tools. > >> > >> See: http://www.phylosoft.org/archaeopteryx/ > >> > >> Example: http://www.phylosoft.org/archaeopteryx/examples/ > >> mollusca.html > >> > >> Archaeopteryx also provides other useful features (at least for > >> comparative genomics use cases). For example, the ability to infer > >> internal taxonomies (if all external nodes have _some_ taxonomic > >> information associated with them; standalone version only; via > >> uniprot > >> taxonomy database). > >> > >> Please let me know if you'd like to know more or have suggestions for > >> improvement (although keep in mind that this Archaeopteryx is just a > >> peculiar hobby of mine). > >> > >> Christian > >> > >> > >> > >> On 10/21/2010 3:39 AM, Rutger Vos wrote: > >>> Hi Dave, > >>> > >>>> The ability to browse large trees seems to be a particular > >>>> limitation of existing tools (I'd love to be corrected if I am > >>>> wrong). Having a tree larger than the widget, as in Phylowidget, > >>>> is one approach, however, an overview window would be nice to > >>>> orientate your view in relation to the entire tree. I have also > >>>> been considering displaying only a subset of nodes and then having > >>>> 'expand', 'contract' and 'pan' (by expanding and contracting) > >>>> functions for navagation. The ability to display node subsets is > >>>> probably more important for networks than trees as reticulation > >>>> will often result in visual occlusion. > >>> > >>> Rod Page has coded a web widget (I believe all javascript) that > >>> has a > >>> small preview window for the whole tree and a larger "zoomed in" > >>> view. > >>> "TreeJuxtaposer" is a java app(let?) that allows you to contract and > >>> expand selections of nodes/clades. I think these come closest to > >>> what > >>> you are talking about, though neither operates on networks. > >>> > >>> Cheers, > >>> > >>> Rutger > >>> > >> > >> _______________________________________________ > >> tdwg-phylo mailing list > >> tdwg-phylo(a)lists.tdwg.org > >> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo > > > > ------- > > Arlin Stoltzfus (arlin(a)umd.edu) > > Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST > > IBBR, 9600 Gudelsky Drive, Rockville, MD > > tel: 240 314 6208; web: www.molevol.org > > > > _______________________________________________ > > tdwg-phylo mailing list > > tdwg-phylo(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-phylo > > > > --------------------------------------------------------- > 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.page(a)bio.gla.ac.uk > Tel: +44 141 330 4778 > Fax: +44 141 330 2792 > AIM: rodpage1962(a)aim.com > 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 > > > > > > > > > > ------------------------------ > > Message: 4 > Date: Fri, 22 Oct 2010 11:25:44 -0400 > From: Arlin Stoltzfus <arlin(a)umd.edu> > Subject: Re: [Tdwg-phylo] Publishing a trees in RDF > To: "tdwg-phylo(a)lists.tdwg.org Interest Group" > <tdwg-phylo(a)lists.tdwg.org> > Message-ID: <B7CBB320-0453-47A9-AC16-6CFD952BA21D(a)umd.edu> > Content-Type: text/plain; charset="US-ASCII"; format=flowed; delsp=yes > > On Oct 22, 2010, at 10:29 AM, Arlin Stoltzfus wrote: > > > QED. The technology is out there. IMHO, the continual propagation of > > new tree-viewers by developers, and the sense of users that there is > > no tree viewer that satisfies their needs, is (in the medium-term and > > long-term) a cultural-organizational-educational problem and not at > > all a technical problem. > > To clarify this-- I didn't mean to imply that there are no gaps. In > the *short-term*, there may be real gaps between what users want (or > think they want) and what developers are providing and maintaining. > I'm just saying that, by virtue of repeated failures, we should have > learned by now that the way to close these gaps is NOT for the Nth > independent developer to go out and developer the Mth independent tree > viewer using the latest GUI fashions. > > Arlin > > > If this is true, then in order to solve the real problem, we need to > > think about things like changes in funding structure, standards > > development, and modes of user engagement, not new graphics libraries > > that do just the right thing with only a few commands. > > > > Arlin > > > > On