May 2011 - tdwg-content - lists.tdwg.org

Re: [tdwg-content] If you need something for referring to a population, then it is probably best to do it as a related class
by Nico Franz 05 Jun '25

05 Jun '25

Hello all: I have a few inserted comments, hopefully with some clarifying effect: On 5/4/2011 10:54 AM, Peter DeVries wrote: > Hi Steve, > > I may have overloaded the term specimen to make the explanation easier > to follow. > > A specimen could be an individual or it could be part of an individual. > > To some extent you need to think about how these models will be used. > > If you subscribe to the model that a species is whatever a taxonomists > says it is then it is difficult to make statements like. > > X% of the world's species will be extinct by 2050. > > If you mean a species as defined by the concept documented at this URI > which is supported by these specimens, images, and DNA then you are on > firmer ground. > > Species in the natural world do a pretty good job recognizing those > individuals that are appropriate mates. In other words members of > their own species. > > Are we modeling species or variations in human conceptualizations of > species? > >> Assuming that there was only one individual organism identified >> there is really one one species (or hybrid). > Aaaaaaaaaaaaaah! Please Nico C., don't take this one up! > > > I stick with this. Assuming you don't have a hybrid individual. That > individual is one species. The fact that human may disagree on what > species it is a human issue. > > Again, Are we modeling species or variations in human > conceptualizations of species? NMF: I believe there is a history of biodiversity database engineering that actually led some people, initially in Australia (Greg Whitbread?) and Europe (Berendsohn's group) to place more emphasis on modeling human conceptualizations of taxa. I understand this happened in the late 80s / early 90s. The motivation was, apparently, that no long-term consensus seemed available to model a single and sufficiently widely accepted taxonomy of, say, Central European vascular plant species or mosses. I believe that projects such as the Euro + Med PlantBase (http://www.emplantbase.org/home.html) are examples of the persistence (success?) of this 20+ year old practice. I think this is the kind of background that Steve is referring to. > > Which of these is of primary importance to decision makers and > non-taxonomist biologists? > Part of the problem with various publications relating to ontologies > and taxonomy is that their species models entail a specific > phylogenetic hypothesis. > > In the real world taxa are not as clean as some would like to make > them out to be. > > Each individual is a unique combination of thousands of separate gene > lineages which often do not follow clean monophyletic paths. > > I would argue that most of those who work with species related data > see them as useful typological constructs which in general follow the > biological species model. NMF: The solution of how to properly model things such as species in RDF, OWL (etc.) should ideally accommodate all "species concepts" (BCS, ESC, PSC, GSC, there's dozens), i.e. it should be neutral towards this issue. The examples below are too simple, ignoring for example cases such as pro parte synonymy, or a concept ("species") that appears unique and monophyletic to one author but (vastly) polyphyletic to another. To do an accurate mapping in that latter case (which is not super-common but it's real), I think one would have to come down on saying we're modeling human conceptualizations. They are not just that, so really it's not a strict dichotomy, meaning that by modeling conceptualizations we do not have to say "the species only exist on our heads", or "well, then anything goes". I agree (sheepishly) that it does come down to what the input data look like, and what the expectations are towards just accommodating the user community versus pushing them in a particular direction. Some of this also on p. 47 of this PDF: https://journals.ku.edu/index.php/jbi/article/view/3927/3852 > > /Aedes triseriatus/ owl:sameAs /Ochlerotatus triseriatus/ > > Others seem to see them as phylogenetic end nodes which entail a > specific phylogenetic history. > > /Aedes triseriatus/ distinctFrom /Ochlerotatus triseriatus/ > / > / > If you are primarily interested in understanding issues of ecology, > disease, diversity and conservation the former model is more > appropriate than the later. > > Respectfully, > > - Pete Regards, Nico Nico M. Franz, Ph.D. Assistant Professor Director, UPRM Invertebrate Collection Department of Biology University of Puerto Rico Call Box 9000 Mayagüez, PR 00681-9000 Phone: (787) 832-4040, ext. 3005 Fax: (787) 834-3673 E-mail: nico.franz(a)upr.edu Laboratory website: http://academic.uprm.edu/~franz/ UPRM-INVCOL: http://uprm-invcol-project.tumblr.com/

