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[tdwg-sdd] Descriptive data at TDWG 2007
by Gregor Hagedorn 23 Jul '07

23 Jul '07

Dear SDD interest group members! Please do consider coming to TDWG 2007 in Bratislava! The following topics may be of interest to you: ============= 1. ============= A 90 minute session on Wednesday, 19 Sep called: "Descriptive model for analysis, identification, description markup, and taxon pages" As the name implies, analyses of all kind of descriptive data models are welcome, regardless whether they use SDD or not. Criticism of SDD version 1.1 is also welcome. Due to the launching of the Encyclopedia of Life the taxon page topic is especially relevant. Pleasse note that the SDD interest group is not just concerned with morphological data. Data useful for identification, genetic, or phylogenetic analyses are limited to morphology, and the interested group considers all that are inherent to a taxon (genetically or environmentally coded so they are stable. This includes molecular descriptive data like sequences or patterns, behavior, physiology, etc. Stressing a general perspective both with regard to the kind of data and with regard to how the data are gathered and used will be important and welcome. In the light of the current parallel development of the SPM model, we need to assess whether separate models are needed for specific purposes, or whether a general model can be maintained as SDD presents currently. If you whish to participate in this session, please send a rough draft (title and abstract may change later) to g.hagedorn(a)bba.de until 20th Juli. Limited travel funds for students without funding may be available, covering one of transport costs, per diem (~US$71/night) or accommodation. ============= 2. ============= Existing applications of SDD are also welcome in further sessions on the following day, where two sessions are reserved for "Applications of TDWG standards". ============= 3. ============= On Saturday the SDD interest group will meet. Possible topics: 1. Which way ahead? XML-schema, natural language markup or RDF? Are these combinable? 2. Who wants to lead task groups for feature-vocabularies and ontologies? 2. Which priorities may help to choose? 3. Usability of current SDD schema for natural language markup Please add to this list or propose what you would consider to be most important. Please note that Éamonn will hold a group discussion about the "Species Profile Model" (previously known as "Taxon Data Model") during the 16.00-18.00 slot on Tues 18th Sept. I suggest that people interested in SDD should also go to that meeting. I therefore propose a meeting on the last day (Saturday) ***If you are interested in in-depth discussion, please check your travel plans and try to stay until Sept. 22nd, afternoon. Thanks! *** ============= 4. ============= We will try to have a "late-night show" (working group) on studying SDD and RDF on one evening, currently Tuesday. All SDD or RDF "experts" are welcome to that. It would probably make sense to suggest a separate task group for descriptive data in SPM? Can you have a name for it? ============= 4. ============= Thank you! Gregor Hagedorn---------------------------------------------------------- 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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[tdwg-ncd] Re: Terminology version 2
by Ruud Altenburg 19 Jul '07

19 Jul '07

Hallo all, Carol, thanks for sending the new terminology. I'm at the point of implementing everything into the new database. However, I haven't seen a formal 'go' yet for the new terminology. As I've seen a few last minute suggestions in the email, where do I find the definite version? A real and related problem comes to mind: I have implemented the ISO standards of countries and languages as per Markus's suggestion. However, both the ISO standards and the new terminology are in English only. How do we mix this with the second language option in the toolkit? The ISO 639-1 standard lists 185 languages, ISO 639-3 no less than 7590! In other words, translating things is no real option, but mixing English and a second language also seems very inelegant solution. Regards, Ruud

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[Biogeosdi] Report from OGC meeting
by Javier de la Torre 18 Jul '07

