February 2006 - tdwg-tag - lists.tdwg.org

Definition of terms: Resolving, Searching Querying
by Roger Hyam 12 Feb '06

12 Feb '06

Hi All, I'd like to start nailing things down a little by getting some terms defined. Recent side discussions at the GUID-1 meeting were around the differences between resolving, searching and querying. These terms are confused so I would like to propose some definitions that we could use going forward. The intent here is to make up something useful rather than work out what people have meant in the past by these terms. 1. *Resolving.* This means to convert a pointer into a data object. Examples would be to resolve an LSID and get back either data or metadata or resolve a url and get back a web page in html. 2. *Searching.* This means to select a set of objects (or their proxies) on the basis of the values of their properties. The objects are predefined (implicitly part of the call) and we are simply looking for them. An example would be finding pages on Google. 3. *Querying.* This means to ask a question of a data source that returns objects that are defined as part of the call. An example would be an SQL query where the response object (tuples) are defined in the query. Using only 'resolving' it would be possible for an agent to crawl around and data harvest (i.e. a web crawler). Using resolving and searching would make the crawler more efficient at gathering data for specific tasks. Querying allows arbitrary data retrieval. At a single data source resolving should be easy to implement technically, searching slightly harder and querying 'non-trivial'. Resolving is 'easy' to do in a distributed environment (e.g. just use DNS like LSID) and searching is harder but can be federated (many examples including Rod's work) or cached (GBIF, Google). Distributed querying is 'non-trivial' in the extreme though some GRID guys will probably solve it for us in the future. Is everyone OK with these definitions? If no one objects then I'll add them to the Wiki and we can work with them. Thanks for your thoughts, Roger -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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RDF versus GML; old but relevant (?)
by Blum, Stan 12 Feb '06

12 Feb '06

I (we) desperately need to solve the puzzle of how to compose (re-use) conceptual specifications. Can we create a flexible system of base classes that can be snapped together to make useful data exchange applications? I think this is one of, if not THE most import tasks for the incipient TDWG Architecture group. So I'm trying to educate myself about RDF versus XML (and their respective schema tools). I came across this comment on RDF versus GML, http://www.mapbureau.com/gml/, which contained this: <excerpt> [...] GML is not directly composable with other XML languages. Entities that are described by other languages cannot legally play the role of geographic features in GML. This because all types of geographic features are required to derive from the GML abstract class gml:AbstractFeatureType. Even if it were not for this formal requirement, the lack of conventions about how to represent even simple semantic notions in XML languages would prevent effective integration of GML with XML languages developed independently. The non-composability of GML requires that it absorb as application schemas the multitude of other domains to which geographical information is relevant. Failing this, non-standard mechanisms of some kind must be used to relate GML content with external data. Indeed, GML positions itself as a universal, rather than geography-specific, semantic standard by including its own general formalisms for collections, assertion of properties (in a style very much like RDF), time and processes, and reference between content in separate files (via Xlink). GML can be viewed as an alternative not just to geography in RDF, but to RDF itself. </excerpt> This seems like a problem for us because some aspects of our biodiversity information are decidedly not spatial. Is this a problem with XML Schema generally or just the way it was used to create GML? Several TDWGers are getting enthusiastic about RDF, despite the cautions of McCool (referenced by Bob Morris earlier on the TDWG-GUID list). Should we go ahead and cast DarwinCore as a GML application while we gear up for a coordinated switch to RDF? -Stan

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Re: Thoughts
by Roderic Page 11 Feb '06

