January 2006 - tdwg-tag - lists.tdwg.org

Re: greetings
by Ricardo Scachetti Pereira 20 Jan '06

20 Jan '06

Ben, Thank you very much for sharing the outline of your presentation with us. It certainly seems ideal for our purposes. We would be very interested in picking your brains on wider semantic interoperability issues during the workshop. Regarding LSIDs specifically, our biggest challange is to find an appropriate way to define stable byte-identical data for our objects. We have therefore been thinking mostly of turning everything to metadata. We would be very interested in knowing what your thoughts are regarding that issue. Best regards, Ricardo Benjamin H Szekely wrote: > > Hi All, > Thank you again for including me in your workshop. From reading > Rod's paper and many of the following comments, it seems that this > community is certainly on the right track and shares a similar vision > for LSIDs and metadata to that of our development team here in > Cambridge, MA. I encourage anybody to ask questions on the list about > LSID or Semantic Web technology in general. Our team has been elbow > deep in the Semantic Web for 3 years and have been working on a wide > variety of projects outside of LSID including Storage and replication, > annotation, workflow, and RDF-based user interfaces, > > I am tentatively planning to organize my talk as follows: > > - Overview of LSID (10-15 minutes) > > - Survey of global LSID participation (10-15 minutes) > > - Brief overview of IBM Cambridge Semantic Web projects (5 minutes) > > I am certainly open to reorganization. I'm not planning on discussing > too many technical and implementation details, but I'd be happy to > discuss these throughout the week at the workshop. > > - Ben

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greetings
by Benjamin H Szekely 19 Jan '06

19 Jan '06

Hi All, Thank you again for including me in your workshop. From reading Rod's paper and many of the following comments, it seems that this community is certainly on the right track and shares a similar vision for LSIDs and metadata to that of our development team here in Cambridge, MA. I encourage anybody to ask questions on the list about LSID or Semantic Web technology in general. Our team has been elbow deep in the Semantic Web for 3 years and have been working on a wide variety of projects outside of LSID including Storage and replication, annotation, workflow, and RDF-based user interfaces, I am tentatively planning to organize my talk as follows: - Overview of LSID (10-15 minutes) - Survey of global LSID participation (10-15 minutes) - Brief overview of IBM Cambridge Semantic Web projects (5 minutes) I am certainly open to reorganization. I'm not planning on discussing too many technical and implementation details, but I'd be happy to discuss these throughout the week at the workshop. - Ben

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Questions to LSID and DOI specialists
by Ricardo Scachetti Pereira 19 Jan '06

19 Jan '06

Folks, As you probably know, some of us will be getting together in a couple of weeks to discuss the use of Globally Unique Identifiers in our community, at the GUID-1 Workshop in Durham, USA. One of the topics we will discuss during the workshop is the adoption of an existing GUID technology. Joining us at the meeting we will have specialists in some of the GUID technologies under consideration. In particular, we will meet at the workshop: - Ben Szekely, who is a Software Engineer at IBM. Ben is one of the creators of the Life Sciences Identifiers (LSID) specification and one of the main developers of a LSID reference implementation in Java; and - George Garrity, who is a Professor at the Department of Microbiology and Molecular Genetics at Michigan State University. Professor Garrity is leading the Names4Life project, a member of the International DOI Foundation which is planning to assign digital object identifiers (DOIs) to semantically meaningful nodes in a nomenclature system. Both Ben Szekely and George Garrity kindly accepted our invitation to give a short 30-minute talk each on the Life Sciences Identifiers (LSID) and Digital Object Identifiers (DOI), respectively, on the first day of our workshop (see the agenda: http://wiki.gbif.org/guidwiki/wikka.php?wakka=GUID1Agenda). So, if you have specific questions regarding either technology, please take advantage of this opportunity and ask your question to the list, or directly to me. We will do whatever we can to address the questions and maybe even address it in their presentations (if time allows). Please ask your questions even if you are not going to attend to the workshop, so you make sure the participants address the concerns you may have. The results will appear on the minutes of the workshop, to be published on our wiki shortly after it ends. Cheers, Ricardo

