June 2007 - tdwg-content - lists.tdwg.org

[Biogeosdi] Re: biogeosdi Digest, Vol 7, Issue 4
by Meganck Bart 04 Jul '07

04 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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[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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[Biogeosdi] Re: itineraries in openmodeller
by Meganck Bart 27 Jun '07

27 Jun '07

Hi Tim, A new week and the rain has started again... time for : Some paragraphs on itinerary modelling With itineraries, we want to retrace the actual expedition route as accurately as possible. For this, we want to make use of all possible data sources, the first of which are of course the georeferenced specimen records (such as come from GBIF et al.). Besides that, we are also looking for other information sources, for example field notes, old maps and the like. When properly encoded in some system of "boundaries", these extra information sources create a set of restrictions that can be used for quality control on the data. For example : if a point by its lat/lon values looks like an outlier of the general set, we could find clues in the other information sources about what is going on. Either some indication that, yes, the point is correct (e.g. its field number fits perfectly in the field number series) or some proof that, indeed, the point is incorrect (e.g. some notes about the camping sites, proving that the expedition was not near that place at the time). Both the data set (points) and the "info set" are fed into the modeller tool, and two outputs are generated : 1/ a judgement about the points in the data set (+ visualisation, indication of faulty points) and 2/ a new "info set", if the points yielded some new information to be used in the future. So, it would be a system that grows in knowledge as more data sets are processed, and more extra information is encoded. In a first stage though, we'll be mostly looking at the internal coherence in the data set points - and that would make the process more "mainstream" and "OM-ready". Later on, the process will add more "semantics" to the geospatial aspect, and I don't see very clear yet how that would fit into OM. The temporal aspect will, however, play a very important part from the beginning - an it's great news that OM will incorporate this. Have you seen the Mapbuilder timeseries demo : http://geoservices.cgdi.ca/mapbuilder/demo/timeSeries/index.html Basically, they perform as many WMS-requests as there are "time slices" on the WMS-server, then store the result and display one after the other in an animation. Best regards, Bart. On Sat, 2007-05-05 at 22:43 -0300, Tim Sutton wrote: > Hi > > Yes a couple of paragraphs of your ideas for itinerary modelling would > probably make your requirements a bit clearer. Currently the > openModeller library has no in built support for temporal analysis. In > a future release of openModeller Desktop, I will add support for > projection of niche models into multiple 'time slices' and producing > an animation of the result. Typically we would use this when > predicting changes in distribution in future climate scenarios. > > PS I dont know if I mentioned the new linux binary thats available > with the 1.0.5 release of openModeller. > > Regardsbiogeosdi(a)lists.tdwg.org > > Tim > > 2007/5/4, Meganck Bart <bart.meganck(a)africamuseum.be>: > > Hi Tim, > > > > > * could OM take in data layers other than environmental data ? > > > > > > > > > > It can use pretty much any raster layer - what did you have in mind? > > > > Well, it would be a bit more difficult than just a raster layer : > > in fact, we try to gather extra information from the data as we process > > it, so there > > would have to be some kind of (temporary) storage. > > > > Also, the data would be more time-oriented, not only spatially (as rasters > > are). > > I don't know if that would be feasible for OM - and if I'm expressing > > myself clearly > > here... ;-) > > > > Perhaps I'll make a short text with some explanation of what exactly > > we would try to do ? > > > > best regards, > > > > Bart. > > > > > > > > On Thu, 2007-05-03 at 13:21 -0300, Tim Sutton wrote: > > > Hi Bart! > > > > > > 2007/5/3, Meganck Bart <bart.meganck(a)africamuseum.be>: > > > > Hi Tim, > > > > > > > > I have been thinking about how to make the "itinerary" project a > > > > use-case for our GeoAppInter workflow. > > > > > > > > It's clear that until now I've been working a bit too enclosed - so > > the > > > > Campinas workshop was an eye-opener. > > > > > > > > In fact the itinerary implementation would not be that different from > > > > the demo we did. It's just another way of looking at the modeling > > part. > > > > For that I have some questions about OpenModeler : > > > > > > > > > > Cool it would be great to include itineray support. > > > > > > > * how easy or how difficult is it to make your own algorithms for OM ? > > > > In what language do they have to be implemented ? > > > > > > > > > > Its pretty easy - requires a basic knowledge of C++ though. > > > > > > > * could OM take in data layers other than environmental data ? > > > > > > > > > > It can use pretty much any raster layer - what did you have in mind? > > > > > > > > > Regards > > > > > > Tim > > > > > > > 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 > > > > > > > > ########################################### > > > > > > > > This message has been scanned by ICT - Africa Museum > > > > > > > > ________________________________________ > > > > 3/5/2007 - Filtered through antispam by ICT > > > > > > > > > > > > > > > > > -- > > -- > > 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 > > > > ________________________________________ > > 4/5/2007 - Filtered through antispam by ICT > > > > > > > -- -- 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 ________________________________________ 7/5/2007 - Filtered through antispam by ICT

