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From: Rutger V. <rut...@gm...> - 2012-02-09 12:55:42
|
Hi all, just to bring this to your attention: the EDAM ontology is amazingly extensive, including terms for all the file formats we all love, tree annotation (for which the concept has been aligned with http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation, terms for reconstruction methods, etc. Maybe you knew all this, but I was quite amazed to see it: http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=EDAM 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 |
From: Vision, T. J <tj...@bi...> - 2011-11-25 00:02:11
|
+1 to Hilmar's suggestion. Some advice from Creative Commons: http://sciencecommons.org/resources/readingroom/ontology-copyright-licensing-considerations/ CC-BY appears to be a common choice, as well, though IMHO it is gratuitious "lawyering up", and could harm adoption by prohibiting 'remix' uses in which attribution is no longer a reasonable expectation. -Todd > Hi all, > > I saw that the license attached to CDAO on the SourceForge project > page is the GPL. This is indeed also what's stated in the paper, so I > should have noted long ago. > > The GPL is, I think, a rather bad choice for licensing CDAO. First, it > was designed for software, and how to apply the terms to an ontology > are not so clear. It's specifically not clear how to interpret the > "viral" terms of the GPL in the case of someone reusing an ontology, > provided that such viral terms were actually desired. Second, as I > think we are all interested in the broadest possible reuse of CDAO, a > "share-alike" requirement in reality I think does more harm than good. > Third, as a license GPL actually implies (and asserts) copyright. > While in some ways one may see an ontology as a work of creative art, > and hence as eligible for copyright protection, much of the things > asserted in CDAO (as in most other life science ontologies) are facts, > which at least in the US are not eligible for copyright protection. So > at least it's a grey zone situation. Perhaps more importantly, > copyright protection and licensing are *legal* instruments, useful for > enforcing one's rights in a court of law. However, what we are > probably rather interested in instead is that certain community norms > for giving credit (attribution) are met by those reusing the ontology > wherever this can be reasonably expected. A public-domain dedication > can state those expectations just as well, and possibly better, than a > license, while removing all barriers to reuse. (For example, licensed > content with copyright assertion, whether with solid or questionable > legal standing, creates all kinds of headaches in aggregations that > would result in mixed licensing situations.) > > Therefore, I would suggest that the CDAO license be changed to a > public-domain waiver, with an attached declaration of expectations for > attribution. > > As an example for how this could look like, here are the terms of > reuse for the Teleost Anatomy Ontology (TAO), as contained in the OWL > file [1]: > > "To the extent possible under law, Wasila M. Dahdul has waived all > copyright and related or neighboring rights to the Teleost Anatomy > Ontology (TAO), under CC0 license (http://creativecommons.org/publicdomain/zero/1.0/ > ). This work is published from the United States. It is requested that > users of this vocabulary cite the following publication: Dahdul, W.M., > Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., > Haendel, M.A., Westerfield, M., and Mabee, P.M. (2010). The Teleost > Anatomy Ontology: anatomical representation for the genomics age. > Systematic Biology 59, 369-383. http://dx.doi.org/10.1093/sysbio/syq013" > > (Note: In comparison, the CDAO at present actually has no such > statement in the OWL file, so a machine accessing the ontology would > have no way to know. [And yes, it would indeed be pretty hard for a > machine to extract the above as the pertinent terms of reuse from the > OWL translation, as I've explained on the OBO format list [2]. But > that's because it is maintained in OBO format - for CDAO we could > choose how to expose this directly in OWL.]) > > -hilmar > > [1] http://purl.obolibrary.org/obo/tao.owl > [2] http://bit.ly/uZBlae > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== |
From: Hilmar L. <hl...@ne...> - 2011-11-21 22:21:14
|
It looks like we are using CVS right now. CVS is obviously better than no version control, but still far inferior from those widely in use these days. (This is a rather diplomatic way to put it compared to other phrases I've seen on the internet. If you really disagree, I can enumerate some of the problems.) Possibly more importantly, there hasn't been much (or any?) development on cvs for a long time, and so it has a variety of vulnerabilities which have caused SourceForge to turn off cvs for significant amounts of time when they were having security incidents in the past. Are there any hurdles or objections to moving to a more modern version control system, such as svn, or git? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
From: Hilmar L. <hl...@ne...> - 2011-11-21 22:06:43
|
Hi all, I saw that the license attached to CDAO on the SourceForge project page is the GPL. This is indeed also what's stated in the paper, so I should have noted long ago. The GPL is, I think, a rather bad choice for licensing CDAO. First, it was designed for software, and how to apply the terms to an ontology are not so clear. It's specifically not clear how to interpret the "viral" terms of the GPL in the case of someone reusing an ontology, provided that such viral terms were actually desired. Second, as I think we are all interested in the broadest possible reuse of CDAO, a "share-alike" requirement in reality I think does more harm than good. Third, as a license GPL actually implies (and asserts) copyright. While in some ways one may see an ontology as a work of creative art, and hence as eligible for copyright protection, much of the things asserted in CDAO (as in most other life science ontologies) are facts, which at least in the US are not eligible for copyright protection. So at least it's a grey zone situation. Perhaps more importantly, copyright protection and licensing are *legal* instruments, useful for enforcing one's rights in a court of law. However, what we are probably rather interested in instead is that certain community norms for giving credit (attribution) are met by those reusing the ontology wherever this can be reasonably expected. A public-domain dedication can state those expectations just as well, and possibly better, than a license, while removing all barriers to reuse. (For example, licensed content with copyright assertion, whether with solid or