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Re: [tdwg-tapir] FAQ page
by "Döring, Markus" 17 Jan '06

17 Jan '06

Chuck, The original BioCASE uses its own registry for service discovery, has its own kind of cache and discovers availble data elements (concepts) through the biocase wrappers(=services) themselves. This "capability" request does also exist in TAPIR. So a service can technically describe itself to clients. The current work on BioCASE makes use of the GBIF UDDI, but adds some extra data to it (mainly for statistics). Markus -----Ursprüngliche Nachricht----- Von: Chuck.Miller(a)mobot.org [mailto:Chuck.Miller@mobot.org] Gesendet: Dienstag, 17. Januar 2006 15:57 An: Döring, Markus; Chuck.Miller(a)mobot.org; tdwg-tapir(a)lists.tdwg.org Cc: Berendsohn, Walter G. Betreff: RE: [tdwg-tapir] FAQ page Thanks, Markus. That helps add more to the ontology of data exchange. But, you also added another term - wrapper. So, we have services, wrappers, protocols, providers and portals. Still confusing to most I'm afraid. My general request is for "someone" to produce a single document that organizes it all into a form understandable by the non-programmers. Also, does BioCASE use UDDI for discovery of the provider metadata and the data elements available from the provider/wrapper? Chuck -----Original Message----- From: "Döring, Markus" [mailto:m.doering@BGBM.org] Sent: Friday, January 13, 2006 4:27 AM To: Chuck.Miller(a)mobot.org; tdwg-tapir(a)lists.tdwg.org Cc: Berendsohn, Walter G. Subject: AW: [tdwg-tapir] FAQ page Chuck, from the BioCASE side I can add the following: BioCASE ------- BioCASE is a European project and its also the name of the protocol (sometimes written as BioCASe). The BioCASE portal (software) is referred to simply as the BioCASE portal. The core of the BioCASE provider software (BPS) is called PyWrapper. This wrapper understands the BioCASE protocol, but also the Species2000/SPICE protocol. So you can use it to serve data in ABCD, SPICE/Species2000, DarwinCore, MCPDH, NaturalCollectionMetadata (NCD) or nearly any other XML standard with some limitations (unfortunately used by SDD). TAPIR ------ TAPIR refers only to the protocol. The primary goal of TAPIR is the unification of DiGIR and BioCASE, thus replacing them so that data providers and clients can access our data in the same way. There is a full TAPIR provider software available based on the PyWrapper which is called TAPIR PyWrapper. There is no TAPIR portal yet or any other client application for TAPIR. RDF ---- In many discussions currently RDF is considered a better way to share our data. To fully go the RDF way we would have to migrate the TDWG XML schema standards to some sort of RDF schema or ontology. There is still a performance problem with RDF if used with millions of records (equivalent to maybe hundreds of millions of rdf statements). So I dont see RDF being used right now in full production, but its surely a promising way to go. Personally I am a bit concerned we are about to split the community again - this time into TAPIR and RDF; but maybe thats how technological progress is made... regards, Markus -----Ursprüngliche Nachricht----- Von: tdwg-tapir-bounces(a)lists.tdwg.org [mailto:tdwg-tapir-bounces@lists.tdwg.org] Im Auftrag von Dave Vieglais Gesendet: Freitag, 13. Januar 2006 16:03 An: Javier privat Cc: tdwg-tapir(a)lists.tdwg.org Betreff: Re: [tdwg-tapir] FAQ page Much of the confusion has come about I guess because DiGIR 2 is actually a code name for a project that is building a data service application that supports pluggable protocols. There is no official name for that application, and there is no release (yet). So to try and help things a little: DiGIR 2 is a data server application, not a protocol. The application supports multiple protocols for accessing the data it serves including: * DiGIR 1.5 (i.e. the current version of DiGIR) * TAPIR (may not be a full implementation) * WFS (OGC Web Feature Service) * possibly SPARQL (an RDF query language) DiGIR 2 data server is being developed because we do not yet feel that there is a single unifying protocol for our community, and that new protocols may emerge and then different versions of the protocols will be developed. Having a single data service application that supports pluggable protocols will, we hope, significantly reduce the maintenance and configuration overhead of those interested in serving their data, since one the application is installed, we expect it to be a relatively trivial matter to add protocols or updates to existing protocols. We will provide more information about the project as updates become available. regards, Dave Vieglais Javier de la Torre said the following on 1/12/2006 8:23 AM: > Dear all, > > We had today the GBIF ICT Expert Group meeting and a lot of people > where making questions about TAPIR. > Seems that there is confusion regarding names. People were asking why > there is Digir 2 if we are all going to TAPIR and things like that. > There were also questions regarding when things are gonna be ready, > what can we expect from Digir2 and TAPIR pywrapper and what would be > the reasons to migrate, how difficult is going to be to migrate, etc. > > I was thinking of extending the FAQ page that Renato started in Madrid > to answer all these questions, but I need some help specially from the > Digir2 people. > > -What is the status of Digir2? > -Is it going to be difficult to update from Digir 1 to 2? > > I will in any case start writing there and maybe you can then modify > extend thins related to you. > > Best regards, > > Javi. > > _______________________________________________ > tdwg-tapir mailing list > tdwg-tapir(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tapir_lists.tdwg.org > _______________________________________________ tdwg-tapir mailing list tdwg-tapir(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tapir_lists.tdwg.org

