July 2008 - tdwg-tag - lists.tdwg.org

Re: [tdwg-tapir] Release of "TapirBuilder" tool (now hosted on the TDWG site)
by Kevin Richards 21 Jul '08

21 Jul '08

I may be missing something, but is there some way to "discover", or search for existing response strucutres, query templates, output models? The reuse of these structures is obviously a key part of TAPIR, and hence the discovery of them. However, the tools look very cool and very useful - hopefully we get a whole bunch of keen people creating useful structures. Kevin >>> "Renato De Giovanni" <renato(a)cria.org.br> 07/18/08 1:12 AM >>> Dear Franck, I would like to say thanks again (now in public) for all your work and also for TDWG's support. These tools are an enormous help in creating XML files that are crucial for TAPIR (Javier was quite right about this when he suggested this kind of development during the last TAPIR meeting). No one deserves to edit XML by hand... I'll find some time during the next weeks to update the network builder's guide making references to these new tools. Many thanks, -- Renato On 17 Jul 2008 at 12:30, THEETEN Franck wrote: > > Dear all, > > We are proud to announce the first release of the "TapirBuilder" > tool. > This application allows the user to define templates facilitating the > configuration of new TAPIR networks, or networks that need to > interact with TAPIR providers. > It can > -Display the nodes of a response structure in a treeview and produce > a TAPIR output model which maps this response structure to the > available conceptual schemas defined in a CNS document. > -Produce templates for inventory and search queries from schemas and > concepts defined in a CNS document. > > You can access this tool on the TDWG website: > http://tapir.tdwg.org/builder/ > This URL also provides you with a default CNS document. > > This tool owes a lot to the TapirLink provider and the TapirChirp > libraries developed by Renato. I would also like to thank Renato for > his huge technical contribution and its assistance when developing > and testing the tool. Lee, Ricardo, Patricia Mergen for the > initiative and implementation of the project which took place in > ideal conditions and Bart Meganck for his help and insights when > conceiving the tools. > > Dońt hesitate to contact us for any suggestions for improvements. > > Best regards, > > Franck > > > Database Manager > Royal Museum for Central Africa > Department of African Zoology > Leuvensesteenweg, 13 > 3080 Tervuren, Belgium > Tel.: +32 2 769 56 24 _______________________________________________ tdwg-tapir mailing list tdwg-tapir(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tapir ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ WARNING: This email and any attachments may be confidential and/or privileged. They are intended for the addressee only and are not to be read, used, copied or disseminated by anyone receiving them in error. If you are not the intended recipient, please notify the sender by return email and delete this message and any attachments. The views expressed in this email are those of the sender and do not necessarily reflect the official views of Landcare Research. http://www.landcareresearch.co.nz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

3 2

[tdwg-tapir] Out of the office
by Jennifer A Pollock 19 Jul '08

19 Jul '08

I will be out of the office starting 07/02/2008 and will not return until 07/21/2008. I will not be checking email and voicemail regularly. Email is a more reliable method of reaching me (japollock(a)usgs.gov) I will get back to you when I return. Please contact Renee Jones at renee_jones(a)usgs.gov or 303.202.4220 if you need assistance.

1 0

Re: [tdwg-tapir] Release of "TapirBuilder" tool (now hosted on the TDWG site)
by THEETEN Franck 18 Jul '08