questionable legal standing, creates all kinds of headaches in aggregations that would result in mixed licensing situations.) Therefore, I would suggest that the CDAO license be changed to a public-domain waiver, with an attached declaration of expectations for attribution. As an example for how this could look like, here are the terms of reuse for the Teleost Anatomy Ontology (TAO), as contained in the OWL file [1]: "To the extent possible under law, Wasila M. Dahdul has waived all copyright and related or neighboring rights to the Teleost Anatomy Ontology (TAO), under CC0 license (http://creativecommons.org/publicdomain/zero/1.0/ ). This work is published from the United States. It is requested that users of this vocabulary cite the following publication: Dahdul, W.M., Lundberg, J.G., Midford, P.E., Balhoff, J.P., Lapp, H., Vision, T.J., Haendel, M.A., Westerfield, M., and Mabee, P.M. (2010). The Teleost Anatomy Ontology: anatomical representation for the genomics age. Systematic Biology 59, 369-383. http://dx.doi.org/10.1093/sysbio/syq013" (Note: In comparison, the CDAO at present actually has no such statement in the OWL file, so a machine accessing the ontology would have no way to know. [And yes, it would indeed be pretty hard for a machine to extract the above as the pertinent terms of reuse from the OWL translation, as I've explained on the OBO format list [2]. But that's because it is maintained in OBO format - for CDAO we could choose how to expose this directly in OWL.]) -hilmar [1] http://purl.obolibrary.org/obo/tao.owl [2] http://bit.ly/uZBlae -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
From: Hilmar L. <hl...@ne...> - 2011-11-21 17:05:28
|
Hi all, the CDAO project wiki as currently hosted on SourceForge should be referenced under the http (unencrypted) protocol, not SSL (https): http://sourceforge.net/apps/mediawiki/cdao If you use https, it will require a login, and thus erroneously seem like it is not publicly visible. I've just fixed this in the SourceForge project description, and it looks like www.evolutionaryontology.org had the correct link already. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
From: Rutger V. <R....@re...> - 2011-11-21 16:01:20
|
Are we having a CDAO telecon now? What are the connection details? On Wed, Nov 9, 2011 at 3:57 PM, Jim Balhoff <ba...@ne...> wrote: > It looks like Monday, November 21, is the only day with time slots where only one interested person can't make it - no time works for everyone. So can we plan on 11 am Eastern time, Monday, November 21? > > Thanks, > Jim > > > On Nov 7, 2011, at 11:16 PM, Jim Balhoff wrote: > >> Hi all, >> >> Arlin has suggested that we hold a conference call to talk about the future of CDAO, organizing development, and finding funding. I think this is a great idea and I have created a Doodle poll to help find a time when everyone who is interested is available: >> >> http://www.doodle.com/5mv7m5mmywsv5sxf >> >> If you would like to participate in this discussion, please fill out your availability in that poll (note that time zone support is enabled, so you can view the times for your area). After a couple of days I'll let everyone know when the call will be, and the number to call. >> >> Anyone interested in the future of CDAO is welcome to join in. Let us know how CDAO in its current form has been useful (or not), and how it can be improved for future use-cases. >> >> Best regards, >> Jim >> >> ____________________________________________ >> James P. Balhoff, Ph.D. >> National Evolutionary Synthesis Center >> 2024 West Main St., Suite A200 >> Durham, NC 27705 >> USA >> >> >> > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading, RG6 6BX, United Kingdom Tel: +44 (0) 118 378 7535 http://rutgervos.blogspot.com |
From: Jim B. <ba...@ne...> - 2011-11-21 15:39:19
|
Reminder - the conference call starts in about 20 minutes. I updated the Google doc with different phone numbers I received this morning, so please look there before calling. Thanks, Jim On Nov 19, 2011, at 8:30 PM, Jim Balhoff wrote: > FYI - I added the call number to the Google doc. > > On Nov 18, 2011, at 11:14 AM, Jim Balhoff wrote: > >> I have added some items to the CDAO teleconference agenda. Please feel free to add and edit as you see fit! I will be putting the call number in that doc once I hear from our IT support. >> >> Here's what I have for now: >> • Projects using CDAO >> • Semantic phenotype annotation in Phenoscape and Hymenoptera taxonomy (Jim) >> • others? please add >> • Summary of current project structure (ontology and version URIs, status of SVN, etc.) >> • Adopt OBO conventions (numeric identifiers, URI templates)? >> • More coordination with OBO Foundry? >> • CDAO content changes >> • Compact matrix representations >> • Matrix subclasses >> • Building community, project funding >> >> Thanks, >> Jim >> >> On Nov 17, 2011, at 1:40 PM, Jim Balhoff wrote: >> >>> I just wanted to remind everyone of the CDAO conference call on Monday. I am working on getting a call-in number, which I will send out tomorrow. Think about anything you want to add to the agenda - I started an empty Google doc here which I will be able to start adding to tomorrow: >>> >>> http://goo.gl/c8QAj >>> >>> If you click that link and request access, I'll add you to the doc. >>> >>> Thanks, >>> Jim >>> >>> ____________________________________________ >>> James P. Balhoff, Ph.D. >>> National Evolutionary Synthesis Center >>> 2024 West Main St., Suite A200 >>> Durham, NC 27705 >>> USA >>> >>> >>> >> >> ____________________________________________ >> James P. Balhoff, Ph.D. >> National Evolutionary Synthesis Center >> 2024 West Main St., Suite A200 >> Durham, NC 27705 >> USA >> >> >> > > ____________________________________________ > James P. Balhoff, Ph.D. > National Evolutionary Synthesis Center > 2024 West Main St., Suite A200 > Durham, NC 27705 > USA > > > |
From: Julie T. <ju...@ig...> - 2011-11-21 06:35:45
|
