September 2011 - tdwg-tag - lists.tdwg.org

RDF/OWL Good Practices Task Group
by joel sachs 17 Oct '11

17 Oct '11

Greetings everyone, After some back and forth amongst Steve Baskauf, myself, Greg Whitbread, and the executive, we've decided to move forward with an RDF/OWL task group, convened under the TAG. Our task will be to deliver a document comprising i. use cases and competency questions; ii. well documented examples of addressing those use cases via rdf and sparql; and iii. discussion of advantages and disadvantages of the approaches illustrated by the examples. Our draft charter is at http://code.google.com/p/tdwg-rdf/wiki/CharterOfTG and we welcome comments, suggestions, and better ideas. One area where we're still open is the question of whether or not our deliverable should be an official Best Current Practice document [1]. The charter reflects our current feeling that it should not. After we deliver our "book of use cases and examples", options would include being re-chartered by the TAG to produce a best practices document, spinning off as a "Semantic Web Interest Group", or disbanding (either in triumph or despair). When we were planning to convene as an Interest Group, several of you accepted our invitation to serve as core members, and we hope that convening as a Task Group does not change your willingness to do so. If you would like to be a core member of the group, and we haven't yet contacted you, there's a good chance that we will. But don't wait! Feel free to volunteer for core membership. (And recall that you don't have to be a "core member to" contribute.) In regards timeline, I'd like to incorporate any feedback we receive, and submit the charter to the executive at the end of this week, in hopes of being chartered by New Orleans. Many thanks! Joel. 1. http://www.tdwg.org/standards/status-and-categories/

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Missing TAPIR standard
by Steve Baskauf 27 Sep '11

27 Sep '11

The downloadable version of the TAPIR standard http://www.tdwg.org/standards/449/ is missing. If you click the "download" link, you get the GUID/LSID applicability statement instead. This is really pretty bad because it means that the "official" standard is not available to the public. 1. Can somebody fix this? 2. Until it gets fixed, can somebody send me a copy of the archive for the standard or direct me to an alternative download location? Thanks, Steve -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 343-6707 http://bioimages.vanderbilt.edu

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Lobbing grenades: a challenge
by Roderic Page 26 Sep '11

26 Sep '11

It's morning and the coffee hasn't quite kicked in yet, but reading through recent TDWG TAG posts, and mindful of the upcoming meeting in New Orleans (which sadly I won't be attending) I'm seeing a mismatch between the amount of effort being expended on discussions of vocabularies, ontologies, etc. and the concrete results we can point to. Hence, a challenge: "What new things have we learnt about biodiversity by converting biodiversity data into RDF?" I'm not saying we can't learn new things, I'm simply asking what have we learnt so far? Since around 2006 we have had literally millions of triples in the wild (uBio, ION, Index Fungorum, IPNI, Catalogue of Life, more recently Biodiversity Collections Index, Atlas of Living Australia, World Register of Marine Species, etc.), most of these using the same vocabulary. What new inferences have we made? Let's make the challenge more concrete. Load all these data sources into a triple store (subchallenge - is this actually possible?). Perhaps add other RDF sources (DBpedia, Bio2RDF, CrossRef). What novel inferences can we make? I may, of course, simply be in "grumpy old arse" mode, but we have millions of triples in the wild and nothing to show for it. I hope I'm not alone in wondering why... Regards Rod --------------------------------------------------------- Roderic Page Professor of Taxonomy Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary and Life Sciences Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK Email: r.page(a)bio.gla.ac.uk Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rodpage1962(a)aim.com Facebook: http://www.facebook.com/profile.php?id=1112517192 Twitter: http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html

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Re: [tdwg-tag] Lobbing grenades: a challenge
by Donald.Hobern＠csiro.au 22 Sep '11

