August 2007 - tdwg-tag - lists.tdwg.org

[tdwg-guid] How to create resource that is not defined in Jena's vocabulary
by Chaohong Xie 28 Nov '07

28 Nov '07

Hi guys, I met the same problem as Peter wrote in the following link: http://lists.tdwg.org/pipermail/tdwg-guid/2006-September/000496.html. Unfortunately, I didn't get the final solution in it. I'm not sure Peter, Ben and Steve are still in this mail group or not. Anyway, can anybody help me solve this problem? Thanks a lot. My code is attached as well. What I want is outputing my vocabulary "Manifest" instead of "rdf:Description". Map<String, String> ns = new HashMap<String, String>(); ns.put("", "http://www.test.com/2007/08/test-vocabulary#"); ns.put("rdfs", "http://www.w3.org/2000/01/rdf-schema#"); ns.put("rdf", "http://www.w3.org/1999/02/22-rdf-syntax-ns#"); Model model = ModelFactory.createDefaultModel(); model.setNsPrefixes(ns); Resource r = model.createResource(" http://www.test.com/2007/08/test_config#MyNodeID").addProperty(model.createProperty("http://www.w3.org/1999/02/22-rdf-syntax-ns#type"), "http://www.test.com/2007/08/test-vocabulary#Manifest"); Property p = model.createProperty(" http://www.test.com/2007/08/test-vocabulary#created_by"); Statement s = model.createStatement(r, p, "Chaohong"); model.add(s); RDFWriter w = model.getWriter("RDF/XML-ABBREV"); w.setProperty("showXMLDeclaration", "true"); w.setProperty("tab", "2"); w.setProperty("xmlbase", "http://www.test.com/2007/08/test_config#"); w.write(model, System.out, "http://www.test.com/2007/08/test-vocabulary #"); Chaohong

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[tdwg-tapir] Microsoft .NET implementation of TAPIR
by Kevin Richards 30 Aug '07

30 Aug '07

Hi all I have recently completed a project funded by the TIP (TDWG Infrastructure Project) funded project that has resulted in a Microsoft .NET version of the TAPIR protocol. TAPIR (TDWG Access Protocol for Information Retrieval) is a computer protocol designed for discovery, search and retrieval of distributed data over the Internet, see http://www.tdwg.org/activities/tapir/ for more information. The .NET implementation of the TAPIR protocol provides the following functionality: All TAPIR operations (metadata, capabilities, inventory, search and ping). KVP and XML request encodings. Inventories on any mapped concepts. Searches with any output models involving concepts from mapped schemas. Response structures with basicSchemaLanguage. Multiple resources can be exposed from a single TAPIRDotNET instance. A simple client (tapir_client.aspx) for testing. OAI-PMH message handling. After mapping the OAI-PMH structure to the data source, OAI-PMH requests can be handled and valid OAI-PMH responses are retuned from the provider. The OAI-PMH message handling was a result of an investigation into the use of the generic, domain independent, protocol, OAI-PMH (http://www.openarchives.org/OAI/openarchivesprotocol.html) over TAPIR. The investigation proved to be an interesting look at integrating similar data harvesting protocols. TapirDotNET is available from http://sourceforge.net/projects/tapirdotnet/ I have also been looking at returning RDF over TAPIR for the herb IMI specimens. I will be presenting this at TDWG next month. Kevin Richards

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[tdwg-guid] Piggy Bank and bioGUID
by Roderic Page 30 Aug '07

30 Aug '07

Biodiversity informatics seems rather short on examples of RDF and Semantic Web browsers, and the promised dream of being able to link data together. Prompted by Jim Balhoff of NESCent asking why bioGUID didn't play with MIT's Piggy Bank, I managed to get bioGUID tom play ball, so now you can extract RDF from bioGUID web pages, and store and browse these in Piggy Bank. Given that bioGUID tries to extract GUIDs from its sources, and renders all the RDF in a consistent fashion, it is possible to navigate around data from PubMed, GenBank, and DiGIR providers. I've put some notes up at http://bioguid.blogspot.com/2007/08/piggy- bank-and-bioguid-browsing.html . 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 iChat: aim://rodpage1962 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: http://darwin.zoology.gla.ac.uk/~rpage/portal/ Find out what we know about a species: http://ispecies.org Rod's rants on phyloinformatics: http://iphylo.blogspot.com Rod's rants on ants: http://semant.blogspot.com