Another issue that might be worth considering is the use of CDAO for phylogenomics, for example, how to represent a supermatrix or a supertree. Another potential field would be systems-level studies: how to represent the evolution of a system such as a structural complex or network, where the characters could be all the residues of the different proteins, or domains/proteins. If you think this is within the scope of CDAO, I could find some use cases. Julie -----Message d'origine----- De : cda...@li... [mailto:cda...@li...] Envoyé : dimanche 20 novembre 2011 13:05 À : cda...@li... Objet : CDAO-discuss Digest, Vol 21, Issue 7 Send CDAO-discuss mailing list submissions to cda...@li... To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/cdao-discuss or, via email, send a message with subject or body 'help' to cda...@li... You can reach the person managing the list at cda...@li... When replying, please edit your Subject line so it is more specific than "Re: Contents of CDAO-discuss digest..." Today's Topics: 1. Re: conference call Monday (Gopalan, Vivek (NIH/NIAID) [C]) 2. Re: conference call Monday (Jim Balhoff) ---------------------------------------------------------------------- Message: 1 Date: Sat, 19 Nov 2011 16:47:44 -0500 From: "Gopalan, Vivek (NIH/NIAID) [C]" <gop...@ni...> Subject: Re: [CDAO-discuss] conference call Monday To: Jim Balhoff <ba...@ne...>, CDAO list <cda...@li...> Message-ID: <CAED81F4.6887%viv...@ni...> Content-Type: text/plain; charset="Windows-1252" Hi Jim, I have added Nexplorer3 project to the agenda item. Nexplorer3 updates: 1. Implemented server-side session to handle user uploaded files 2. Added history option in the client side so users can save a specific view of Nexplorer view with description and title tag. 3. Implemented functionality to share the saved view as Url. 4. Minor additions & Issues fixed - Flickering issue of popup Menu option over tree nodes has been fixed, Added Vertical slider bar for adjusting the width of the viewer, the total time taken to process the data in the server is now displayed in the client side. I have not deployed the latest changes to the exon.niaid.nih.gov/nexplorer site yet, since it is still in testing. If you want to see these changes, Please follow the 3 steps in the following README.txt file to setup the local version of Nexplorer (with embedded web server) in you computer. http://nexplorer.svn.sourceforge.net/viewvc/nexplorer/trunk/nexplorer3/READ ME.txt?view=markup Cheers, Vivek On 11/18/11 11:14 AM, "Jim Balhoff" <ba...@ne...> wrote: >I have added some items to the CDAO teleconference agenda. Please feel >free to add and edit as you see fit! I will be putting the call number in >that doc once I hear from our IT support. > >Here's what I have for now: > ? Projects using CDAO > ? Semantic phenotype annotation in Phenoscape and Hymenoptera taxonomy >(Jim) > ? others? please add > ? Summary of current project structure (ontology and version URIs, >status of SVN, etc.) > ? Adopt OBO conventions (numeric identifiers, URI templates)? > ? More coordination with OBO Foundry? > ? CDAO content changes > ? Compact matrix representations > ? Matrix subclasses > ? Building community, project funding > >Thanks, >Jim > >On Nov 17, 2011, at 1:40 PM, Jim Balhoff wrote: > >> I just wanted to remind everyone of the CDAO conference call on Monday. >>I am working on getting a call-in number, which I will send out >>tomorrow. Think about anything you want to add to the agenda - I started >>an empty Google doc here which I will be able to start adding to >>tomorrow: >> >> http://goo.gl/c8QAj >> >> If you click that link and request access, I'll add you to the doc. >> >> Thanks, >> Jim >> >> ____________________________________________ >> James P. Balhoff, Ph.D. >> National Evolutionary Synthesis Center >> 2024 West Main St., Suite A200 >> Durham, NC 27705 >> USA >> >> >> > >____________________________________________ >James P. Balhoff, Ph.D. >National Evolutionary Synthesis Center >2024 West Main St., Suite A200 >Durham, NC 27705 >USA > > > > >-------------------------------------------------------------------------- >---- >All the data continuously generated in your IT infrastructure >contains a definitive record of customers, application performance, >security threats, fraudulent activity, and more. Splunk takes this >data and makes sense of it. IT sense. And common sense. >http://p.sf.net/sfu/splunk-novd2d >_______________________________________________ >CDAO-discuss mailing list >CDA...@li... >https://lists.sourceforge.net/lists/listinfo/cdao-discuss ------------------------------ Message: 2 Date: Sat, 19 Nov 2011 20:30:28 -0500 From: Jim Balhoff <ba...@ne...> Subject: Re: [CDAO-discuss] conference call Monday To: CDAO list <cda...@li...> Message-ID: <5FA...@ne...> Content-Type: text/plain; charset=windows-1252 FYI - I added the call number to the Google doc. On Nov 18, 2011, at 11:14 AM, Jim Balhoff wrote: > I have added some items to the CDAO teleconference agenda. Please feel free to add and edit as you see fit! I will be putting the call number in that doc once I hear from our IT support. > > Here's what I have for now: > ? Projects using CDAO > ? Semantic phenotype annotation in Phenoscape and Hymenoptera taxonomy (Jim) > ? others? please add > ? Summary of current project structure (ontology and version URIs, status of SVN, etc.) > ? Adopt OBO conventions (numeric identifiers, URI templates)? > ? More coordination with OBO Foundry? > ? CDAO content changes > ? Compact matrix representations > ? Matrix subclasses > ? Building community, project funding > > Thanks, > Jim > > On Nov 17, 2011, at 1:40 PM, Jim Balhoff wrote: > >> I just wanted to remind everyone of the CDAO conference call on Monday. I am working on getting a call-in number, which I will send out tomorrow. Think about anything you want to add to the agenda - I started an empty Google doc here which I will be able to start adding to tomorrow: >> >> http://goo.gl/c8QAj >> >> If you click that link and request access, I'll add you to the doc. >> >> Thanks, >> Jim >> >> ____________________________________________ >> James P. Balhoff, Ph.D. >> National Evolutionary Synthesis Center >> 2024 West Main St., Suite A200 >> Durham, NC 27705 >> USA >> >> >> > > ____________________________________________ > James P. Balhoff, Ph.D. > National Evolutionary Synthesis Center > 2024 West Main St., Suite A200 > Durham, NC 27705 > USA > > > ____________________________________________ James P. Balhoff, Ph.D. National Evolutionary Synthesis Center 2024 West Main St., Suite A200 Durham, NC 27705 USA ------------------------------ ------------------------------------------------------------------------------ All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ------------------------------ _______________________________________________ CDAO-discuss mailing list CDA...@li... https://lists.sourceforge.net/lists/listinfo/cdao-discuss End of CDAO-discuss Digest, Vol 21, Issue 7 ******************************************* |
From: Jim B. <ba...@ne...> - 2011-11-20 01:30:39
|