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Fwd: [Biogeosdi] Re: Search on the GBIF REST services
by Javier de la Torre 26 Jun '07

26 Jun '07

Begin forwarded message: > From: Donald Hobern <dhobern(a)gbif.org> > Date: 26 de junio de 2007 22:47:00 GMT+02:00 > To: Javier de la Torre <jatorre(a)gmail.com> > Cc: Tim Sutton <tim(a)linfiniti.com>, biogeosdi(a)lists.tdwg.org > Subject: Re: [Biogeosdi] Re: Search on the GBIF REST services > > The tests we perform correspond to the following bits: > > /** > * Set if latitude appears to have the wrong sign > */ > public static final int > GEOSPATIAL_PRESUMED_NEGATED_LATITUDE = 0x01; > /** > * Set if longitude appears to have the wrong sign > */ > public static final int > GEOSPATIAL_PRESUMED_NEGATED_LONGITUDE = 0x02; > /** > * Set if latitude and longitude appears to have been switched > */ > public static final int > GEOSPATIAL_PRESUMED_INVERTED_COORDINATES = 0x04; > /** > * Set if coordinates are (0,0) > */ > public static final int > GEOSPATIAL_ZERO_COORDINATES = 0x08; > /** > * Set if coordinates not in range -90 to 90 and -180 to 180 > */ > public static final int > GEOSPATIAL_COORDINATES_OUT_OF_RANGE = 0x10; > /** > * Set if coordinates do not match country name (covers > cases not handled above) > */ > public static final int > GEOSPATIAL_COUNTRY_COORDINATE_MISMATCH = 0x20; > > 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 >>>>> >>>> >>>> >> >> >>

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[Biogeosdi] Fwd: Auto-discard notification
by Javier de la Torre 26 Jun '07

26 Jun '07

I think Donald is not on the mailing list... Begin forwarded message: > From: biogeosdi-bounces(a)lists.tdwg.org > Date: 26 de junio de 2007 22:12:59 GMT+02:00 > To: biogeosdi-owner(a)lists.tdwg.org > Subject: Auto-discard notification > > The attached message has been automatically discarded. > From: Donald Hobern <dhobern(a)gbif.org> > Date: 26 de junio de 2007 22:13:02 GMT+02:00 > To: Tim Sutton <tim(a)linfiniti.com> > Cc: Javier de la Torre <jatorre(a)gmail.com>, biogeosdi(a)lists.tdwg.org > Subject: Re: [Biogeosdi] Re: Search on the GBIF REST services > > > 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 >>> >> >> >> >>

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Re: [Biogeosdi] Re: Search on the GBIF REST services
by Javier de la Torre 26 Jun '07

26 Jun '07

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 >>> >> >>

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[Biogeosdi] Re: Search on the GBIF REST services
by Javier de la Torre 26 Jun '07

26 Jun '07

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 > ------------------------------------------------------------ >

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[Biogeosdi] Fwd: Search on the GBIF REST services
by Javier de la Torre 26 Jun '07

26 Jun '07

Cool!! Begin forwarded message: > From: Donald Hobern <dhobern(a)gbif.org> > Date: 26 de junio de 2007 14:29:18 GMT+02:00 > To: Javier de la Torre <jatorre(a)gmail.com> > Subject: Re: Search on the GBIF REST services > > 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 > ------------------------------------------------------------ >

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[Biogeosdi] Long time ago...
by Javier de la Torre 26 Jun '07

26 Jun '07

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. Tecnología Tel: 91 536 05 03 Mov: 629 69 38 70 skype:jatorre555 jatorre(a)imaste-ips.com

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Re: [Biogeosdi] the EDIT connection
by Javier de la Torre 25 Jun '07