18 Jul '07

Hey Lee, Here I send you what I have written at my return from the OGC meeting. You asked me also for a comment on how i think TDWG should continue working with OGC. I will write that in a later message ok? By the way... i couldnt find any news announcing the MoU between TDWG and OGC :( Cheers. --------- Report of the July 2007 OGC Technical Committee Meeting --------------------- The Open Geospatial Consortium (OGC) held its 61st Technical Committee and Planning Committee Meetings during the week of July 9, 2007 in Paris. TDWG was there represented by Donald Hobern and Javier de la Torre who gave two presentations on the Earth Observation and Natural Resources and Environment Working Group. OGC Technical Committees meetings are a fundamental tool for OGC process in building standards and assure interoperability. During a week, OGC members meet in different working groups, discuss and vote in the process of making or reviewing standards. Thanks to the new MoU between TDWG & OGC (link here but I could not find any news item about this ???) now there can be a representation of TDWG in every OGC meeting and push the interest from the biodiversity informatics community in the development of geospatial standards. In this meeting topics varied from Geographic Markup Language, coverages, the GEOSS project, Web Map Service, Sensor Web Enables and many more. During the Earth Observation, Natural Resources & Environment Working Group Meeting TDWG was presented in two different presentations from Donald Hobern and Javier de la Torre. Donald Hobern presented (available here) the TDWG infrastructure project and GBIF. The new GBIF REST services were presented together with how TDWG is creating a new set of vocabularies that can be use by services which data has something to do with biodiversity. Javier de la Torre presented (available here) the results of the BioGeoSDI meeting (link http://wiki.tdwg.org/twiki/bin/view/ Geospatial/InteroperabilityWorkshop1) with a presentation that made emphasis on the use of primary data and niche modelling together with OGC and TDWG standards. In the other hand there has been several presentations about the Global Earth System of Systems (GEOSS) and the pilot projects that are starting now. GEOSS have recently released their catalog service, a registry where geographic data providers and services can be found to create a truly world wide Spatial Data Infrastructure for the observation of the earth. For the moment only a few services are registered, but they plan in the upcomming months to complete the catalog with every service related to the observation of the earth. Related to the observation of the earth, there is the Sensor Web Enabled (SWE) working group in OGC that has presented several papers in their continuos effort to provide an interoperability framework where all kind of sensors can "talk to each other" in a seamless way. During the meeting the new OGC interoperability program, OWS-5, was discussed. This new initiative include more than a hundred participants with a budget of at least a million dollars. The program is organized in 6 different threads: Sensor Web Enablement (SWE), Geo Processing Workflow (GPW), Information Communities' Semantics (ICS), CAD/GIS/BIM, Agile Geography, Compliance Testing (CITE). Significant work items include geospatial Web service chaining and workflow, enhancements to the KML language, practical application of the Sensor Web, and application of GML to real-world scenarios. There were also discussions on the so called GeoAPI. Together with the creation of standards there are efforts to provide APIs that implement the standards so that different vendor, software producers, can implement them using the same interfaces. The API is available in sourceforge and is implemented in Java. The Web Coverage Service (WCS) was also discussed. There is open discussions on implementing asynchronous services and the use of SOAP encodings, although this seems to be a general discussion among all OGC standards. The meeting about OGC for the Mass was a very crowded one. The aim of the meeting was to identify current trends on the use of geospatial information on Internet. Things like GeoRSS, KML, WMS tiling, etc. Specially interesting is the process of making KML an OGC standard. This has been included in the OWS-5 initiative. In general it has been a nice meeting with lot of ongoing discussions. The OGC procedures seems to work quite well and lots of discussion papers are being prepared continuously that expand or improve OGC vision and their standards. [maybe you want some more personal comments Lee?]

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[tdwg-tnc] TCS problems
by Wouter Addink 17 Jul '07

17 Jul '07

Hi, I am currently experiencing some problems with implementing TCS 1.01 There are a couple of elements that do not have a simple element, like Genus (type=ReferenceType) or Rank (type=TaxonomicRank), therefore you don't expect a value for these elements, although it is not invalid and the documentation suggests that there is a value. If there is a value, you don't know if it is a string or something else. Based on the schema you would expect <Genus ref="ref1" linkType="local" /> but in an instance doc you will probably get: <Genus ref="ref1" linkType="local" />Xyz</Genus> or even <Genus>Xyz</Genus> Applications that generate sample docs based on the schema, like oXygen, or parse the schema, like Pywrapper Schema Parser will not treat the element as having a value. This is probably also the cause that aliases for these elements are missing in the TAPIR Concept Name server at TDWG: http://rs.tdwg.org/tapir/cns/alias.txt Regards, Wouter Addink

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[Biogeosdi] Re: biogeosdi Digest, Vol 8, Issue 14
by Meganck Bart 16 Jul '07