FYI - I added the call number to the Google doc. On Nov 18, 2011, at 11:14 AM, Jim Balhoff wrote: > I have added some items to the CDAO teleconference agenda. Please feel free to add and edit as you see fit! I will be putting the call number in that doc once I hear from our IT support. > > Here's what I have for now: > • Projects using CDAO > • Semantic phenotype annotation in Phenoscape and Hymenoptera taxonomy (Jim) > • others? please add > • Summary of current project structure (ontology and version URIs, status of SVN, etc.) > • Adopt OBO conventions (numeric identifiers, URI templates)? > • More coordination with OBO Foundry? > • CDAO content changes > • Compact matrix representations > • Matrix subclasses > • Building community, project funding > > Thanks, > Jim > > On Nov 17, 2011, at 1:40 PM, Jim Balhoff wrote: > >> I just wanted to remind everyone of the CDAO conference call on Monday. I am working on getting a call-in number, which I will send out tomorrow. Think about anything you want to add to the agenda - I started an empty Google doc here which I will be able to start adding to tomorrow: >> >> http://goo.gl/c8QAj >> >> If you click that link and request access, I'll add you to the doc. >> >> Thanks, >> Jim >> >> ____________________________________________ >> James P. Balhoff, Ph.D. >> National Evolutionary Synthesis Center >> 2024 West Main St., Suite A200 >> Durham, NC 27705 >> USA >> >> >> > > ____________________________________________ > James P. Balhoff, Ph.D. > National Evolutionary Synthesis Center > 2024 West Main St., Suite A200 > Durham, NC 27705 > USA > > > ____________________________________________ James P. Balhoff, Ph.D. National Evolutionary Synthesis Center 2024 West Main St., Suite A200 Durham, NC 27705 USA |
From: Gopalan, V. (NIH/N. [C] <gop...@ni...> - 2011-11-19 21:58:25
|
Hi Jim, I have added Nexplorer3 project to the agenda item. Nexplorer3 updates: 1. Implemented server-side session to handle user uploaded files 2. Added history option in the client side so users can save a specific view of Nexplorer view with description and title tag. 3. Implemented functionality to share the saved view as Url. 4. Minor additions & Issues fixed - Flickering issue of popup Menu option over tree nodes has been fixed, Added Vertical slider bar for adjusting the width of the viewer, the total time taken to process the data in the server is now displayed in the client side. I have not deployed the latest changes to the exon.niaid.nih.gov/nexplorer site yet, since it is still in testing. If you want to see these changes, Please follow the 3 steps in the following README.txt file to setup the local version of Nexplorer (with embedded web server) in you computer. http://nexplorer.svn.sourceforge.net/viewvc/nexplorer/trunk/nexplorer3/READ ME.txt?view=markup Cheers, Vivek On 11/18/11 11:14 AM, "Jim Balhoff" <ba...@ne...> wrote: >I have added some items to the CDAO teleconference agenda. Please feel >free to add and edit as you see fit! I will be putting the call number in >that doc once I hear from our IT support. > >Here's what I have for now: > € Projects using CDAO > € Semantic phenotype annotation in Phenoscape and Hymenoptera taxonomy >(Jim) > € others? please add > € Summary of current project structure (ontology and version URIs, >status of SVN, etc.) > € Adopt OBO conventions (numeric identifiers, URI templates)? > € More coordination with OBO Foundry? > € CDAO content changes > € Compact matrix representations > € Matrix subclasses > € Building community, project funding > >Thanks, >Jim > >On Nov 17, 2011, at 1:40 PM, Jim Balhoff wrote: > >> I just wanted to remind everyone of the CDAO conference call on Monday. >>I am working on getting a call-in number, which I will send out >>tomorrow. Think about anything you want to add to the agenda - I started >>an empty Google doc here which I will be able to start adding to >>tomorrow: >> >> http://goo.gl/c8QAj >> >> If you click that link and request access, I'll add you to the doc. >> >> Thanks, >> Jim >> >> ____________________________________________ >> James P. Balhoff, Ph.D. >> National Evolutionary Synthesis Center >> 2024 West Main St., Suite A200 >> Durham, NC 27705 >> USA >> >> >> > >____________________________________________ >James P. Balhoff, Ph.D. >National Evolutionary Synthesis Center >2024 West Main St., Suite A200 >Durham, NC 27705 >USA > > > > >-------------------------------------------------------------------------- >---- >All the data continuously generated in your IT infrastructure >contains a definitive record of customers, application performance, >security threats, fraudulent activity, and more. Splunk takes this >data and makes sense of it. IT sense. And common sense. >http://p.sf.net/sfu/splunk-novd2d >_______________________________________________ >CDAO-discuss mailing list >CDA...@li... >https://lists.sourceforge.net/lists/listinfo/cdao-discuss |
From: Jim B. <ba...@ne...> - 2011-11-18 16:14:40
|
I have added some items to the CDAO teleconference agenda. Please feel free to add and edit as you see fit! I will be putting the call number in that doc once I hear from our IT support. Here's what I have for now: • Projects using CDAO • Semantic phenotype annotation in Phenoscape and Hymenoptera taxonomy (Jim) • others? please add • Summary of current project structure (ontology and version URIs, status of SVN, etc.) • Adopt OBO conventions (numeric identifiers, URI templates)? • More coordination with OBO Foundry? • CDAO content changes • Compact matrix representations • Matrix subclasses • Building community, project funding Thanks, Jim On Nov 17, 2011, at 1:40 PM, Jim Balhoff wrote: > I just wanted to remind everyone of the CDAO conference call on Monday. I am working on getting a call-in number, which I will send out tomorrow. Think about anything you want to add to the agenda - I started an empty Google doc here which I will be able to start adding to tomorrow: > > http://goo.gl/c8QAj > > If you click that link and request access, I'll add you to the doc. > > Thanks, > Jim > > ____________________________________________ > James P. Balhoff, Ph.D. > National Evolutionary Synthesis Center > 2024 West Main St., Suite A200 > Durham, NC 27705 > USA > > > ____________________________________________ James P. Balhoff, Ph.D. National Evolutionary Synthesis Center 2024 West Main St., Suite A200 Durham, NC 27705 USA |
From: Jim B. <ba...@ne...> - 2011-11-17 18:40:47
|
I just wanted to remind everyone of the CDAO conference call on Monday. I am working on getting a call-in number, which I will send out tomorrow. Think about anything you want to add to the agenda - I started an empty Google doc here which I will be able to start adding to tomorrow: http://goo.gl/c8QAj If you click that link and request access, I'll add you to the doc. Thanks, Jim ____________________________________________ James P. Balhoff, Ph.D. National Evolutionary Synthesis Center 2024 West Main St., Suite A200 Durham, NC 27705 USA |
From: Enrico P. <epo...@cs...> - 2011-11-10 14:48:06
|