25 Jun '07

Hey Tim, Well, this is definetly wired but I am on it... In any case I get a lot of layers like .svn/text-base/meanRad.asc.svn- base that I suspect are not real layers but is just that the omws fetch the layers from the file system and does not exclude hidden files like the ones from subversion. We are gonna get a lot of wrong layers like this. But in any case this is not the problem... it is the nusoap library... Did we mention enough in the report that SOAP document style web services are almost impossible to use from PHP? There is only nusoap available and is pretty buggy... I am really considering rewriting the piece of code that connect to the service and get the data... at the end we are not really making use of any serialization deserialization mechanism... definelty AMF rules!! JAvi. On 25/06/2007, at 20:22, Tim Sutton wrote: > Hi > > Yup I should have said I checked using openModeller desktop and the ws > is working fine so the issue seems to be a nusoapy one. If its still > using the omtest ws url (it was last I checked) then no the available > layers list should not have changed and it should return a result > pretty quickly since it has only a handful of layers in it... > > I think a swift conk on the nusoap lib with a coconut may fix it... > > Regards > > Tim > > 2007/6/25, Javier de la Torre <jatorre(a)gmail.com>: >> Hey, >> >> This is very weird. I checked with another tool and the OMWS is >> working fine returning layers as it should... then I check on the >> NUSOAP library and it seems that the problem is that the call to the >> method >> >> $omSoapService->document >> >> which should return the document that the omws returned is truncated >> almost at the end and therefore the XML does not validate... >> accessing the response inna an object way seems to work so I am >> checking if I can solve that. >> >> So... the difference from the workshop might be that there more >> layers now available under omws? >> >> Cheers. >> >> On 25/06/2007, at 18:00, Tim Sutton wrote: >> >> > Hi Javi >> > >> > If you watch the logs (/tmp/phperrors.log) while clicking onto the >> > getlayers link you will see only this: >> > >> > [25-Jun-2001 09:50:42] nlayers: 1 >> > [25-Jun-2001 09:50:46] >> > http://omtest.cria.org.br:80/cgi-bin/om_soap_server.cgi<-- ctor >> om end >> > point >> > [25-Jun-2001 09:50:46] >> > http://omtest.cria.org.br:80/cgi-bin/om_soap_server.cgi <-- >> > getAvailable Layers endpoint >> > >> > When I installed the omtest code on my mac here the mac console >> gives >> > me a bit more detail: >> > >> > [Mon Jun 25 12:59:57 2007] [error] nlayers: 1 >> > [Mon Jun 25 13:00:02 2007] [error] [client 200.144.120.115] File >> does >> > not exist: /Users/timlinux/Sites/biogeosdi/frontend/openlayers/ >> > theme/default/style.css >> > [Mon Jun 25 13:02:06 2007] [error] >> > http://omtest.cria.org.br:80/cgi-bin/om_soap_server.cgi<-- ctor >> om end >> > point >> > [Mon Jun 25 13:02:06 2007] [error] >> > http://omtest.cria.org.br:80/cgi-bin/om_soap_server.cgi <-- >> > getAvailable Layers endpoint >> > [Mon Jun 25 13:02:06 2007] [error] PHP Notice: Undefined property: >> > nusoapclient::$operation in >> > /Users/timlinux/dev/php/biogeosdi/backend/libs/nusoap/nusoap.php on >> > line 6837 >> > >> > Does that mean anything to you? >> > >> > Regards >> > >> > Tim >> > >> > 2007/6/7, Javier de la Torre <jatorre(a)gmail.com>: >> >> Give it to me!! I am the master of strange nusoap errors and >> you know >> >> it :D >> >> >> >> >> >> On 06/06/2007, at 20:49, Tim Sutton wrote: >> >> >> >> > Hi Guys >> >> > >> >> > Yes absolutely its all available as opensource already - they >> >> can get >> >> > it using anonymouse svn account. I've been working on getting >> the >> >> > prototype completed yesterday and on and off this week. >> Something >> >> > seems to have been broken with the layer selection screen and Im >> >> > gettin g a strange error from nusoap at this point. Ill post >> the >> >> > exact message in a follow up email. >> >> > >> >> > Regards >> >> > >> >> > Tim >> >> > >> >> > 2007/5/30, Javier de la Torre <jatorre(a)gmail.com>: >> >> >> Hi all, >> >> >> >> >> >> I am trying to finish what we did in the biodgeosdi meeting >> and >> >> >> going through the emails. >> >> >> >> >> >> > Some people from partner institutes are visiting us now >> for the >> >> >> EDIT >> >> >> > project. I have shown them what we have done in Campinas, and >> >> they >> >> >> > were >> >> >> > really interested. >> >> >> > >> >> >> > We got some nice interaction from them concerning >> Mapbuilder and >> >> >> other >> >> >> > softwares, and they were asking specifically for how we went >> >> >> about to >> >> >> > get the XMl from the OGC services, and pass it on to PHP. >> >> >> > >> >> >> > So, a quick check with all of the team : am I right that our >> >> code, >> >> >> > once >> >> >> > finished, will be available on the web as open source ? >> For the >> >> >> moment >> >> >> > you have to log into the CVS server. >> >> >> >> >> >> >> >> >> From my side this is clearly the idea. And expect it really >> soon. >> >> >> >> >> >> Cheers. >> >> >> _______________________________________________ >> >> >> biogeosdi mailing list >> >> >> biogeosdi(a)lists.tdwg.org >> >> >> http://lists.tdwg.org/mailman/listinfo/biogeosdi >> >> >> >> >> > >> >> > >> >> > -- >> >> > -- >> >> > Tim Sutton >> >> > >> >> > Visit http://qgis.org for a great Open Source GIS >> >> > Home Page: http://linfiniti.com >> >> > Skype: timlinux >> >> > MSN: tim_bdworld(a)msn.com >> >> > Yahoo: tim_bdworld(a)yahoo.com >> >> > Jabber: timlinux >> >> > Irc: timlinux on #qgis at freenode.net >> >> >> >> >> > >> > >> > -- >> > Tim Sutton >> > QGIS Project Steering Committee Member - Release Manager >> > Visit http://qgis.org for a great open source GIS >> > openModeller Desktop Developer >> > Visit http://openModeller.sf.net for a great open source ecological >> > niche modelling tool >> > Home Page: http://tim.linfiniti.com >> > Skype: timlinux >> > Irc: timlinux on #qgis at freenode.net >> >> > > > -- > Tim Sutton > QGIS Project Steering Committee Member - Release Manager > Visit http://qgis.org for a great open source GIS > openModeller Desktop Developer > Visit http://openModeller.sf.net for a great open source ecological > niche modelling tool > Home Page: http://tim.linfiniti.com > Skype: timlinux > Irc: timlinux on #qgis at freenode.net

