May 2009 - tdwg-tag - lists.tdwg.org

e-Biosphere 09 Challenge: visualising biodiversity digitisation in real time
by Roderic Page 27 May '09

27 May '09

Dear All, As many of you know, e-Biosphere '09 is on next week in London, and the organisers have issued a bioinformatic challenge. Since challenges tend to focus my mind, I'm entering a tool that aggregates and displays biodiversity digitisation in "real time". The organisers were keen on "real time", and this is not an easy thing to do (unless we're in the middle of a flu pandemic). However, there's enough happening in our field the space of a month (and even a week) to give people a sense of what is going on. To this end I've created http://bioguid.info/ebio09/www/3d/ , which aggregates RSS feeds (mostly from http://bioguid.info/rss ), does some geotagging, then uses Poly9's Globe to display the result (inspired by David Troys http://twittervision.com). I've put some background up at http://iphylo.blogspot.com/2009/05/e-biosphere-challenge-visualising.html . I welcome any comments, and suggestions for improvements, extra feeds, etc. I plan to have this updated during the conference. Regards Rod --------------------------------------------------------- Roderic Page Professor of Taxonomy DEEB, FBLS 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

1 0

Darwin Core cover page a bit of a mess
by Hilmar Lapp 26 May '09

26 May '09

The Darwin Core cover page at http://www.tdwg.org/standards/450/ (which is linked from the Standards page) looks like a bit of a mess - I'm assuming the Package Contents aren't meant to be rendered the way they are (which is rather gobbledygook), and clicking any of the links doesn't result in anything useful. Is this the result of some auto- generation? -hilmar -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at duke dot edu : ===========================================================

2 1

TDWG ontology revisited ... a newcomer's perspective
by Lynette.Woodburn＠csiro.au 25 May '09

25 May '09

Back to basics ... Anyone new to biodiversity informatics (in general) and TDWG (in particular) might be expected, as a first step, to seek a broad understanding of the scope of the knowledge domain which is of interest to the community they've just joined. Next, they're likely to want to gain an understanding of each of the main concepts and to discover how those concepts relate to one other. Delving yet deeper, curiosity will lead them to seek details about features used by the community to characterise each of those main concepts. So, gradually, it is anticipated that newcomers will gain an understanding of the meaning associated by their fellow community members with elements (concepts, features, relationships) within the knowledge domain. (Those elements are, after all, the chief subjects of discourse amongst community members.) This fantastic voyage of discovery, these first steps into Aladdin's Cave, ought to be made easy for any newcomer. Instead, TDWG presents a dizzying array of perspectives on disparate subsets of elements within the knowledge domain, often with only cryptic, tenuous links binding them together. 'Horses-for-courses'-drivers clearly exist for these subsets, but where is the common community understanding of where each element fits into the broader, shared knowledge domain which is TDWG's scope? I fully support any initiative which more effectively leads newcomers (and not-so-newcomers) to that place: that place where I would hope to find, in plain expressions devoid of techno-speak, a description of each real world element (concept, feature, relationship), together with a simple representation (a label?) by which the TDWG community prefers each to be referred; that place which evolves, but endures, independently of technological fashions and particular implementations; that place I can visit to paint a picture in my mind's eye of TDWG's own Aladdin's Cave. Lynette Woodburn Atlas of Living Australia

16 27

DC: was Re: Re-organisation of TDWG Ontology: Danger silence will == acquiescence!
by Bob Morris 20 May '09