16 Jul '07

Hi all, I won't be able to attend to TDWG this year - but I'm in for an IRC meeting on the 21st. best regards, Bart. > > Pitty. But still would you be available for a telephone meeting on > > Friday 21th? > > > > Anybody else going to TDWG? > > > > If possible I would like to organize a meeting about our little > > subgroup. > > > > Cheers. > > > > On 12/07/2007, at 17:41, Tim Sutton wrote: > > > > > Hi > > > > > > I wont be able to attend this year. Will be great if someone can > > > present ours tuff though. > > > > > > Regards > > > > > > Tim > > > > > > 2007/7/10, Javier de la Torre <jatorre(a)gmail.com>: > > >> Hi all, > > >> > > >> is there anybody thinking in attending TDWG this year? I was just > > >> lookig at the program and wondering if we should present and abstract > > >> to present this. Renato already asked me to present in his slot for > > >> "Integrating biodiversity data - 2" at 11:00 12:30. That is ok for > > >> me. This year i will not be able to make it the whole week so i plan > > >> to travel on wednesday late 19th. > > >> > > >> But if there is people from the team around... we could make try to > > >> find a slot to work further on this... specially on creating > > >> documentation to go for funding for next workshop :) If there is many > > >> people away we can maybe ask for conference equipment (they do it a > > >> lot here in OGC and is cool). > > >> Sooo what about Friday at 17:30 for a meeting? > > >> > > >> Cheers. > > >> _______________________________________________ > > >> biogeosdi mailing list > > >> biogeosdi(a)lists.tdwg.org > > >> http://lists.tdwg.org/mailman/listinfo/biogeosdi > > >> > > > > > > > > > -- > > > 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 > > > ------------------------------ > > Message: 2 > Date: Sun, 15 Jul 2007 18:54:27 -0300 > From: "Tim Sutton" <tim(a)linfiniti.com> > Subject: Re: [Biogeosdi] OMWS getAlgorithms > To: "Javier de la Torre" <jatorre(a)gmail.com> > Cc: biogeosdi(a)lists.tdwg.org > Message-ID: > <d368056f0707151454w722d1888ga6b0653671d1af3a(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi > > Im back now. I will try to resolve the rest of the issues in the > Parallels vm (relating to the om service) this week and upload a new > image. Did you give your ogc presentation already? > > Regards > > Tim > > 2007/7/13, Javier de la Torre <jatorre(a)gmail.com>: > > Dont worry, > > > > As I said I hacked it on the client side. > > And yes I did not manage to actually run models but I am a little bit > > lost there so I was trying to make sure that the rest is working... > > > > When do you get back from your little country? How is extrema going? > > I miss it! > > > > Cheers. > > > > On 12/07/2007, at 17:39, Tim Sutton wrote: > > > > > Hi Renato & Javi > > > > > > A quick note from an icafe in extreme... > > > Renato I discovered there is a problem with the xml coming back from > > > teh svm alg - open it with ffox to see the error. Javi for now you can > > > resolve teh issue by simply removing > > > /usr/local/lib/openmodeller/libomsvm.so . Also it seems the cron job > > > for the om service is not running - in the parallels image the crontab > > > for www-data is set up but I think you may need to check the cron > > > configs to ensure that www-data is allowed to run cronjobs. > > > > > > Hope that helps! > > > > > > Regards > > > > > > Tim > > > > > > 2007/7/9, Javier de la Torre <jatorre(a)gmail.com>: > > >> I am using the OMWS that Tim left me in a parallels image. I believe > > >> it is the last version as it is taken from repository and compiled... > > >> In any case I am not sure at all. > > >> > > >> I just made a hack on my side and now is working so I will wait for > > >> Tim to come back and figure out this as I dont know how openmodeller > > >> has been installed on this debian that I have. > > >> > > >> Cheers. > > >> > > >> Javier. > > >> > > >> > > >> On 09/07/2007, at 19:18, Renato De Giovanni wrote: > > >> > > >> > Hello Javi, > > >> > > > >> > Can you tell me which omws service address are you using? > > >> > > > >> > The library does escape the special characters &, < and >, but I've > > >> > just noticed that double quotes were not being escaped (fixed now). > > >> > The library returns content in latin1. However, the soap server > > >> will > > >> > always return content in utf-8. > > >> > > > >> > I tested with the "official" omws service > > >> > (http://modeller.cria.org.br/cgi-bin/om_soap_server.cgi) and it > > >> seems > > >> > to be working with the most recent list of algorithms. I've dumped > > >> > the response and copied to a static document if you want to check: > > >> > > > >> > http://www.cria.org.br/~renato/omws_alg_metadata_dump.xml > > >> > > > >> > Maybe you're