We could use http://sourceforge.net/apps/mediawiki/cdao/index.php?title=Main_Page Enrico -- Dept. Computer Science, New Mexico State University MSC CS, Box 30001, Las Cruces, NM 88003 Voice: 575-646-6239 Fax: 575-646-1002 On 11/10/11 7:24 AM, "Hilmar Lapp" <hl...@ne...> wrote: > >On Nov 10, 2011, at 4:49 AM, Rutger Vos wrote: > >> Sure, what's the best place for that? > > >I thought CDAO now has a wiki (hosted at SourceForge). But perhaps >that's not true? As far as I'm concerned, the EvoIO wiki would be at >least as good if not even a better place. > > -hilmar >-- >=========================================================== >: Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : >=========================================================== > > |
From: Hilmar L. <hl...@ne...> - 2011-11-10 14:25:07
|
On Nov 10, 2011, at 4:49 AM, Rutger Vos wrote: > Sure, what's the best place for that? I thought CDAO now has a wiki (hosted at SourceForge). But perhaps that's not true? As far as I'm concerned, the EvoIO wiki would be at least as good if not even a better place. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
From: Rutger V. <R....@re...> - 2011-11-10 09:49:51
|
Sure, what's the best place for that? On Wed, Nov 9, 2011 at 5:48 PM, Hilmar Lapp <hl...@ne...> wrote: > Rutger - > > can you document your query needs as a use-case on the wiki? I think it's > important to retain this and other cases for continuous validation. > > -hilmar > > On Nov 8, 2011, at 10:38 AM, Rutger Vos wrote: > >>> I also feel that some of these are not difficult to address - e.g., it is >>> not hard to envision new subclasses to provide alternative forms of data >>> to be used in the matrix representation. E.g., the matrix representation >>> already allows compound characters that can be used to provide a sequence >>> as a single entity (instead of breaking it down into smaller characters). >>> We also need to remember that an ontology is not a data format (thus >>> succinctness is not one criteria to drive its design) - it should provide >>> whatever level of detail one desires to annotate any existing source of >>> data. >> >> I certainly agree with your point that an ontology is not a data >> format, but verbosity is still an issue: if we transformed all of >> TreeBASE's NeXML to CDAO/RDF it would become, to the best of my >> knowledge, the biggest public triple store currently in use in the >> life sciences (I'm basing this on the presentations of Jerven Bolleman >> from UniProt). In other words, it will not scale. Also, we really do >> want to be able to find out with a relatively simple SPARQL query >> whether a matrix/alignment is DNA, RNA, Protein, or something else >> without too many joins and interpretation of the used alphabet. >> >> Rutger >> >>> On 11/8/11 3:57 AM, "Rutger Vos" <R....@re...> wrote: >>> >>>> Hey Jim, >>>> >>>> thanks for pushing this. I think it's crucial that CDAO continues to >>>> be under development. At the BioHackathon in Kyoto I spent my time >>>> working on improving the NeXML-to-CDAO stylesheet and on querying >>>> CDAO/RDF graphs to extract known objects (taxa, trees, matrices) out >>>> of it. >>>> >>>> I discovered some inconvenient design decisions in terms of the >>>> verbosity of the generated RDF and the circumlocution in which certain >>>> important facts are expressed (e.g.: how do I find out the data type >>>> of a character state matrix through a SPARQL query? This is >>>> surprisingly hard to do in CDAO). >>>> >>>> I would be happy to share these findings on the call as I feel it is >>>> important that these issues are addressed in the run up to, or at, the >>>> HIP meetings. >>>> >>>> Best wishes, >>>> >>>> Rutger >>>> >>>> On Tue, Nov 8, 2011 at 4:16 AM, Jim Balhoff <ba...@ne...> wrote: >>>>> >>>>> Hi all, >>>>> >>>>> Arlin has suggested that we hold a conference call to talk about the >>>>> future of CDAO, organizing development, and finding funding. I think >>>>> this is a great idea and I have created a Doodle poll to help find a >>>>> time when everyone who is interested is available: >>>>> >>>>> http://www.doodle.com/5mv7m5mmywsv5sxf >>>>> >>>>> If you would like to participate in this discussion, please fill out >>>>> your availability in that poll (note that time zone support is enabled, >>>>> so you can view the times for your area). After a couple of days I'll >>>>> let everyone know when the call will be, and the number to call. >>>>> >>>>> Anyone interested in the future of CDAO is welcome to join in. Let us >>>>> know how CDAO in its current form has been useful (or not), and how it >>>>> can be improved for future use-cases. >>>>> >>>>> Best regards, >>>>> Jim >>>>> >>>>> ____________________________________________ >>>>> James P. Balhoff, Ph.D. >>>>> National Evolutionary Synthesis Center >>>>> 2024 West Main St., Suite A200 >>>>> Durham, NC 27705 >>>>> USA >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> >>>> -- >>>> Dr. Rutger A. Vos >>>> School of Biological Sciences >>>> Philip Lyle Building, Level 4 >>>> University of Reading >>>> Reading, RG6 6BX, United Kingdom >>>> Tel: +44 (0) 118 378 7535 >>>> http://rutgervos.blogspot.com >>> >>> >>> >> >> >> >> -- >> Dr. Rutger A. Vos >> School of Biological Sciences >> Philip Lyle Building, Level 4 >> University of Reading >> Reading, RG6 6BX, United Kingdom >> Tel: +44 (0) 118 378 7535 >> http://rutgervos.blogspot.com >> >> >> ------------------------------------------------------------------------------ >> RSA(R) Conference 2012 >> Save $700 by Nov 18 >> Register now >> http://p.sf.net/sfu/rsa-sfdev2dev1 >> _______________________________________________ >> CDAO-discuss mailing list >> CDA...@li... >> https://lists.sourceforge.net/lists/listinfo/cdao-discuss > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading, RG6 6BX, United Kingdom Tel: +44 (0) 118 378 7535 http://rutgervos.blogspot.com |
From: Rutger V. <R....@re...> - 2011-11-10 09:48:16
|
Me too. On Wed, Nov 9, 2011 at 5:47 PM, Hilmar Lapp <hl...@ne...> wrote: > > On Nov 9, 2011, at 10:57 AM, Jim Balhoff wrote: > >> So can we plan on 11 am Eastern time, Monday, November 21? > > > Works for me. -hilmar > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : > =========================================================== > > > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading, RG6 6BX, United Kingdom Tel: +44 (0) 118 378 7535 http://rutgervos.blogspot.com |
From: Rutger V. <R....@re...> - 2011-11-10 09:47:39
|