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An individual identified to a higher group like Order, is still an instance of a species - just a species that is currently unspecified
by Peter DeVries 25 Sep '11

25 Sep '11

What I would recommend is that you treat a specimen that is identified to an order (Perciformes) with something like the following. Species => Order Perciformes species undetermined. The individual is still an instance of a species, however that species has yet to be determined. What would work best is to have some standard way of writing the green string above. This would allow the occurrences that are of individuals identified only to the Order Perciformes, to be interpreted as a species that falls somewhere within the Order Perciformes. - 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/> ------------------------------------------------------------

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Re: [tdwg-content] ITIS TSNID to uBio NamebankIDs mapping
by Nicolson, David 09 Jun '11

09 Jun '11

Hi Steve (and Dave), [NB: After having composed the email below, just before sending it, I re-read your initial email more carefully and realized that you said you already had the ITIS TSNs, and were looking to add the NamebankIDs! Doh! Well, in case you (or anyone else) is interested in methods of matching names to get TSNs, I'll go ahead and send this anyway. But do note the comments below about the ITIS "versions" and ongoing overhaul of the vascular plant data in ITIS!!! -Dave] I noticed this just before leaving work last week, and was out yesterday, but I wanted to chime in on this. I'm glad the uBio tools are meeting your needs (they do have some cool stuff!), but it should be noted that those tools are using a static snapshot of ITIS data from January 2009, and we have added about 50,000 additional scientific names, and updated tens of thousands of names beyond that (most of that in the last 6 months, as the frequency of loads dropped off in 2009-2010 due to technical issues). I also want to note that ITIS is right in the middle of a full update of the vascular plant data in ITIS, and we're loading updated families on a monthly basis... and at long last we are tackling all the leftover issues from several bulk loads from USDA PLANTS data that left unreconciled bits of ITIS' older vascular plant data in various confusing states... so it is a VAST improvement that is underway. There are several options for bouncing your names off the current version of ITIS. One is to automate a matching process using the live ITIS data, based on the existing ITIS Web Services. I am CC'ing Alan Hampson, our IT fellow who built the Web Services ( http://www.itis.gov/web_service.html ), in case you'd like to follow up with him on that option. The advantage is that once you have a process in place it is completely self-serve and can always utilize the current ITIS data. If you have the resources to do this I think it would be greatly to your advantage to use this approach. You can explore some ideas for client software to use the services at: http://www.itis.gov/ws_develop.html And for more information on ITIS web services try http://www.itis.gov/ws_description.html http://www.itis.gov/ITISWebService.xml The ability to flag multiply-matched names (as you noted) should probably be considered, so that appropriate manual steps can be taken. This solution will allow you to take advantage of subsequent updates to ITIS with a minimum of additional effort, and given that the plant data are in the middle of a major overhaul, this bears consideration! Another possibility is to grab a full snapshot of the ITIS data, and load it into a database so you can do what you wish. The obvious drawback is that it goes out of date, as with the ITIS snapshot uBio is currently using. But it puts you in the driver's seat re what to do & getting new versions of ITIS. Some general information about the full exports is in the following page, although conspicuously absent is any mention of the MySQL version which (assuming you have the free MySQL properly installed & configured) can be loaded with just a few clicks or a few command lines (depending on your platform): http://www.itis.gov/ftp_download.html And the current ITIS data are all here for downloading: http://www.itis.gov/downloads/ A third option, which I note with some