using another service address with an older version of > > >> > the library? Or maybe there's something doing some conversions > > >> > between the real raw XML you receive and your parser? > > >> > > > >> > Regards, > > >> > -- > > >> > Renato > > >> > > > >> > On 9 Jul 2007 at 13:19, Javier de la Torre wrote: > > >> > > > >> >> Hey all, > > >> >> > > >> >> Finally I had to hack two things to handle incorrect messages from > > >> >> OMWS. I could not find where the metadata about the algorithms is > > >> >> stored so I hack in the biogeosdi code... that is what I made: > > >> >> > > >> >> //HACK BECUASE OMWS IS RETURNING INVALID XML > > >> >> $rawXml = str_replace("&oldid","&oldid",$rawXml); > > >> >> $rawXml = str_replace("& Shawe","& Shawe",$rawXml); > > >> >> $rawXml = utf8_encode($rawXml); > > >> >> //HACK FINISHED > > >> >> > > >> >> The first two are to handle the not scaped parethesis. The > > >> third one > > >> >> is to encode the result as UTF8 because if not is not valid XML > > >> >> without a encoding definition, which the response does not > > >> include. > > >> >> If the encoding is not defined I think the default is UTF8 and > > >> this > > >> >> seems to be latin1, but in any case I would really recommend being > > >> >> explicit about the encoding bein used. > > >> >> > > >> >> Cheers. > > >> > > > >> > _______________________________________________ > > >> > biogeosdi mailing list > > >> > biogeosdi(a)lists.tdwg.org > > >> > http://lists.tdwg.org/mailman/listinfo/biogeosdi > > >> > > >> _______________________________________________ > > >> biogeosdi mailing list > > >> biogeosdi(a)lists.tdwg.org > > >> http://lists.tdwg.org/mailman/listinfo/biogeosdi > > >> > > > > > > > > > -- > > > 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 > > > ------------------------------ > > Message: 3 > Date: Sun, 15 Jul 2007 23:56:44 +0200 > From: Javier de la Torre <jatorre(a)gmail.com> > Subject: Re: [Biogeosdi] Someone attending TDWG > To: "Tim Sutton" <tim(a)linfiniti.com> > Cc: biogeosdi(a)lists.tdwg.org > Message-ID: <4397B2AB-E4AA-459B-BB5A-0788438F120F(a)gmail.com> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Yes, sure we can do it through IRC, but the idea is that there might > be people at TDWG that are interested in what we do and therefore I > would prefer to open the discussion for everybody there... > > I will ask if there will be teleconferencing support at Bratislava. > > Cheers. > > PD: agghhh I am having problems with openModeller web services > installed on the parallels image... and any advice on the cron work > that i have to set up would be appreciated. > > > On 15/07/2007, at 23:39, Tim Sutton wrote: > > > Hi Javi > > > > Sure I will be available - preferably early in the day brazil time for > > me. If we are meeting with all the workshop participants a meeting on > > IRC will be better...? > > > > Regards > > > > Tim > > > > 2007/7/13, Javier de la Torre <jatorre(a)gmail.com>: > >> Hi Tim, > >> > >> Pitty. But still would you be available for a telephone meeting on > >> Friday 21th? > >> > >> Anybody else going to TDWG? > >> > >> If possible I would like to organize a meeting about our little > >> subgroup. > >> > >> Cheers. > >> > >> On 12/07/2007, at 17:41, Tim Sutton wrote: > >> > >> > Hi > >> > > >> > I wont be able to attend this year. Will be great if someone can > >> > present ours tuff though. > >> > > >> > Regards > >> > > >> > Tim > >> > > >> > 2007/7/10, Javier de la Torre <jatorre(a)gmail.com>: > >> >> Hi all, > >> >> > >> >> is there anybody thinking in attending TDWG this year? I was just > >> >> lookig at the program and wondering if we should present and > >> abstract > >> >> to present this. Renato already asked me to present in his slot > >> for > >> >> "Integrating biodiversity data - 2" at 11:00 12:30. That is ok for > >> >> me. This year i will not be able to make it the whole week so i > >> plan > >> >> to travel on wednesday late 19th. > >> >> > >> >> But if there is people from the team around... we could make > >> try to > >> >> find a slot to work further on this... specially on creating > >> >> documentation to go for funding for next workshop :) If there > >> is many > >> >> people away we can maybe ask for conference equipment (they do > >> it a > >> >> lot here in OGC and is cool). > >> >> Sooo what about Friday at 17:30 for a meeting? > >> >> > >> >> Cheers. > >> >> _______________________________________________ > >> >> biogeosdi mailing list > >> >> biogeosdi(a)lists.tdwg.org > >> >> http://lists.tdwg.org/mailman/listinfo/biogeosdi > >> >> > >> > > >> > > >> > -- > >> > 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 > > > > ------------------------------ > > Message: 4 > Date: Mon, 16 Jul 2007 10:26:00 +1200 > From: Dave Vieglais <vieglais(a)ku.edu> > Subject: Re: [Biogeosdi] Someone attending TDWG > To: "Tim Sutton" <tim(a)linfiniti.com> > Cc: biogeosdi(a)lists.tdwg.org > Message-ID: <4C8B1D7A-3209-48D1-A813-9C70D2E67CD4(a)ku.edu> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > I was hoping to get to TDWG but now can't due to some family > obligations. > > Dave V. > > > On Jul 16, 2007, at 09:39, Tim Sutton wrote: > > > Hi Javi > > > > Sure I will be available - preferably early in the day brazil time for > > me. If we are meeting with all the workshop participants a meeting on > > IRC will be better...? > > > > Regards > > > > Tim > > > > 2007/7/13, Javier de la Torre <jatorre(a)gmail.com>: > >> Hi Tim, > >> > >> Pitty. But still would you be available for a telephone meeting on > >> Friday 21th? > >> > >> Anybody else going to TDWG? > >> > >> If possible I would like to organize a meeting about our little > >> subgroup. > >> > >> Cheers. > >> > >> On 12/07/2007, at 17:41, Tim Sutton wrote: > >> > >> > Hi > >> > > >> > I wont be able to attend this year. Will be great if someone can > >> > present ours tuff though. > >> > > >> > Regards > >> > > >> > Tim > >> > > >> > 2007/7/10, Javier de la Torre <jatorre(a)gmail.com>: > >> >> Hi all, > >> >> > >> >> is there anybody thinking in attending TDWG this year? I was just > >> >> lookig at the program and wondering if we should present and > >> abstract > >> >> to present this. Renato already asked me to present in his slot > >> for > >> >> "Integrating biodiversity data - 2" at 11:00 12:30. That is ok for > >> >> me. This year i will not be able to make it the whole week so i > >> plan > >> >> to travel on wednesday late 19th. > >> >> > >> >> But if there is people from the team around... we could make > >> try to > >> >> find a slot to work further on this... specially on creating > >> >> documentation to go for funding for next workshop :) If there > >> is many > >> >> people away we can maybe ask for conference equipment (they do > >> it a > >> >> lot here in OGC and is cool). > >> >> Sooo what about Friday at 17:30 for a meeting? > >> >> > >> >> Cheers. > >> >> _______________________________________________ > >> >> biogeosdi mailing list > >> >> biogeosdi(a)lists.tdwg.org > >> >> http://lists.tdwg.org/mailman/listinfo/biogeosdi > >> >> > >> > > >> > > >> > -- > >> > 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 > > _______________________________________________ > > biogeosdi mailing list > > biogeosdi(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/biogeosdi > > > > ------------------------------ > > Message: 5 > Date: Mon, 16 Jul 2007 00:27:28 +0200 > From: Javier de la Torre <jatorre(a)gmail.com> > Subject: Re: [Biogeosdi] OMWS getAlgorithms > To: "Tim Sutton" <tim(a)linfiniti.com> > Cc: biogeosdi(a)lists.tdwg.org > Message-ID: <2E41BF87-2452-4BD6-BA68-E02452FE0408(a)gmail.com> > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > Hi Tim, > > I have been continue taking a look at the parallels image... there > were several configs wrong in regard to the occurrences part... > hopefully now they are solved... at least in my parallels now is > working fine. > > But I do not manage to run models... I am trying trough the HTML, > once this is ready i will go for the Flex one ok?. When running the > model after a while I get this error back: > > ---------- > Warning: SimpleXMLElement::__construct() [function.SimpleXMLElement--- > construct]: namespace error : Namespace prefix SOAP-ENV on Fault is > not defined in /opt/biogeosdiTrunk/backend/services/OmService.php on > line 346 > > Warning: SimpleXMLElement::__construct() [function.SimpleXMLElement--- > construct]: <?xml version='1.0'?><SOAP-ENV:Fault><faultcode>SOAP- > ENV:Server</faultcode><faul in /opt/biogeosdiTrunk/backend/services/ > OmService.php on line 346 > > Warning: SimpleXMLElement::__construct() [function.SimpleXMLElement--- > construct]: ^ in /opt/biogeosdiTrunk/backend/services/OmService.php > on line 346 > > Fatal error: Call to a member function asXml() on a non-object in / > opt/biogeosdiTrunk/backend/services/OmService.php on line 347 > ---------- > > This is because I eventually get this from the omws: > > <?xml version='1.0'?