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RE: [Biogeosdi] RE: [tdwg-tapir] Executive summary available
by Meganck Bart 25 Jun '07

25 Jun '07

Hi Tim, Thanks a lot ! That's quick service, from the other end of the globe... ;-) An additional (not related) question : as a QGIS-developer, do you know anything about GPSbabel ? I know the tool just as a user, but now for EDIT we're looking at tools to do format conversions and GPSbabel just sprung to mind (strange how these umpteen formats it lists grab hold of the mind...). We would particularly be interested in KML, csv and GML - but I don't think GML is there as yet... ? Do you know any of the people working on it ? best regards, Bart. -----Original Message----- From: Tim Sutton [mailto:tim@linfiniti.com] Sent: Tue 6/5/2007 4:00 PM To: Meganck Bart Cc: Renato De Giovanni; biogeosdi(a)lists.tdwg.org Subject: Re: [Biogeosdi] RE: [tdwg-tapir] Executive summary available Hi Bart et al Ok the machine is up and running again. I think the lid fell closed and it went to sleep. Javi and I are investigating getting a dedicated server to host the site. Regards Tim PS. tim.sutton(a)cria.org.br, <-- doesnt exist! 2007/6/5, Tim Sutton <tim(a)linfiniti.com>: > Hi Bart > > Thanks for the note. I will spend some time on the demo today and try > to see whats going on! > > Best regards > > Tim > > 2007/6/5, Meganck Bart <bart.meganck(a)africamuseum.be>: > > Hi Tim, hi Renato, > > > > The link to our demo website > > > > http://omtest.cria.org.br/biogeosdi/ > > > > seems to be working slowly or not at all... ? > > > > This is a pity, because what we did in Campinas was really relevant to > > the other projects we're working on, and I often refer to our demo > > implementation to demonstrate how standard-compliant existing services can > > be strung together in a user-friendly way. > > I'll be referring to it next Tuesday on the DeeGree user's day in Bonn > > (which is nice, given the fact that we didn't even use DeeGree as WMS - > > but OGC is OGC, no ? ;-) and the 18th in the bioinformatics block of the > > 7th Flora Malesiana symposium 2007, Leiden. > > > > Could you see if the server is still fully functional ? > > > > > > best regards - I often miss the coconuts... > > > > > > Bart. > > > > > > > > > > ########################################### > > > > This message has been scanned by ICT - Africa Museum > > > > ________________________________________ > > 5/6/2007 - Filtered through antispam by ICT > > > > _______________________________________________ > > biogeosdi mailing list > > biogeosdi(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/biogeosdi > > > > > -- > -- > Tim Sutton > > Visit http://qgis.org for a great Open Source GIS > Home Page: http://linfiniti.com > Skype: timlinux > MSN: tim_bdworld(a)msn.com > Yahoo: tim_bdworld(a)yahoo.com > Jabber: timlinux > Irc: timlinux on #qgis at freenode.net > -- -- Tim Sutton Visit http://qgis.org for a great Open Source GIS Home Page: http://linfiniti.com Skype: timlinux MSN: tim_bdworld(a)msn.com Yahoo: tim_bdworld(a)yahoo.com Jabber: timlinux Irc: timlinux on #qgis at freenode.net ########################################### This message has been scanned by ICT - Africa Museum ________________________________________ 5/6/2007 - Filtered through antispam by ICT

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[tdwg-ncd] NCD v0.70 + Ontology
by Döring, Markus 20 Jun '07