trepidation, is the old "Compare Nomenclature/Taxonomy" function on the ITIS site: http://www.itis.gov/taxmatch_ftp.html This is a VERY old function that we do plan on replacing (timeframe not yet certain), and it is vulnerable to timeouts, etc., which is why it notes to limit the number of names per pass. But with smaller chunks of names it does work quite well. The caveat is that I would make sure to choose the 4th option in Step 4, as it is at least aware (unlike the 3 other options) of multiply-matched name cases, and lists them separately at the bottom of the report. Just a bare listing of the scientific names, with the word "name" at the top, saved as plain text, is all that is needed for input. A final option would be to ask someone at ITIS to handle the matching for you (leaving you to decide re the multiply-matched names). This might be simple from your end, but is suboptimal as it leaves you in the same position as you are now should you want or need to compare names again in the future (whether due to acquiring new names in your system, or wanting to check against a later updated version of ITIS), and it pulls someone here (probably me) off of the push to get more updates into ITIS. But in a pinch, I'm certainly willing to try to help you, should it come down to that! I would just ask that you seriously consider the web services option (in particular) or the others above first. I hope this helps some. If you have already run all your matches against the old "ITIS" data via uBio then you might consider re-running (against the current ITIS data) at least the leftover names that you did not yet get matched. Let us know if you have questions (the itiswebmaster(a)itis.gov address goes to myself and Alan and several others, so that might be the best bet for a follow-up unless you have a question specifically for me). Regards, Dave David Nicolson Data Development Coordinator, Integrated Taxonomic Information System Biologist, USGS Core Science Systems, Biological Informatics Program nicolsod(a)si.edu Office 202-633-2149 Fax 202-786-2934 http://www.itis.gov/ http://www.cbif.gc.ca/itis/ "Nihil sumas necesse est..." -----Original Message----- Date: Fri, 20 May 2011 05:42:03 -0500 From: Steve Baskauf <steve.baskauf(a)vanderbilt.edu> Subject: Re: [tdwg-content] ITIS TSNID to uBio NamebankIDs mapping To: "David Remsen (GBIF)" <dremsen(a)gbif.org> Cc: "tdwg-content(a)lists.tdwg.org" <tdwg-content(a)lists.tdwg.org> Message-ID: <4DD6457B.2080204(a)vanderbilt.edu> Content-Type: text/plain; charset="iso-8859-1" Thanks, all, for the responses. The "Compare to ITIS" function does just what I want. I did a test run of 1000 names and it worked like a charm. I will need to do a little massaging because sometimes two or more ITIS IDs come back for each uBio ID. But I can handle that. Steve David Remsen (GBIF) wrote: > Steve > > Have you tried this? > http://www.ubio.org/clients/ITIS/index.php > > or this? > http://www.ubio.org/services/mapper/index2.php > > All this ubio talk makes me think we were on to something. Worth a thought about adopting the new stnadrds and tools and making it really smooth. > > DR > > > On 20 May 2011, at 04:46, Steve Baskauf wrote: > > >> I have generated a csv spreadsheet of about 39 000 plant names for the >> U.S. which has the ITIS TSNIDs for the names in a column. I would like >> to have the uBio Namebank IDs in another column of the table. I have >> been looking them up on the uBio website by typing in the names as I >> need to know the IDs, but after doing about 300 of them, I'm getting >> tired of it. Does anybody have a clever idea of a way to get the other >> 38 000 Namebank IDs without looking them up. I'm sure that it would be >> possible to find this out because uBio gets names from ITIS. However, I >> haven't seen any clues about how to do it in an automated fashion. I'm >> guessing that there might be some way to use the uBio web services, but >> if so, it isn't obvious and I probably don't have the skills to carry it >> out anyway. >> >> Any ideas? >> 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 >> >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> >> > > . > > -- 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 _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

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DwC Occurrence [SEC=UNCLASSIFIED]
by Paul Murray 06 Jun '11