Oct 21, 2010, at 12:57 PM, Christian M Zmasek wrote: > > > >> Hi, Dave and Rutger: > >> > >> My own tree viewer "Archaeopteryx" provides such an overview when > >> zoomed > >> in, plus some other features described as "missing" in most current > >> tools. > >> > >> See: http://www.phylosoft.org/archaeopteryx/ > >> > >> Example: http://www.phylosoft.org/archaeopteryx/examples/ > >> mollusca.html > >> > >> Archaeopteryx also provides other useful features (at least for > >> comparative genomics use cases). For example, the ability to infer > >> internal taxonomies (if all external nodes have _some_ taxonomic > >> information associated with them; standalone version only; via > >> uniprot > >> taxonomy database). > >> > >> Please let me know if you'd like to know more or have suggestions for > >> improvement (although keep in mind that this Archaeopteryx is just a > >> peculiar hobby of mine). > >> > >> Christian > >> > >> > >> > >> On 10/21/2010 3:39 AM, Rutger Vos wrote: > >>> Hi Dave, > >>> > >>>> The ability to browse large trees seems to be a particular > >>>> limitation of existing tools (I'd love to be corrected if I am > >>>> wrong). Having a tree larger than the widget, as in Phylowidget, > >>>> is one approach, however, an overview window would be nice to > >>>> orientate your view in relation to the entire tree. I have also > >>>> been considering displaying only a subset of nodes and then having > >>>> 'expand', 'contract' and 'pan' (by expanding and contracting) > >>>> functions for navagation. The ability to display node subsets is > >>>> probably more important for networks than trees as reticulation > >>>> will often result in visual occlusion. > >>> > >>> Rod Page has coded a web widget (I believe all javascript) that > >>> has a > >>> small preview window for the whole tree and a larger "zoomed in" > >>> view. > >>> "TreeJuxtaposer" is a java app(let?) that allows you to contract and > >>> expand selections of nodes/clades. I think these come closest to > >>> what > >>> you are talking about, though neither operates on networks. > >>> > >>> Cheers, > >>> > >>> Rutger > >>> > >> > >> _______________________________________________ > >> tdwg-phylo mailing list > >> tdwg-phylo(a)lists.tdwg.org > >> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo > > > > ------- > > Arlin Stoltzfus (arlin(a)umd.edu) > > Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST > > IBBR, 9600 Gudelsky Drive, Rockville, MD > > tel: 240 314 6208; web: www.molevol.org > > > > _______________________________________________ > > tdwg-phylo mailing list > > tdwg-phylo(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-phylo > > ------- > Arlin Stoltzfus (arlin(a)umd.edu) > Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST > IBBR, 9600 Gudelsky Drive, Rockville, MD > tel: 240 314 6208; web: www.molevol.org > > > > ------------------------------ > > Message: 5 > Date: Fri, 22 Oct 2010 12:22:29 -0400 > From: William Piel <william.piel(a)yale.edu> > Subject: Re: [Tdwg-phylo] Publishing a trees in RDF > To: "tdwg-phylo(a)lists.tdwg.org Interest Group" > <tdwg-phylo(a)lists.tdwg.org> > Message-ID: <ED033676-380C-4CBF-B5BE-C0E465DAF1B0(a)yale.edu> > Content-Type: text/plain; charset=us-ascii > > > On Oct 22, 2010, at 11:00 AM, Roderic Page wrote: > > > There are other issues here as well. Technology advances rapidly, and > > what once seemed a good choice may rapidly become dated > > True.. but another aspect is just that in order to explore whether a > particular graphical concept or tool will work, or will benefit people, you > have to knock out prototypes and implementations. e.g., drag-and-drop branch > rearrangement in MacClade was great for small trees but not for big ones, > hence phylowidget was looking to implement something that worked for large > trees (via concentric menus on nodes) and to experiment with auto-pruing, > etc. People have to keep knocking out GUI software efforts to test the > waters for new features. And the search is not over, for example: > > - Do we really have a completely satisfying way of visualizing patterns of > gene duplication within a species tree? > - If I handed you a tree with 200k nodes, is there a visual / GUI way that > would allow you to easily find