April 2006 - tdwg-tag - lists.tdwg.org

Central LSID registration authority?
by Donald Hobern 19 Apr '06

19 Apr '06

I've added some starting comments on the question of whether or not a "central LSID registration authority" would be useful to our community: http://wiki.gbif.org/guidwiki/wikka.php?wakka=GUIDCentralRegistrationAuthori ty (text appended below) This is one of the Infrastructure Working Group topics. As I have noted, there are topics which could be addressed under this title but which I have deliberately excluded. Please address these if you think they are valuable. Please provide your input. Thanks, Donald --------------------------------------------------------------- Donald Hobern (dhobern(a)gbif.org) Programme Officer for Data Access and Database Interoperability Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 --------------------------------------------------------------- A central LSID registration authority could take several different forms. The following is an attempt to outline some options, so that subsequent discussion can focus more clearly on the benefits of each. I'm going to start by ignoring the possibility of establishing a central LSID registration authority as some kind of registrar approving or recording new LSID authorities within our domain. I'm also going to ignore the possibility of requiring all LSIDs to be registered within a single namespace. I cannot see value in either of these "options". If anyone wishes to propose them, please go ahead. It is assumed here that the purpose of such an authority would be to provide a mechanism for data providers to associate LSIDs with their records without having to establish and maintain an LSID resolver in their own namespace. This could for example be because the data set in question is likely to be moved to a different home, or because the data provider cannot get permission to register an LSID provider with DNS, or because the data provider's host institution has restrictive rules on firewall access. Under these circumstances a data provider may still wish to be able to assign LSIDs to each data record and to have the LSID resolve correctly to the appropriate data and metadata. Some options: 1. Central hosting of data/metadata The simplest option technically (or at least simplest with respect to the assignment of LSIDs) may be for the central LSID registration authority actually to host the data sets in question on behalf of the data provider. 2. Central proxy LSID resolver If the data provider is able to establish an LSID resolver but is unable or unwilling to register this resolver with DNS, a central LSID registration authority might establish a proxy LSID resolver, which redirects to the known location of the actual LSID resolver. In other words, assuming that the central LSID registration authority has an LSID resolver registered for clra.org and running on lsid.clra.org, and the data provider has established its own unregistered LSID resolver on lsid.dp.org, the data provider can issue LSIDs of the form urn:lsid:clra.org:<DatasetName <http://wiki.gbif.org/guidwiki/wikka.php?wakka=DatasetName/edit> >:<RecordId <http://wiki.gbif.org/guidwiki/wikka.php?wakka=RecordId/edit> >. Requests for data or metadata will be directed to lsid.clra.org, which resolves <DataSetName <http://wiki.gbif.org/guidwiki/wikka.php?wakka=DataSetName/edit> > to be associated with the unregistered LSID resolver on lsid.dp.org, and directs the request to lsid.dp.org for resolution. This again should be relatively simple to implement, and could be of use in some circumstances. The data provider and the central LSID registration authority clearly need to coordinate the elements included in the LSID string. 3. Central LSID resolver with non-LSID proxy resolution Slightly more complex (and potentially with too many uncertainties), a data provider could register a provider tool using some other protocol (e.g. TAPIR) and rely on an external proxy LSID resolver to map LSID requests to the appropriate protocol. For example, assume that a TAPIR provider is set up on tapir.dp.org to serve data in some version of darwin core which includes a <darwin:lsid> element. The records in the TAPIR provider are all set up to include values for this element of the form urn:lsid:clra.org:<DatasetName <http://wiki.gbif.org/guidwiki/wikka.php?wakka=DatasetName/edit> >:<RecordId <http://wiki.gbif.org/guidwiki/wikka.php?wakka=RecordId/edit> >. Requests for data or metadata will be directed to lsid.clra.org, which resolves <DataSetName <http://wiki.gbif.org/guidwiki/wikka.php?wakka=DataSetName/edit> > to be associated with the TAPIR provider on tapir.dp.org, issues an appropriate TAPIR request for the record with the appropriate value for <darwin:lsid> and then formats the data or metadata appropriately for an LSID response. This is again not complex to implement, but requires even more coordination than with option 2. It could however be applicable in any case in which a data provider has any mechanism for sharing their data online, regardless of what additional firewall restrictions are in place. This is doubtless not a complete set of options, but should be enough to begin discussion. So, do you see value in considering any of these options as part of the infrastructure we plan to adopt. It may of course be that any and all of these can be used transparently within any LSID-based network, but we should consider whether there are immediate benefits in offering some kind of central service (through TDWG, GBIF or others) for these purposes.

