- tdwg-content - lists.tdwg.org

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 22 May '11

22 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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Updated Example of TDWG BioBlitz Records showing the utility of dwc_area
by Peter DeVries 13 May '11

13 May '11

One of the advantages of the dwc_area:*Area* encoding, is that it creates one urn for each combination of lat, long, radius. In practice, this is similar to one urn for each GPS reading. An alternative way to get the same list would be a query that includes geo:lat, geo:long and radius. Most people want to think of this as one thing, a point with a PointRadiusSpatialFit- type error measure. I created this demonstration query that finds the BioBlitz observations with geo coordinates and sorts the resulting data by Observer. It also allows you to pick and display different *Areas* from the list of returned records. *Note I have only 708 occurrence records with GPS coordinates. * I still include the geo:lat and geo:long since most toolkits do not understand the proposed ietf.org proposed geo standard. Screenshots of the Pivot Views and a link for the query itself can be found at this bit.ly bundle http://bit.ly/m6c5hI Here is the query REFIX 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 foaf: <http://xmlns.com/foaf/0.1/> PREFIX cc: <http://creativecommons.org/ns#> PREFIX time: <http://www.w3.org/2006/time#> PREFIX geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> select distinct ?s, ?o as ?image, ?class, ?order, ?family, ?sciname, ?cname, ?observer, ?lat, ?long, ?area where { ?s rdf:type txn:Occurrence. ?s dcterms:isPartOf < http://lod.taxonconcept.org/ontology/txn.owl#TDWG2010_BioBlitz>. ?s txn:class ?class. ?s txn:order ?order. ?s txn:family ?family. ?s txn:hasScientificName ?sciname. ?s cc:attributionName ?observer. ?s geo:lat ?lat. ?s geo:long ?long. ?s txn:occurrenceHasArea ?area. optional {?s foaf:depiction ?o. ?s txn:commonName ?cname. }. } limit 708 -- 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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Updated Rich's Two Species and additional thoughts and example on how to handle alternative conceptualizations
by Peter DeVries 10 May '11

10 May '11

I have added some additional information the the TaxonConcept KB for Rich's two fish About: Centropyge fisheri se:q72fd Orange Angelfish http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org… bit.ly http://bit.ly/j1c7NF About: Centropyge flavicauda se:Mj6j4 Whitetail Angelfish http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org… bit.ly http://bit.ly/mwQIyh * Assuming the photo's are correct, these examples still need links to representative specimens and other related data. This was done by creating this file and adding it to the triplestore http://assets.taxonconcept.org/fb/index.rdf Data about the image http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Fassets.taxonconcept.… bit.ly http://bit.ly/jjmnsd If I understand Rich correctly all these images would be instances of the concept *Centropyge fisheri sensu lato* * * *That would need it own URI and could be related by something like this:* * * <http://lod.taxonconcept.org/ses/q72fd#Species> txn:hasWiderAlternativeConceptualization < http://lod.alternativeconcepts.org/ses/10252#Species> <http://lod.taxonconcept.org/ses/Mj6j4#Species> txn:hasWiderAlternativeConceptualization < http://lod.alternativeconcepts.org/ses/10252#Species> and <http://lod.alternativeconcepts.org/ses/10252#Species > txn:hasNarrowerTXNConceptualization < http://lod.taxonconcept.org/ses/q72fd#Species> <http://lod.alternativeconcepts.org/ses/10252#Species > txn:hasNarrowerTXNConceptualization < http://lod.taxonconcept.org/ses/Mj6j4#Species> I think it is cleaner to have the overlapping concepts separated into a different namespace. This implies that the set of alternativeconcepts don't overlap with each other. So what I am proposing allows for alternative concepts. It does not appear that The Plant List has alternative concepts, each species has a current name and the set represents their form of a set of non overlapping concepts. Why isn't this controversial? Note also that things like The Plant List don't do much to improve the lot of those who document and describe species. You cite the authors of The Plant List. This is in contrast to TaxonConcept where you site the species editors and the original author is linked via their DBpedia description. (In many cases these will need to be added to Wikipedia, about 6,000 already) Respectfully, - 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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Fwd: [Fwd: Re: If you need something for referring to a population, then it is probably best to do it as a related class]
by Nico Cellinese 10 May '11