20 Jun '07

Dear list, I have released the 0.70 version of the NCD schema that we have created during the Amsterdam workshop and also finalised the NCD Collection Ontology. Files can be found here: XML Schema: http://rs.tdwg.org/ncd/ http://rs.tdwg.org/ncd/0.70/ncd.xsd Ontology: http://rs.tdwg.org/ontology/voc/Collection.rdf Discussion and class overview diagram: http://wiki.tdwg.org/twiki/bin/view/TAG/OntDiscussCollection The 0.80 version of the xml schema that will validate RDF instances based on the ontology will be available soon too. Best wishes, Markus

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[tdwg-spm] Species profile model instance examples
by Eamonn O Tuama 14 Jun '07

14 Jun '07

Bob has created a page on the Species Profile Model wiki for instance examples (http://wiki.tdwg.org/twiki/bin/view/SPM/InstanceExamples) You are all encouraged to put your own examples there and add comments too. In reaction to the AbiesAlba example and observations from Marcus, I have put up one on SalmoSalar and posed some further questions. Please contribute. Best regards, Éamonn

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[taxon-data-model] Re: taxon data model
by Markus Döring 12 Jun '07

12 Jun '07

Éamonn, I have prepared a simple SpeciesPage example based on the current ontology. http://ww3.bgbm.org/tmp/abiesalba.rdf I hope this helps and also that it's really correct. At least it validates with w3c's validator. You can also view it with the new AJAX based OpenLink RDF browser: http://demo.openlinksw.com/DAV/JS/rdfbrowser/index.html two things struck me when writing this example: - where do I put a PublicationCitation? I would want to cite all sources for every information and I dont know where/how. Is this missing or part of the base/core ontology already? - hasInformation is a bit redundant, but the validator did complain when I declared all InfoItems under a single hasInformation node. Was this intended? I guess yes, cause otherwise the InfoItems would have to be properties. best wishes -- Markus On 28.06.2007, at 13:11, Eamonn O Tuama wrote: > Dear Gregor, > > I do not see it being a case of SDD versus SPM. SPM will only be > needed if > SDD cannot fulfill the use cases of the latter. It would be great > if you > would accept Roger's invitation to act as champion of an interest > group that > covers descriptive data, whether covered by SDD, SPM, whatever. Bob > would be > a good person to talk to because of his knowledge of SDD and his > attendance > at the GBIF SPM workshop where we initiated discussions. > > Question to Marcus: did you manage to develop the SPM instance > examples we > talked about? I think they will help the interest group, particularly > non-modellers, to understand what's involved. > > Best regards, > > Éamonn > > -----Original Message----- > From: Roger Hyam [mailto:rogerhyam@googlemail.com] On Behalf Of > Roger Hyam > Sent: 28 May 2007 12:36 > To: G. Hagedorn > Cc: Eamonn O Tuama; Markus Döring; Lee Belbin > Subject: Re: taxon data model > > > Hi Gregor, > > I had hoped that Bob would have talked to you about this. We spoke to > him very deliberately in Copenhagen before he came to see you about > the overlap with SDD and he said he would discuss it with you. > > There was a consensus at the meeting I believe that there should be > an interest group that covers descriptive data that contained task > groups to do things on SDD, SDD-Lite? TDM (now called SPM I believe) > perhaps images or whatever. That way there would be a forum to deal > with any of these potential overlaps. I was hoping that he would > persuade you to step forward as a champion for such a group! > > Please discuss with Eammon who is championing the SPM and Markus who > is looking at re-modeling what we came up with. I have cc'd them in > on the email. > > All the best, > > Roger > > > > On 22 May 2007, at 17:48, Gregor Hagedorn wrote: > > > >> Hi Roger >> >> I am just responding because of Adrian's call for the TDWG program. >> >> I understand that the Taxon data model redevelops a lot of the >> concepts of SDD >> in a different light. >> >> I do not say what you do is wrong if you are only interested in >> free-form text. >> SDD is about structured data and about mixed situations. But I >> wonder whether >> you really never want to move into more structured forms. >> >> I am worried or just don't see how your future extensibility would >> work. How >> can I learn that? >> >> We did have reasons to consider text characters a form of >> character, but the >> reasons we did it is to have typed characters and free-form text >> mixtures >> supported. In the markup part, you can also markup with any number >> of high- >> level concepts. >> >> I would really like to have discussions on this, on what you >> learned, and that >> would include possibly changing SDD into something new. I hope both >> sides could >> learn. >> >> What can you suggest? Should we have a session on SDD versus TDM at >> TDWG? >> >> Would you be willing to talk on the descriptive data part? Do you >> suggest other >> talks? >> >> I appreciate your help if you can! >> >> Gregor---------------------------------------------------------- >> Gregor Hagedorn (G.Hagedorn(a)bba.de) >> Institute for Plant Virology, Microbiology, and Biosafety >> Federal Research Center for Agriculture and Forestry (BBA) >> Königin-Luise-Str. 19 Tel: +49-30-8304-2220 >> 14195 Berlin, Germany Fax: +49-30-8304-2203 >> > > >

