August 2007 - tdwg-content

[Biogeosdi] generic query tool
by Meganck Bart 28 Aug '07

28 Aug '07

Hi all, I've been working on SYNTHESYS NA-D 1.6 for some time, and this has produced a tool that I think could be of some use in a general TDWG/Gbif context. It's a small (medium) PHP program meant for integration in workflows such as the one we've done in Campinas : querying servers, combining data and displaying them on maps... There is no graphical front-end, the tool is meant for developers. You communicate with it via HTTP GET parameters, and you get result back in a TAPIR-like response XML (though I'm not sure it would pass Renato's close scrutiny ;) What is does is get info about, and query, any server that talks in either the BioCase, DiGIR or TAPIR protocol. In the current version, this means : * you can ask info for any server, and you'll get the server type, some other metadata, and the specific data for the different protocols (e.g. the possible resources for diGIR servers). * you can search any BioCase, DiGIR or TAPIR server for the scientific names of specimens. For the moment, only one "version" of each protocol is implemented, and no other fields than scientific name can be searched. But more of this should be not too difficult to implement in further versions. The tool is meant to be simple, meaning that for most parameters default values are used, and that it's functionality is -at the moment- quite limited. But it should be good at what is does, and is designed to be as programmer-friendly as possible, with extensive documentation, useful error messages, and plenty of debugging info. You'll find the tool on : http://synthesys.africamuseum.be/GQT.html Here you can download the PHP code (e.g. for a local install), which includes some examples as well. Or try the online version at http://synthesys.africamuseum.be/GQT/generic.php, for example with : http://synthesys.africamuseum.be/GQT/generic.php?op=help (help function, overview of parameters) http://synthesys.africamuseum.be/GQT/generic.php?op=info &endpoint=http://193.190.223.48/biocase/pywrapper.cgi?dsa=RMCA_Amphibians (info about our biocase server) http://synthesys.africamuseum.be/GQT/generic.php?op=search &endpoint=http://193.190.223.48/biocase/pywrapper.cgi?dsa=RMCA_Amphibians &filter=A (&timeout=5) (&count=true) (search (count) our biocase server for names starting with A) http://synthesys.africamuseum.be/GQT/generic.php?op=search &endpoint=http://digir.austmus.gov.au:80/ozcam/DiGIR.php &filter=Fel &count=false ( search (full) the DiGIR server for names starting with "Fel" ) Any comments are welcome, though I will not be in office next week (holiday(a)belgian.coast) to respond immediately. best regards, Bart. -- Bart Meganck, ICT & GIS engineer, African Zoology Department. Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium. Tel : +32(0)2 769 56 92 Fax : +32(0)2 767 02 42 Email : bart.meganck(a)africamuseum.be Website : www.africamuseum.be

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[tdwg-lit] TDWG Lit interest group revitalisation!
by Weitzman, Anna 16 Aug '07

16 Aug '07

Hi all, I am sending this to everyone who has signed up for the list and to a few people who have expressed continued interest, but who have not yet signed up. If you wish to join this list, please do so at: http://lists.tdwg.org/mailman/listinfo/tdwg-lit. First, the Lit group charter is under review. I presume that it will be approved before the upcoming TDWG meeting in Bratislava. Second, I want to let you know that we have scheduled (I apologize for the short notice) a 'formal' Lit interest group meeting on Sunday, 16 September 2007 from 2:30-5:00 pm in Bratislava (prior to the TDWG meeting which starts the following morning and before the opening reception). For those of you who cannot attend the meeting, I'll send out minutes (or at least a summary after the TDWG meeting). Third, and most importantly, I have been receiving some pressure from the TDWG TIP program to apply for funds for a workshop to bring as many of us together as possible so we can quickly 'knock out' version one of a standard ASAP (by the end of 2007???). There was not time to pull this together at the time of the TDWG meeting, so I have been thinking about potentials for this and the best I can think of is 2-3 days in mid-November (the week of 12 November). Please let me know if that time is possible for you. Once I get an idea of who might be able to come (and the geographic distribution of those able to do so), I will figure out the most cost-effective location and put in a proposal for funds. I look forward to seeing as many of you as possible in Bratislava and at the workshop! Regards, Anna Anna L. Weitzman, PhD Editor, TDWG Proceedings Botanical and Biodiversity Informatics Research National Museum of Natural History Smithsonian Institution office: 202.633.0846 mobile: 202.415.4684 weitzman(a)si.edu

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[tdwg-obs] Observation Associations Controlled Vocabulary
by Kevin Richards 13 Aug '07