06 Jun '11

> An Occurrence is a combination of an Individual and an Event. > An Occurrence is a coupling of an Individual and an Event. > An Occurrence is a pairing of an Individual and an Event. How about: An Occurrence is the reification of an individual's involvement in (entaglement with? presence at? relationship to?) an event. It reifies an "Event involvesIndividual Individual" fact. The need for this construct is that we often need to say a number of additional things about an individual's involvement with (presence at) an event beyond simply assertin that there is some relationship. We need to say what tokens that individual left, what role that individual had (Predator? Prey? Parasite?), perhaps temporal or other limits of that particular individual at the event. Occurrence is the object to which these facts may be attached. An individual might meaningfully have more than one occurrence at an event - particularly in cases where events are part-of larger events, or where an individual somehow has multiple roles (hyenas chased away from their kill by a lion - or is it the other way around?). To put it another way: "reification" = "tuple" = "association table" = "pulling a property out into an object". More or less. To put it another another way, an Occurence object stands in relation to an event and an individual much as a TaxonRelationship object stands in relation to the two taxa it mentions. You could simply model taxonomy with a "hasSubtaxon" predicate, but we usually need to say a great deal more about taxonomic relationships than that. If you have received this transmission in error please notify us immediately by return e-mail and delete all copies. If this e-mail or any attachments have been sent to you in error, that error does not constitute waiver of any confidentiality, privilege or copyright in respect of information in the e-mail or attachments. Please consider the environment before printing this email.

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Fwd: error in TDWG geogrphic classification
by David Remsen (GBIF) 25 May '11

25 May '11

This is probably worth posting here. Begin forwarded message: > From: David Eades <dceades(a)illinois.edu> > Date: 25 May 2011 00:17:20 CEST > To: "'David Remsen (GBIF)'" <dremsen(a)gbif.org> > Cc: "'Burke Chih-Jen Ko (GBIF)'" <bko(a)gbif.org>, 'Hernán Pereira' <ellocodelassembler(a)gmail.com>, "Flood, Rich" <jrflood(a)illinois.edu> > Subject: error in TDWG geogrphic classification > Reply-To: <dceades(a)illinois.edu> > > Dear David, > > Hernán Pereira and Rich Flood have located what we believe is an error in > the TDWG data that has been widely used. The geographic coordinates > associated with Sardinia actually form the outline of Corsica. The > geographic coordinates associated with Corsica actually outline Sardinia. > We got the data from TDWG in 2001. I have separately notified Kew, which > has the same data we got from TDWG available for download at > http://kew.org/gis/tdwg/. > > David > >

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Re: [tdwg-content] ITIS TSNID to uBio NamebankIDs mapping
by Cynthia Parr 24 May '11