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GML expressed in RDF
by Roger Hyam 17 Jan '06

17 Jan '06

I just came across a couple of pages pertinent to the recent discussion regarding GML. http://danbri.org/words/2005/07/26/110 http://www.w3.org/2003/01/geo/ Among the general noise made by people in St Petersburg were the comments that GML as a whole was "too complex". Perhaps profiling a subset in RDF (especially under the umbrella of W3C) would solve several problems. Anyhow worth thinking about if we want to freely mix geographic data with our biodiversity data. What do you think? Roger -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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EGU General Assembly - call for TDWG GUID contribution
by Robert Huber 17 Jan '06

17 Jan '06

Dear Colleagues, I apologize this very late information, but it seems as if my participation in this TDWG group is so new that I didn't see the obvious! The obvious is that I am co convener of a geoinformatics session at the EGU 2006 one of the most important geoscience conferences. The session is dedicated to database and information management topics in sedimentology , stratigraphy and paleontology. And of course, taxonomy and the management of taxonomic knowledge is of special importance here. So my question is: is anybody interested to introduce the GUID thing there? Any other contribution is of course also welcome! The deadline for abstract submission to this year's European Geosciences Union (EGU) General Assembly is approaching fast! Deadline for receipt of abstracts : 20 January 2006 . The official deadline was already last friday, but additional contributions can be sent to me : rhuber(a)wdc.mare.org. Here is the info on the session: SSP21 "Geoinformatics and Information Management in Stratigraphy, Sedimentology & Paleontology". Conveners: Jens Klump (GeoForschungsZentrum Potsdam), Kerstin Lehnert (Lamont-Doherty Earth Observatory of Columbia University) Robert Huber (MARUM, University of Bremen). This session continues the discussion process initiated at the EGU General Assembly 2005 and at the AGU Fall Meeting 2005. At both meetings iGeoInfo (http://www.igeoinfo.org) had organised sessions dedicated to networking scientists working in informatics and information management in the geological sciences. Both the oral sessions and the poster sessions were very well attended. Data on stratigraphy, sedimentology and paleontology are heterogeneous and diverse. In many countries around the globe, an increasing number of Geoscience projects are developing and maintaining digital data and information systems together with tools for data analysis and visualization. Coordination and collaboration among these projects, and their integration are essential in order to maximize the impact of these globally distributed Geoinformatics resources. This session emphasizes the importance of international collaboration in the development of a Geoscience cyberinfrastructure that will successfully promote advances in Geoscience research and enable new approaches to addressing scientific problems that lead to new discoveries and an improved understanding of the Earth. We have defined two objectives for this session: (1) to draw attention to and discuss the many political, cultural, organizational, and technical challenges that need to be addressed and overcome in order to achieve a truly global cyberinfrastructure for the Geosciences. (2) to highlight examples of international collaborations that successfully coordinate and integrate their efforts. Important Dates: (Abstract Deadline 13 January 2006) EGU General Assembly Vienna, Austria, 2-7 April 2006 http://meetings.copernicus.org/egu2006/ Deadline for support applications : 9 December 2005 (passed) Deadline for receipt of abstracts : 13 January 2006 Deadline for pre-registration : 10 March 2006 Please, forward this message also to your colleagues. We are looking forward to seeing you at this meeting. Regards, Jens Klump, Kerstin Lehnert and Robert Huber Dr. Robert Huber WDC-MARE / PANGAEA - www.pangaea.de, www.wdc-mare.org Stratigraphy.net - www.stratigraphy.net _____________________________________________ MARUM - Institute for Marine Environmental Sciences (location) University Bremen Leobener Strasse POP 330 440 28359 Bremen Phone ++49 421 218-65593, Fax ++49 421 218-65505 e-mail rhuber@@wdc-mare.org, robert.huber(a)stratigraphy.net