><SOAP-ENV:Fault><faultcode>SOAP-ENV:Server</ > faultcode><faultstring>Model unavailable</faultstring></SOAP-ENV:Fault> > > So... Any idea os what is going wrong? > > Cheers. > > > > On 15/07/2007, at 23:54, Tim Sutton wrote: > > > Hi > > > > Im back now. I will try to resolve the rest of the issues in the > > Parallels vm (relating to the om service) this week and upload a new > > image. Did you give your ogc presentation already? > > > > Regards > > > > Tim > > > > 2007/7/13, Javier de la Torre <jatorre(a)gmail.com>: > >> Dont worry, > >> > >> As I said I hacked it on the client side. > >> And yes I did not manage to actually run models but I am a little bit > >> lost there so I was trying to make sure that the rest is working... > >> > >> When do you get back from your little country? How is extrema going? > >> I miss it! > >> > >> Cheers. > >> > >> On 12/07/2007, at 17:39, Tim Sutton wrote: > >> > >> > Hi Renato & Javi > >> > > >> > A quick note from an icafe in extreme... > >> > Renato I discovered there is a problem with the xml coming back > >> from > >> > teh svm alg - open it with ffox to see the error. Javi for now > >> you can > >> > resolve teh issue by simply removing > >> > /usr/local/lib/openmodeller/libomsvm.so . Also it seems the cron > >> job > >> > for the om service is not running - in the parallels image the > >> crontab > >> > for www-data is set up but I think you may need to check the cron > >> > configs to ensure that www-data is allowed to run cronjobs. > >> > > >> > Hope that helps! > >> > > >> > Regards > >> > > >> > Tim > >> > > >> > 2007/7/9, Javier de la Torre <jatorre(a)gmail.com>: > >> >> I am using the OMWS that Tim left me in a parallels image. I > >> believe > >> >> it is the last version as it is taken from repository and > >> compiled... > >> >> In any case I am not sure at all. > >> >> > >> >> I just made a hack on my side and now is working so I will wait > >> for > >> >> Tim to come back and figure out this as I dont know how > >> openmodeller > >> >> has been installed on this debian that I have. > >> >> > >> >> Cheers. > >> >> > >> >> Javier. > >> >> > >> >> > >> >> On 09/07/2007, at 19:18, Renato De Giovanni wrote: > >> >> > >> >> > Hello Javi, > >> >> > > >> >> > Can you tell me which omws service address are you using? > >> >> > > >> >> > The library does escape the special characters &, < and >, > >> but I've > >> >> > just noticed that double quotes were not being escaped (fixed > >> now). > >> >> > The library returns content in latin1. However, the soap server > >> >> will > >> >> > always return content in utf-8. > >> >> > > >> >> > I tested with the "official" omws service > >> >> > (http://modeller.cria.org.br/cgi-bin/om_soap_server.cgi) and it > >> >> seems > >> >> > to be working with the most recent list of algorithms. I've > >> dumped > >> >> > the response and copied to a static document if you want to > >> check: > >> >> > > >> >> > http://www.cria.org.br/~renato/omws_alg_metadata_dump.xml > >> >> > > >> >> > Maybe you're using another service address with an older > >> version of > >> >> > the library? Or maybe there's something doing some conversions > >> >> > between the real raw XML you receive and your parser? > >> >> > > >> >> > Regards, > >> >> > -- > >> >> > Renato > >> >> > > >> >> > On 9 Jul 2007 at 13:19, Javier de la Torre wrote: > >> >> > > >> >> >> Hey all, > >> >> >> > >> >> >> Finally I had to hack two things to handle incorrect > >> messages from > >> >> >> OMWS. I could not find where the metadata about the > >> algorithms is > >> >> >> stored so I hack in the biogeosdi code... that is what I made: > >> >> >> > >> >> >> //HACK BECUASE OMWS IS RETURNING INVALID XML > >> >> >> $rawXml = str_replace("&oldid","&oldid",$rawXml); > >> >> >> $rawXml = str_replace("& Shawe","& Shawe", > >> $rawXml); > >> >> >> $rawXml = utf8_encode($rawXml); > >> >> >> //HACK FINISHED > >> >> >> > >> >> >> The first two are to handle the not scaped parethesis. The > >> >> third one > >> >> >> is to encode the result as UTF8 because if not is not valid XML > >> >> >> without a encoding definition, which the response does not > >> >> include. > >> >> >> If the encoding is not defined I think the default is UTF8 and > >> >> this > >> >> >> seems to be latin1, but in any case I would really recommend > >> being > >> >> >> explicit about the encoding bein used. > >> >> >> > >> >> >> Cheers. > >> >> > > >> >> > _______________________________________________ > >> >> > biogeosdi mailing list > >> >> > biogeosdi(a)lists.tdwg.org > >> >> > http://lists.tdwg.org/mailman/listinfo/biogeosdi > >> >> > >> >> _______________________________________________ > >> >> biogeosdi mailing list > >> >> biogeosdi(a)lists.tdwg.org > >> >> http://lists.tdwg.org/mailman/listinfo/biogeosdi > >> >> > >> > > >> > > >> > -- > >> > 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 > > > > ------------------------------ > > _______________________________________________ > biogeosdi mailing list > biogeosdi(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/biogeosdi > > > End of biogeosdi Digest, Vol 8, Issue 14 > **************************************** -- 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 ________________________________________ 16/7/2007 - Filtered through antispam by ICT