> I agree with Enrico about the importance of annotating data at a given level of detail. It's true that the current, "fully triplified", matrix representation can be quite large as a datastore. But if you think of referencing characters, states, and data cells in a linked data context, you can have URIs which reference any detailed node in a matrix, but actually maps back to some other matrix store implementation (which you probably recognize already). The most fine-grained CDAO content can be used to exchange metadata for given nodes in the matrix graph without instantiating the entire matrix in triples. I am not sure how we could reference all the different pieces of a character matrix with a smaller number of triples, but it would be useful to explore alternatives. Even given that, it seems like it would be useful to include ways to reference compact versions of data elements as suggested by you and Enrico. Great points. Yes, we do want the *ability* to go to a very granular representation of individual matrix cells - especially, perhaps, for morphological matrices - and some way of faking that for the 80% of use cases is something to be explored. Just as long as it's not the only possible way of doing things in CDAO. Not so dissimilar a situation from TreeBASE, where we can imagine individual matrix cells usefully having their own PhyloWS URIs for some use cases, yet we can't really support an ever expanding matrixelement table that has every cell in every matrix ever submitted to TreeBASE as individual records (as we found out). > In your earlier email, you mentioned handling ordering of lists (taxa and characters). I don't think we can use rdf:List within OWL DL - there is an interesting presentation here: > > http://www.co-ode.org/resources/tutorials/bio/slides/owl-lists29_11_05.ppt > > We might be best off with simple character numbers rather than maintaining an actual list data structure, which would just add to our verbosity problem. Ah, ok - I wasn't aware of those issues. Thanks. Best wishes, Rutger -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading, RG6 6BX, United Kingdom Tel: +44 (0) 118 378 7535 http://rutgervos.blogspot.com |
From: Hilmar L. <hl...@ne...> - 2011-11-09 16:49:13
|
Rutger - can you document your query needs as a use-case on the wiki? I think it's important to retain this and other cases for continuous validation. -hilmar On Nov 8, 2011, at 10:38 AM, Rutger Vos wrote: >> I also feel that some of these are not difficult to address - e.g., >> it is >> not hard to envision new subclasses to provide alternative forms of >> data >> to be used in the matrix representation. E.g., the matrix >> representation >> already allows compound characters that can be used to provide a >> sequence >> as a single entity (instead of breaking it down into smaller >> characters). >> We also need to remember that an ontology is not a data format (thus >> succinctness is not one criteria to drive its design) - it should >> provide >> whatever level of detail one desires to annotate any existing >> source of >> data. > > I certainly agree with your point that an ontology is not a data > format, but verbosity is still an issue: if we transformed all of > TreeBASE's NeXML to CDAO/RDF it would become, to the best of my > knowledge, the biggest public triple store currently in use in the > life sciences (I'm basing this on the presentations of Jerven Bolleman > from UniProt). In other words, it will not scale. Also, we really do > want to be able to find out with a relatively simple SPARQL query > whether a matrix/alignment is DNA, RNA, Protein, or something else > without too many joins and interpretation of the used alphabet. > > Rutger > >> On 11/8/11 3:57 AM, "Rutger Vos" <R....@re...> wrote: >> >>> Hey Jim, >>> >>> thanks for pushing this. I think it's crucial that CDAO continues to >>> be under development. At the BioHackathon in Kyoto I spent my time >>> working on improving the NeXML-to-CDAO stylesheet and on querying >>> CDAO/RDF graphs to extract known objects (taxa, trees, matrices) out >>> of it. >>> >>> I discovered some inconvenient design decisions in terms of the >>> verbosity of the generated RDF and the circumlocution in which >>> certain >>> important facts are expressed (e.g.: how do I find out the data type >>> of a character state matrix through a SPARQL query? This is >>> surprisingly hard to do in CDAO). >>> >>> I would be happy to share these findings on the call as I feel it is >>> important that these issues are addressed in the run up to, or at, >>> the >>> HIP meetings. >>> >>> Best wishes, >>> >>> Rutger >>> >>> On Tue, Nov 8, 2011 at 4:16 AM, Jim Balhoff <ba...@ne...> >>> wrote: >>>> Hi all, >>>> >>>> Arlin has suggested that we hold a conference call to talk about >>>> the >>>> future of CDAO, organizing development, and finding funding. I >>>> think >>>> this is a great idea and I have created a Doodle poll to help >>>> find a >>>> time when everyone who is interested is available: >>>> >>>> http://www.doodle.com/5mv7m5mmywsv5sxf >>>> >>>> If you would like to participate in this discussion, please fill >>>> out >>>> your availability in that poll (note that time zone support is >>>> enabled, >>>> so you can view the times for your area). After a couple of days >>>> I'll >>>> let everyone know when the call will be, and the number to call. >>>> >>>> Anyone interested in the future of CDAO is welcome to join in. >>>> Let us >>>> know how CDAO in its current form has been useful (or not), and >>>> how it >>>> can be improved for future use-cases. >>>> >>>> Best regards, >>>> Jim >>>> >>>> ____________________________________________ >>>> James P. Balhoff, Ph.D. >>>> National Evolutionary Synthesis Center >>>> 2024 West Main St., Suite A200 >>>> Durham, NC 27705 >>>> USA >>>> >>>> >>>> >>>> >>> >>> >>> >>> -- >>> Dr. Rutger A. Vos >>> School of Biological Sciences >>> Philip Lyle Building, Level 4 >>> University of Reading >>> Reading, RG6 6BX, United Kingdom >>> Tel: +44 (0) 118 378 7535 >>> http://rutgervos.blogspot.com >> >> >> > > > > -- > Dr. Rutger A. Vos > School of Biological Sciences > Philip Lyle Building, Level 4 > University of Reading > Reading, RG6 6BX, United Kingdom > Tel: +44 (0) 118 378 7535 > http://rutgervos.blogspot.com > > ------------------------------------------------------------------------------ > RSA(R) Conference 2012 > Save $700 by Nov 18 > Register now > http://p.sf.net/sfu/rsa-sfdev2dev1 > _______________________________________________ > CDAO-discuss mailing list > CDA...@li... > https://lists.sourceforge.net/lists/listinfo/cdao-discuss -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
From: Hilmar L. <hl...@ne...> - 2011-11-09 16:47:47
|
On Nov 9, 2011, at 10:57 AM, Jim Balhoff wrote: > So can we plan on 11 am Eastern time, Monday, November 21? Works for me. -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org : =========================================================== |
From: Jim B. <ba...@ne...> - 2011-11-09 16:41:03
|