interesting patterns in it, such as points of > incongruence with a conventional taxonomy? > - If I gave you 1,000 trees, is there a visual / GUI way that would allow > you to see which branches in each tree probably crossed an ancient land > bridge together? > > So I think we still have lots more GUI / visual / ergonomic challenges that > still need to be solved (even if lots of challenges have already been > solved). And we should not expect each new idea to be implemented in a > pristine killer app that does everything that everyone wants out of a tree > visualizer -- that takes too long to build, and the right person for > dreaming up a new idea is not necessarily the best person for creating > clean, robust, off-the-shelf software. > > We need to be okay with seeing a rich plethora of quick-and-dirty efforts, > each focusing on articulating/investigating sets of novel ideas -- despite > some obvious redundancy in some of the more general functions. And then > periodically, someone's got to assemble the best of these ideas into a > robust, jack-of-all-trades, off-the-shelf software package. > > bp > > > > > ------------------------------ > > Message: 6 > Date: Fri, 22 Oct 2010 12:38:37 -0400 > From: Hilmar Lapp <hlapp(a)nescent.org> > Subject: Re: [Tdwg-phylo] Publishing a trees in RDF > To: William Piel <william.piel(a)yale.edu> > Cc: "tdwg-phylo(a)lists.tdwg.org Interest Group" > <tdwg-phylo(a)lists.tdwg.org> > Message-ID: <F56AA1E2-8162-486C-9D74-C04563957BC4(a)nescent.org> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > > On Oct 22, 2010, at 12:22 PM, William Piel wrote: > > > We need to be okay with seeing a rich plethora of quick-and-dirty > > efforts, each focusing on articulating/investigating sets of novel > > ideas -- despite some obvious redundancy in some of the more general > > functions. And then periodically, someone's got to assemble the > > best of these ideas into a robust, jack-of-all-trades, off-the-shelf > > software package. > > > That sounds nice indeed, but frankly I've never seen it happen. The > quick-and-dirty efforts that I have seen become standard parts of > reusable and sustainable software have almost all started from their > early beginnings as parts of reusable software. For a while rather > experimental and unstable parts, obviously, but the future course was > charted not as an afterthought. > > Truth of the matter is that we're all scientists. No scientist is > interested in, or gets promotion, scientific recognition, or > publications from assembling entirely incompatible, mostly redundant > except for a few features, quick-and-dirty pieces of software into > some grand jack-of-all-trades software package. > > My $0.02, from about 13 years of software engineering. > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > > ------------------------------ > > Message: 7 > Date: Fri, 22 Oct 2010 11:39:44 -0500 > From: Richard Ree <rree(a)fieldmuseum.org> > Subject: Re: [Tdwg-phylo] Publishing a trees in RDF > To: "tdwg-phylo(a)lists.tdwg.org Interest Group" > <tdwg-phylo(a)lists.tdwg.org> > Message-ID: > <AANLkTimHXsPgiL4J=f5C1b=eXoTA3dusJYO0vXOcbdmF(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Both technology and users' needs evolve rapidly - so the "gaps" will > never be closed, at least in the time frame required by grants, etc. > Also, in phylogenetics a lot of developers are themselves users, so > quick and dirty solutions to scratch individual itches is inevitable. > It's a good thing, IMO. > > -Rick > > > On Fri, Oct 22, 2010 at 11:22 AM, William Piel <william.piel(a)yale.edu> > wrote: > > > > On Oct 22, 2010, at 11:00 AM, Roderic Page wrote: > > > >> There are other issues here as well. Technology advances rapidly, and > >> what once seemed a good choice may rapidly become dated > > > > True.. but another aspect is just that in order to explore whether a > particular graphical concept or tool will work, or will benefit people, you > have to knock out prototypes and implementations. e.g., drag-and-drop branch > rearrangement in MacClade was great for small trees but not for big ones, > hence phylowidget was looking to implement something that worked for large > trees (via concentric menus on nodes) and to experiment with auto-pruing, > etc. People