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[Biogeosdi] OMWS getAlgorithms
by Javier de la Torre 16 Jul '07

16 Jul '07

Hey all, Finally I had to hack two things to handle incorrect messages from OMWS. I could not find where the metadata about the algorithms is stored so I hack in the biogeosdi code... that is what I made: //HACK BECUASE OMWS IS RETURNING INVALID XML $rawXml = str_replace("&oldid","&oldid",$rawXml); $rawXml = str_replace("& Shawe","& Shawe",$rawXml); $rawXml = utf8_encode($rawXml); //HACK FINISHED The first two are to handle the not scaped parethesis. The third one is to encode the result as UTF8 because if not is not valid XML without a encoding definition, which the response does not include. If the encoding is not defined I think the default is UTF8 and this seems to be latin1, but in any case I would really recommend being explicit about the encoding bein used. Cheers.

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[tdwg-ncd] Re: Terminology version 2
by Markus Döring 16 Jul '07

16 Jul '07

Hi, Id like to reformulate some queries cause they seem to be targeted at specimens (unit level) rather than collections. I think all queries are good real world use cases, but to be honest I think most of them are way too complex to be answered by NCD datasets. This is mostly due to the lack of standardised keywords (India, SE Asia, fallout area of cherynoble) but also because of too detailed questions (species names like 'bufo bufo' are unlikely to be listed for collections). But one lesson learned here is again the need for keyword standardisation. We should at least recommend ISO country codes or kind of enforce them through the editor. Not sure if NCD should mandate this cause you really might want to use different region schemas. Markus > Here are some sample queries to consider, and I'm sure you have > others in mind: > - All the birds from India all collections having birds from india > - All the instances of Bufo bufo resources in a single > institution's holdings all collections of the institution X that have specimens of Bufo bufo (what is a resource ???) > - All specimens collected in the fall-out area within a year after > the Cherynoble disaster all collections that have specimens collected in the fall-out area within a year after the Cherynoble disaster > - Specimens from SE Asia all collections that have specimens from SE Asia > - Endangered species, worldwide all collections that have worldwide endagered species > - All the herbarium collections in Europe > - All the herbarium and insect collections in Africa > - Published and unpublished resources relating to Darwin's collections > - Molecular collections available for destructive analysis > - Living collections of plants and animals > - Living collections for which observation of mating displays exists > > > I'm hoping we can come to a conclusion on this soon, to give Ruud > and Wouter what they need to keep moving on their work, and Connie > what she needs towards documentation. > > Best wishes to all! > Carol > > > > > > -----Original Message----- > From: Markus Döring [mailto:m.doering@bgbm.org] > Sent: Wednesday, July 11, 2007 9:39 AM > To: Constance Rinaldo; Neil Thomson; Butler, Carol; > Guenter.Waibel(a)rlg.org; Barbara Mathe; Doug Holland; Natural > Collections Descriptions mailing list; Wouter Addink; Ruud Altenburg > Subject: Re: Terminology version 2 > > Hi, > I've been talking to Anton Güntsch about the use of NCD and the > different proposals about controlled keywords. > We came to the conclusions that from an biological point of view we > would need an easy way to enter and extract at least the information > which collection is a herbarium, zoo, garden, aquarium, mineral > collection. > Some terms are specialisations of broader terms we had (herbarium < > specimen collection). We can model this in the ontology so that > applications know that every herbarium is also a specimen collection > (or "dead" collection as opposed to living collection?) and simply > keep all terms in the schema list. Would that be an option? We will > have all the broad terms and some frequently occuring > specialisations. for example: > > archive > library > facsimile > digital data # what exactly is this? arent observations also data, > maybe just a specialisation > observation > specimen > - herbarium > - nat.hist.collection # or how you call those dead animal > collections in general? > living collection > - garden > - zoo > - aquarium > > > > The other option to know whether a collection is a herbarium is to > say its a specimen collection and have a taxonomic indication of > "plants". For this we would need a short list of very broad taxonomic > terms. I think that would be very useful anyways. something along the > lines of plants, animals, fungus, bacteria, viruses and minerals. And > of course additionally the free taxonomic keywords list. Does this > sound strange from a librarian point of view? > > Markus > > > > > On Jul 9, 2007, at 3:37 PM, Döring, Markus wrote: > >> I do like the idea of having a very short high level list for a first >> categorisation. I would like to add "Living collection" and maybe >> also "DNA >> samples" or more generic "molecular samples" to the list though. So >> we have >> dead specimens, living beings and some molecular (?) samples like >> DNA, cell >> culture, proteins and alike. Well, cell cultures are not really >> molecular >> samples. Anyone with a better term for this? >> >> Markus >> >> >> Am 09.07.2007 15:17 Uhr schrieb "Constance Rinaldo" unter >> <crinaldo(a)oeb.harvard.edu>: >> >>> Have we absolutely agreed to merge ctype and pfocus? I still think >>> there is value in keeping them separate. Carol had an idea about >>> Ctype having a few, high-level choices with pfocus as a modifier. >>> The two fields really are different, although it is easy to see how >>> they can be a bit confusing. If we offer the right choices, though, >>> it will not be so confusing. Carol suggested to me: <ctype> " >>> should >>> become a very short, high level list - - only having: Archive, >>> Library, specimen/Object, Observation, Data/Information, >>> Representation/Facsimilie. Then <pFocus> would be something of a >>> modifier. " >>> >>> Can we still talk about this? I am not convinced that merging them >>> is the best idea. It seems even more confusing to me. >>> >>> >>> ************************************************************ >>> Constance Rinaldo, Librarian of the Ernst Mayr Library >>> Museum of Comparative Zoology, Harvard University, >>> 26 Oxford St., Cambridge, MA 02138 >>> voice: 617-495-4576; fax: 617-496-6838 >>> email: crinaldo(a)fas.harvard.edu >>> http://library.mcz.harvard.edu >>> ************************************************************ >>> "To a person uninstructed in natural history, his country or seaside >>> stroll is a walk through a gallery filled with wonderful works of >>> art, nine-tenths of which have their faces turned to the wall" >>> Thomas >>> Henry Huxley >>> >>> >>> On Jul 9, 2007, at 5:28 AM, Neil Thomson wrote: >>> >>>> Hi Carol, >>>> >>>> I'm happy that we have the right elements now and a good selection >>>> of terms within each. >>>> >>>> Just one comment on the collectionType terms - since they refer to >>>> collections, then maybe some of them should be in the plural? For >>>> example, image should be images. This wouldn't apply to all, for >>>> example event and expedition should remain as they are. >>>> >>>> Any other views? >>>> >>>> With thanks, >>>> Neil >>>> >>>> From: Butler, Carol [mailto:ButlerCR@si.edu] >>>> Sent: 06 July 2007 19:04 >>>> To: Neil Thomson; Guenter.Waibel(a)rlg.org; Markus Döring; Barbara >>>> Mathe; Constance Rinaldo; Doug Holland; Wouter Addink; Ruud >>>> Altenburg >>>> Subject: Terminology version 2 >>>> Importance: High >>>> >>>> Hi All, >>>> >>>> Thanks for your comments. I've attached version 2. You'll see >>>> that it collapses <primaryFocus> into <collectionType> (which we >>>> had in the past called "collection class"). I included examples >>>> for the terms that correspond to this revised element. >>>> >>>> >>>> As we're on a time schedule and need to agree on the property/ >>>> elements so that Ruud and Wouter can proceed, would you please send >>>> me your final comments on 1) the Property Comment definitions, and >>>> 2) updated Terms, no later than the end of your day on Monday, July >>>> 9th? My recollection is that we needed to complete this review by >>>> July 10th. I expect we may want to tune the term definitions and >>>> examples a bit, which Neil tells me can have a bit more time as >>>> long as the elements themselves are agreed. If I don't hear from >>>> you, I'll conclude that you don't have comments or edits on this >>>> version. >>>> >>>> >>>> I've also sent this to our wiki. >>>> >>>> >>>> Thanks! >>>> >>>> Carol >>>> >>>> >>>> >>>> >>> >> > > <NCD terms version 3_July11.xls>

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[Biogeosdi] Someone attending TDWG
by Javier de la Torre 16 Jul '07

16 Jul '07

Hi all, is there anybody thinking in attending TDWG this year? I was just lookig at the program and wondering if we should present and abstract to present this. Renato already asked me to present in his slot for "Integrating biodiversity data - 2" at 11:00 12:30. That is ok for me. This year i will not be able to make it the whole week so i plan to travel on wednesday late 19th. But if there is people from the team around... we could make try to find a slot to work further on this... specially on creating documentation to go for funding for next workshop :) If there is many people away we can maybe ask for conference equipment (they do it a lot here in OGC and is cool). Sooo what about Friday at 17:30 for a meeting? Cheers.