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Re: [tdwg-tapir] FAQ page
by Chuck.Miller＠mobot.org 17 Jan '06

17 Jan '06

Thanks, Markus. That helps add more to the ontology of data exchange. But, you also added another term - wrapper. So, we have services, wrappers, protocols, providers and portals. Still confusing to most I'm afraid. My general request is for "someone" to produce a single document that organizes it all into a form understandable by the non-programmers. Also, does BioCASE use UDDI for discovery of the provider metadata and the data elements available from the provider/wrapper? Chuck -----Original Message----- From: "Döring, Markus" [mailto:m.doering@BGBM.org] Sent: Friday, January 13, 2006 4:27 AM To: Chuck.Miller(a)mobot.org; tdwg-tapir(a)lists.tdwg.org Cc: Berendsohn, Walter G. Subject: AW: [tdwg-tapir] FAQ page Chuck, from the BioCASE side I can add the following: BioCASE ------- BioCASE is a European project and its also the name of the protocol (sometimes written as BioCASe). The BioCASE portal (software) is referred to simply as the BioCASE portal. The core of the BioCASE provider software (BPS) is called PyWrapper. This wrapper understands the BioCASE protocol, but also the Species2000/SPICE protocol. So you can use it to serve data in ABCD, SPICE/Species2000, DarwinCore, MCPDH, NaturalCollectionMetadata (NCD) or nearly any other XML standard with some limitations (unfortunately used by SDD). TAPIR ------ TAPIR refers only to the protocol. The primary goal of TAPIR is the unification of DiGIR and BioCASE, thus replacing them so that data providers and clients can access our data in the same way. There is a full TAPIR provider software available based on the PyWrapper which is called TAPIR PyWrapper. There is no TAPIR portal yet or any other client application for TAPIR. RDF ---- In many discussions currently RDF is considered a better way to share our data. To fully go the RDF way we would have to migrate the TDWG XML schema standards to some sort of RDF schema or ontology. There is still a performance problem with RDF if used with millions of records (equivalent to maybe hundreds of millions of rdf statements). So I dont see RDF being used right now in full production, but its surely a promising way to go. Personally I am a bit concerned we are about to split the community again - this time into TAPIR and RDF; but maybe thats how technological progress is made... regards, Markus -----Ursprüngliche Nachricht----- Von: tdwg-tapir-bounces(a)lists.tdwg.org [mailto:tdwg-tapir-bounces@lists.tdwg.org] Im Auftrag von Dave Vieglais Gesendet: Freitag, 13. Januar 2006 16:03 An: Javier privat Cc: tdwg-tapir(a)lists.tdwg.org Betreff: Re: [tdwg-tapir] FAQ page Much of the confusion has come about I guess because DiGIR 2 is actually a code name for a project that is building a data service application that supports pluggable protocols. There is no official name for that application, and there is no release (yet). So to try and help things a little: DiGIR 2 is a data server application, not a protocol. The application supports multiple protocols for accessing the data it serves including: * DiGIR 1.5 (i.e. the current version of DiGIR) * TAPIR (may not be a full implementation) * WFS (OGC Web Feature Service) * possibly SPARQL (an RDF query language) DiGIR 2 data server is being developed because we do not yet feel that there is a single unifying protocol for our community, and that new protocols may emerge and then different versions of the protocols will be developed. Having a single data service application that supports pluggable protocols will, we hope, significantly reduce the maintenance and configuration overhead of those interested in serving their data, since one the application is installed, we expect it to be a relatively trivial matter to add protocols or updates to existing protocols. We will provide more information about the project as updates become available. regards, Dave Vieglais Javier de la Torre said the following on 1/12/2006 8:23 AM: > Dear all, > > We had today the GBIF ICT Expert Group meeting and a lot of people > where making questions about TAPIR. > Seems that there is confusion regarding names. People were asking why > there is Digir 2 if we are all going to TAPIR and things like that. > There were also questions regarding when things are gonna be ready, > what can we expect from Digir2 and TAPIR pywrapper and what would be > the reasons to migrate, how difficult is going to be to migrate, etc. > > I was thinking of extending the FAQ page that Renato started in Madrid > to answer all these questions, but I need some help specially from the > Digir2 people. > > -What is the status of Digir2? > -Is it going to be difficult to update from Digir 1 to 2? > > I will in any case start writing there and maybe you can then modify > extend thins related to you. > > Best regards, > > Javi. > > _______________________________________________ > tdwg-tapir mailing list > tdwg-tapir(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tapir_lists.tdwg.org > _______________________________________________ tdwg-tapir mailing list tdwg-tapir(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tapir_lists.tdwg.org