22 Sep '11

"Grumpy old arse" or not, this is an important question. However, I'd also like to suggest that the move to RDF has likely benefits which are not related to our ability to use semantic technologies over the data. Given our current stage of standardisation of biodiversity data, RDF has always seemed to me primarily to be the most convenient technology to treat disparate data records as bags of properties that are asserted about a real-world object or concept. In other words, I want to use RDF primarily as a data-transfer technology, without the closed-model or versioning issues that can arise with XML Schema, and with greater clarity and flexibility for complex data than is possible with CSV. RDF makes it much easier for any project to reuse a set of core properties and supplement them with others specific to their interests. This is the first and primary driver for moving to RDF. Standardising vocabularies and semantics and moving toward the possibility of semantic exploration seems to me to be a bigger, more long-term goal. Donald Donald Hobern, Director, Atlas of Living Australia CSIRO Ecosystem Sciences, GPO Box 1700, Canberra, ACT 2601 Phone: (02) 62464352 Mobile: 0437990208 Email: Donald.Hobern(a)csiro.au Web: http://www.ala.org.au/ Roderic Page wrote: > It's morning and the coffee hasn't quite kicked in yet, but reading > through recent TDWG TAG posts, and mindful of the upcoming meeting in > New Orleans (which sadly I won't be attending) I'm seeing a mismatch > between the amount of effort being expended on discussions of > vocabularies, ontologies, etc. and the concrete results we can point to. > > Hence, a challenge: > > "What new things have we learnt about biodiversity by converting > biodiversity data into RDF?" > > I'm not saying we can't learn new things, I'm simply asking what have > we learnt so far? > > Since around 2006 we have had literally millions of triples in the > wild (uBio, ION, Index Fungorum, IPNI, Catalogue of Life, more > recently Biodiversity Collections Index, Atlas of Living Australia, > World Register of Marine Species, etc.), most of these using the same > vocabulary. What new inferences have we made? > > Let's make the challenge more concrete. Load all these data sources > into a triple store (subchallenge - is this actually possible?). > Perhaps add other RDF sources (DBpedia, Bio2RDF, CrossRef). What novel > inferences can we make? > > I may, of course, simply be in "grumpy old arse" mode, but we have > millions of triples in the wild and nothing to show for it. I hope I'm > not alone in wondering why... > > Regards > > Rod > > --------------------------------------------------------- > Roderic Page > Professor of Taxonomy > Institute of Biodiversity, Animal Health and Comparative Medicine > College of Medical, Veterinary and Life Sciences > Graham Kerr Building > University of Glasgow > Glasgow G12 8QQ, UK > > Email: r.page(a)bio.gla.ac.uk <mailto:r.page@bio.gla.ac.uk> > Tel: +44 141 330 4778 > Fax: +44 141 330 2792 > AIM: rodpage1962(a)aim.com <mailto:rodpage1962@aim.com> > Facebook: http://www.facebook.com/profile.php?id=1112517192 > Twitter: http://twitter.com/rdmpage > Blog: http://iphylo.blogspot.com > Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html >

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Part-of in RDF/OWL
by Gregor Hagedorn 22 Sep '11

22 Sep '11

We are seeking advice in the context of using semantic mediawiki to document terms, at present as an example the taxpub vocabularly, which ontology to use to document the following: 1. generic part-of relations of concepts. Example: the taxpub nomenclature section is part of the taxpub treatment We consider using DublinCore for this. We found nothing in SKOS for this. 2. part of relations of things both petal and sepal are part of the corolla. Bob Morris recommends the ro ontology: http://obofoundry.org/ro/ However, this one says that it is undergoing strong changes in the near future. 3. When documenting legacy xml ontologies, the xml variant requires documenting a difference between element and attribute children. How to express this in RDF form? ("why would you want do that" -> Bob Morris likes to answer that, but in fact we just want to have an orthogonal form to simplify things). Any help or insight is appreciated. Gregor -- --------------------------------- Dr. G. Hagedorn +49-(0)30-8304 2220 (work) +49-(0)30-831 5785 (private) http://www.linkedin.com/in/gregorhagedorn This communication (including all attachments) is sent on a personal basis. It is intended only for the person(s) to whom it is addressed. Redistributing or publishing it without permission is a violation of privacy rights and copyright.