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Request for Comments on the TDWG LSID Applicability Statement
by Ricardo Pereira 30 Aug '07

30 Aug '07

Dear GUID and TAG members, The TDWG Infrastructure Project (TIP) <http://www.tdwg.org/activities/tip/> has been working on a *new* draft of the *TDWG LSID Applicability Statement*. This document- 1. provides guidance on how to use Life Sciences Identifiers (LSID) to meet specific requirements of the biodiversity information community and 2. defines how to identify shared data objects in biodiversity information applications using LSID. This specification, soon to be submitted to TDWG for ratification, summarizes all agreed decisions by the TDWG-GUID group <http://www.tdwg.org/activities/guid/> and addresses the requirements of the TAG group <http://www.tdwg.org/activities/tag/>. We would like to ask you to please *review* the applicability statement and provide feedback. The document is available at: http://www.tdwg.org/standards/150/download/ (it is also available in PDF format <http://wiki.tdwg.org/twiki/pub/GUID/LsidApplicabilityStatementRfC2007Sep/TD…>) This version of the applicability statement is significantly different from the version reviewed last year <http://wiki.tdwg.org/twiki/bin/view/GUID/LsidApplicabilityStatementRfC2006O…>. For that reason, we would like to ask those who kindly reviewed the previous version of the document to review this one as well. Please make your comments using one (or more) of the following methods: 1. Send your comments to tdwg-guid(a)lists.tdwg.org <mailto:tdwg-guid@listsREMOVE-THIS.tdwg.org> or directly to ricardo(a)tdwg.org <mailto:ricardo@tdwgREMOVE-THIS.org>; 2. Revise the MS Word document posted above using the /Track Changes/ feature and send it to ricardo(a)tdwg.org <mailto:ricardo@tdwgREMOVE-THIS.org>; or 3. Post your comments at the end of the wiki page at: http://wiki.tdwg.org/twiki/bin/view/GUID/LsidApplicabilityStatementRfC2007S… All comments will be later collated at the end of the wiki page mentioned above. When we are all satisfied with the contents of this applicability statement, we intend to ratify it as a TDWG standard. We would really appreciate your feedback. Best regards, The TDWG Infrastructure Team (TIP)

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2007 Roadmap Document - last call
by Roger Hyam 20 Aug '07

20 Aug '07

Dear Tagistas, The 2007 Roadmap document is nearing completion. The vast majority of content is now in place. http://wiki.tdwg.org/twiki/bin/view/TAG/RoadMap2007 Please take a look and feed back either on the page or to me. This document makes recommendations to the executive and members of TDWG. Do you agree with them? Feedback now - before the document is frozen. I intend to freeze the wiki page and produce a PDF document for circulation next Monday (27 August). This is a little later than I would have liked but is in plenty of time for Bratislava - which is what is required by the TAG charter. We are all working towards Bratislava now and I look forward to seeing you there if you will be attending. Please be aware of the TAG meeting on the Sunday 16th immediately before the main TDWG Meeting. The agenda for this meeting is here: http://wiki.tdwg.org/twiki/bin/view/TAG/TagMeeting2 Please add issues to this agenda that you wish discussed - even if you can't attend. If you can attend please add your name to the list so we can order enough beer (only joking). All the best, Roger ____________________________________________________________ Roger Hyam <roger(a)tdwg.org> ____________________________________________________________ Biodiversity Information Standards: http://www.tdwg.org/ "Working To Make Biodiversity Data Global" ____________________________________________________________ TDWG Standards Architecture: http://wiki.tdwg.org/twiki/bin/view/TAG LSID RDF Vocabularies: http://wiki.tdwg.org/twiki/bin/view/TAG/ LsidVocs ____________________________________________________________

