- tdwg-content - lists.tdwg.org

poking from TDWG wiki's
by Bob Morris 14 Apr '11

14 Apr '11

What if the list tdwg-content received a notification from each TDWG wiki when a page changed? These are fairly unobtrusive and presently infrequent (because most TDWG wiki's are inactive). They summarize the change and give links to the new content. I believe that they are set to notify only once a day. I \think/ this can be accomplished without more than edit privilege on the wikis, and if nobody raises major objection, I'll try to implement it for SDD, MRTG, and AnnotationsIG and we can see if it is a help or an annoyance. Pros: No need to make announcements or comments in two places. WikiLuddites can still respond in the mailing list. No need to opt-in for Wiki change notices. One click to relevant information. Cons: Default is to summarize changes, so people who want to respond in the mailing list have to proactively visit the relevant Wiki and perhaps cut/paste into their reply. Spammy feeling if a wiki suddenly become very active. Wiki users who do not subscribe to tdwg-content won't see email discussion of wiki pages. Another possibility is to do this in some other mailing list, perhaps even one devoted to entirely to the notifications. But to me, an active mailing list seems more productive. After all, wiki content is nothing if not TDWG content.... Bob Morris -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 IT Staff Filtered Push Project Department of Organismal and Evolutionary Biology Harvard University email: morris.bob(a)gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile)

5 6

GBIF Darwin Core data publishing documents and tools
by David Remsen (GBIF) 11 Apr '11

11 Apr '11

Dear TDWG Content GBIF has produced a series of documents and supporting tools that focus primarily on Darwin Core publishing. They are divided into three profiles each of which presents a series of documents based on the different content types in which GBIF focuses: 1. primary biodiversity data, http://www.gbif.org/informatics/primary-data/publishing/ 2. checklists, http://www.gbif.org/informatics/name-services/publishing/ 3. resource metadata http://www.gbif.org/informatics/discoverymetadata/publishing/ While you may have seen the announcement of the GBIF Integrated Publishing Toolkit earlier in the year, we also have developed two additional tools for producing Darwin Core Archives, which are featured on these sites. First, we have produced a suite of MS Excel templates, currently under evaluation, which are coupled with a web service that processes completed files and returns a validated Darwin Core Archive. Templates exist for primary biodiversity data, simple checklists, and EML metadata. See http://tools.gbif.org/spreadsheet-processor/ Second, the Darwin Core Archive Assistant is a tool that composes a XML metafile, the only XML component of a Darwin Core Archive, for you. It presents a pick list of Darwin Core and extension terms, accessed dynamically from the GBIF registry, and presents these to the user who describe their data files. This allows Darwin Core Archives to be created for sharing with no installed software at all. See http://tools.gbif.org/dwca-assistant/ We would appreciate any feedback on any or all of this as we roll these tools and documents out to the GBIF community. Best, David Remsen ---------------------------------------------------------------------------- David Remsen, Senior Programme Officer Electronic Catalog of Names of Known Organisms Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321472 Fax: +45-35321480 Mobile +45 28751472 Skype: dremsen ----------------------------------------------------------------------------

1 0

TDWG 2011 - New Orleans - October 16-21, 2011
by Chuck Miller 08 Apr '11

08 Apr '11

The TDWG Executive Committee is pleased to announce that the 2011 TDWG annual conference will be held on October 16-21, 2011 at the Astor Crowne Plaza Hotel in New Orleans, Louisiana located at the entrance to the famous Bourbon Street district. Hank Bart, Director of Tulane Museum of Natural History, will be the local sponsor. Information on accommodations, registration, program, abstract submission and other meeting details will soon be made available at www.tdwg.org. We hope to have an informative and productive meeting and a lot of fun in The Big Easy. Chuck Miller TDWG Chair