Hi Rutger, On Nov 8, 2011, at 10:38 AM, Rutger Vos wrote: >> I also feel that some of these are not difficult to address - e.g., it is >> not hard to envision new subclasses to provide alternative forms of data >> to be used in the matrix representation. E.g., the matrix representation >> already allows compound characters that can be used to provide a sequence >> as a single entity (instead of breaking it down into smaller characters). >> We also need to remember that an ontology is not a data format (thus >> succinctness is not one criteria to drive its design) - it should provide >> whatever level of detail one desires to annotate any existing source of >> data. > > I certainly agree with your point that an ontology is not a data > format, but verbosity is still an issue: if we transformed all of > TreeBASE's NeXML to CDAO/RDF it would become, to the best of my > knowledge, the biggest public triple store currently in use in the > life sciences (I'm basing this on the presentations of Jerven Bolleman > from UniProt). In other words, it will not scale. Also, we really do > want to be able to find out with a relatively simple SPARQL query > whether a matrix/alignment is DNA, RNA, Protein, or something else > without too many joins and interpretation of the used alphabet. I think this should be straightforward with some subclasses of CharacterStateDataMatrix that have the appropriate restrictions. I agree with Enrico about the importance of annotating data at a given level of detail. It's true that the current, "fully triplified", matrix representation can be quite large as a datastore. But if you think of referencing characters, states, and data cells in a linked data context, you can have URIs which reference any detailed node in a matrix, but actually maps back to some other matrix store implementation (which you probably recognize already). The most fine-grained CDAO content can be used to exchange metadata for given nodes in the matrix graph without instantiating the entire matrix in triples. I am not sure how we could reference all the different pieces of a character matrix with a smaller number of triples, but it would be useful to explore alternatives. Even given that, it seems like it would be useful to include ways to reference compact versions of data elements as suggested by you and Enrico. In your earlier email, you mentioned handling ordering of lists (taxa and characters). I don't think we can use rdf:List within OWL DL - there is an interesting presentation here: http://www.co-ode.org/resources/tutorials/bio/slides/owl-lists29_11_05.ppt We might be best off with simple character numbers rather than maintaining an actual list data structure, which would just add to our verbosity problem. Cheers, Jim ____________________________________________ James P. Balhoff, Ph.D. National Evolutionary Synthesis Center 2024 West Main St., Suite A200 Durham, NC 27705 USA |
From: Jim B. <ba...@ne...> - 2011-11-09 15:58:04
|
It looks like Monday, November 21, is the only day with time slots where only one interested person can't make it - no time works for everyone. So can we plan on 11 am Eastern time, Monday, November 21? Thanks, Jim On Nov 7, 2011, at 11:16 PM, Jim Balhoff wrote: > Hi all, > > Arlin has suggested that we hold a conference call to talk about the future of CDAO, organizing development, and finding funding. I think this is a great idea and I have created a Doodle poll to help find a time when everyone who is interested is available: > > http://www.doodle.com/5mv7m5mmywsv5sxf > > If you would like to participate in this discussion, please fill out your availability in that poll (note that time zone support is enabled, so you can view the times for your area). After a couple of days I'll let everyone know when the call will be, and the number to call. > > Anyone interested in the future of CDAO is welcome to join in. Let us know how CDAO in its current form has been useful (or not), and how it can be improved for future use-cases. > > Best regards, > Jim > > ____________________________________________ > James P. Balhoff, Ph.D. > National Evolutionary Synthesis Center > 2024 West Main St., Suite A200 > Durham, NC 27705 > USA > > > |
From: Rutger V. <R....@re...> - 2011-11-08 15:38:33
|
> I also feel that some of these are not difficult to address - e.g., it is > not hard to envision new subclasses to provide alternative forms of data > to be used in the matrix representation. E.g., the matrix representation > already allows compound characters that can be used to provide a sequence > as a single entity (instead of breaking it down into smaller characters). > We also need to remember that an ontology is not a data format (thus > succinctness is not one criteria to drive its design) - it should provide > whatever level of detail one desires to annotate any existing source of > data. I certainly agree with your point that an ontology is not a data format, but verbosity is still an issue: if we transformed all of TreeBASE's NeXML to CDAO/RDF it would become, to the best of my knowledge, the biggest public triple store currently in use in the life sciences (I'm basing this on the presentations of Jerven Bolleman from UniProt). In other words, it will not scale. Also, we really do want to be able to find out with a relatively simple SPARQL query whether a matrix/alignment is DNA, RNA, Protein, or something else without too many joins and interpretation of the used alphabet. Rutger > On 11/8/11 3:57 AM, "Rutger Vos" <R....@re...> wrote: > >>Hey Jim, >> >>thanks for pushing this. I think it's crucial that CDAO continues to >>be under development. At the BioHackathon in Kyoto I spent my time >>working on improving the NeXML-to-CDAO stylesheet and on querying >>CDAO/RDF graphs to extract known objects (taxa, trees, matrices) out >>of it. >> >>I discovered some inconvenient design decisions in terms of the >>verbosity of the generated RDF and the circumlocution in which certain >>important facts are expressed (e.g.: how do I find out the data type >>of a character state matrix through a SPARQL query? This is >>surprisingly hard to do in CDAO). >> >>I would be happy to share these findings on the call as I feel it is >>important that these issues are addressed in the run up to, or at, the >>HIP meetings. >> >>Best wishes, >> >>Rutger >> >>On Tue, Nov 8, 2011 at 4:16 AM, Jim Balhoff <ba...@ne...> wrote: >>> Hi all, >>> >>> Arlin has suggested that we hold a conference call to talk about the >>>future of CDAO, organizing development, and finding funding. I think >>>this is a great idea and I have created a Doodle poll to help find a >>>time when everyone who is interested is available: >>> >>> http://www.doodle.com/5mv7m5mmywsv5sxf >>> >>> If you would like to participate in this discussion, please fill out >>>your availability in that poll (note that time zone support is enabled, >>>so you can view the times for your area). After a couple of days I'll >>>let everyone know when the call will be, and the number to call. >>> >>> Anyone interested in the future of CDAO is welcome to join in. Let us >>>know how CDAO in its current form has been useful (or not), and how it >>>can be improved for future use-cases. >>> >>> Best regards, >>> Jim >>> >>> ____________________________________________ >>> James P. Balhoff, Ph.D. >>> National Evolutionary Synthesis Center >>> 2024 West Main St., Suite A200 >>> Durham, NC 27705 >>> USA >>> >>> >>> >>> >> >> >> >>-- >>Dr. Rutger A. Vos >>School of Biological Sciences >>Philip Lyle Building, Level 4 >>University of Reading >>Reading, RG6 6BX, United Kingdom >>Tel: +44 (0) 118 378 7535 >>http://rutgervos.blogspot.com > > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading, RG6 6BX, United Kingdom Tel: +44 (0) 118 378 7535 http://rutgervos.blogspot.com |