have to keep knocking out GUI software efforts to test the > waters for new features. And the search is not over, for example: > > > > - Do we really have a completely satisfying way of visualizing patterns > of gene duplication within a species tree? > > - If I handed you a tree with 200k nodes, is there a visual / GUI way > that would allow you to easily find interesting patterns in it, such as > points of incongruence with a conventional taxonomy? > > - ?If I gave you 1,000 trees, is there a visual / GUI way that would > allow you to see which branches in each tree probably crossed an ancient > land bridge together? > > > > So I think we still have lots more GUI / visual / ergonomic challenges > that still need to be solved (even if lots of challenges have already been > solved). And we should not expect each new idea to be implemented in a > pristine killer app that does everything that everyone wants out of a tree > visualizer -- that takes too long to build, and the right person for > dreaming up a new idea is not necessarily the best person for creating > clean, robust, off-the-shelf software. > > > > We need to be okay with seeing a rich plethora of quick-and-dirty > efforts, each focusing on articulating/investigating sets of novel ideas -- > despite some obvious redundancy in some of the more general functions. ?And > then periodically, someone's got to assemble the best of these ideas into a > robust, jack-of-all-trades, off-the-shelf software package. > > > > bp > > > > > > _______________________________________________ > > tdwg-phylo mailing list > > tdwg-phylo(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-phylo > > > > > ------------------------------ > > Message: 8 > Date: Fri, 22 Oct 2010 12:42:10 -0400 > From: Nico Cellinese <ncellinese(a)flmnh.ufl.edu> > Subject: Re: [Tdwg-phylo] Publishing a trees in RDF > To: Richard Ree <rree(a)fieldmuseum.org> > Cc: "tdwg-phylo(a)lists.tdwg.org Interest Group" > <tdwg-phylo(a)lists.tdwg.org> > Message-ID: <48C2E497-DAB3-47E0-8F77-0F4921F51CC5(a)flmnh.ufl.edu> > Content-Type: text/plain; charset=us-ascii > > Inevitable. Good thing inded. But not enough to make significant progress > and fill the gaps. I agree with Hilmar. > > Nico > > > On Oct 22, 2010, at 12:39 PM, Richard Ree wrote: > > > Both technology and users' needs evolve rapidly - so the "gaps" will > > never be closed, at least in the time frame required by grants, etc. > > Also, in phylogenetics a lot of developers are themselves users, so > > quick and dirty solutions to scratch individual itches is inevitable. > > It's a good thing, IMO. > > > > -Rick > > > > > > On Fri, Oct 22, 2010 at 11:22 AM, William Piel <william.piel(a)yale.edu> > wrote: > >> > >> On Oct 22, 2010, at 11:00 AM, Roderic Page wrote: > >> > >>> There are other issues here as well. Technology advances rapidly, and > >>> what once seemed a good choice may rapidly become dated > >> > >> True.. but another aspect is just that in order to explore whether a > particular graphical concept or tool will work, or will benefit people, you > have to knock out prototypes and implementations. e.g., drag-and-drop branch > rearrangement in MacClade was great for small trees but not for big ones, > hence phylowidget was looking to implement something that worked for large > trees (via concentric menus on nodes) and to experiment with auto-pruing, > etc. People have to keep knocking out GUI software efforts to test the > waters for new features. And the search is not over, for example: > >> > >> - Do we really have a completely satisfying way of visualizing patterns > of gene duplication within a species tree? > >> - If I handed you a tree with 200k nodes, is there a visual / GUI way > that would allow you to easily find interesting patterns in it, such as > points of incongruence with a conventional taxonomy? > >> - If I gave you 1,000 trees, is there a visual / GUI way that would > allow you to see which branches in each tree probably crossed an ancient > land bridge together? > >> > >> So I think we still have lots more GUI / visual / ergonomic challenges > that still need to be solved (even if lots of challenges have already been > solved). And we should not expect each new idea to be implemented