1 0

A Little More on the TDWG BioBlitz Records
by Peter DeVries 29 Mar '11

29 Mar '11

Here is a little more on the latest version of the TDWG BioBlitz records. This bit.ly link will run a SPARQL query to give you what you need SPARQL Query for TableView of TDWG BioBlitz Records http://bit.ly/gcA3ox Here is the query used: Note it returns those records that have identifications and a lat/long but includes those without a photo. PREFIX foaf: <http://xmlns.com/foaf/0.1/> PREFIX txn: <http://lod.taxonconcept.org/ontology/txn.owl#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX dcterms: <http://purl.org/dc/terms/> PREFIX geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> PREFIX time: <http://www.w3.org/2006/time#> select distinct ?s, ?area, ?lat, ?long, ?kingdom, ?phylum, ?class, ?order, ?family, ?scientific_name, ?collector, ?recorder, ?individual, ?date, ?day_of_year, ?depiction where { ?s rdf:type txn:Occurrence. ?s dcterms:isPartOf txn:TDWG2010_BioBlitz. ?s geo:lat ?lat. ?s geo:long ?long. ?s txn:startDate ?date. ?s time:dayOfYear ?day_of_year. ?s txn:occurrenceHasArea ?area. ?s txn:kingdom ?kingdom. ?s txn:phylum ?phylum. ?s txn:class ?class. ?s txn:order ?order. ?s txn:family ?family. ?s txn:hasScientificName ?scientific_name. ?s txn:hasCollector ?collector. ?s txn:recordedBy ?recorder. ?s txn:occurrenceHasIndividual ?individual. OPTIONAL {?s foaf:depiction ?depiction }. } ORDER BY ASC(?area) limit 1000 =========== Here is a map base view of those records. http://bit.ly/ids5hX It uses the following query: PREFIX foaf: <http://xmlns.com/foaf/0.1/> PREFIX txn: <http://lod.taxonconcept.org/ontology/txn.owl#> PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX dcterms: <http://purl.org/dc/terms/> PREFIX geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> PREFIX time: <http://www.w3.org/2006/time#> describe ?s where { ?s rdf:type txn:Occurrence. ?s dcterms:isPartOf txn:TDWG2010_BioBlitz. ?s geo:lat ?lat. ?s geo:long ?long. ?s txn:startDate ?date. ?s time:dayOfYear ?day_of_year. ?s txn:occurrenceHasArea ?area. ?s txn:kingdom ?kingdom. ?s txn:phylum ?phylum. ?s txn:class ?class. ?s txn:order ?order. ?s txn:family ?family. ?s txn:hasScientificName ?scientific_name. ?s txn:hasCollector ?collector. ?s txn:recordedBy ?recorder. ?s txn:occurrenceHasIndividual ?individual. ?s foaf:depiction ?depiction . } limit 1000 This PivotView (requires Silverlight) is an interactive way to look at the data. It shows the TDWG Observations by Observer http://bit.ly/fzR3cv * It maybe a little slow to load (~1000 records) Here are two screenshots to give you an idea of what this looks like Small Version http://assets.taxonconcept.org/ss/PivotView_BioBlitz_by_Ob_800x457.png Large Version http://assets.taxonconcept.org/ss/PivotView_BioBlitz_by_Ob_1614x923.png Respectfully, - Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies Knowledge Base <http://lod.geospecies.org/> About the GeoSpecies Knowledge Base <http://about.geospecies.org/> ------------------------------------------------------------

1 0

Original TDWGBioblitz needs geo:lat geo:long fixed to match geo vocabulary
by Peter DeVries 28 Mar '11

28 Mar '11

I noticed this when someone wrote me about querying the original tdwgbioblitz RDF. In the file available here: http://www.cs.umbc.edu/~jsachs/occurrences/TechnoBioblitzOccurrences.rdf the geo:lat and geo:long are geo:latitude and geo:longitude. I separated the original version from my modified version. They are in two separate graphs on in my SPARQL endpoint. Original <urn:org:linkedopenspeciesdata:dataspace:tdwg2010bioblitz> The modified version is in the graph <urn:org:linkedopenspeciesdata:dataspace:taxonconcept> I can reload a fixed version of the original RDF when it is ready. The new version can be seen here: http://ocs.taxonconcept.org/ocs/index.html The highlighted species names takes you to the species concepts, while the "HTML" and "RDF" take you to the HTML and RDF for the occurrences themselves. For instance here is one observation http://ocs.taxonconcept.org/ocs/e08c6f06-ee59-4f2b-8f46-a3f66a65431e.html Here is the RDF for that observation http://ocs.taxonconcept.org/ocs/e08c6f06-ee59-4f2b-8f46-a3f66a65431e.rdf There are still some issues with the identifications, and I think that there are multiple rows "observations" for an individual observation. It seems as if one "observation" was made for the gps and another for the photograph but it is hard to tell. - Pete -- --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies Knowledge Base <http://lod.geospecies.org/> About the GeoSpecies Knowledge Base <http://about.geospecies.org/> ------------------------------------------------------------