18 Jul '08

Thanks Lee and Renato, it was a very valuable experience for me and my team and we learnt a lot both technically and about the way to contribute to community projects. TAPIR is now embedded in a suite of tools and libraries which will improve its interoperability with other protocols and the development of extensions or modules based on the existing TAPIR providers. I must also say that the initial description of the awaited product that we received was pretty clear and has greatly facilitated the implementation of the tool. Cheers, Franck -----Original Message----- From: tdwg-tapir-bounces(a)lists.tdwg.org [mailto:tdwg-tapir-bounces@lists.tdwg.org] On Behalf Of Lee Belbin Sent: vendredi 18 juillet 2008 0:01 To: tdwg-tapir(a)lists.tdwg.org Subject: Re: [tdwg-tapir] Release of "TapirBuilder" tool (now hosted onthe TDWG site) I would echo Renato's thanks to you Franck. Nice to see another TAPIR tool out there for people to use! Many thanks Lee Lee Belbin TDWG Secretariat -----Original Message----- From: tdwg-tapir-bounces(a)lists.tdwg.org [mailto:tdwg-tapir-bounces@lists.tdwg.org] On Behalf Of Renato De Giovanni Sent: Thursday, 17 July 2008 11:12 PM To: tdwg-tapir(a)lists.tdwg.org Subject: Re: [tdwg-tapir] Release of "TapirBuilder" tool (now hosted on the TDWG site) Dear Franck, I would like to say thanks again (now in public) for all your work and also for TDWG's support. These tools are an enormous help in creating XML files that are crucial for TAPIR (Javier was quite right about this when he suggested this kind of development during the last TAPIR meeting). No one deserves to edit XML by hand... I'll find some time during the next weeks to update the network builder's guide making references to these new tools. Many thanks, -- Renato On 17 Jul 2008 at 12:30, THEETEN Franck wrote: > > Dear all, > > We are proud to announce the first release of the "TapirBuilder" > tool. > This application allows the user to define templates facilitating the > configuration of new TAPIR networks, or networks that need to > interact with TAPIR providers. > It can > -Display the nodes of a response structure in a treeview and produce > a TAPIR output model which maps this response structure to the > available conceptual schemas defined in a CNS document. > -Produce templates for inventory and search queries from schemas and > concepts defined in a CNS document. > > You can access this tool on the TDWG website: > http://tapir.tdwg.org/builder/ This URL also provides you with a > default CNS document. > > This tool owes a lot to the TapirLink provider and the TapirChirp > libraries developed by Renato. I would also like to thank Renato for > his huge technical contribution and its assistance when developing > and testing the tool. Lee, Ricardo, Patricia Mergen for the > initiative and implementation of the project which took place in > ideal conditions and Bart Meganck for his help and insights when > conceiving the tools. > > Don´t hesitate to contact us for any suggestions for improvements. > > Best regards, > > Franck > > > Database Manager > Royal Museum for Central Africa > Department of African Zoology > Leuvensesteenweg, 13 > 3080 Tervuren, Belgium > Tel.: +32 2 769 56 24 _______________________________________________ tdwg-tapir mailing list tdwg-tapir(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tapir _______________________________________________ tdwg-tapir mailing list tdwg-tapir(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tapir ########################################### This message has been scanned by ICT - Africa Museum ________________________________________ 18/7/2008 - Filtered through antispam by ICT

2 1

[tdwg-tapir] Release of "TapirBuilder" tool (now hosted on the TDWG site)
by THEETEN Franck 17 Jul '08

17 Jul '08

Dear all, We are proud to announce the first release of the "TapirBuilder" tool. This application allows the user to define templates facilitating the configuration of new TAPIR networks, or networks that need to interact with TAPIR providers. It can -Display the nodes of a response structure in a treeview and produce a TAPIR output model which maps this response structure to the available conceptual schemas defined in a CNS document. -Produce templates for inventory and search queries from schemas and concepts defined in a CNS document. You can access this tool on the TDWG website: http://tapir.tdwg.org/builder/ This URL also provides you with a default CNS document. This tool owes a lot to the TapirLink provider and the TapirChirp libraries developed by Renato. I would also like to thank Renato for his huge technical contribution and its assistance when developing and testing the tool. Lee, Ricardo, Patricia Mergen for the initiative and implementation of the project which took place in ideal conditions and Bart Meganck for his help and insights when conceiving the tools. Don't hesitate to contact us for any suggestions for improvements. Best regards, Franck Database Manager Royal Museum for Central Africa <http://www.africamuseum.be/> Department of African Zoology Leuvensesteenweg, 13 3080 Tervuren, Belgium Tel.: +32 2 769 56 24 ########################################### This message has been scanned by ICT - Africa Museum ________________________________________ 17/7/2008 - Filtered through antispam by ICT

3 2

[tdwg-tapir] openModeller querying TAPIR providers
by Renato De Giovanni 17 Jul '08

17 Jul '08

Dear all, I should also say that I already used these new tools (TAPIR builders) when I was writing a new openModeller driver to read species occurrence data from TAPIR/DarwinCore providers. If anyone is interested in this kind of development (deciding about how to interact with TAPIR providers) these are the steps that I followed: 1) Create a response structure to define how search results will be returned. In this case I used XML Spy to define an XML Schema which would be used to produce the easiest XML to be parsed with expat (all data returned as XML attributes). This document was made available here: http://openmodeller.cria.org.br/xml/tapir/1.0/rs.xsd 2) Create a TAPIR output model for the response structure. I used the output model builder to map all nodes from the response structure to DarwinCore concepts. This document was made available here: http://openmodeller.cria.org.br/xml/tapir/1.0/om.xml 3) Create a TAPIR search template to facilitate interaction with TAPIR providers, pre-filter records and allow the existence of TAPIRLite providers that can understand the same request. I used the search template builder and made the document available here: http://openmodeller.cria.org.br/xml/tapir/1.0/st_v3.xml If I need to make any change in these documents, I save them with a new name to avoid problems with providers that could be using older cached versions based on the document URL. So now the client (openModeller) just needs to check if the provider has the necessary capabilities before sending search requests. I'm basically checking if the provider supports the search operation, if all needed concepts are mapped, and if it supports "any output model" (full TAPIR providers) or if it supports the specific query template that I created (TAPIRLite providers). By the way, this driver is already available in the latest release of the openModeller library (yet to be included in a new release of openModeller Desktop). Best Regards, -- Renato