in a > pristine killer app that does everything that everyone wants out of a tree > visualizer -- that takes too long to build, and the right person for > dreaming up a new idea is not necessarily the best person for creating > clean, robust, off-the-shelf software. > >> > >> We need to be okay with seeing a rich plethora of quick-and-dirty > efforts, each focusing on articulating/investigating sets of novel ideas -- > despite some obvious redundancy in some of the more general functions. And > then periodically, someone's got to assemble the best of these ideas into a > robust, jack-of-all-trades, off-the-shelf software package. > >> > >> bp > >> > >> > >> _______________________________________________ > >> tdwg-phylo mailing list > >> tdwg-phylo(a)lists.tdwg.org > >> http://lists.tdwg.org/mailman/listinfo/tdwg-phylo > >> > > _______________________________________________ > > tdwg-phylo mailing list > > tdwg-phylo(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-phylo > > > > ------------------------------ > > Message: 9 > Date: Fri, 22 Oct 2010 12:56:21 -0400 > From: Hilmar Lapp <hlapp(a)nescent.org> > Subject: Re: [Tdwg-phylo] Publishing a trees in RDF > To: Richard Ree <rree(a)fieldmuseum.org> > Cc: "tdwg-phylo(a)lists.tdwg.org Interest Group" > <tdwg-phylo(a)lists.tdwg.org> > Message-ID: <D5F11390-E3DB-4712-8444-2A136876E58F(a)nescent.org> > Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes > > > On Oct 22, 2010, at 12:39 PM, Richard Ree wrote: > > > Both technology and users' needs evolve rapidly - so the "gaps" will > > never be closed, at least in the time frame required by grants, etc. > > Also, in phylogenetics a lot of developers are themselves users, so > > quick and dirty solutions to scratch individual itches is inevitable. > > It's a good thing, IMO. > > > I agree entirely with the "solutions to scratch individual itches is > inevitable and a Good Thing(tm)". > > What I don't agree with is if this is portrayed as being mutually > exclusive with reusable and more sustainable software. Projects like > Bioconductor, the Bio* libraries, and other similar ones demonstrate > that it clearly does not need to be mutually exclusive if we don't > want it to be. Every piece of code in BioPerl is there because it > first scratched someone's itch. The rate of innovation in Bioconductor > is pretty rapid. > > The barrier, if there is perceived to be one, is social, not technical > or scientific. If we as a community of practice don't care about > sustainable software, it won't happen, and we'll continue to lose > software. If we want to think that the software we produce is an > integral part of our science, we lose part of our science every time a > piece of software is no longer maintained. And if we want to think > that writing a new piece of software is part of our scientific > progress, then every time someone writes code for something that code > has already been written for, our rate of scientific progress is > slowed down unnecessarily. > > Again, just my own $0.02. > > -hilmar > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > > > ------------------------------ > > Message: 10 > Date: Fri, 22 Oct 2010 13:06:06 -0400 > From: Arlin Stoltzfus <arlin(a)umd.edu> > Subject: Re: [Tdwg-phylo] Publishing a trees in RDF > To: "tdwg-phylo(a)lists.tdwg.org Interest Group" > <tdwg-phylo(a)lists.tdwg.org> > Message-ID: <7C7A6642-2219-429C-BC2D-4F88BBC3CAA0(a)umd.edu> > Content-Type: text/plain; charset="US-ASCII"; format=flowed; delsp=yes > > This discussion doesn't really belong here, but I'm not sure where > else it belongs, and I sure would hate to stop, because its > interesting and valuable. > > Hilmar, are you referring to various quick-and-dirty BioPerl modules, > for instance, as cases in which software that ended up being reusable > started out as part of a reusable software package? Are there other > kinds of contexts where this would work? How could we get different > developers working on the same architecture, building a shared > foundation but creating different solutions from it? > > One idea used in nexplorer3 (and in some other viewers) is a Model- > View-Controller design pattern that separates the business logic from > the user interface. > > It seems to me