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[tdwg-ncd] Re: Terminology version 2
by Markus Döring 11 Jul '07

11 Jul '07

Hi, I've been talking to Anton Güntsch about the use of NCD and the different proposals about controlled keywords. We came to the conclusions that from an biological point of view we would need an easy way to enter and extract at least the information which collection is a herbarium, zoo, garden, aquarium, mineral collection. Some terms are specialisations of broader terms we had (herbarium < specimen collection). We can model this in the ontology so that applications know that every herbarium is also a specimen collection (or "dead" collection as opposed to living collection?) and simply keep all terms in the schema list. Would that be an option? We will have all the broad terms and some frequently occuring specialisations. for example: archive library facsimile digital data # what exactly is this? arent observations also data, maybe just a specialisation observation specimen - herbarium - nat.hist.collection # or how you call those dead animal collections in general? living collection - garden - zoo - aquarium The other option to know whether a collection is a herbarium is to say its a specimen collection and have a taxonomic indication of "plants". For this we would need a short list of very broad taxonomic terms. I think that would be very useful anyways. something along the lines of plants, animals, fungus, bacteria, viruses and minerals. And of course additionally the free taxonomic keywords list. Does this sound strange from a librarian point of view? Markus On Jul 9, 2007, at 3:37 PM, Döring, Markus wrote: > I do like the idea of having a very short high level list for a first > categorisation. I would like to add "Living collection" and maybe > also "DNA > samples" or more generic "molecular samples" to the list though. So > we have > dead specimens, living beings and some molecular (?) samples like > DNA, cell > culture, proteins and alike. Well, cell cultures are not really > molecular > samples. Anyone with a better term for this? > > Markus > > > Am 09.07.2007 15:17 Uhr schrieb "Constance Rinaldo" unter > <crinaldo(a)oeb.harvard.edu>: > >> Have we absolutely agreed to merge ctype and pfocus? I still think >> there is value in keeping them separate. Carol had an idea about >> Ctype having a few, high-level choices with pfocus as a modifier. >> The two fields really are different, although it is easy to see how >> they can be a bit confusing. If we offer the right choices, though, >> it will not be so confusing. Carol suggested to me: <ctype> " should >> become a very short, high level list - - only having: Archive, >> Library, specimen/Object, Observation, Data/Information, >> Representation/Facsimilie. Then <pFocus> would be something of a >> modifier. " >> >> Can we still talk about this? I am not convinced that merging them >> is the best idea. It seems even more confusing to me. >> >> >> ************************************************************ >> Constance Rinaldo, Librarian of the Ernst Mayr Library >> Museum of Comparative Zoology, Harvard University, >> 26 Oxford St., Cambridge, MA 02138 >> voice: 617-495-4576; fax: 617-496-6838 >> email: crinaldo(a)fas.harvard.edu >> http://library.mcz.harvard.edu >> ************************************************************ >> "To a person uninstructed in natural history, his country or seaside >> stroll is a walk through a gallery filled with wonderful works of >> art, nine-tenths of which have their faces turned to the wall" Thomas >> Henry Huxley >> >> >> On Jul 9, 2007, at 5:28 AM, Neil Thomson wrote: >> >>> Hi Carol, >>> >>> I'm happy that we have the right elements now and a good selection >>> of terms within each. >>> >>> Just one comment on the collectionType terms - since they refer to >>> collections, then maybe some of them should be in the plural? For >>> example, image should be images. This wouldn't apply to all, for >>> example event and expedition should remain as they are. >>> >>> Any other views? >>> >>> With thanks, >>> Neil >>> >>> From: Butler, Carol [mailto:ButlerCR@si.edu] >>> Sent: 06 July 2007 19:04 >>> To: Neil Thomson; Guenter.Waibel(a)rlg.org; Markus Döring; Barbara >>> Mathe; Constance Rinaldo; Doug Holland; Wouter Addink; Ruud >>> Altenburg >>> Subject: Terminology version 2 >>> Importance: High >>> >>> Hi All, >>> >>> Thanks for your comments. I’ve attached version 2. You’ll see >>> that it collapses <primaryFocus> into <collectionType> (which we >>> had in the past called “collection class”). I included examples >>> for the terms that correspond to this revised element. >>> >>> >>> As we’re on a time schedule and need to agree on the property/ >>> elements so that Ruud and Wouter can proceed, would you please send >>> me your final comments on 1) the Property Comment definitions, and >>> 2) updated Terms, no later than the end of your day on Monday, July >>> 9th? My recollection is that we needed to complete this review by >>> July 10th. I expect we may want to tune the term definitions and >>> examples a bit, which Neil tells me can have a bit more time as >>> long as the elements themselves are agreed. If I don’t hear from >>> you, I’ll conclude that you don’t have comments or edits on this >>> version. >>> >>> >>> I’ve also sent this to our wiki. >>> >>> >>> Thanks! >>> >>> Carol >>> >>> >>> >>> >> >

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[Biogeosdi] Problem with getting avaialble algorithms in OMWS
by Javier de la Torre 08 Jul '07

08 Jul '07

Hi all, Well this is from Tim and Renato... I have troubles dealing with the response from the getAvailableAlgorithms method. The XML it returns is invalid (some & not scaped in biographies and things like that). I am going to try to fake it for my demostration but you probably have forgotten to include code to escape text. Cheers.

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