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Re: [taxon-model] Re: Owl polymorphism
by Markus Döring 11 Jun '07

11 Jun '07

Im not sure why we are talking about inheritance. My primary goal is to see how useful TDM is for data exchange and integration. I am very interested for example to use TDM to exchange species distribution data. If every application defines its own occurence status terminology noone would be able to merge datasets. So I was hoping TDWG would at least define a default standard for those kind of things. I am aware that some communities will use a different standard, but if they want to be interoperable with the outside world how can you see this happen if we dont define a common terminology? Reason over hundreds of SameAs statements? It would be nice to have at least a standard "backbone" where you can relate your terminology against. And if we agree that this is needed, why not have a strongly typed property for the respective InfoItem classes that only allows terms of the recommended terminology? But maybe I misinterpreted the purpose of TDM and/or are still too heavily influenced by xml schema ;) cheers -- Markus On 11.05.2007, at 13:56, Bob Morris wrote: > Alas, for some of the intended audiences, there are requirements of > practice, or even of law, to use particular controlled vocabularies. > Often, there are several in wide use. This is especially true in the > invasive species community, but also, I believe, for many > agriculture, public health and other communities. > > My inclination is to share Roger's concern about an inheritance tree > adding complexity that might add to the complexity of either > application building or adoption. (I can't believe I'm agreeing with > Roger in this domain... :-) ). Unfortunately, my intuition is that > two related problems will quickly arise: > > (a). The inexperience, and a small stake in the outcome, of the > various communities will quickly lead to an undisciplined inheritance > tree in which most people derive from the base, not from other > derivations. This in turn makes effective and easily extended > polymorphic application programming difficult or impossible to put in > place. If the utility of polymorphic programming is compromised, > there seems small point accepting the maintenance hit of polymorphic > ontology. It's a little like the difference between tags and property > lists. You can go an awfully long way with the former even though they > just float by like clouds. > > (b)For similar reasons to (a), even when disciplined extension > lineages emerge, there will be rooted at them further undisciplined > derivations as above, and that these will lead to \semantic/ > multipaths through the inheritance trees as people map undisciplined > leaf nodes in one branch to those in another. > > For a number of the TDMTerm categories there are already multiple well > established controlled vocabularies. Many of the relevant > subcommunities are communities of practice, not of theory, and feel > more constrained to "get on with it" about their work than to make > sure it is easily related to the vocabularies of other subcommunities > much less apparently unrelated communities. I believe this is > especially true where ecology, public policy, commercial or health > data are in play. It is a little regrettable that the list and wiki > name got abbreviated from Taxon Data Model to Taxon Model. The latter > might give taxonomists the mistaken (I hope) view that TDM is about a > theory of what a Taxon is. > > > > > On 5/11/07, Markus Döring <m.doering(a)bgbm.org> wrote: >> Roger, >> this was not targeted directly at TDM. I was mainly exploring OWL and >> definitely not suggesting multiple inheritance! >> >> But in regards to TDM I was thinking about the consequences of >> allowing any defined term as a "controlled" value for >> InfoItems.hasValue. Is this desired? Having individual classes for >> the InfoItem categories now would allow us to define a specific >> controlled vocabulary for each category - or None if we dont think >> this is a good idea. These vocabularies, like CyclicityTerm, can >> easily be extended by anyone who really needs to. And all InfoItems >> are allowed to contain uncontrolled values via the hasContent >> property in any case. >> -- >> Markus >> >> >> >> On 11.05.2007, at 11:30, Roger Hyam wrote: >> >> > >> > Hi Markus, >> > >> > Sounds like interesting and complex stuff and exactly what I am >> > trying to avoid ;) >> > >> > If this is for exchange standards we want to keep things as simple >> > as possible. We also need our ontology to entail as little as >> > possible so people can understand it and (if they are up on the >> > technology) import it into their own business ontologies. >> > >> > The role of the exchange ontology is to denote the meaning of >> > simple fields it is not to enable connotations but to avoid them. >> > >> > This is why I was sticking to simple properties with domains and >> > ranges. Really just one up from RDFS. If it is important for a >> > consumer to assert a hierarchy of properties then they can do that >> > in their own ontology and import it. Who is to say that all >> > consumers will have the same notion of that hierarchy and what is >> > the business case for trying to impose one at this point? >> > >> > If there were polymorphism of properties (overriding them in sub >> > classes) then it would get confusing because of the multiple >> > inheritance. I am not sure what would happen to meaning with the >> > diamond problem - where the same property is inherited via several >> > routes but has it's meaning changed differently on each route. It >> > is always possible to subclass the property though and it may be >> > possible to forbid the use of the parent property in a class - >> > perhaps - but this is getting beyond my reading level. >> > >> > Not sure if this helps, >> > >> > All the best, >> > >> > Roger >> > >> > >> > >> > >> > On 11 May 2007, at 09:54, Markus Döring wrote: >> > >> >> Roger, >> >> is it possible with OWL to have polymorph class properties? >> >> As properties are global and only bound to classes via range/ >> >> domain it doesnt seem to be possible to me, but maybe Im wrong. >> >> Can I redefine a propertys range depending upon the class it >> >> belongs to, so its domain? Well, that would mean to declare the >> >> same property twice with different domains and ranges. Probably >> >> impossible. It is different from classic OO thinking... >> >> -- >> >> Markus >> >> >> >> >> >> >> > >> >> _______________________________________________ >> taxon-model mailing list >> taxon-model(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/taxon-model >>