that ATV has been pretty successful. I've seen half a > dozen sites that use it (that's a success by my standards). > > Arlin > > On Oct 22, 2010, at 12:38 PM, Hilmar Lapp wrote: > > > > > On Oct 22, 2010, at 12:22 PM, William Piel wrote: > > > >> We need to be okay with seeing a rich plethora of quick-and-dirty > >> efforts, each focusing on articulating/investigating sets of novel > >> ideas -- despite some obvious redundancy in some of the more general > >> functions. And then periodically, someone's got to assemble the > >> best of these ideas into a robust, jack-of-all-trades, off-the-shelf > >> software package. > > > > > > That sounds nice indeed, but frankly I've never seen it happen. The > > quick-and-dirty efforts that I have seen become standard parts of > > reusable and sustainable software have almost all started from their > > early beginnings as parts of reusable software. For a while rather > > experimental and unstable parts, obviously, but the future course was > > charted not as an afterthought. > > > > Truth of the matter is that we're all scientists. No scientist is > > interested in, or gets promotion, scientific recognition, or > > publications from assembling entirely incompatible, mostly redundant > > except for a few features, quick-and-dirty pieces of software into > > some grand jack-of-all-trades software package. > > > > My $0.02, from about 13 years of software engineering. > > > > -hilmar > > -- > > =========================================================== > > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > > =========================================================== > > > > > > > > _______________________________________________ > > tdwg-phylo mailing list > > tdwg-phylo(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-phylo > > ------- > Arlin Stoltzfus (arlin(a)umd.edu) > Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST > IBBR, 9600 Gudelsky Drive, Rockville, MD > tel: 240 314 6208; web: www.molevol.org > > > > ------------------------------ > > _______________________________________________ > tdwg-phylo mailing list > tdwg-phylo(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-phylo > > > End of tdwg-phylo Digest, Vol 2, Issue 8 > **************************************** > -- Chris Baron

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Publishing a tree in RDF
by Chris Baron 19 Oct '10

19 Oct '10

Hi, My name is Chris Baron - a software developer, computer science graduate student interested in linked data, working in BioSync at the Field Museum on tree visualization. I have a few ideas on how to publish trees in RDF (have even created a tool to do so) and would like to speak to Biologists about how their data exists at publication so I can form a proper solution. On Tue, Oct 19, 2010 at 5:00 AM, <tdwg-phylo-request(a)lists.tdwg.org> wrote: > Send tdwg-phylo mailing list submissions to > tdwg-phylo(a)lists.tdwg.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.tdwg.org/mailman/listinfo/tdwg-phylo > or, via email, send a message with subject or body 'help' to > tdwg-phylo-request(a)lists.tdwg.org > > You can reach the person managing the list at > tdwg-phylo-owner(a)lists.tdwg.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of tdwg-phylo digest..." > > > Today's Topics: > > 1. publishing trees in CDAO as linked open data? (Arlin Stoltzfus) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 18 Oct 2010 12:32:39 -0400 > From: Arlin Stoltzfus <arlin(a)umd.edu> > Subject: [Tdwg-phylo] publishing trees in CDAO as linked open data? > To: CDAO list <cdao-discuss(a)lists.sourceforge.net>, Phylogenetics > Standards Interest Group <tdwg-phylo(a)lists.tdwg.org> > Message-ID: <BAAFA68C-2622-409A-B530-1CABADC36016(a)umd.edu> > Content-Type: text/plain; charset="US-ASCII"; format=flowed; delsp=yes > > Dear all-- > > At the Biodiversity Information Standards (TDWG) meeting last month, a > sub-group of the phylogenetic standards working group started a > project to assess "current best practices for publishing trees > electronically". At present, probably the best way to publish a tree > is to use the TreeBASE submission process, which makes it possible to > upload a NEXUS file and create associations of OTUs with taxon IDs, > and