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[Biogeosdi] report
by Javier de la Torre 05 Jul '07

05 Jul '07

this is how it looks like... in PDF and in HTML check it on subversion... (HTML looks nicer)

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[tdwg-ncd] NCD Workshop report and deliverables
by Neil Thomson 05 Jul '07

05 Jul '07

Dear NCD'ers, The meeting report from the NCD 2007 Workshop is available, along with other workshop deliverables, on the NCD wiki. Please take a look at: http://wiki.tdwg.org/twiki/bin/view/NCD/NCDWorkShop and let me know if any changes are required, With thanks, Neil ------- Neil Thomson Head of Data & Digital Systems The Natural History Museum, Cromwell Road, London SW7 5BD Tel: +44 (0)20 7942 5294, Fax: +44 (0)20 7942 5559, Email: n.thomson(a)nhm.ac.uk http://www.nhm.ac.uk

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[Biogeosdi] Re: biogeosdi Digest, Vol 8, Issue 4
by Meganck Bart 05 Jul '07

05 Jul '07

Hi Javier, It has become a neat report ! The text seems ok, I had nothing really to add - I only put the definitions and links for PHP and SPICE in the Terms Definition part. best regards, Bart. On Thu, 2007-07-05 at 07:51 +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. Hey guys, last chance to touch the report... (Javier de la Torre) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 5 Jul 2007 07:51:09 +0200 > From: Javier de la Torre <jatorre(a)gmail.com> > Subject: [Biogeosdi] Hey guys, last chance to touch the report... > To: biogeosdi(a)lists.tdwg.org, Lee Belbin <leebel(a)netspace.net.au> > Message-ID: <FA773FD2-C4BE-48A1-8824-F273370F79DE(a)gmail.com> > Content-Type: text/plain; charset="us-ascii" > > Hey guys, > > Here I send you the latest version of the report with serious > editings and adapted for the txt2tags that we agree on use. I have > produced the PDF and HTML and everything is in subversion. > > Please edit as soon as possible as I plan to start circulating this > now now!! > > Javi. > > >

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RE: [tdwg-spm] SPM session at TDWG Conference
by Eamonn O Tuama 03 Jul '07

03 Jul '07

Thanks, Bob. I think this could be very informative in helping people get to grips with RDf and SPM. I'll add you to the list. Best regards, Éamonn -----Original Message----- From: Bob Morris [mailto:morris.bob@gmail.com] Sent: 03 July 2007 18:05 To: Eamonn O Tuama Cc: tdwg-spm(a)lists.tdwg.org Subject: Re: [tdwg-spm] SPM session at TDWG Conference I can give a little demo of how Protege and Altova SemanticWorks can help one come to terms (pun intended) with SPM. An abstract might be something like this: ---- Coming to Terms with SPM/RDF. Although the ultimate point is to generate SPM programmatically, the use of tools like Protege and Altova SemanticWorks can ease the learning burden, and of course serve as a debugging aid, if properly configured. I will discuss, with demonstration, how I used these tools to come to terms with SPM. ---- Actually, someone should probably give a survey of tools at least by name and function, and it should be on the wiki in advance. But a stroll through Protege and SemanticWorks after such a talk would warrant 15 minutes, I think. Bob On 7/3/07, Eamonn O Tuama <eotuama(a)gbif.org> wrote: > > Hello there, > > As you probably know, TDWG are devoting a special session to the Species > Profile Model at the upcoming Bratislava conference. It is scheduled for > 08.30 to 10.00 on Wed 19 Sept and we hope to fill the slot with up to six > short (10-15 min) presentations. Marcus has already agreed to talk about the > modelling aspects of SPM on which he has been working (see the wiki for > more info: http://wiki.tdwg.org/twiki/bin/view/SPM/InstanceExamples). > > You are invited to make suggestions for contributions to this session. Any > aspect can be considered - vocabularies, use cases, relationship to other > species profile schemas, etc. Or do you know of a potential contribution > from another TDWG member outside this immediate subtask group? I intend to > mail a request for contributions to the wider TDWG community later in the > week but, in the meantime, would welcome your input. > > Best regards, > > Éamonn > ________________________________________________________________ > Éamonn Ó Tuama, Ph.D. (eotuama(a)gbif.org), > Senior Programme Officer for Data Access & Database Interoperability (DADI), > Global Biodiversity Information Facility Secretariat, > Universitetsparken 15, DK-2100 Copenhagen Ø, DENMARK > Phone: +45 3532 1494; Fax: +45 3532 1480 > > _______________________________________________ > tdwg-spm mailing list > tdwg-spm(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-spm > -- Robert A. Morris Professor of Computer Science UMASS-Boston ram(a)cs.umb.edu http://www.cs.umb.edu/bdei http://www.cs.umb.edu/~ram http://www.cs.umb.edu/~ram/calendar.html phone (+1)617 287 6466