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Re: [Tdwg-tag] rdf stores and SPARQL
by Kennedy, Jessie 19 Apr '06

19 Apr '06

Hi Marcus I've been meaning to announce this on the TAG and GUID group lists and your email has just prompted me... I'm organising a workshop on RDF, Ontologies and Meta-data at the eScience Centre in Edinburgh from the 7-9th June - immediately preceding the GUID-2 workshop. The workshop will begin with a morning devoted to a tutorial session from Oracle on RDF and their triple store. The afternoon follows this with presentations from researchers on building triple stores and then a discussion session on the scalability of RDF - which I believe is still a problem. So with any luck your questions might get answered there. Details of the workshop are being firmed up on the wiki at: http://wiki.esi.ac.uk/RDF%2C_Ontologies_and_Meta-Data_Workshop Registration for the even is open at: http://www.nesc.ac.uk/esi/events/683/ The aim of the workshop is to try and understand exactly where we are with these technologies, what are the main issues facing us, what is achievable in the near future and what are real problems that need longer term research to answer. I'm sure many of you would find the workshop interesting and could contribute to the discussion sessions, so feel free to sign up and come along. Jessie > -----Original Message----- > From: Tdwg-tag-bounces(a)lists.tdwg.org [mailto:Tdwg-tag- > bounces(a)lists.tdwg.org] On Behalf Of "Döring, Markus" > Sent: 19 April 2006 10:10 > To: Tdwg-tag(a)lists.tdwg.org > Subject: [Tdwg-tag] rdf stores and SPARQL > > Hello TAG, > > I believe scalability and performance in RDF stores IS a major problem and > I think we should try to gather as much information about it as possible. > Roger, could we start to collect resources in the TAG wiki about it? > So far I am aware of the following +/- recent articles: > > * http://crschmidt.net/blog/archives/90/rdf-as-backing-storage/ > * http://simile.mit.edu/reports/stores/ > * http://km.aifb.uni-karlsruhe.de/ws/psss03/proceedings/harris-et-al.pdf > * other interesting papers from the same conference "Practical and > Scalable Semantic Systems Service": http://km.aifb.uni- > karlsruhe.de/ws/psss03/proceedings > * http://eprints.ecs.soton.ac.uk/11985/01/owens-semanticStorageOverview- > ecs.pdf > * http://www.w3.org/2001/sw/Europe/reports/rdf_scalable_storage_report/ > > Most of them are sceptical about having large scale rdf stores in the > intermediate future and usually suggest to go with a specialised stores > for specific appllication purposes. Especially the combination of storing > large amounts of data based on complex ontologies with good > inference/reasoning/querying support seems unreasonable in a generic > solution. > > But maybe Oracle can do much better. Has anyone heard claims about their > performance yet? > > -- > Markus > > > > > _______________________________________________ > Tdwg-tag mailing list > Tdwg-tag(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tag_lists.tdwg.org

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Re: [Tdwg-tag] rdf stores and SPARQL
by Kennedy, Jessie 19 Apr '06