From: Enrico P. <epo...@cs...> - 2011-11-08 15:27:27
|
I do agree with some of the points that Rutger raises, and I am glad to see the discussion starting. I also feel that some of these are not difficult to address - e.g., it is not hard to envision new subclasses to provide alternative forms of data to be used in the matrix representation. E.g., the matrix representation already allows compound characters that can be used to provide a sequence as a single entity (instead of breaking it down into smaller characters). We also need to remember that an ontology is not a data format (thus succinctness is not one criteria to drive its design) - it should provide whatever level of detail one desires to annotate any existing source of data. I'm happy to see this discussion moving forward and I am looking forward a conversation with everyone interested in pushing CDAO forward. Enrico -- Dept. Computer Science, New Mexico State University MSC CS, Box 30001, Las Cruces, NM 88003 Voice: 575-646-6239 Fax: 575-646-1002 On 11/8/11 3:57 AM, "Rutger Vos" <R....@re...> wrote: >Hey Jim, > >thanks for pushing this. I think it's crucial that CDAO continues to >be under development. At the BioHackathon in Kyoto I spent my time >working on improving the NeXML-to-CDAO stylesheet and on querying >CDAO/RDF graphs to extract known objects (taxa, trees, matrices) out >of it. > >I discovered some inconvenient design decisions in terms of the >verbosity of the generated RDF and the circumlocution in which certain >important facts are expressed (e.g.: how do I find out the data type >of a character state matrix through a SPARQL query? This is >surprisingly hard to do in CDAO). > >I would be happy to share these findings on the call as I feel it is >important that these issues are addressed in the run up to, or at, the >HIP meetings. > >Best wishes, > >Rutger > >On Tue, Nov 8, 2011 at 4:16 AM, Jim Balhoff <ba...@ne...> wrote: >> Hi all, >> >> Arlin has suggested that we hold a conference call to talk about the >>future of CDAO, organizing development, and finding funding. I think >>this is a great idea and I have created a Doodle poll to help find a >>time when everyone who is interested is available: >> >> http://www.doodle.com/5mv7m5mmywsv5sxf >> >> If you would like to participate in this discussion, please fill out >>your availability in that poll (note that time zone support is enabled, >>so you can view the times for your area). After a couple of days I'll >>let everyone know when the call will be, and the number to call. >> >> Anyone interested in the future of CDAO is welcome to join in. Let us >>know how CDAO in its current form has been useful (or not), and how it >>can be improved for future use-cases. >> >> Best regards, >> Jim >> >> ____________________________________________ >> James P. Balhoff, Ph.D. >> National Evolutionary Synthesis Center >> 2024 West Main St., Suite A200 >> Durham, NC 27705 >> USA >> >> >> >> > > > >-- >Dr. Rutger A. Vos >School of Biological Sciences >Philip Lyle Building, Level 4 >University of Reading >Reading, RG6 6BX, United Kingdom >Tel: +44 (0) 118 378 7535 >http://rutgervos.blogspot.com |
From: Rutger V. <R....@re...> - 2011-11-08 10:57:39
|
Hey Jim, thanks for pushing this. I think it's crucial that CDAO continues to be under development. At the BioHackathon in Kyoto I spent my time working on improving the NeXML-to-CDAO stylesheet and on querying CDAO/RDF graphs to extract known objects (taxa, trees, matrices) out of it. I discovered some inconvenient design decisions in terms of the verbosity of the generated RDF and the circumlocution in which certain important facts are expressed (e.g.: how do I find out the data type of a character state matrix through a SPARQL query? This is surprisingly hard to do in CDAO). I would be happy to share these findings on the call as I feel it is important that these issues are addressed in the run up to, or at, the HIP meetings. Best wishes, Rutger On Tue, Nov 8, 2011 at 4:16 AM, Jim Balhoff <ba...@ne...> wrote: > Hi all, > > Arlin has suggested that we hold a conference call to talk about the future of CDAO, organizing development, and finding funding. I think this is a great idea and I have created a Doodle poll to help find a time when everyone who is interested is available: > > http://www.doodle.com/5mv7m5mmywsv5sxf > > If you would like to participate in this discussion, please fill out your availability in that poll (note that time zone support is enabled, so you can view the times for your area). After a couple of days I'll let everyone know when the call will be, and the number to call. > > Anyone interested in the future of CDAO is welcome to join in. Let us know how CDAO in its current form has been useful (or not), and how it can be improved for future use-cases. > > Best regards, > Jim > > ____________________________________________ > James P. Balhoff, Ph.D. > National Evolutionary Synthesis Center > 2024 West Main St., Suite A200 > Durham, NC 27705 > USA > > > > -- Dr. Rutger A. Vos School of Biological Sciences Philip Lyle Building, Level 4 University of Reading Reading, RG6 6BX, United Kingdom Tel: +44 (0) 118 378 7535 http://rutgervos.blogspot.com |
From: Jim B. <ba...@ne...> - 2011-11-08 04:17:03
|
Hi all, Arlin has suggested that we hold a conference call to talk about the future of CDAO, organizing development, and finding funding. I think this is a great idea and I have created a Doodle poll to help find a time when everyone who is interested is available: http://www.doodle.com/5mv7m5mmywsv5sxf If you would like to participate in this discussion, please fill out your availability in that poll (note that time zone support is enabled, so you can view the times for your area). After a couple of days I'll let everyone know when the call will be, and the number to call. Anyone interested in the future of CDAO is welcome to join in. Let us know how CDAO in its current form has been useful (or not), and how it can be improved for future use-cases. Best regards, Jim ____________________________________________ James P. Balhoff, Ph.D. National Evolutionary Synthesis Center 2024 West Main St., Suite A200 Durham, NC 27705 USA |