20 May '09

Sometimes DC works and sometimes it doesn't. See http://www.keytonature.eu/wiki/MRTG_Schema_v0.7 where we spent and continue to spend a lot of effort to sort out (in the case of multimedia resources) what does and doesn't. I hope people will join that discussion. At the simplest level, what we do is use DC (and other standards) URI's for the URI of the term we are adopting. Some DC remains very vague and sloppy, even in the 2008 revision. The current "controversy" on the MRTG wiki is whether too much complexity gets introduced by trying to provide for data provenance. To me, this is an issue very important for science data, but only somewhat so in the communities classically served by DC---the cultural artifacts community possibly being the biggest exception. Bob On Tue, May 12, 2009 at 10:17 AM, Roderic Page <r.page(a)bio.gla.ac.uk> wrote: > Dear Roger, > This is probably off topic (and maybe I missed something), but it really > worries me that much of the TDWG vocabulary is unique to TDWG. Journal > publishers are busy pumping out Dublin Core and PRISM (sometimes with FOAF). > I'm trying to link this to records nomenclators pump out. I seem to recall > some statement that where possible TDWG would reuse existing vocabularies, > but I don't see this happening. In the meantime, I'm busy mapping our > idiosyncratic vocabulary to that used by publishers. > > Regards > > Rod > > > > > On 12 May 2009, at 09:59, Roger Hyam wrote: > > Hi All, > I need to do some work on the Taxon Name and Taxon Concept vocabularies and > believe I have come up with a good way of organising the TDWG ontology space > (everything within http:/rs.tdwg.org/ontology). > > The following are the changes I suggest: > > > - All files should be OWL DL compliant > - All files should be openable in Protege 4 (I believe this is now good > enough to use for editing these small ontologies) > - We take a highly structured modular approach I call this the Bricks > and Mortar design pattern > - Some files are 'Bricks' and as such *import or reference no other > files, classes or individuals*. e.g. TaxonName does not mention a > higher 'Name' object in the class hierarchy. > - Other files are 'Mortar'. These files import Bricks and stipulate > relationships between things. Because we are using OWL it is easy to define > things like the class hierarchy or the range of a property in a separate > file to the file the original class or property was defined in. > - This pattern gives us maximum re-usability as the same Brick could > be used in different ways. It does not bind us to any one implementation of > one object. > - An example of the usage pattern would be to define TaxonName, > TaxonConcept, Rank, NomenclaturalCode as separate bricks that don't > reference each other at all then create a TCS ontology that imports these 4 > bricks and defines their relationships. > - We move to some other method of presenting the ontologies on line - > possibly the OWLDoc plug-in for Protege. This would lose us the branded look > we have at the moment but would be more flexible and consistent in the long > run. > > > As I need to do this for the TaxonName TaxonConcept vocabularies I > volunteer to do manage the space this year if people are happy going down > this route. > > From the point of view of deployed systems (the nomenclators) there may be > a need for a namespace change on some properties but I would review what is > in use and this would be trivial - if necessary at all. > > What do you think? I will take silence as acquiescence on the grounds that > any movement is better than none - though I don't suppose I will get round > to doing anything about changes till after e-Biosphere in June. > > All the best, > > Roger > > > ----------------------------------------------------- > Roger Hyam - Project Officer WP4 > Pan European Species Infrastructure > +44 75 90 60 80 16 > ----------------------------------------------------- > > > > > _______________________________________________ > tdwg-tag mailing list > tdwg-tag(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tag > > > --------------------------------------------------------- > Roderic Page > Professor of Taxonomy > DEEB, FBLS > 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 > > > > > > > > _______________________________________________ > tdwg-tag mailing list > tdwg-tag(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tag > > -- Robert A. Morris Professor of Computer Science UMASS-Boston ram(a)cs.umb.edu http://bdei.cs.umb.edu/ http://www.cs.umb.edu/~ram http://www.cs.umb.edu/~ram/calendar.html phone (+1)617 287 6466

3 4

Re-organisation of TDWG Ontology: Danger silence will == acquiescence!
by Roger Hyam 17 May '09