11 Feb '06

For my take on McCool's articles see http://iphylo.blogspot.com/2006/02/rob-mccool-on-rethinking-semantic- web.html Regards Rod On 11 Feb 2006, at 20:44, Bob Morris wrote: > > Rethinking the semantic Web. Part I > McCool, R.; > Internet Computing, IEEE > Volume 9, Issue 6, Nov.-Dec. 2005 Page(s):88, 86 - 87 > Abstract: > > The semantic Web is a compelling vision, in which the World Wide Web > will include a notion of meaning in data and services. Intelligent > agents will exchange information and rules for how to interact with > that information, with or without human intervention; appointments > will be automatically scheduled; and automated agents will select and > invoke services. Information will be easy to find without depending > solely on keywords. In part one of this column, the author propose > several reasons that this vision hasn't yet been adopted despite > substantial research funding in the US and European Union (EU). These > reasons will provide the foundation for a new approach, which propose > in part two. > > McCool is one of the architects of a number of RDF and RDF related > systems. This doesn't bear very much on LSID vs. something else, but > it does argue that RDF is burdened by its weight and hasn't achieved > certain of its aims. A question arises about whether this has > implications for other applications that have ontological overtones, > including many of TDWGs. > > The second columm is in the January issue of the same journal. > > > > > On 2/10/06, Sally Hinchcliffe < S.Hinchcliffe(a)kew.org> wrote:Hi Rod, >> Your comment facility is down or I would have added this to the blog >> ... >> I think that most of the talk re serving XML from LSIDs was by way of >> an upgrade path rather than as a final goal. As you say (rightly or >> wrongly) the community has put a lot of effort into XML schemas and >> it worried me (and others) that tying LSIDs to RDF might mean that >> the LSID baby got thrown out with the RDF bathwater as the community >> rejected it wholesale. But I was persuaded this wouldn't happen and >> now I face some scepticism here at Kew about the benefits of RDF so a >> killer app would be good... >> >> On the meeting itself, yes it was frustrating (and interesting and >> useful as well) and it struck me on my return that we might have got >> further had we had some professional (and neutral) facilitators - not >> to say that the chairs didn't do a good job getting us all to a >> decision in the end, but that we are all (me included) so parti pris >> and bound up in the subject that herding cats didn't even come close >> ... For the next meeting the decisions will be harder and more >> concrete and there will be a lot to decide. It might help having >> people who know how to facilitate useful debate and close off some of >> the blind alleys and circular pathways we have a tendency to wander >> into >> Sally >> >> >> >> > For those at the workshop, it was great to meet you and to discuss >> > GUIDs. I've posted a personal view on proceedings on one of my >> blogs: >> > http://iphylo.blogspot.com/2006/02/globally-unique-identifiers.html >> . >> > Comments are welcome. >> > >> > Regards >> > >> > Rod >> > >> > >> ---------------------------------------------------------------------- >> -- >> > ---------------------------------------- >> > Professor Roderic D. M. Page >> > Editor, Systematic Biology >> > DEEB, IBLS >> > Graham Kerr Building >> > University of Glasgow >> > Glasgow G12 8QP >> > United Kingdom >> > >> > Phone: +44 141 330 4778 >> > Fax: +44 141 330 2792 >> > email: r.page(a)bio.gla.ac.uk >> > web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html >> > reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html >> > >> > Subscribe to Systematic Biology through the Society of Systematic >> > Biologists Website: http://systematicbiology.org >> > Search for taxon names at >> http://darwin.zoology.gla.ac.uk/~rpage/portal/ >> > Find out what we know about a species at http://ispecies.org >> >> *** Sally Hinchcliffe >> *** Computer section, Royal Botanic Gardens, Kew >> *** tel: +44 (0)20 8332 5708 >> *** S.Hinchcliffe(a)rbgkew.org.uk >> ------------------------------------------------------------------------ ---------------------------------------- Professor Roderic D. M. Page Editor, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page(a)bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org Search for taxon names at http://darwin.zoology.gla.ac.uk/~rpage/portal/ Find out what we know about a species at http://ispecies.org ___________________________________________________________ To help you stay safe and secure online, we've developed the all new Yahoo! Security Centre. http://uk.security.yahoo.com

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Re: Thoughts
by Bob Morris 11 Feb '06