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[tdwg-tapir] Adoption figures and hopes for 2008
by Roger Hyam 17 Aug '07

17 Aug '07

Hi All, I am just putting together a roadmap for TDWG 2007. This document must be produced by the TAG before the meeting to summarize the current situation and make suggestions for the coming year. TAPIR is obviously mentioned! http://wiki.tdwg.org/twiki/bin/view/TAG/RoadMap2007 I would be grateful if you would take a look at this document and either feedback to me or change it. In particular on the section on Exchange Protocols http://wiki.tdwg.org/twiki/bin/view/TAG/RoadMap2007#Exchange_Protocols I would like to give some indication of the roll out of TAPIR. What has been done and what is expected? Please fill in your own figures. I am taking a "tough love" approach this year with the recommendations. I make several specific ones about TAPIR. TAPIR should be used in preference to DiGIR or BioCASe in any new networks http://wiki.tdwg.org/twiki/bin/view/TAG/RoadMap2007#DiGIR http://wiki.tdwg.org/twiki/bin/view/TAG/RoadMap2007#BioCASe TAPIR should be the preferred XML exchange protocol. http://wiki.tdwg.org/twiki/bin/view/TAG/ RoadMap2007#TDWG_Access_Protocol_for_Informa If you have any comments on the rest of the document I'd love to hear them. It is still work in progress. Now is the time to influence it! Many thanks, Roger

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[tdwg-guid] Observation Associations Controlled Vocabulary
by Kevin Richards 12 Aug '07

12 Aug '07

Hi all I apologise for any cross postings, and Im not sure Ive even got the right mailing lists here. I am trying to get hold of a controlled vocabularly / list of terms that define associations between organisms with respect to observations or specimens. For example parasites, hosts etc - eg to specify that a specimen/observation was found living on another specimen (host). I need this for the specimens RDF/LSID presentation I am giving at TDWG this year. Any help would be appreciated. Thanks Kevin Richards ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 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. Landcare Research http://www.landcareresearch.co.nz ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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TAG Meeting Agenda
by Roger Hyam 09 Aug '07

09 Aug '07

Dear All, I have started a wiki page for the TAG meeting in Bratislava. It will take place Sunday 16th September 14:00 - 17:00 prior to the main TDWG 2007 meeting. http://wiki.tdwg.org/twiki/bin/view/TAG/TagMeeting2 Please add any issues you would like discussed to this page. Please do this even if you can not attend the meeting. If you can attend the meeting please add your name to the attendees list so that other people can approach you and ask you to represent their needs. Can I remind you that we should be thinking about the Roadmap document for 2007. Anything you think that should be put forward to the Executive this year regarding the new Architecture (love it or hate it) please enter on this page. http://wiki.tdwg.org/twiki/bin/view/TAG/RoadMap2007 I hope to work on this page in the next few days. All the best, Roger ____________________________________________________________ Roger Hyam <roger(a)tdwg.org> ____________________________________________________________ Biodiversity Information Standards: http://www.tdwg.org/ "Working To Make Biodiversity Data Global" ____________________________________________________________ TDWG Standards Architecture: http://wiki.tdwg.org/twiki/bin/view/TAG LSID RDF Vocabularies: http://wiki.tdwg.org/twiki/bin/view/TAG/ LsidVocs ____________________________________________________________

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Re: [tdwg-tapir] TAPIRLink and memory
by Peter Neish 02 Aug '07