13 Aug '07

Hi all I apologise for any cross postings, and Im not sure Ive even got the right mailing lists here. I am trying to get hold of a controlled vocabularly / list of terms that define associations between organisms with respect to observations or specimens. For example parasites, hosts etc - eg to specify that a specimen/observation was found living on another specimen (host). I need this for the specimens RDF/LSID presentation I am giving at TDWG this year. Any help would be appreciated. Thanks Kevin Richards ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ WARNING: This email and any attachments may be confidential and/or privileged. They are intended for the addressee only and are not to be read, used, copied or disseminated by anyone receiving them in error. If you are not the intended recipient, please notify the sender by return email and delete this message and any attachments. The views expressed in this email are those of the sender and do not necessarily reflect the official views of Landcare Research. Landcare Research http://www.landcareresearch.co.nz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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[Biogeosdi] Good reading, someone wants to write an article?
by Javier de la Torre 08 Aug '07

08 Aug '07

Hi all, Some of you might now already this article about the use of GBIF data for developing biodiversity change indicators. Its lecture will probably not provide much more info of what you know already, it has been written by A. T. Peterson and J. Soberon so you know what their ideas are. I just thought it is a good base for our biogeosdi experiment. If you take a look at their proposed approach we have already fulfilled some of the steps. I think that taking this article as a base and talk about what we have done will probably create a nice article we could publish somewhere... anybody interested in doing this? Is there anybody interested in gaining publications? Cheers. >>> >>> >>

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[Biogeosdi] News item at TDWG site
by Javier de la Torre 08 Aug '07

08 Aug '07

Hey people! We got a news item at the TDWG site :) Check it out at: http://www.tdwg.org/homepage-news-item/article/geointeroperability- workshop-outcomes/ Cheers.

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[Biogeosdi] Re: TDWG presentation
by Meganck Bart 03 Aug '07

03 Aug '07

Hi Javier, Yes we had a cool headline on the TDWG site... ;-) It's a good thing that you'll be presenting our work at the TDWG : there was much interesting stuff in there, an I think there's lots of opportunities for follow-up work. You were asking for telephone support, but I couldn't find out clearly when you were giving your talk. Patricia Mergen and Franck Theeten from RMCA will be attending TDWG for the RMCA. best regards, Bart. On Thu, 2007-08-02 at 18:12 +0200, biogeosdi-request(a)lists.tdwg.org wrote: > Send biogeosdi mailing list submissions to > biogeosdi(a)lists.tdwg.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.tdwg.org/mailman/listinfo/biogeosdi > or, via email, send a message with subject or body 'help' to > biogeosdi-request(a)lists.tdwg.org > > You can reach the person managing the list at > biogeosdi-owner(a)lists.tdwg.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of biogeosdi digest..." > > > Today's Topics: > > 1. News item at TDWG site (Javier de la Torre) > 2. Abstract for TDWG 2007 (Javier de la Torre) > 3. Here goes the abstract submission (Javier de la Torre) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 2 Aug 2007 13:16:31 +0200 > From: Javier de la Torre <jatorre(a)gmail.com> > Subject: [Biogeosdi] News item at TDWG site > To: biogeosdi(a)lists.tdwg.org > Message-ID: <132BE569-4300-4590-9647-454D4F4AFBF2(a)gmail.com> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Hey people! > > We got a news item at the TDWG site :) Check it out at: > > http://www.tdwg.org/homepage-news-item/article/geointeroperability- > workshop-outcomes/ > > Cheers. > > > ------------------------------ > > Message: 2 > Date: Thu, 2 Aug 2007 17:36:06 +0200 > From: Javier de la Torre <jatorre(a)gmail.com> > Subject: [Biogeosdi] Abstract for TDWG 2007 > To: biogeosdi(a)lists.tdwg.org > Message-ID: <5E64E7DF-9F50-47D5-8211-3419630E0D6B(a)gmail.com> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Hi all, > > As you know I will attend TDWG 2007 and from the lasts messages I > received seems that I am the only one attending. Therefore I take the > liberty to send an abstract about the workshop we had with all the > participants as co-authors. I am mainly taking the abstract from the > report and briefly reformulating it for a talk. My first idea was to > present this at Renato's session on "integrating biodiversity data" > on Thursday 20th, but due to some things going on I might move it to > the spatial Model session on Wednesday (Renato I will keep you updated). > > My idea at the presentation is just to demonstrate the prototype and > highlight some of the issues we had with it. More or less what I did > at OGC but without explaining what a plant is ,like I did there :D > > I am asking for teleconference facilities to see if some of you can > at least join me remotely for questions or comments. Is there anybody > avaialble at least for telephone call then? > > Hopefully during next week I can work with Tim to set the whole code > in TDWG server and we can have it finally host it somewhere > permanently. If not and if someone is interested we have it working > in a Parallels image that you can run in a mac (and maybe somewhere > else Tim?) > > Cheers and see you all soon. > > Javi. > > > > > > > > > ------------------------------ > > Message: 3 > Date: Thu, 2 Aug 2007 18:12:42 +0200 > From: Javier de la Torre <jatorre(a)gmail.com> > Subject: [Biogeosdi] Here goes the abstract submission > To: biogeosdi(a)lists.tdwg.org > Message-ID: <E84BFEEE-234C-4F47-97A4-79AF104A5F8C(a)gmail.com> > Content-Type: text/plain; charset="us-ascii" > > Just in case someone is interested here it goes the submission i just > have made. > > Cheers. > > Javi. >

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[Biogeosdi] Here goes the abstract submission
by Javier de la Torre 02 Aug '07

02 Aug '07

Just in case someone is interested here it goes the submission i just have made. Cheers. Javi.