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[Biogeosdi] Fwd: Auto-discard notification
by Javier de la Torre 03 Jul '07

03 Jul '07

> > > Hey guys, > > I do not have ssh access to anythign from my hotel here so i cant > update the omtest server... if so one can try... > > cheers. > > Javier de la Torre > IMASTE-IPS > Dtor. Tecnología > Tel: 91 536 05 03 > Mov: 629 69 38 70 > skype:jatorre555 > jatorre(a)imaste-ips.com > >

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[Biogeosdi] Re: biogeosdi Digest, Vol 7, Issue 4
by Meganck Bart 03 Jul '07

03 Jul '07

Hi Javier, Yes, I totally agree that we should finish this noble task of saving the world... For a title, how about : "How to save the world with standards and coconuts" "90 coconuts can't be mad" "OGC : Open Geospatial Coconuts ? " I've taken a look at the report text again, and made some small changes (mostly in style and typos) - but I think the text is quite good now as it is, and I especially liked the addition of a bit more text on the workings of the "backend" : it made things clearer for me (though I do not know who put it there). As for the demo, I see two big things that are still missing : 1/ the maps shown in the GUI are just GBIF demo maps, not the WMS maps provided by our own work : this is actually something that I should implement (mea maxima culpa). 2/ we had the last step (the modelling returning a WMS (WCS?) layer and displaying it working in Campinas, but in the online demo this doesn't work. That's a pity, because you always have to break off the demonstration there, and ask people to believe that it was actually working (and tough audiences going "yeah, right !"). Could we perhaps insert some sort of mock-up there ? Or would it be possible to get it working again (would be fantastic) ? best regards to all, I hope that some day we'll meet up and work together again - and have a coconut, aahhh ! Bart. On Mon, 2007-06-25 at 01:27 +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. Long time ago... (Javier de la Torre) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 25 Jun 2007 01:27:20 +0200 > From: Javier de la Torre <jatorre(a)gmail.com> > Subject: [Biogeosdi] Long time ago... > To: biogeosdi(a)lists.tdwg.org > Message-ID: <2C324760-7B1C-41DC-9B26-85F38D4F4ABB(a)gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hey people!! > > Long time ago there was a meeting in Campinas... 6 incredible person > met there to create an amazing prototype that would save the world... > but they forgot to finish the documentation!! > > What a pity, the world would have been a much better place.... > > > We can be different! We still have the opportunity to save the world > if we finish the report from our last meeting! > > I have edited several parts of the document and sent it to Lee to ask > him for comments. He is very happy with the status of the report, but > I have to say I would still edit a little bit more... in any case I > think we can start a fast process... let say we put the document > under ask for comments until wednesday, if no one complain before I > will send it then. > > If someone, for any reason, does not have access to the document on > the SVN server > > Lee also asked me to present the report and the prototype on the next > OGC meeting in Paris, the 12th of June. Flip will give us 20min and 5 > more for questions... > I hope everybody is fine with me going there. This is part of the > TDWG-OGC MoU, we have to demonstrate that we take them seriously. > > I will be on holidays from the 28th til the 8th of July. I will > travel to the states for a friends wedding in Kentucky. If things get > crazy I might finish getting marriage in Las Vegas as Elvis Presley, > but if not I will probably fly then directly tom Paris. My trip is NY- > Chicago-Kentucky if someone is on the road those days. > > So... I did it again... I will use my holidays to work on the > presentation and on the prototype. Ideally I will present a finish > prototype on HTML and Flex, with the design that the designer did > here and with Yahoo maps integration. Of course also with a nice > presentation, not a boring one, and with lot of preparation. But > somewhere between this ideal situation and a total disaster I will > finish, if someone want to help please go ahead!! First thing I need > to have is a title for the presentation. I have some ideas but more > are welcome: > > -90 coconuts and an old Dell laptop to save biodiversity using > geospatial standards. > -Demonstration on how tropical weather influence programming > productivity and happiness... using OGC standards! > -OGC is not enough > -Biodioversity 2.0 > > And some more classical, and more probable like: > -OGC standards and biodiversity: the biogeosdi experiment. > > > Javier de la Torre > IMASTE-IPS > Dtor. Tecnologa > Tel: 91 536 05 03 > Mov: 629 69 38 70 > skype:jatorre555 > jatorre(a)imaste-ips.com > > > >