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[tdwg-tapir] FAQ page
by Roger Hyam 16 Jan '06

16 Jan '06

I should add my 2 cents here. I think it is my role (when I can get the documentation thing out the way) to pull together an overview of the whole TDWG 'thing'. This will be part of the architecture along with a vision of where we should be going. A glossary of terms is a start but their needs to be more than that. We need a Bush (senior) "Vision Thing" here. I imagine the vision will crystallize out after the GUID meeting at which point lots of people will say "it will never work" and we will have to change things or build demo systems or whatever. At the moment it looks likely (as Donald says) that we will need to move toward an RDF/OWL way of doing things but I don't see this as being based on big triple stores as I don't think all services will give the ability to search on all possible assertions (I have not had a chance to look at the logs I received properly but it doesn't look to me that people want to do complex searches and we should perhaps have clear test cases before we engineer a solution to support arbitrary requests rather than basing it on what we thing people might want to do). What is clear is that people want to extend and mix and match schemas. ABCD has been added to repeatedly and DarwinCore has been forked. Also we don't make use of metadata standards like DublinCore of vCard which means that engineering generic solutions is likely to be difficult. RDF/OWL type approach definitely solves these kinds of problem. Even if we still exchange templated chunks of XML those chunks can also be RDF compliant, served through Tapir and reference a central OWL ontology. Everything changes but things remain the same. Hope this helps, Roger -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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Re: [tdwg-tapir] FAQ page
by "Döring, Markus" 16 Jan '06