1 0

Stability of tdwg-content postings?
by Steve Baskauf 28 Mar '11

28 Mar '11

I have been reviewing some posts in the tdwg-content archives and got to this one: http://lists.tdwg.org/pipermail/tdwg-content/2010-August/000060.html It references a number of previous posts related to background on the DwC standard, such as http://lists.tdwg.org/pipermail/tdwg-content/2009-June/000019.html However, those links don't seem to do anything any more. There are other emails whose URLs begin with http://lists.tdwg.org/pipermail/tdwg-content/2009-June/ found in the June 2009 archives: http://lists.tdwg.org/pipermail/tdwg-content/2009-June/thread.html but not the ones referenced in the August 2010 message. I have been assuming that although it is a bit inconvenient to look things up in the list archives, the messages that have been sent would nevertheless be permanently archived. Is that not true? 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

7 10

FW: Habitat classifications?
by Tony.Rees＠csiro.au 25 Mar '11

25 Mar '11

Apologies for cross-posting - below is a message I just sent to the TAXACOM list, but if there are TDWG persons not on TAXACOM who have not seen it and may have useful information, I'd be happy to receive it. Regards - Tony > -----Original Message----- > From: taxacom-bounces(a)mailman.nhm.ku.edu [mailto:taxacom- > bounces(a)mailman.nhm.ku.edu] On Behalf Of Tony.Rees(a)csiro.au > Sent: Thursday, 17 March 2011 2:22 PM > To: Taxacom(a)mailman.nhm.ku.edu > Subject: [ExternalEmail] [Taxacom] Habitat classifications? > > Dear all, > > I am interested in extending the habitat classification presently used in > my IRMNG genera and species database from the present "very basic" > (marine/nonmarine/both) to something a bit more detailed - maybe marine, > freshwater, terrestrial with up to perhaps a dozen or so subcategories of > each, as appropriate (e.g. end up with a little nested hierarchy of maybe > 30-50 terms total). > > So, I am looking for suggestions of such classifications as may already be > in use in order to either pick one up more or less unchanged, or develop > something with the best features of several. For example I am familiar > with the following off the top of my head: > > http://sn2000.taxonomy.nl/SyntaxHabitat.htm - 23 terms, coverage a bit > uneven > > http://mave.tweakdsl.nl/tn/syntax.html - scroll down to the section headed > "% HABITAT" -- 56 terms, looks quite useable. > > Something like the EUNIS classification e.g. as accessible via > > http://eunis.eea.europa.eu/habitats-code-browser.jsp possibly gets too > detailed too quickly at this time for my needs, but you never know what > may end up being of value. > > If list persons can point me at any other resources worth looking at, or > comment on details of the above, I would be very appreciative. It also > occurs to me that some people may have been through this exercise > previously, e.g. for "species / structured descriptive data" purposes, so > any pointers to the results of those deliberations would also be useful. > > Thanks in advance, > > Tony Rees > Manager, Divisional Data Centre, > CSIRO Marine and Atmospheric Research, > GPO Box 1538, > Hobart, Tasmania 7001, Australia > Ph: 0362 325318 (Int: +61 362 325318) > Fax: 0362 325000 (Int: +61 362 325000) > e-mail: Tony.Rees(a)csiro.au > Manager, OBIS Australia regional node, http://www.obis.org.au/ > Biodiversity informatics research activities: > http://www.cmar.csiro.au/datacentre/biodiversity.htm > Personal info: > http://www.fishbase.org/collaborators/collaboratorsummary.cfm?id=1566 > > > > _______________________________________________ > > Taxacom Mailing List > Taxacom(a)mailman.nhm.ku.edu > http://mailman.nhm.ku.edu/mailman/listinfo/taxacom > > The Taxacom archive going back to 1992 may be searched with either of > these methods: > > (1) http://taxacom.markmail.org > > Or (2) a Google search specified as: > site:mailman.nhm.ku.edu/pipermail/taxacom your search terms here