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DwC change review: geo terms
by John Wieczorek 06 Sep '11

06 Sep '11

Hi TAGers, I am deep in the review process for the proposed changes to Darwin Core, trying to do due diligence. Some of the change requests are challenging to summarize to determine if there is consensus, in spite of, or because of the discussions. One of the requests on which I’d like some TAG help before proposing a solution is the request for the inclusion of the terms from the geo: namespace (xmlns:geo="http://www.w3.org/2003/01/geo/wgs84_pos#"). Support in tdwg-content for this request comes from multiple independent sources. There has been a long history of discussion (http://lists.tdwg.org/pipermail/tdwg-tag/2010-August/000050.html), beginning in anticipation of the 2010 TDWG BioBlitz. The proposal has gone through the minimum 30-day public review and discussion on the forum tdwg-content(a)lists.tdwg.org: http://lists.tdwg.org/pipermail/tdwg-content/2011-July/002581.html There seems to be general support for the additions, however, after reviewing the discussions and the references. I have the following observations/concerns: 1) The discussions presented geo:lat and geo:lng as W3C standards. This is not actually the case. These terms were created by the W3C Semantic Web Interest Group in 2003. The documentation for these terms (http://www.w3.org/2003/01/geo/) states: "This document was created as an informal collaboration within W3C's Semantic Web Interest Group. This work is not currently on the W3C recommendation track for standardization, and has not been subject to the associated review process, quality assurance, etc. If there is interest amongst the W3C membership in standards work on a location/mapping RDF vocabulary, this current work may inform any more formal efforts to follow." These terms do seem to have widespread usage in the semantic web. Should we be concerned that they are not part of a standard? 2) geo:lat and geo:lng are not semantically equivalent to the existing Darwin Core terms decimalLatitude and decimalLongitude, which have been a part of the Darwin Core since it 2003 (or before, if we ignore the missing Datum term in earlier versions). The addition of the geo: terms as a third set of geolocation terms for Darwin Core raised concerns about confusion. I share this concern. An option would be to adopt these terms and deprecate dwc:decimalLatitude, dwc:Longitude, and dwc:geodeticDatum. Data that would have occupied these terms would go instead to dwc:verbatimLatitude dwc:verbatimLongitude, and dwc:verbatimSRS. I see a couple of problems with this. First, most of the time the data in the decimal coordinate fields are not the verbatim originals, so this would be a misuse of the Darwin Core terms. Second, this change would make it more difficult for data consumer’s to use existing georeferences. Here’s how. Right now the verbatim fields are meant to hold the original coordinate information, which means they have a wide variety of content - everything from UTMs to custom-encoded coordinates, in any conceivable format. Meanwhile, the data in the decimal coordinates fields can be much more readily transformed into the desired standardized spatial reference system afforded by the geo: terms, because the values are at least standardized on decimal degrees and only a datum transformation has to be done on them. Do we abandon the dwc: terms decimalLatitude, decimalLongitude, and geodeticDatum? Do we abandon them now? Do we build the simplest possible tools necessary for anyone to do the transformations so that these terms are no longer needed? If so, do we wait until those tools exist? 3) Additional concern was expressed that the term geo:alt should also be added. No one has made a formal request for this. However, if the other geo: terms were adopted, it might be silly not to adopt this one as well. Doing so would raise a host of issues similar to those raised for lat and lng. I don’t have a good solution. The best short-term one, in my opinion, is to leave Darwin Core as it is, and to recommend that if applications (or aggregators) want to share “cleansed” point-based georeferences, that they do so with the geo: tags, the values for which they derive through transformations to WGS84 of the DwC decimal coordinates and geodeticDatum. Options: 1) Accept the proposal, adding geo:lat, geo:lng, and geo:alt to the list of recommended terms for DwC. 2) Reject the proposal pending further directed research into a comprehensive solution that considers all geospatial terms in Darwin Core (including footprintWKT, for example). 3) Reject the proposal for now, reopening the public discussion with these concerns. Others?

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