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[tdwg-tnc] Species profile model group meeting at TDWG 2007 Conference
by Eamonn O Tuama 08 Jun '07

08 Jun '07

Dear TDWG TNC Member, We plan to hold a group discussion about the "Species Profile Model" SPM (previously known as "Taxon Data Model") at the TDWG 2007 conference, possibly on Sunday 16th during the group meetings slot (09.00-17.00). We are trying to gauge interest and potential numbers and to avoid clashes with other parallel discussions that might be taking place. The SPM is intended to describe species facts (organised into categories) as might appear in "species bank" type web applications like Encyclopedia of Life or FishBase/SeaLifePortal. We do not intend to duplicate the work of TCS and SDD for nomenclature and taxonomy but rather draw on them, and other TDWG standards, wherever appropriate. We want it to fit in with the TDWG technical architecture and will work closely with all concerned to do this. It seemed to us that the SPM was sufficiently distinct to warrant set up a new group within TDWG with cross linkages to other groups where appropriate. For a background, see the wiki here: http://wiki.tdwg.org/TaxonDataModel, and the summary of a recent workshop held at GBIF here: http://wiki.tdwg.org/twiki/bin/view/TaxonDataModel/SpeciesModelWorkshopRepor t. You can subscribe to the taxon-data-model mailing list here to follow developments and contribute: http://lists.tdwg.org/mailman/listinfo/taxon-data-model (mailing list information web page) taxon-data-model(a)lists.tdwg.org <mailto:taxon-data-model@lists.tdwg.org> (mailing list web address) Please reply to me directly to let me know if you are interested in attending the SPM workgroup during the TDWG conference. At this stage it is purely to get a rough indication of numbers so there is no real commitment required on your part. 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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[tdwg-ncd] RE: NCD status summary
by Neil Thomson 05 Jun '07