16 Jan '06

Chuck, from the BioCASE side I can add the following: BioCASE ------- BioCASE is a European project and its also the name of the protocol (sometimes written as BioCASe). The BioCASE portal (software) is referred to simply as the BioCASE portal. The core of the BioCASE provider software (BPS) is called PyWrapper. This wrapper understands the BioCASE protocol, but also the Species2000/SPICE protocol. So you can use it to serve data in ABCD, SPICE/Species2000, DarwinCore, MCPDH, NaturalCollectionMetadata (NCD) or nearly any other XML standard with some limitations (unfortunately used by SDD). TAPIR ------ TAPIR refers only to the protocol. The primary goal of TAPIR is the unification of DiGIR and BioCASE, thus replacing them so that data providers and clients can access our data in the same way. There is a full TAPIR provider software available based on the PyWrapper which is called TAPIR PyWrapper. There is no TAPIR portal yet or any other client application for TAPIR. RDF ---- In many discussions currently RDF is considered a better way to share our data. To fully go the RDF way we would have to migrate the TDWG XML schema standards to some sort of RDF schema or ontology. There is still a performance problem with RDF if used with millions of records (equivalent to maybe hundreds of millions of rdf statements). So I dont see RDF being used right now in full production, but its surely a promising way to go. Personally I am a bit concerned we are about to split the community again - this time into TAPIR and RDF; but maybe thats how technological progress is made... regards, Markus -----Ursprüngliche Nachricht----- Von: tdwg-tapir-bounces(a)lists.tdwg.org [mailto:tdwg-tapir-bounces@lists.tdwg.org] Im Auftrag von Dave Vieglais Gesendet: Freitag, 13. Januar 2006 16:03 An: Javier privat Cc: tdwg-tapir(a)lists.tdwg.org Betreff: Re: [tdwg-tapir] FAQ page Much of the confusion has come about I guess because DiGIR 2 is actually a code name for a project that is building a data service application that supports pluggable protocols. There is no official name for that application, and there is no release (yet). So to try and help things a little: DiGIR 2 is a data server application, not a protocol. The application supports multiple protocols for accessing the data it serves including: * DiGIR 1.5 (i.e. the current version of DiGIR) * TAPIR (may not be a full implementation) * WFS (OGC Web Feature Service) * possibly SPARQL (an RDF query language) DiGIR 2 data server is being developed because we do not yet feel that there is a single unifying protocol for our community, and that new protocols may emerge and then different versions of the protocols will be developed. Having a single data service application that supports pluggable protocols will, we hope, significantly reduce the maintenance and configuration overhead of those interested in serving their data, since one the application is installed, we expect it to be a relatively trivial matter to add protocols or updates to existing protocols. We will provide more information about the project as updates become available. regards, Dave Vieglais Javier de la Torre said the following on 1/12/2006 8:23 AM: > Dear all, > > We had today the GBIF ICT Expert Group meeting and a lot of people > where making questions about TAPIR. > Seems that there is confusion regarding names. People were asking why > there is Digir 2 if we are all going to TAPIR and things like that. > There were also questions regarding when things are gonna be ready, > what can we expect from Digir2 and TAPIR pywrapper and what would be > the reasons to migrate, how difficult is going to be to migrate, etc. > > I was thinking of extending the FAQ page that Renato started in Madrid > to answer all these questions, but I need some help specially from the > Digir2 people. > > -What is the status of Digir2? > -Is it going to be difficult to update from Digir 1 to 2? > > I will in any case start writing there and maybe you can then modify > extend thins related to you. > > Best regards, > > Javi. > > _______________________________________________ > tdwg-tapir mailing list > tdwg-tapir(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tapir_lists.tdwg.org > _______________________________________________ tdwg-tapir mailing list tdwg-tapir(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tapir_lists.tdwg.org

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[tdwg-tapir] FAQ page
by Javier de la Torre 13 Jan '06

13 Jan '06

Dear all, We had today the GBIF ICT Expert Group meeting and a lot of people where making questions about TAPIR. Seems that there is confusion regarding names. People were asking why there is Digir 2 if we are all going to TAPIR and things like that. There were also questions regarding when things are gonna be ready, what can we expect from Digir2 and TAPIR pywrapper and what would be the reasons to migrate, how difficult is going to be to migrate, etc. I was thinking of extending the FAQ page that Renato started in Madrid to answer all these questions, but I need some help specially from the Digir2 people. -What is the status of Digir2? -Is it going to be difficult to update from Digir 1 to 2? I will in any case start writing there and maybe you can then modify extend thins related to you. Best regards, Javi.

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