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[tdwg-spm] SPM session at TDWG Conference
by Eamonn O Tuama 03 Jul '07

03 Jul '07

Hello there, As you probably know, TDWG are devoting a special session to the Species Profile Model at the upcoming Bratislava conference. It is scheduled for 08.30 to 10.00 on Wed 19 Sept and we hope to fill the slot with up to six short (10-15 min) presentations. Marcus has already agreed to talk about the modelling aspects of SPM on which he has been working (see the wiki for more info: http://wiki.tdwg.org/twiki/bin/view/SPM/InstanceExamples). You are invited to make suggestions for contributions to this session. Any aspect can be considered - vocabularies, use cases, relationship to other species profile schemas, etc. Or do you know of a potential contribution from another TDWG member outside this immediate subtask group? I intend to mail a request for contributions to the wider TDWG community later in the week but, in the meantime, would welcome your input. Best regards, Éamonn ________________________________________________________________ Éamonn Ó Tuama, Ph.D. (eotuama(a)gbif.org), Senior Programme Officer for Data Access & Database Interoperability (DADI), Global Biodiversity Information Facility Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, DENMARK Phone: +45 3532 1494; Fax: +45 3532 1480

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[Biogeosdi] GBIF REST services
by Javier de la Torre 28 Jun '07

28 Jun '07

Hey guys, Seems that the GBIF REST services have changed since we coded... the GbifOccurrenceSax.php class that Dave programmed is hadling manually namespaces expecting things like "dwc:ScientificName". In the response from the REST services now you will get things like "<tn:nameComplete>" so... Another change on the format that the data is comming and another crash on the application... What do you think? Should we update this to the new format? or we make a note on the report and explain that because people keep changing the XML format they are using behind their services, without changing the semantics, it is a pain for applications? Aghh. There should be like in Google Maps a parameter specifying which version you wanna have returned to keep things stable. In any case I could not resist and updated the GbifOccurrenceSax class to use the new format.... Still there is no way to tell GBIF only to return occurrences with coordinates. I will ask Donald. Cheers. Javier.

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[Biogeosdi] Who is working on the code?
by Javier de la Torre 28 Jun '07

28 Jun '07

Hey guys, While editing the code to improve a little bit the documentation I am more and more realizing that there has been some work on it after the workshop. I see ocurrencesModel now have methids to serialize to RSS and things like that... Who is working on this? For what purpose? Just for curiosity! Thanks Javier.

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Fwd: [Biogeosdi] Re: Search on the GBIF REST services
by Javier de la Torre 27 Jun '07