02 Aug '07

Hi Renato and Roger, One thing that might be worth trying is including the command ini_set to override the php.ini setting for the memory limit e.g. ini_set('memory_limit', '16M'); This has worked for me on a shared host to run a content management system that choked at the lower default value. Regards, Peter >>> "Renato De Giovanni" <renato(a)cria.org.br> 2/08/07 2:21 >>> Hi Roger, I do think it's worth adding your changes related to the "fopen" workaround. Please don't hesitate. I should say that I'm actually surprised that TapirLink requires only 10M with such a complex RDF output model. I wonder how many records were being returned in your request? I also don't have much experience with profiling, but I'm sure there's room for improvements since I didn't pay much attention to optimization. By the way, the main new feature for the next version will be caching. I'm expecting significant improvements in performance since query templates, output models, and response structures will be all cached by default as serialized PHP. When TapirLink can use cached content, I suppose this will also reduce memory use. However, the first time it receives a particular output model in a request, then it will require the same memory if we don't make additional optimizations and if we want it to run below the 8M limit. Anyway, I also wonder how many people and organizations will need to run a TAPIR provider software under the conditions you described (external ISP with such a low memory use limit). I still never heard of any case in our community (maybe someone from GBIF could give us a better picture?). Best Regards, -- Renato On 1 Aug 2007 at 14:11, Roger Hyam wrote: > Hi All > > I spent a couple of hours this morning adapting TAPIRLink so that it > uses a work around of fopen() because many ISPs will not support > opening remote files (there is a php config option to stop it). > > Anyhow I got past this and found that my output model still wouldn't > run on my ISP account (Easyspace.com) but would run on my local > machine. After a while I found that it was running out of memory. > > My ISP limits memory to 8meg per running script. That seems pretty > tight until you imagine having a hundred scripts running > simultaneously. It was the default setting prior to php 5.2 when it > jumped to 128meg! This may explain why ISPs are very slow to migrate > to PHP5.* > > The TAPIRLink request was using almost 10meg under PHP 5.2 according > to memory_get_peak_usage() to parse the rather complex > TaxonOccurrence output model. There is no peak usage method on > earlier PHP versions. Ten meg seems quite reasonable considering the > cost of RAM these days - but there you have it. > > Anyhow I am nervous because this means that deployers might need to > mess with php.ini to get scripts running which means shared servers > may be problematic for deployments that use complex output models. > Basically it won't run everywhere php is available but only where php > in a certain config is available. It also means that if you are being > crawled by a 10 threaded robot you will be using close to 100meg to > service the requests plus memory allocation and deallocation etc. > > It is all seems pretty trivial if you have a newer machine and even > more so if you install PHP 5.2+ on it but it does mean that that old > departmental webserver that has an old install of PHP on may not run > the RDF based output models out of the box. > > Never done any profiling with PHP and wouldn't like to get into it. I > guess Python will have a similar memory footprint as it is doing a > similar job but the install scenario is different for PyWrapper - you > really need shell access. > > It may not be worth adding the fopen() work round if the deployment > environment requires access to php.ini. > > Would be grateful for your thoughts on this. > > Roger _______________________________________________ tdwg-tapir mailing list tdwg-tapir(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tapir

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Re: [tdwg-tapir] Is the current schema valid?
by Döring, Markus 01 Aug '07

01 Aug '07

Renato, Honetly I dont really understand the validation error, but it has to do with the all group for sure: """ E cos-all-limited.1.2: An 'all' model group must appear in a particle with '{'min occurs'}' = '{'max occurs'}' = 1, and that particle must be part of a pair which constitutes the '{'content type'}' of a complex type definition. """ I therefore have replaced the all with a sequence and the schema validates again. I also raised the schema version to 1.01 which we never did before. I think we should really do so while remaining the namespace under http://rs.tdwg.org/tapir/1.0 cheers Markus Am 31.07.2007 19:00 Uhr schrieb "Renato De Giovanni" unter <renato(a)cria.org.br>: > Hi Markus, > > Would you like to try to make the schema valid again? (I don't use > oxygen here). Or should we just replace xsd:all by xsd:sequence? > > Thanks, > -- > Renato > > On 31 Jul 2007 at 17:31, Döring, Markus wrote: > >> Renato, >> Afaik oxygen is using xerces for validation - which is a very good >> parser/validator. Not sure if the w3c xsv validator is more trustable, but I >> feel very uncomfortable if xerces doesnt validate the schema. >> >> Markus >

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