19 Apr '06

Hi Marcus I've been meaning to announce this on the TAG and GUID group lists and your email has just prompted me... I'm organising a workshop on RDF, Ontologies and Meta-data at the eScience Centre in Edinburgh from the 7-9th June - immediately preceding the GUID-2 workshop. The workshop will begin with a morning devoted to a tutorial session from Oracle on RDF and their triple store. The afternoon follows this with presentations from researchers on building triple stores and then a discussion session on the scalability of RDF - which I believe is still a problem. So with any luck your questions might get answered there. Details of the workshop are being firmed up on the wiki at: http://wiki.esi.ac.uk/RDF%2C_Ontologies_and_Meta-Data_Workshop Registration for the even is open at: http://www.nesc.ac.uk/esi/events/683/ The aim of the workshop is to try and understand exactly where we are with these technologies, what are the main issues facing us, what is achievable in the near future and what are real problems that need longer term research to answer. I'm sure many of you would find the workshop interesting and could contribute to the discussion sessions, so feel free to sign up and come along. Jessie > -----Original Message----- > From: Tdwg-tag-bounces(a)lists.tdwg.org [mailto:Tdwg-tag- > bounces(a)lists.tdwg.org] On Behalf Of "Döring, Markus" > Sent: 19 April 2006 10:10 > To: Tdwg-tag(a)lists.tdwg.org > Subject: [Tdwg-tag] rdf stores and SPARQL > > Hello TAG, > > I believe scalability and performance in RDF stores IS a major problem and > I think we should try to gather as much information about it as possible. > Roger, could we start to collect resources in the TAG wiki about it? > So far I am aware of the following +/- recent articles: > > * http://crschmidt.net/blog/archives/90/rdf-as-backing-storage/ > * http://simile.mit.edu/reports/stores/ > * http://km.aifb.uni-karlsruhe.de/ws/psss03/proceedings/harris-et-al.pdf > * other interesting papers from the same conference "Practical and > Scalable Semantic Systems Service": http://km.aifb.uni- > karlsruhe.de/ws/psss03/proceedings > * http://eprints.ecs.soton.ac.uk/11985/01/owens-semanticStorageOverview- > ecs.pdf > * http://www.w3.org/2001/sw/Europe/reports/rdf_scalable_storage_report/ > > Most of them are sceptical about having large scale rdf stores in the > intermediate future and usually suggest to go with a specialised stores > for specific appllication purposes. Especially the combination of storing > large amounts of data based on complex ontologies with good > inference/reasoning/querying support seems unreasonable in a generic > solution. > > But maybe Oracle can do much better. Has anyone heard claims about their > performance yet? > > -- > Markus > > > > > _______________________________________________ > Tdwg-tag mailing list > Tdwg-tag(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tag_lists.tdwg.org

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rdf stores and SPARQL
by "Döring, Markus" 19 Apr '06

19 Apr '06

Hello TAG, I believe scalability and performance in RDF stores IS a major problem and I think we should try to gather as much information about it as possible. Roger, could we start to collect resources in the TAG wiki about it? So far I am aware of the following +/- recent articles: * http://crschmidt.net/blog/archives/90/rdf-as-backing-storage/ * http://simile.mit.edu/reports/stores/ * http://km.aifb.uni-karlsruhe.de/ws/psss03/proceedings/harris-et-al.pdf * other interesting papers from the same conference "Practical and Scalable Semantic Systems Service": http://km.aifb.uni-karlsruhe.de/ws/psss03/proceedings * http://eprints.ecs.soton.ac.uk/11985/01/owens-semanticStorageOverview-ecs.p… * http://www.w3.org/2001/sw/Europe/reports/rdf_scalable_storage_report/ Most of them are sceptical about having large scale rdf stores in the intermediate future and usually suggest to go with a specialised stores for specific appllication purposes. Especially the combination of storing large amounts of data based on complex ontologies with good inference/reasoning/querying support seems unreasonable in a generic solution. But maybe Oracle can do much better. Has anyone heard claims about their performance yet? -- Markus

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UML limitations for our uses?
by Roger Hyam 17 Apr '06

17 Apr '06

There is an interesting article here: http://www.cs.vu.nl/~guus/public/owl-restrictions/ That discusses the differences between OWL and UML. One of the features of OWL that I like is the notion of a necessary and sufficient properties but alas this is lacking in UML. Sufficient conditions allow you to determine if an instance is a member of a class when it in not explicitly stated. You can therefore receive and object and work out what it is according to an ontology of your choice - which seems pretty useful to me. It is a mechanism, I believed, could enable us to integrate a simple core ontology with more complex specialist ontologies that some network participants may choose to use. It is not available in UML but could be used to reason about a UML ontology expressed in OWL or RDFS. OWL doesn't do qualified cardinality restrictions as well as UML - but there are work rounds and proposals and I am not sure how important this is. There is also a good quote in the article on data modeling versus building ontologies: "A data model is a model of the information in some restricted well-delimited application domain, whereas an ontology is intended to provide a set of shared concepts for multiple users and applications. To put it simply: data models live in a relatively small closed world; ontologies are meant for an open, distributed world (hence their importance for the Web)." I think we are sometime confusing the two in our discussions. Bottom line is: * You can't express everything in UML or OWL. * If we want to assure that we can swap between two or more modeling languages then we can't use all the feature of any of them but have to come up with a subset. The answer never includes a single TLA. <- apart from this answer! My personal feeling is that anything that is defined centrally by TDWG should use the lowest common denominator of features anyhow. As usual I am grateful for you comments/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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LSID resolver for analyses and models
by Matt Jones 14 Apr '06