27 Jun '07

Here is a comment from Donald, I have to say I have no idea why this statement is on the report... was like this in the previous too no? Cheers. Begin forwarded message: > From: Donald Hobern <dhobern(a)gbif.org> > Date: 27 de junio de 2007 12:17:27 GMT+02:00 > To: Javier de la Torre <jatorre(a)gmail.com> > Subject: Re: [Biogeosdi] Re: Search on the GBIF REST services > > Thanks, Javier. > > I'll take a look. By the way, the report says: > > */ GBIF data does not reference the original data providers > > Are you having a problem with this? Every occurrence record (and > every taxon concept) is nested within a DataResource metadata > block, which is itself nested within a DataProvider block. For > each you can use the appropriate web service (with the supplied key > values) to retrieve full information (including access points for > DataResources). > > If you need help, please let me know. > > Many thanks, > > Donald > > Javier de la Torre wrote: >> jaja. >> >> Well, >> >> Let me send you the report as it is today. The doxygen still looks >> very bad, maybe is easier for you to just try the service >> interface we have for the code: >> >> http://omtest.cria.org.br/biogeosdi/backend/libs/amfphp/browser/ >> >> The doxygen is here (we are working to clean it): >> >> http://omtest.cria.org.br/biogeosdi/doc/html/ >> >> The two prototypes themselves can be found at: >> >> http://omtest.cria.org.br/biogeosdi/doc/html/ >> >> >> Have fun. >> >> Javier. >> >> >> >> >> On 27/06/2007, at 10:36, Donald Hobern wrote: >> >> >> >>> Do you have any current presentation/document outlining what you >>> are doing in BioGeoSDI? A web search tells me that you have >>> exceptionally well commented code... >>> >>> >>> >>> Donald >>> >>> >>> >>> Javier de la Torre wrote: >>> >>>> Buff... that is more than enough!! >>>> >>>> I suppose you also drop latitude=longitude=0 right? >>>> >>>> >>>> >>>> I think we have to change our report on this topic jeje. >>>> >>>> >>>> >>>> Cheers. >>>> >>>> >>>> >>>> On 26/06/2007, at 22:13, Donald Hobern wrote: >>>> >>>> >>>> >>>>> Right now the dodginess is only detected for records where we >>>>> interpret the Country name as a particular country and also >>>>> have coordinates and the coordinates do not intersect the >>>>> country. In many cases we actually also determine that the >>>>> latitude is negated, the longitude is negated and/or the >>>>> latitude and longitude are transposed. >>>>> >>>>> >>>>> >>>>> Donald >>>>> >>>>> >>>>> >>>>> Tim Sutton wrote: >>>>> >>>>>> Hi >>>>>> >>>>>> >>>>>> >>>>>> Great stuff that we can now exclude dodgy / non existant >>>>>> occurrences - >>>>>> >>>>>> we could probably make th e second (coordinate issues) option >>>>>> user >>>>>> >>>>>> settable (or at the least a setting in our global config file). >>>>>> >>>>>> >>>>>> >>>>>> Regards >>>>>> >>>>>> >>>>>> >>>>>> Tim >>>>>> >>>>>> >>>>>> >>>>>> 2007/6/26, Javier de la Torre <jatorre(a)gmail.com>: >>>>>> >>>>>>> Great, >>>>>>> >>>>>>> >>>>>>> >>>>>>> I will then uncomment the code :) >>>>>>> >>>>>>> >>>>>>> >>>>>>> Javier. >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 26/06/2007, at 17:24, Donald Hobern wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> > Thanks, Javier - found the problem - will get the fix deployed >>>>>>> >>>>>>> > tomorrow. >>>>>>> >>>>>>> > >>>>>>> >>>>>>> > Best wishes, >>>>>>> >>>>>>> > >>>>>>> >>>>>>> > Donald >>>>>>> >>>>>>> > >>>>>>> >>>>>>> > Javier de la Torre wrote: >>>>>>> >>>>>>> >> Great Donald, >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> We have now some comments to remove on the report about >>>>>>> the GBIF >>>>>>> >>>>>>> >> REST service ;) >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> Still I have an issue when using the &coordinateissues=false >>>>>>> >>>>>>> >> parameter >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> This URL returns 195 records: >>>>>>> >>>>>>> >> http://data.gbif.org/ws/rest/occurrence/list? >>>>>>> >>>>>>> >> format=brief&scientificname=Puma+concolor >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> This one none: >>>>>>> >>>>>>> >> http://data.gbif.org/ws/rest/occurrence/list? >>>>>>> >>>>>>> >> format=brief&coordinateissues=false&scientificname=Puma >>>>>>> +concolor >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> And I suppose not all coordinates are wrong no? >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> Cheers. >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> On 26/06/2007, at 14:29, Donald Hobern wrote: >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >>> Dear Javier, >>>>>>> >>>>>>> >>> >>>>>>> >>>>>>> >>> The structures are now stable. Sorry not to have copied >>>>>>> you on >>>>>>> >>>>>>> >>> my emails on what was changing. Adding >>>>>>> "&coordinatestatus=true" >>>>>>> >>>>>>> >>> should limit responses to those with coordinates. You >>>>>>> can also >>>>>>> >>>>>>> >>> use "&coordinateissues=false" to exclude records where we >>>>>>> have >>>>>>> >>>>>>> >>> detected that the coordinates do not match the supplied >>>>>>> country >>>>>>> >>>>>>> >>> name. >>>>>>> >>>>>>> >>> >>>>>>> >>>>>>> >>> Donald >>>>>>> >>>>>>> >>> >>>>>>> >>>>>>> >>> Javier de la Torre wrote: >>>>>>> >>>>>>> >>>> Hey Donald, >>>>>>> >>>>>>> >>>> >>>>>>> >>>>>>> >>>> I am fixing some stuff on the prototype we did in Brasil >>>>>>> and I >>>>>>> >>>>>>> >>>> had to change my code to reflect the new format that the >>>>>>> rest >>>>>>> >>>>>>> >>>> services are sending now. Is this more or less stable now? >>>>>>> >>>>>>> >>>> >>>>>>> >>>>>>> >>>> And another question, would be possible to ask the >>>>>>> service to >>>>>>> >>>>>>> >>>> return only occurrences with coordinates. For us is not >>>>>>> of much >>>>>>> >>>>>>> >>>> use occurrences without coordinates. >>>>>>> >>>>>>> >>>> >>>>>>> >>>>>>> >>>> Thats the query I am trying >>>>>>> >>>>>>> >>>> >>>>>>> >>>>>>> >>>> http://newportal.gbif.org/ws/rest/occurrence/list? >>>>>>> >>>>>>> >>>> >>>>>>> format=brief&minLatitude=-90&maxLatitude=90&scientificname=Puma >>>>>>> >>>>>>> >>>> +concolor >>>>>>> >>>>>>> >>>> >>>>>>> >>>>>>> >>>> Thanks in advance. >>>>>>> >>>>>>> >>>> >>>>>>> >>>>>>> >>>> Javier. >>>>>>> >>>>>>> >>>> >>>>>>> >>>>>>> >>>> >>>>>>> >>>>>>> >>>> >>>>>>> >>>>>>> >>> >>>>>>> >>>>>>> >>> -- >>>>>>> >>>>>>> >>> ------------------------------------------------------------ >>>>>>> >>>>>>> >>> Donald Hobern (dhobern(a)gbif.org) >>>>>>> >>>>>>> >>> Deputy Director for Informatics Global Biodiversity >>>>>>> Information >>>>>>> >>>>>>> >>> Facility Secretariat Universitetsparken 15, DK-2100 >>>>>>> Copenhagen, >>>>>>> >>>>>>> >>> Denmark >>>>>>> >>>>>>> >>> Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 >>>>>>> >>>>>>> >>> ------------------------------------------------------------ >>>>>>> >>>>>>> >>> >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> >> >>>>>>> >>>>>>> > >>>>>>> >>>>>>> > -- >>>>>>> >>>>>>> > ------------------------------------------------------------ >>>>>>> >>>>>>> > Donald Hobern (dhobern(a)gbif.org) >>>>>>> >>>>>>> > Deputy Director for Informatics Global Biodiversity >>>>>>> Information >>>>>>> >>>>>>> > Facility Secretariat Universitetsparken 15, DK-2100 >>>>>>> Copenhagen, >>>>>>> >>>>>>> > Denmark >>>>>>> >>>>>>> > Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 >>>>>>> >>>>>>> > ------------------------------------------------------------ >>>>>>> >>>>>>> > >>>>>>> >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> >>>>>>> biogeosdi mailing list >>>>>>> >>>>>>> biogeosdi(a)lists.tdwg.org >>>>>>> >>>>>>> http://lists.tdwg.org/mailman/listinfo/biogeosdi >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> >>> -- >>> ------------------------------------------------------------ >>> >>> Donald Hobern (dhobern(a)gbif.org) >>> >>> Deputy Director for Informatics Global Biodiversity Information >>> Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, >>> Denmark >>> >>> Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 >>> >>> ------------------------------------------------------------ >>> >>> >>> >> >> >> > > -- > ------------------------------------------------------------ > Donald Hobern (dhobern(a)gbif.org) > Deputy Director for Informatics > Global Biodiversity Information Facility Secretariat > Universitetsparken 15, DK-2100 Copenhagen, Denmark > Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 > ------------------------------------------------------------

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