24 May '11

> > Quick note -- EOL is also aligning ITIS tsn's with Catalogue of Life, NCBI > identifiers and many other partner sources. They don't all update with the > same frequency on EOL but shouldn't be too stale. > > It might be a little complicated, but you can use the EOL API and find out > the cross-walks http://www.eol.org/api (see expecially the PAGES method) > > Steve, since Bioimages is an EOL partner you could even see exactly how we > align your specific taxa with others. > > Cyndy > > Cynthia Sims Parr, parrc(a)si.edu > Director, Species Pages Group > Encyclopedia of Life http://www.eol.org > Office: 202.633.9513, Fax: 202.633.8742 > > Mailing address: > National Museum of Natural History > Smithsonian Institution > P.O. Box 37012, MRC 106 > Washington, DC 20013-7012 > > > On Tue, May 24, 2011 at 4:50 PM, Nicolson, David <NICOLSOD(a)si.edu>wrote: > >> Hi Steve (and Dave), >> >> [NB: After having composed the email below, just before sending it, I >> re-read your initial email more carefully and realized that you said you >> already had the ITIS TSNs, and were looking to add the NamebankIDs! Doh! >> Well, in case you (or anyone else) is interested in methods of matching >> names to get TSNs, I'll go ahead and send this anyway. But do note the >> comments below about the ITIS "versions" and ongoing overhaul of the >> vascular plant data in ITIS!!! -Dave] >> >> I noticed this just before leaving work last week, and was out yesterday, >> but I wanted to chime in on this. I'm glad the uBio tools are meeting your >> needs (they do have some cool stuff!), but it should be noted that those >> tools are using a static snapshot of ITIS data from January 2009, and we >> have added about 50,000 additional scientific names, and updated tens of >> thousands of names beyond that (most of that in the last 6 months, as the >> frequency of loads dropped off in 2009-2010 due to technical issues). >> >> I also want to note that ITIS is right in the middle of a full update of >> the vascular plant data in ITIS, and we're loading updated families on a >> monthly basis... and at long last we are tackling all the leftover issues >> from several bulk loads from USDA PLANTS data that left unreconciled bits of >> ITIS' older vascular plant data in various confusing states... so it is a >> VAST improvement that is underway. >> >> There are several options for bouncing your names off the current version >> of ITIS. >> >> One is to automate a matching process using the live ITIS data, based on >> the existing ITIS Web Services. I am CC'ing Alan Hampson, our IT fellow who >> built the Web Services ( http://www.itis.gov/web_service.html ), in case >> you'd like to follow up with him on that option. The advantage is that once >> you have a process in place it is completely self-serve and can always >> utilize the current ITIS data. If you have the resources to do this I think >> it would be greatly to your advantage to use this approach. >> >> You can explore some ideas for client software to use the services at: >> http://www.itis.gov/ws_develop.html >> >> And for more information on ITIS web services try >> http://www.itis.gov/ws_description.html >> http://www.itis.gov/ITISWebService.xml >> >> The ability to flag multiply-matched names (as you noted) should probably >> be considered, so that appropriate manual steps can be taken. This solution >> will allow you to take advantage of subsequent updates to ITIS with a >> minimum of additional effort, and given that the plant data are in the >> middle of a major overhaul, this bears consideration! >> >> Another possibility is to grab a full snapshot of the ITIS data, and load >> it into a database so you can do what you wish. The obvious drawback is that >> it goes out of date, as with the ITIS snapshot uBio is currently using. But >> it puts you in the driver's seat re what to do & getting new versions of >> ITIS. Some general information about the full exports is in the following >> page, although conspicuously absent is any mention of the MySQL version >> which (assuming you have the free MySQL properly installed & configured) can >> be loaded with just a few clicks or a few command lines (depending on your >> platform): >> http://www.itis.gov/ftp_download.html >> And the current ITIS data are all here for downloading: >> http://www.itis.gov/downloads/ >> >> A third option, which I note with some trepidation, is the old "Compare >> Nomenclature/Taxonomy" function on the ITIS site: >> http://www.itis.gov/taxmatch_ftp.html >> This is a VERY old function that we do plan on replacing (timeframe not >> yet certain), and it is vulnerable to timeouts, etc., which is why it notes >> to limit the number of names per pass. But with smaller chunks of names it >> does work quite well. The caveat is that I would make sure to choose the 4th >> option in Step 4, as it is at least aware (unlike the 3 other options) of >> multiply-matched name cases, and lists them separately at the bottom of the >> report. Just a bare listing of the scientific names, with the word "name" at >> the top, saved as plain text, is all that is needed for input. >> >> A final option would be to ask someone at ITIS to handle the matching for >> you (leaving you to decide re the multiply-matched names). This might be >> simple from your end, but is suboptimal as it leaves you in the same >> position as you are now should you want or need to compare names again in >> the future (whether due to acquiring new names in your system, or wanting to >> check against a later updated version of ITIS), and it pulls someone here >> (probably me) off of the push to get more updates into ITIS. But in a pinch, >> I'm certainly willing to try to help you, should it come down to that! I >> would just ask that you seriously consider the web services option (in >> particular) or the others above first. >> >> I hope this helps some. If you have already run all your matches against >> the old "ITIS" data via uBio then you might consider re-running (against the >> current ITIS data) at least the leftover names that you did not yet get >> matched. Let us know if you have questions (the itiswebmaster(a)itis.govaddress goes to myself and Alan and several others, so that might be the >> best bet for a follow-up unless you have a question specifically for me). >> >> Regards, >> Dave >> >> David Nicolson >> Data Development Coordinator, Integrated Taxonomic Information System >> Biologist, USGS Core Science Systems, Biological Informatics Program >> nicolsod(a)si.edu Office 202-633-2149 Fax 202-786-2934 >> http://www.itis.gov/ >> http://www.cbif.gc.ca/itis/ >> "Nihil sumas necesse est..." >> >> >> -----Original Message----- >> Date: Fri, 20 May 2011 05:42:03 -0500 >> From: Steve Baskauf <steve.baskauf(a)vanderbilt.edu> >> Subject: Re: [tdwg-content] ITIS TSNID to uBio NamebankIDs mapping >> To: "David Remsen (GBIF)" <dremsen(a)gbif.org> >> Cc: "tdwg-content(a)lists.tdwg.org" <tdwg-content(a)lists.tdwg.org> >> Message-ID: <4DD6457B.2080204(a)vanderbilt.edu> >> Content-Type: text/plain; charset="iso-8859-1" >> >> Thanks, all, for the responses. The "Compare to ITIS" function does >> just what I want. I did a test run of 1000 names and it worked like a >> charm. I will need to do a little massaging because sometimes two or >> more ITIS IDs come back for each uBio ID. But I can handle that. >> Steve >> >> David Remsen (GBIF) wrote: >> > Steve >> > >> > Have you tried this? >> > http://www.ubio.org/clients/ITIS/index.php >> > >> > or this? >> > http://www.ubio.org/services/mapper/index2.php >> > >> > All this ubio talk makes me think we were on to something. Worth a >> thought about adopting the new stnadrds and tools and making it really >> smooth. >> > >> > DR >> > >> > >> > On 20 May 2011, at 04:46, Steve Baskauf wrote: >> > >> > >> >> I have generated a csv spreadsheet of about 39 000 plant names for the >> >> U.S. which has the ITIS TSNIDs for the names in a column. I would like >> >> to have the uBio Namebank IDs in another column of the table. I have >> >> been looking them up on the uBio website by typing in the names as I >> >> need to know the IDs, but after doing about 300 of them, I'm getting >> >> tired of it. Does anybody have a clever idea of a way to get the other >> >> 38 000 Namebank IDs without looking them up. I'm sure that it would be >> >> possible to find this out because uBio gets names from ITIS. However, >> I >> >> haven't seen any clues about how to do it in an automated fashion. I'm >> >> guessing that there might be some way to use the uBio web services, but >> >> if so, it isn't obvious and I probably don't have the skills to carry >> it >> >> out anyway. >> >> >> >> Any ideas? >> >> 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 >> >> >> >> _______________________________________________ >> >> tdwg-content mailing list >> >> tdwg-content(a)lists.tdwg.org >> >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> >> >> >> >> > >> > . >> > >> > >> >> -- >> 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 >> >> >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> >> >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> > >