17 May '09

Hi All, I need to do some work on the Taxon Name and Taxon Concept vocabularies and believe I have come up with a good way of organising the TDWG ontology space (everything within http:/rs.tdwg.org/ontology). The following are the changes I suggest: All files should be OWL DL compliant All files should be openable in Protege 4 (I believe this is now good enough to use for editing these small ontologies) We take a highly structured modular approach I call this the Bricks and Mortar design pattern Some files are 'Bricks' and as such import or reference no other files, classes or individuals. e.g. TaxonName does not mention a higher 'Name' object in the class hierarchy. Other files are 'Mortar'. These files import Bricks and stipulate relationships between things. Because we are using OWL it is easy to define things like the class hierarchy or the range of a property in a separate file to the file the original class or property was defined in. This pattern gives us maximum re-usability as the same Brick could be used in different ways. It does not bind us to any one implementation of one object. An example of the usage pattern would be to define TaxonName, TaxonConcept, Rank, NomenclaturalCode as separate bricks that don't reference each other at all then create a TCS ontology that imports these 4 bricks and defines their relationships. We move to some other method of presenting the ontologies on line - possibly the OWLDoc plug-in for Protege. This would lose us the branded look we have at the moment but would be more flexible and consistent in the long run. As I need to do this for the TaxonName TaxonConcept vocabularies I volunteer to do manage the space this year if people are happy going down this route. From the point of view of deployed systems (the nomenclators) there may be a need for a namespace change on some properties but I would review what is in use and this would be trivial - if necessary at all. What do you think? I will take silence as acquiescence on the grounds that any movement is better than none - though I don't suppose I will get round to doing anything about changes till after e-Biosphere in June. All the best, Roger ----------------------------------------------------- Roger Hyam - Project Officer WP4 Pan European Species Infrastructure +44 75 90 60 80 16 -----------------------------------------------------

9 14

TDWG ontology revisited ... a newcomer'sperspective [SEC=UNCLASSIFIED]
by Lee Belbin 17 May '09

17 May '09

Point taken Bob, but I'd refer back to Rupert's point about mentoring. How are the experts of tomorrow recruited and trained? TDWG has a role to play here. Lee Lee Belbin TDWG Secretariat

1 0

Re: [tdwg-tag] [BULK] TDWG ontology revisited ... a newcomer's perspective
by rupertwilson＠rhs.org.uk 15 May '09

15 May '09

As one of those not-so-newcomers who has been attending TDWG meetings for the last few years I feel I should speak out in agreement with Lynette. Whilst I may understand the general ideas the techno-speak is truly baffling. I appreciate that technology is evolving and the TDWG community is looking for the best way to embrace it but could you not spare a thought for those organisations like mine who have information they would like to share but are bewildered by the multitude of ways to do it? Having limited development resources the last thing I want my organisation to do is deliver information using technology "a" which is currently flavour of the moment only to find in twelve months that we should really be using technology "b" because that is what everyone else is using. I feel there is also a divide here between the research community which can chop and change the way it handles its data and the more constrained organisations such as mine where the data is of critical/core use to the organisation and can't be re-purposed as easily. Perhaps TDWG would also consider identifying mentors who would be willing to offer support to those lurking in the back of Aladdin's Cave currently too scared to come out into the light? Rupert Wilson RHS Horticultural Database Royal Horticultural Society Wisley, UK. ________________________________ From: tdwg-tag-bounces(a)lists.tdwg.org [mailto:tdwg-tag-bounces@lists.tdwg.org] On Behalf Of Lynette.Woodburn(a)csiro.au Sent: 14 May 2009 04:31 To: tdwg-tag(a)lists.tdwg.org Subject: [BULK] [tdwg-tag] TDWG ontology revisited ... a newcomer's perspective Importance: Low Back to basics ... Anyone new to biodiversity informatics (in general) and TDWG (in particular) might be expected, as a first step, to seek a broad understanding of the scope of the knowledge domain which is of interest to the community they've just joined. Next, they're likely to want to gain an understanding of each of the main concepts and to discover how those concepts relate to one other. Delving yet deeper, curiosity will lead them to seek details about features used by the community to characterise each of those main concepts. So, gradually, it is anticipated that newcomers will gain an understanding of the meaning associated by their fellow community members with elements (concepts, features, relationships) within the knowledge domain. (Those elements are, after all, the chief subjects of discourse amongst community members.) This fantastic voyage of discovery, these first steps into Aladdin's Cave, ought to be made easy for any newcomer. Instead, TDWG presents a dizzying array of perspectives on disparate subsets of elements within the knowledge domain, often with only cryptic, tenuous links binding them together. 'Horses-for-courses'-drivers clearly exist for these subsets, but where is the common community understanding of where each element fits into the broader, shared knowledge domain which is TDWG's scope? I fully support any initiative which more effectively leads newcomers (and not-so-newcomers) to that place: that place where I would hope to find, in plain expressions devoid of techno-speak, a description of each real world element (concept, feature, relationship), together with a simple representation (a label?) by which the TDWG community prefers each to be referred; that place which evolves, but endures, independently of technological fashions and particular implementations; that place I can visit to paint a picture in my mind's eye of TDWG's own Aladdin's Cave. Lynette Woodburn Atlas of Living Australia