05 Jun '07

Hi Markus, Sorry for the delay in responding to this. I have interspersed comments below and Cc:'d in the RAVNS since there are some changes here that are potential workshop agenda items. Thanks for your help with this ... -----Original Message----- From: Markus Döring [mailto:m.doering@BGBM.org] Sent: 01 June 2007 14:51 To: Neil Thomson Cc: Ruud Altenburg Subject: NCD status summary Neil, I have been working on the schema and the ontology lately. They don't match a 100%. In my opinion it would be best to focus on one specification only instead of trying to maintain and keep in sync 2 specifications for different target platforms (XML+RDF). If we need to do that, I strongly suggest to do the real modelling in an abstract form with UML and derive a schema and ontology from that! You can also create a suitable database schema from UML automatically if you want. Im not sure how to go about this decision. Maybe its best to discuss this during the workshop? ## NT: We should complete the schema v1.0 at least before transferring to another technology. Maybe you could cover the reasons for moving and how it will affect future developments in your session at the workshop? ----------------------- In regard to the php toolkit I think this decision doesnt have a very strong impact as long as the toolkit doesn't implement im/export via xml or rdf yet. I suggest to work with the schema for now cause this is 99% complete. On the other hand I believe the RDF version is the preferred tdwg format, so we should use this ontology as the reference. And as I said its not exactly the same as the ncd schema, as it is part of the tdwg ontology and uses external ontologies too (like vcard). ## NT: ok, that's good in that it should not hold Ruud up too much. --------- Detailed issues that still need to be resolved are: *** SCHEMA *** - what IDs should exist? 1 NCD guid (lsid or whatever) + many others with source. Is this correct? ##NT: Only the NCDID needs to be generated, probably as an LSID. All other identifiers are taken from elsewhere (i.e.the "source") ------------------ - are multiple parent collections & parent institutions allowed? currently this is not ##NT: Yes, they should be allowed ------------------ - person roles not fixed or at least core suggested? I think we need this ##NT: Yes, we do need this ------------------ - what is "richRecordSearchString" in contrast to "collectionDatabaseURL"? what about "objectAccessService" and simply "furtherInformation" ? ##NT: The "collectionDatabaseURL" is the URL of the database that holds item-level data for the collection being described in this NCD record. The "richRecordSearchString" is what should be used in that database to get directly to the relevant record. To take an example, there will be an NCD record describing a herbarium. The "collectionDatabaseURL" will be to the Index Herbariorum WebDatabase and the "richRecordSearchString" will contain the coden for the herbarium so that the full description of the herbarium can be found by adding the two together. I have no objection to "objectAccessService" for the latter, but the former is more explicit than "furtherInformation". ------------------- - I have replaced all address information with vcard elements. That is vc:N for person names and vc:ADR for addresses. Some existing NCD elements do not exist in vcard though. How shall we treat them? Right now Ive simply left them as they were before in addition the vcard elements. It looks a bit weird, but its ok I believe. In particular that is byear and deathyear for persons (full birthday exists in vcard) and fax, email, logourl for institutional addresses. Maybe we can remove the email and fax and add a website instead? The collection have real contacts anyway already, so institutions dont really need this, do they? ##NT: Yes, institutions do require contact details too so I would prefer that these elements remain. If they are not present as vc: elements then can they just be ncd: elements? ------------------- - many elements cover the same ideas that dublin core covers. Should we use the explicit dublin core elements for title, description, other resources, keyword, rights, modified, created and citation? I would be in favor to do so. It would mean that NCD mainly is about the extra metadata bits that dublin core doesn't cover! ##NT: We certainly could do this and Doug has produced an NCD <--> DC mapping. Since this would just be a re-labelling exercise we can have this as a discussion item at the workshop. NCD would then be an application profile, re-using elements from mets:, dc: and vc: along with its own. ------------------- *** ONTOLOGY *** - collection extent is a pure integer without a unit definition. I know this is bad, but having complex data (i.e. with multiple elements or attributes) in an ontology means I would have to define a new class just for this. And Roger is very keen on keeping the number of classes low. ##NT: In this case the single attribute should be a string not an integer. Describing a collection extent as "2" is spectacularly meaningless. If the string is "2 shelves" or "2 cupboards" or "2 rooms" it means a little bit more. Not much, but enough for someone to assess whether it is worth a visit or not. -------------------- - all keywords lacking strength flag cause I have created a single keyword class that is used by all keyword types. And the strewngth flag didnt exist for all keywords. Should it or should we drop it? ##NT: I would like to keep the strength flag if possible fot those elements where it makes sense - it would be good to indicate where the collection owner believe's the collection to be particularly strong. -------------------- - a persons role in regard to a specific collection is missing. I think we need it, but then again we need at least a basic controlled vocabulary ##NT: Yesm we do need this. Example terms would be owner, adminstrator, collector, preparator etc. ------------------- I think thats all there is. It looks like a lot, but most issues are of a cosmetic nature and do not change the abstract standard. Some like multiple parents do of cause. I would be glad if you could reply to these questions as soon as possible, even if its only partly, cause I hope to find some time over the weekend to settle some of them. ##NT: Thanks again for looking at these details. It was always known that changes would be needed for the toolkit to work and others may well come to light during testing. We can also talk that through at the workshop, since I think that some of the RAVNS are keen to help with the testing. Is everyone in agreement with the changes proposed above? We need to quickly move to v1.0 so that Ruud can strut his stuff. Apologies again for the unintended out-time recently. All best wishes, Neil ----------- best wishes -- Markus http://rs.tdwg.org/ontology/voc/ http://rs.tdwg.org/ncd/dev/schema/ncd.xsd

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[Biogeosdi] RE: [tdwg-tapir] Executive summary available
by Meganck Bart 05 Jun '07

05 Jun '07

Hi Tim, hi Renato, The link to our demo website http://omtest.cria.org.br/biogeosdi/ seems to be working slowly or not at all... ? This is a pity, because what we did in Campinas was really relevant to the other projects we're working on, and I often refer to our demo implementation to demonstrate how standard-compliant existing services can be strung together in a user-friendly way. I'll be referring to it next Tuesday on the DeeGree user's day in Bonn (which is nice, given the fact that we didn't even use DeeGree as WMS - but OGC is OGC, no ? ;-) and the 18th in the bioinformatics block of the 7th Flora Malesiana symposium 2007, Leiden. Could you see if the server is still fully functional ? best regards - I often miss the coconuts... Bart. ########################################### This message has been scanned by ICT - Africa Museum ________________________________________ 5/6/2007 - Filtered through antispam by ICT

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