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[Biogeosdi] Abstract for TDWG 2007
by Javier de la Torre 02 Aug '07

02 Aug '07

Hi all, As you know I will attend TDWG 2007 and from the lasts messages I received seems that I am the only one attending. Therefore I take the liberty to send an abstract about the workshop we had with all the participants as co-authors. I am mainly taking the abstract from the report and briefly reformulating it for a talk. My first idea was to present this at Renato's session on "integrating biodiversity data" on Thursday 20th, but due to some things going on I might move it to the spatial Model session on Wednesday (Renato I will keep you updated). My idea at the presentation is just to demonstrate the prototype and highlight some of the issues we had with it. More or less what I did at OGC but without explaining what a plant is ,like I did there :D I am asking for teleconference facilities to see if some of you can at least join me remotely for questions or comments. Is there anybody avaialble at least for telephone call then? Hopefully during next week I can work with Tim to set the whole code in TDWG server and we can have it finally host it somewhere permanently. If not and if someone is interested we have it working in a Parallels image that you can run in a mac (and maybe somewhere else Tim?) Cheers and see you all soon. Javi.

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[tdwg-ncd] French metadata interfaces based on the NCD
by Neil Thomson 02 Aug '07

02 Aug '07

Forwarded on behalf on Patricia Kelbert ... -----Original Message----- From: kelbert(a)bohm.snv.jussieu.fr [mailto:kelbert@bohm.snv.jussieu.fr] Sent: 02 August 2007 12:43 To: tdwg-ncd(a)lists.tdwg.org Cc: gbif-fr(a)gbif.fr Subject: [tdwg-ncd] French metadata interfaces based on the NCD As we announced it in january, the french GBIF node developed its own interface for metadata, based on the NCD schema. We made an new interface in PHP for adding metadata, and adapted the Synthesys Web Portal for browsing and updating the data (Python). We started to develop the interfaces in february-march, thus "our" NCD version might not fit to the current version; we added some fields too. You can have a look at the interface (only in french, sorry) : http://www.gbif.fr/?q=fr/node/97 and the portal (still in development and in french) : http://lis-02.snv.jussieu.fr/portail/ Hope it can be useful. Selon lancelot(a)bohm.snv.jussieu.fr: > > > >>>I am pleased to say the the French GBIF node have expressed an early > >>> interest > >>> in making use of the toolkit and have joined this mailing list so > >>> that they > >>> can participate in the discussions - welcome Gaël Lancelot. > >>> > >> > Thank you very much for your warm welcome. I would like, however, to point > out > that I'm not alone in the French GBIF team. In fact, I'm quite certain that > most of the contributions on this list will come from my colleagues, Adil El > Filali and Patricia Kelbert, who have vastly superior computer know-how to > mine. > > This being said, the French node is indeed looking at using NCD for its > metadata > gathering campaign. Due to our timekeeping constraints, we cannot afford to > wait for the NCD toolkit, useful as it would be, and we might well develop > our > NCD tools (database, interface) in parallel to the work done in Amsterdam. > Of > course, we'd be glad to share these developments with the list, in case it > might be of any help. > > Thanks a lot for your support and your work, > > Gaël Lancelot > Scientific Resource Management > GBIF France > 12, rue Cuvier > 75005 PARIS > FRANCE > _______________________________________________ > tdwg-ncd mailing list > tdwg-ncd(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-ncd > >

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[Biogeosdi] Re: path kludge
by Meganck Bart 02 Aug '07

02 Aug '07

Hi Pete, Well, it certainly is a bit more elegant than Dave's string & duct tape solution - still, it worked fine, though. Hope you got through the worst of the red tape by now, and starting to get settled. How is the US in comprison with the UK ? best regards, Bart. On Wed, 2007-08-01 at 12:00 +0200, biogeosdi-request(a)lists.tdwg.org wrote: -- Bart Meganck, ICT & GIS engineer, African Zoology Department. Royal Museum for Central Africa, Leuvensesteenweg 13, B-3080 Tervuren, Belgium. Tel : +32(0)2 769 56 92 Fax : +32(0)2 767 02 42 Email : bart.meganck(a)africamuseum.be Website : www.africamuseum.be ########################################### This message has been scanned by ICT - Africa Museum ________________________________________ 2/8/2007 - Filtered through antispam by ICT

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