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GBIF Seeks a Knowledge Systems Engineer
by David Remsen (GBIF) 24 May '11

24 May '11

Dear TDWG-content-ers GBIF is seeking a committed and proactive Knowledge Systems Engineer to develop a framework for creating and managing controlled vocabularies, thesauri and other knowledge organisation systems. Interested candidates should review the document, “Recommendations for the Use of Knowledge Organisation Systems by GBIF” at http://links.gbif.org/gbif_kos_whitepaper_v1.pdf for a fuller understanding of our requirements. Interested candidates should have knowledge of RDF, OWL, SKOS, the OBO Foundry, Open Ontology Repository principles, the TDWG ontologies and the broad Life Sciences ontology landscape, as well as an understanding of other well-known, generic vocabularies such as Dublin Core, FOAF, etc. Knowledge of principles of the semantic web and Linked Open Data are desirable. Practical experience with existing KOS systems such as the OBO Foundry, BioPortal, Collaborative Protégé, Pool Party or other systems would be highly beneficial. A key asset is the capacity to identify, communicate and facilitate the practical and pragmatic application of KOS principles that facilitate the uptake and use of GBIF-mediated data and infrastructure. Please circulate this posting to relevant lists and parties. This post is an exciting career-enhancing opportunity to work in a multicultural environment for an international organisation at the cutting edge of scientific developments in biodiversity informatics. The post is for two years with a possibility it may be extended. Residence in Denmark is preferred. Deadline for applications is 15 June. I'm happy to answer any questions about the posting. More information can be found on our website at http://www.gbif.org/communications/news-and-events/showsingle/article/gbif-… 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 ----------------------------------------------------------------------------

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Question about "vocabulary" in Darwin Core Archives assistant
by Steve Baskauf 23 May '11

23 May '11

I am playing around with Darwin Core Arcives, in particular the DwC-A Assistant (http://tools.gbif.org/dwca-assistant/) One thing that I am not exactly clear about is how to use the "Vocabulary" column in the assistant. The description that comes up when you mouse over the column heading says that it should ideally be a URI that identifies the vocabulary and resolves to some machine readable form like RDF. So what I'm wondering is whether I can put what effectively amounts to as a namespace in that spot. For example, a URI for the name "Acer rubrum L." that actually resolves to RDF is: http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:… I think that would qualify as a valid HTTP URI guid because it's the proxied form of an LSID. So I would like to use it as a value for the dwc:scientificNameID column in a DwC-A taxon record. However, the only part of the identifier that makes the string unique within uBio's domain is the last number - if I'm always using a uBio guid, the first approximately 75 characters will be the same for all of the guids. So can I just put "http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:" in the Vocabulary column and then just put the locally unique numbers (e.g. "456216") in the column for dwc:scientificNameID? Should an application using a DwC-A file be smart enough to append the "vocabulary" string on the front of the actual value in the text file? Or is that not how the "Vocabulary" column is intended to be used? 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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ITIS TSNID to uBio NamebankIDs mapping
by Steve Baskauf 20 May '11

20 May '11

I have generated a csv spreadsheet of about 39 000 plant names for the U.S. which has the ITIS TSNIDs for the names in a column. I would like to have the uBio Namebank IDs in another column of the table. I have been looking them up on the uBio website by typing in the names as I need to know the IDs, but after doing about 300 of them, I'm getting tired of it. Does anybody have a clever idea of a way to get the other 38 000 Namebank IDs without looking them up. I'm sure that it would be possible to find this out because uBio gets names from ITIS. However, I haven't seen any clues about how to do it in an automated fashion. I'm guessing that there might be some way to use the uBio web services, but if so, it isn't obvious and I probably don't have the skills to carry it out anyway. Any ideas? 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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Another example of non-overlapping concepts
by Peter DeVries 19 May '11

19 May '11

I thought that I would also mention that in addition to The Plants List, the eBird project also uses on overlapping concepts in its bird list (it does have concepts for common hybrids) What is clear to me is that you cannot create graphs like these if every observation can have X number of species (especially those that overlapping ) without any indication which is is the most appropriate one. eBird Occurrence Maps Northern Cardinal http://ebird.org/content/ebird/about/occurrence-maps/northern-cardinal NCBI is also similar. Perhaps a member of the consensus committee can comment? -- Pete ------------------------------------------------------------------------------------ Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 Email: pdevries(a)wisc.edu TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies<http://about.geospecies.org/> Knowledge Bases A Semantic Web, Linked Open Data <http://linkeddata.org/> Project --------------------------------------------------------------------------------------

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