11 Feb '06

** *Rethinking the semantic Web. Part I* McCool, R.; Internet Computing, IEEE Volume 9, Issue 6, Nov.-Dec. 2005 Page(s):88, 86 - 87 *Abstract:* The semantic Web is a compelling vision, in which the World Wide Web will include a notion of meaning in data and services. Intelligent agents will exchange information and rules for how to interact with that information, with or without human intervention; appointments will be automatically scheduled; and automated agents will select and invoke services. Information will be easy to find without depending solely on keywords. In part one of this column, the author propose several reasons that this vision hasn't yet been adopted despite substantial research funding in the US and European Union (EU). These reasons will provide the foundation for a new approach, which propose in part two. McCool is one of the architects of a number of RDF and RDF related systems. This doesn't bear very much on LSID vs. something else, but it does argue that RDF is burdened by its weight and hasn't achieved certain of its aims. A question arises about whether this has implications for other applications that have ontological overtones, including many of TDWGs. The second columm is in the January issue of the same journal. On 2/10/06, Sally Hinchcliffe <S.Hinchcliffe(a)kew.org> wrote: > > Hi Rod, > Your comment facility is down or I would have added this to the blog > ... > I think that most of the talk re serving XML from LSIDs was by way of > an upgrade path rather than as a final goal. As you say (rightly or > wrongly) the community has put a lot of effort into XML schemas and > it worried me (and others) that tying LSIDs to RDF might mean that > the LSID baby got thrown out with the RDF bathwater as the community > rejected it wholesale. But I was persuaded this wouldn't happen and > now I face some scepticism here at Kew about the benefits of RDF so a > killer app would be good... > > On the meeting itself, yes it was frustrating (and interesting and > useful as well) and it struck me on my return that we might have got > further had we had some professional (and neutral) facilitators - not > to say that the chairs didn't do a good job getting us all to a > decision in the end, but that we are all (me included) so parti pris > and bound up in the subject that herding cats didn't even come close > ... For the next meeting the decisions will be harder and more > concrete and there will be a lot to decide. It might help having > people who know how to facilitate useful debate and close off some of > the blind alleys and circular pathways we have a tendency to wander > into > Sally > > > > > For those at the workshop, it was great to meet you and to discuss > > GUIDs. I've posted a personal view on proceedings on one of my blogs: > > http://iphylo.blogspot.com/2006/02/globally-unique-identifiers.html . > > Comments are welcome. > > > > Regards > > > > Rod > > > > ------------------------------------------------------------------------ > > ---------------------------------------- > > Professor Roderic D. M. Page > > Editor, Systematic Biology > > DEEB, IBLS > > Graham Kerr Building > > University of Glasgow > > Glasgow G12 8QP > > United Kingdom > > > > Phone: +44 141 330 4778 > > Fax: +44 141 330 2792 > > email: r.page(a)bio.gla.ac.uk > > web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html > > reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html > > > > Subscribe to Systematic Biology through the Society of Systematic > > Biologists Website: http://systematicbiology.org > > Search for taxon names at http://darwin.zoology.gla.ac.uk/~rpage/portal/ > > Find out what we know about a species at http://ispecies.org > > *** Sally Hinchcliffe > *** Computer section, Royal Botanic Gardens, Kew > *** tel: +44 (0)20 8332 5708 > *** S.Hinchcliffe(a)rbgkew.org.uk >

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Re: Thoughts
by Matt Jones 11 Feb '06

11 Feb '06

I'm away until January 21, 2006 and will not be reading email until I return. Please direct any critical issues to 'help(a)nceas.ucsb.edu' or to Mark Schildhauer 'schild(a)nceas.ucsb.edu'. Thanks. Matt

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TAG Technical Architecture Group Meeting Call
by Roger Hyam 10 Feb '06

10 Feb '06

Dear GUID List Member, As you will be all too aware the GUID-1 meeting has now taken place. The outcome of this meeting has wide ranging repercussions for all TDWG standards and their future interoperability. I am therefore calling a Technical Architecture Group meeting as soon as possible to discuss the best way to proceed. This meeting will be able to discuss issues, such as shared vocabularies, which are outside the scope of the GUID project and this list. You can read more about the proposed meeting here: http://www.tdwg.hyam.net/twiki/bin/view/TAG/TagMeeting1 I would be grateful if you would consider whether you might attend or nominate some one to attend. If you would like to discuss the meeting further please join the TAG list to save generating traffic on this list (http://www.tdwg.org/mailinglists.htm) Best wishes, Roger (apologies if you have received this multiple times as it is going to several TDWG lists). -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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[tdwg-tapir] TDWG Technical Architecture Group Meeting Call
by Roger Hyam 10 Feb '06