14 Apr '06

In addition to the resolver I described in my previous message, we've started work on an LSID resolver for published analyses and models that are stored using Modeling Markup Language in the Kepler actor library (http://library.kepler-project.org). This modeling system also utilizes data that can be obtained from EcoGrid-enabled and eventually LSID enabled data servers (see my previous post). Details on the wiki at: http://wiki.gbif.org/guidwiki/wikka.php?wakka=LSIDResolverForAnalyticalMode… Matt -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Matt Jones Ph: 907-789-0496 jones(a)nceas.ucsb.edu SIP #: 1-747-626-7082 National Center for Ecological Analysis and Synthesis (NCEAS) UC Santa Barbara http://www.nceas.ucsb.edu/ecoinformatics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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prototype LSID resolver for observations
by Matt Jones 14 Apr '06

14 Apr '06

Hi, We've been working on an LSID resolver prototype for observational data that is described using Ecological Metadata Language. During the last GUID meeting I said I would work on this, and we have made some progress, although the demo is currently without data (we'll fix that soon over the next few days). The resolver is located at "esa.org", and the data that has LSIDs can be found using the web interface at http://data.esa.org. Wait a couple of days for us to populate the server with data and the demo will be more interesting. We'll eventually also install this demo on our KNB network (http://knb.ecoinformatics.org), which currently contains over 5000 observational datasets and their associated EML metadata. I've described some of our work, including various existing bugs in our resolver, on the GUID wiki here: http://wiki.gbif.org/guidwiki/wikka.php?wakka=LSIDResolverForObservations I won't be able to make the next GUID meeting, but I am hoping to stay involved with this project as it evolves. Cheers, Matt PS Rods LSID tester has been very useful in showing that we still have a number of bugs in our resolver, especially with our SOAP methods. Thanks! -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Matt Jones Ph: 907-789-0496 jones(a)nceas.ucsb.edu SIP #: 1-747-626-7082 National Center for Ecological Analysis and Synthesis (NCEAS) UC Santa Barbara http://www.nceas.ucsb.edu/ecoinformatics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Re: New LSID resolver: TDWG standards cover pages
by Lee Belbin 13 Apr '06

13 Apr '06

Hi Ricardo & Roger That is really neat guys! A great idea. Well done!!!! Lee Lee Belbin Manager, TDWG Infrastructure Project Email: lee(a)tdwg.org Phone: +61(0)419 374 133 -----Original Message----- From: Taxonomic Databases Working Group GUID Project [mailto:TDWG-GUID@LISTSERV.NHM.KU.EDU] On Behalf Of Ricardo Scachetti Pereira Sent: Thursday, 13 April 2006 6:20 AM To: TDWG-GUID(a)LISTSERV.NHM.KU.EDU Subject: New LSID resolver: TDWG standards cover pages Hi folks, I thouhg I would let you know that Roger and I have just set up yet another LSID resolver. But this one resolves very peculiar objects: TDWG standards cover pages. If you are curious, find out more at: http://wiki.gbif.org/guidwiki/wikka.php?wakka=LSIDResolverTdwgStandards Cheers, Ricardo PS. Rod, your LSID testing tool is really a blast. It really helps developers setting up LSID resolvers. Many thanks!!!

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New LSID resolver: TDWG standards cover pages
by Ricardo Scachetti Pereira 12 Apr '06

12 Apr '06

Hi folks, I thouhg I would let you know that Roger and I have just set up yet another LSID resolver. But this one resolves very peculiar objects: TDWG standards cover pages. If you are curious, find out more at: http://wiki.gbif.org/guidwiki/wikka.php?wakka=LSIDResolverTdwgStandards Cheers, Ricardo PS. Rod, your LSID testing tool is really a blast. It really helps developers setting up LSID resolvers. Many thanks!!!

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HP RDF Analysis - Regarded as Balanced
by Roger Hyam 12 Apr '06

12 Apr '06

Bob (inspired by Damian) asked me to post this for him as he is away from his email account just now . http://www.hpl.hp.com/techreports/2005/HPL-2005-189.pdf is touted on some blogs as extremely balanced. Looks good to me to - though not gone through it in detail yet. Roger -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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