7 8

Forgot to mention: MS Pivot Heuristics are putting non-gps occurrences in NC, sorry
by Peter DeVries 11 Mar '11

11 Mar '11

I forgot to mention in the earlier email that MS Pivot Heuristics are putting non-gps occurrences in NC, sorry. I hope to have this fixed in the future. - Pete -- --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies Knowledge Base <http://lod.geospecies.org/> About the GeoSpecies Knowledge Base <http://about.geospecies.org/> ------------------------------------------------------------

1 0

Not condemning DarwinCore, but trying to support my argument for the development of an additional LOD RDF format
by Peter DeVries 11 Mar '11

11 Mar '11

I thought I should be clear that my point is not that there is something wrong with the DarwinCore for what it is good for, it is that I think we should develop some additional form that works well as LOD data. Perhaps expressed after processing by GBIF? Also the web applications just serve as a framework for exposing the data structure. I would *not* suggest that my occurrence example web app is ideal for showing / editing BioBlitz records. The idea I am trying to get across is meshups and possibilities of structured LOD data For example this view from Sig.ma http://sig.ma/search?pid=ba0db41b7772e1b06231a8975dcf903b <http://sig.ma/search?pid=ba0db41b7772e1b06231a8975dcf903b>I recently changed the occurrence RDF slightly and ID'd two previously unidentified wasps. http://ocs.taxonconcept.org/ocs/9f0fc9c7-a522-44d8-a0c3-327fea9351f0.html http://ocs.taxonconcept.org/ocs/e08c6f06-ee59-4f2b-8f46-a3f66a65431e.html In the listing of the occurrence records here http://ocs.taxonconcept.org/ocs/index.html The occurrence HTML and RDF are linked at the end of each row. The species names on the table link to the species concepts (the most interesting thing there is the RDF structure and LOD representations) A new Pivot View should be online shortly. The entire dataset is described with a void file and CKAN description http://ckan.net/package/taxonconcept I am sorry if some had problems with the earlier Pivot SPARQL query. The bit.ly link runs a SPARQL query which feeds into MS Pivot for viewing. For some people Pivot had problems parsing the results of the SPARQL query. In the future the current working Pivot example will be available here: http://www.delicious.com/taxonconcept.org <http://www.delicious.com/taxonconcept.org>This and other Pivot example can be found here: http://www.delicious.com/kidehen/pivot_collection_app * The MS Pivot example require Silverlight, which you might already have if you use netflix or similar apps, but they won't work on iPhone or iPad. :-( Respectfully, - Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies Knowledge Base <http://lod.geospecies.org/> About the GeoSpecies Knowledge Base <http://about.geospecies.org/> ------------------------------------------------------------

1 0

New views and RDF representations of the TDWG BioBlitz data
by Peter DeVries 09 Mar '11

09 Mar '11

Hi TDWG'ers, I decided that rather than tweak Joel's RDF by hand it might make more sense to just import the data and express in a different RDF representation. These examples are not about the web application or relatively small differences in how to name fields, they are more about how in general to format occurrence records in a way that maximizes their utility. I added the identified TDWG records to my small set of occurrence examples here: http://ocs.taxonconcept.org/ocs/index.html Here is one example http://ocs.taxonconcept.org/ocs/a5bd890c-c1db-4194-8347-796621105ae6.html On that page are highlighted links that take you into a view of the entity in my sparql endpoint knowledgebase. The data is also on the URIburner endpoint which allows a browsable Pivot interface. Here is the short link http://t.co/03WriMA The actual URI looks like this since it contains a SPARQL query: < http://uriburner.com/PivotViewer/?url=http%3A%2F%2Furiburner.com%2Fsparql%2… > There are still things that are not ideal in these examples, or instance I was not able to add the occurrenceRemarks simply but I hope to do so in the future. This also allows me to host the original DarwinCore RDF for comparison. Here is the url to the endpoint view of one of those records. Current DarwinCore < http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Fwww.cs.umbc.edu%2F~j…> Bit.ly < http://bit.ly/i1gfCK > Current TaxonConcept < http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/a…> Bit.ly < http://bit.ly/ezU2BA > Respectfully, - Pete --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies Knowledge Base <http://lod.geospecies.org/> About the GeoSpecies Knowledge Base <http://about.geospecies.org/> ------------------------------------------------------------

1 0