1 0

[tdwg-tapir] interesting position available for experienced PHP programmer
by Wouter Addink 11 Jul '08

11 Jul '08

Hi all, Sorry for cross posting. Job opportunity at ETI BioInformatics: Experienced Software Engineer Internet Applications ETI BioInformatics (www.eti.uva.nl) develops cutting edge information systems that facilitate information sharing in the field of biodiversity on a global scale. Connecting distributed databases into interoperable networks with dedicated information portals provides an efficient, customizable solution that meets information needs in science, education, policy making and environmental awareness in general. ETI, an NGO in operational relation with UNESCO, promotes equal access to quality biodiversity information. We develop information networks in international initiatives such as the Global Biodiversity Information Facility (GBIF), the Catalogue of Life (Species2000 & ITIS), and build user-targeted systems for species identification in European projects (e.g. KeyToNature, MARBEF, EDIT, Synthesys). In the Netherlands ETI works for NLBIF (national GBIF Node), and the Ministry of Agriculture (BioWIE). We participate in bilateral projects with Tanzania, Colombia, Bulgaria, and Italy. ETI BioInformatics (NL) has a staff of 13, and ETI-IS (based in UK) a staff of 4. For our expanding portfolio we are looking for an experienced software engineer to strengthen our team in Amsterdam in developing rich internet PHP applications, with service orientated architecture and semantic web technologies. We offer varied and challenging, international projects; support to express your own ideas, solutions and initiatives; a dedicated, enthusiastic and experienced team; a working environment with the latest hardware and software; a competitive salary; 25 vacation days and a good pension arrangement. Qualifications: Programming languages: provable very experienced in PHP 5 (OOP, Smarty), JavaScript (Ajax, Json, Jquery), and HTML; recommended: working knowledge of JAVA/JSP/JAVA Applets, and Python. Database management systems: very experienced with MySQL, and PostgreSQL; recommended: working knowledge of PostGIS, AdoDB abstraction layer, Oracle. Further: experience with MVC frameworks, CVS, and recommended skills in XML, XSLT, XML Schema, RDF/OWL, REST and SOAP Web services, UML, Drupal, Apache, Open Source development, Multilanguage solutions, Mobile application development Personality: engaged, team worker, pro-active, innovative. Education: university degree in (Biodiversity) informatics or a comparable demonstrable level of knowledge and experience. Languages: English (required), (Dutch, French or Spanish are an advantage). Please send your application and CV to jobs(a)eti.uva.nl. For more information please contact Peter Schalk (pschalk(a)eti.uva.nl) Wouter Addink (waddink(a)eti.uva.nl) or Marc Brugman (mbrugman(a)eti.uva.nl)

1 0

ontology bug tracking
by Bob Morris 08 Jul '08

08 Jul '08

Is there a bug tracking facility for the ontology? I am trying to get SPM to be OWL DL, which in turn depends on the core being OWL DL, but I run into various lint in the core. For example, Base.rdf is not valid RDF according to the w3 validator, even if the document is pasted into the validator. Thanks Bob -- Robert A. Morris Professor of Computer Science UMASS-Boston ram(a)cs.umb.edu http://bdei.cs.umb.edu/ http://www.cs.umb.edu/~ram http://www.cs.umb.edu/~ram/calendar.html phone (+1)617 287 6466

1 0

[tdwg-tapir] Content Delivery Networks (CDN) options
by Phil Cryer 01 Jul '08

01 Jul '08

(Offtopic, but hoping some other institution has some exerience on this) Does anyone have any CDN experience they'd like to share? Currently we need to move about 80-100GB of PDFs to a provider, because we're serving up ~8.5GB/day, and it's killing our internal bandwidth. We've considered things as basic as GoDaddy, but at 6.99$/month that has to just be file hosting, not a CDN right? A package for that amount of data at Cachefly looks like it'd be around 99$/month. Other things like Amazon's S3 are being priced out, but what about Akami, Level3, etc. Any advice, guidance appreciated, we see this as a short term fix, with a new strategy to come for next year. Thanks P -- Phil Cryer | Open Source Development Missouri Botanical Garden | Lat: 38.6112700 | Lon: -90.2583440 Email: phildotcryeratmobotdotorg | IM GoogleTalk/Skype: phil.cryer

1 0