4 4

Call for participation in GEO BON work groups
by Eamonn O Tuama (GBIF) 12 May '09

12 May '09

[apologies for cross posting] The establishment of the Group on Earth Observations Biodiversity Observation Network (GEO BON) was approved by GEO members at the GEO V Plenary in Bucharest last November (http://www.gbif.org/Stories/geobon). This is a culmination of efforts by many organisations, including GBIF, who have devoted time to developing both a concept document and implementation overview document for GEO BON. As a worldwide initiative, GEO BON, a component of the Global Earth Observation System of Systems (GEOSS) seeks to link and build on the work of countries, organisations and individuals to collect, manage, share and analyse data on the status of the world's biodiversity. For further information, visit the GEO BON home page: http://www.earthobservations.org/cop_bi_geobon.shtml GEO BON is now entering its implementation phase, and to aid this, a number of topical working groups are being established. Work Group 8 "Data Integration and Inter-operability; Informatics and Portals" is being lead by GBIF through co-chairs Hannu Saarenmaa (GBIF Finland) and Éamonn Ó Tuama (GBIF Secretariat). The attached document describes how the working groups should get started. If you are interested in participating in a work group, please contact the chair of the group as listed in the document. In particular, for work group 8 (Data Integration and Interoperability), please contact the co-chairs below by Friday, 5th June. Best regards, Hannu and Éamonn Hannu Saarenmaa GBIF Finland hannu.saarenmaa(a)helsinki.fi Telephone +358-9-191-28688 Mobile +358-50-3102689 http://www.gbif.fi/ Éamonn Ó Tuama GBIF Secretariat eotuama(a)gbif.org Telephone +45 3532 1494 http://www.gbif.org

1 0

Zootaxa RSS feed
by Roderic Page 08 May '09

08 May '09

Dear All, Continuing on from yesterday's theme of RSS feeds for names, I've created a RSS feed for Zootaxa. The feed is in the list on http://bioguid.info/rss , or can be accessed directly here: http://bioguid.info/rss/zootaxa.php The feed contains a list of the latest articles published in the journal, links to those articles, and a list of names extracted from the article title using uBio's findIT tool. If you use a feed reader it should be a useful way to keep track of what Zootaxa is publishing. For the geeks, the RSS feed is RSS 1.0, so you can get bibliographic details and uBIO LSIDs from the feed source. Regards Rod --------------------------------------------------------- Roderic Page Professor of Taxonomy DEEB, FBLS 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

1 0

Test Example of Occurrence RDF with DarwinCore/TDWG (might not be correct :-\)
by Peter DeVries 08 May '09

08 May '09

I thought I would try to start using the DarwinCore vocabulary in my observation RDF. I thought it might be easiest to start with the SimpleDarwinCore. The following URL takes you to an RDF file that combines my older vocabulary with my attempt at the SimpleDarwinCore. There is some redundancy in this version but it looks like I can probably replace a number of my terms with DarwinCore terms. The DarwinCore representation appears at the bottom of the RDF. http://species.geospecies.org/observations/a3c39dad-6756-4129-9a61-fbd32883… I would appreciate comments or suggestions. Thanks! Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 ------------------------------------------------------------

1 0