10 Feb '06

Dear Tapir List Member, As you will probably be aware the GUID-1 meeting has now taken place. The outcome of this meeting has wide ranging repercussions for all TDWG standards and their future interoperability. I am therefore calling a Technical Architecture Group meeting as soon as possible to discuss the best way to proceed. This meeting will be able to discuss issues, such as shared vocabularies and *protocols* which are outside the scope of the GUID project. You can read more about the proposed meeting here: http://www.tdwg.hyam.net/twiki/bin/view/TAG/TagMeeting1 I would be grateful if you would consider whether you might attend or nominate some one to attend. Best wishes, Roger (apologies if you have received this multiple times as it is going to several TDWG lists). -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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TDWG Technical Architecture Group Meeting Call
by Roger Hyam 10 Feb '06

10 Feb '06

Dear TAG List Member, As you will probably be aware the GUID-1 meeting has now taken place. The outcome of this meeting has wide ranging repercussions for all TDWG standards and their future interoperability. I am therefore calling a Technical Architecture Group meeting as soon as possible to discuss the best way to proceed. This meeting will be able to discuss issues, such as shared vocabularies, which are outside the scope of the GUID project. You can read more about the proposed meeting here: http://www.tdwg.hyam.net/twiki/bin/view/TAG/TagMeeting1 I would be grateful if you would consider whether you might attend or nominate some one to attend. Best wishes, Roger (apologies if you have received this multiple times as it is going to several TDWG lists). -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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Re: Thoughts
by Sally Hinchcliffe 10 Feb '06

10 Feb '06

Hi Rod, Your comment facility is down or I would have added this to the blog ... I think that most of the talk re serving XML from LSIDs was by way of an upgrade path rather than as a final goal. As you say (rightly or wrongly) the community has put a lot of effort into XML schemas and it worried me (and others) that tying LSIDs to RDF might mean that the LSID baby got thrown out with the RDF bathwater as the community rejected it wholesale. But I was persuaded this wouldn't happen and now I face some scepticism here at Kew about the benefits of RDF so a killer app would be good... On the meeting itself, yes it was frustrating (and interesting and useful as well) and it struck me on my return that we might have got further had we had some professional (and neutral) facilitators - not to say that the chairs didn't do a good job getting us all to a decision in the end, but that we are all (me included) so parti pris and bound up in the subject that herding cats didn't even come close ... For the next meeting the decisions will be harder and more concrete and there will be a lot to decide. It might help having people who know how to facilitate useful debate and close off some of the blind alleys and circular pathways we have a tendency to wander into Sally > For those at the workshop, it was great to meet you and to discuss > GUIDs. I've posted a personal view on proceedings on one of my blogs: > http://iphylo.blogspot.com/2006/02/globally-unique-identifiers.html . > Comments are welcome. > > Regards > > Rod > > ------------------------------------------------------------------------ > ---------------------------------------- > Professor Roderic D. M. Page > Editor, Systematic Biology > DEEB, IBLS > Graham Kerr Building > University of Glasgow > Glasgow G12 8QP > United Kingdom > > Phone: +44 141 330 4778 > Fax: +44 141 330 2792 > email: r.page(a)bio.gla.ac.uk > web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html > reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html > > Subscribe to Systematic Biology through the Society of Systematic > Biologists Website: http://systematicbiology.org > Search for taxon names at http://darwin.zoology.gla.ac.uk/~rpage/portal/ > Find out what we know about a species at http://ispecies.org *** Sally Hinchcliffe *** Computer section, Royal Botanic Gardens, Kew *** tel: +44 (0)20 8332 5708 *** S.Hinchcliffe(a)rbgkew.org.uk

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GUID-1 Workshop Report
by Ricardo Scachetti Pereira 10 Feb '06

10 Feb '06

Hi all, I've posted a report of the GUID-1 workshop on the Wiki at: http://wiki.gbif.org/guidwiki/wikka.php?wakka=GUID1Report Please, feel free to add your comments. The powerpoint presentations and other materials used during the workshop will be posted there soon. Again, thank you very much for your attendance and participation. Best regards, Ricardo

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