of data rows with accessions, and so on. But there are also some > other possibilities. The preliminary report is being assembled here: > > http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/LinkingTrees2010 > > Our plan is (over the next 6 weeks) to get feedback on this > preliminary report, then analyze the results and prepare a more > extensive report for publication. > > One possibility that we haven't examined yet is to publish a tree > electronically by rendering it in RDF in the language of CDAO > (Comparative Data Analysis Ontology) and then contributing it to the > Linked-Open-Data cloud in some way. > > Does anyone out there want to explore this idea and contribute the > results to the TDWG project? If so, please let me know. > > Arlin > ------- > Arlin Stoltzfus (arlin(a)umd.edu) > Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST > IBBR, 9600 Gudelsky Drive, Rockville, MD > tel: 240 314 6208; web: www.molevol.org > > > > ------------------------------ > > _______________________________________________ > tdwg-phylo mailing list > tdwg-phylo(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-phylo > > > End of tdwg-phylo Digest, Vol 2, Issue 3 > **************************************** > -- Chris Baron

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publishing trees in CDAO as linked open data?
by Arlin Stoltzfus 19 Oct '10

19 Oct '10

Dear all-- At the Biodiversity Information Standards (TDWG) meeting last month, a sub-group of the phylogenetic standards working group started a project to assess "current best practices for publishing trees electronically". At present, probably the best way to publish a tree is to use the TreeBASE submission process, which makes it possible to upload a NEXUS file and create associations of OTUs with taxon IDs, and of data rows with accessions, and so on. But there are also some other possibilities. The preliminary report is being assembled here: http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/LinkingTrees2010 Our plan is (over the next 6 weeks) to get feedback on this preliminary report, then analyze the results and prepare a more extensive report for publication. One possibility that we haven't examined yet is to publish a tree electronically by rendering it in RDF in the language of CDAO (Comparative Data Analysis Ontology) and then contributing it to the Linked-Open-Data cloud in some way. Does anyone out there want to explore this idea and contribute the results to the TDWG project? If so, please let me know. Arlin ------- Arlin Stoltzfus (arlin(a)umd.edu) Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST IBBR, 9600 Gudelsky Drive, Rockville, MD tel: 240 314 6208; web: www.molevol.org

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TDWG 2010 working meeting outcomes
by Hilmar Lapp 04 Oct '10

04 Oct '10

The event home page for the 2010 working meeting at TDWG in Woods Hole has now been updated with documentation of outcomes: http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/WorkingMeeting2010 Thank you to everyone who participated. This was a a short, single-day meeting, yet I think it was pretty productive, and led to some clear follow-ups and next steps. Thanks also to Arlin for presenting the meeting summary to the TDWG audience on Friday morning. Outcomes from targets #3 (Kate) and #4 (Chris) are based on my notes from the wrap-up. Kate and Chris, please feel free to update and/or correct. Your wiki accounts should now be approved, let me know if you have trouble logging in. Kate - it'd be great if you could add the source code URL for your XSLT code. Arlin - if you don't mind, could you attach your summary slides to the page? It's too bad we forgot to take a group photo at the event. Maybe it'd be better to have a gallery of individual pictures on the page rather than the sub-group of people we photographed later (and which is on the wiki right now)? If anyone here who hasn't participated has questions or suggestions on what else should be on that event page, please let us know. On behalf of the others, -Hilmar & Nico -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : ===========================================================

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