10 May '11

Hi Pete, > 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. I would have stopped here! If someone wants to point to a series of objects to indicate his own concept of a "species", then that's ok. That's a convention we can work with. Everything else you talk about below seem to be a confused mashup of "species" as a taxon and "species" as ranks. > 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. Really? Maybe in animals but everywhere else I don't think so! And what about asexual organisms? I guess they do not deserve the status of "species". So, the biological species concept you are referring to can't be universally applied = not a good concept to use for ALL organisms, right? > Are we modeling species or variations in human conceptualizations of species? Is there anything else out there besides the human conceptualization of species? Do we have an absolute concept of what a species represent? Last time I checked we have been arguing about this for the past century and more. Species defined by the 25+ species concepts out there can't possibly be real. They are defined by human conceptualization = artificial. The only think we can clearly try to discern are clades and often those clades may correspond with someone's concept of a species. In other words, you can take the rank of species and point it at a node that define a taxon. Or you can take the rank of species and point it to an assemblage of lineages, regardless if that assemblage represents a monophyletic group or not. Traditionally recognized species are most likely polyphyletic anyways. > 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. What do you really mean by individuals? Are species created by the gods and we just can't figure out what they meant? Human issue? We, humans came up with this impossible to define concept. Individuals are just that: individuals. The individuals = species hypothesis has been argued in the literature and is not an accepted notion by far (note: I am not saying I agree or disagree, this is just another non-absolute concept). But maybe you don't mean it that way. > Again, Are we modeling species or variations in human conceptualizations of species? Your statement is recursive. You have an idea of species that is above all of the other variations on the theme. I don't understand what you mean and that's why I think there is a confusion between the usage of "species" as a taxon and "species" as an arbitrary rank. > 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. Even in the lack of a phylogenetic framework, every species is a hypothesis. When we lump and split we generate hypotheses. A new name points to a new hypothesis. Adding a new genus to a family or a new species to a genus refines and modifies the original hypothesis. > In the real world taxa are not as clean as some would like to make them out to be. In fact, the only way we can discover a little more clarity is through phylogenies. When it comes to low level taxa, population studies help a lot too. > Each individual is a unique combination of thousands of separate gene lineages which often do not follow clean monophyletic paths. But as you stated above you equate individuals with species. if that's correct, then you admit that individuals can be polyphyletic, and as such do we really care about polyphyletic entities? As such you admit that species as you define them are artificial. > 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. I actually don't and I can name many others who don't. The rank of species may be useful to many as communication tool but the way it is applied vary a lot. The biological species concept is not widely accept and certainly not followed by the vast majority as you indicate. The only think we can really achieve from an informatics standpoint is to reconcile objects (specimens, images, sequences, descriptions, etc.etc.) with the many names that may have been associated with those and leave the rest (philosophical masturbation) to the users. Reconciling names with concepts, given the nature of the concepts and the idiosyncratic way that names have been historically used, is a Quixoterian challenge. Cheers, Nico > > 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 > > On Wed, May 4, 2011 at 8:35 AM, Steve Baskauf <steve.baskauf(a)vanderbilt.edu> wrote: > I beg to differ. > > > Peter DeVries wrote: >> >> About occurrences. >> >> It is the specimen (individual) that gets identified and it can have several identifications. > I do not believe it is a good idea to equate "specimen" with individual. I have reached the conclusion that a specimen CAN be an individual if one chooses to type a particular "thing" as both a specimen and and an Individual but I'm not comfortable with saying that they are owl:sameAs . It is my opinion, and I think one that was supported to some extent in the discussion of last Oct/Nov that when we "identify" some kind of evidence like a a branch cut from a tree we are really making a statement about what taxon we think the tree represents, not the branch per se. This is an important distinction, because if we are identifying the tree, then any branch that is dcterms:partOf the tree shares that identification. This may seem like an esoteric point, but it is one that has a fairly significant bearing on how one chooses to construct a model. I will stop there because I don't want to re-plough the same ground again. The relevant posts are summarized and referenced on the DSW pages explaining the IndividualOrganism and Specimen classes. >> >> There is an issue with occurrence records that we saw with one of the initial TDWG BioBlitz RDF Versions. >> >> There were multiple identifications but there was no way of indicating which was the preferred. > Again, I beg to differ. It was my understanding (again from the extensive conversation about this in Oct/Nov) that the creation of multiple Identifications were "preference agnostic". Each Identification represented an expressed opinion about the concept/TNU that the determiner asserted that the individual represented. They were not flagged as "right" or "wrong". In fact, it is possible that there could be several Identifications by different determiners that asserted the same concept/TNU, indicating that the determiners agreed with each other. > >> >> 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! > >> >> Different human identifiers make assertions about what that species is, those different identifications are then tied to the individual organism. > Yes I agree entirely. > >> >> In other words it is the specimen that is identified not the occurrence. > Yes, the occurrence was not identified. But I would say the individual, not the specimen (as explained above). > >> >> If your additional identification RDF links to the specimen then it will be linked to the occurrence so someone can browse from the occurrence and look at the identification history of the specimen. >> >> Does, this answer your question? > Not really, but I think the issue here is that the way you are conceptualizing specimens, individuals, and identifications is NOT the same as DSW defines them. So I retract my earlier statement that the taxonconcept.org ontology and DSW are really the same thing with different term names . > > Steve > >> >> - Pete >> >> On Mon, May 2, 2011 at 8:16 AM, Steve Baskauf <steve.baskauf(a)vanderbilt.edu> wrote: >> OK, Pete, I'm going to try to write the other email that I mentioned in the previous one. This email relates to the actual suggestion that you made in the email, that is to use the URIs of the form like: "http://lod.taxonconcept.org/ses/mCcSp#Occurrence". In the RDF that defines what this URI means, the URI is described as "A lightweight tag that can be used to label occurrences of this species". What I'm not sure about is what exactly one is supposed to do with it. From the example that I was talking about in the previous email (http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9.rdf) this "tag" is the object of the predicate txn:occurrenceHasSpeciesOccurrenceTag . So I guess that it is another way that one could query Occurrence records to find out which ones are Occurrences of the species having the identifier "ICmLC" (Boloria selene). But I'm not sure what the advantage of that is. The RDF for the Occurrence already tells me that the Occurrence has the txn:occurrenceHasSpeciesConcept property with object URI http://lod.taxonconcept.org/ses/ICmLC#Species . I can resolve that URI and "find out" that the "species concept" (sensu DeVries) is Boloria selene . But if I used the "lightweight tag" I'd also have to resolve its URI to find out about it and the RDF for the tag directs me to the http://lod.taxonconcept.org/ses/ICmLC#Species URI anyway via the dcterms:isPartOf property of the tag. I guess the point is that if one wants to "find out" about the Occurrence, it takes two steps to get to the species concept description if I use the tag (first through txn:occurrenceHasSpeciesOccurrenceTag, then through dcterms:isPartOf) which is no advantage over just getting there in one step (via txn:occurrenceHasSpeciesConcept). If the only point is to have something to put in as a search term, then why not just make the txn:occurrenceHasSpeciesOccurrenceTag a data property with the literal object the string "ICmLC"? >> >> I suppose that one could say that an advantage of the "lightweight tag" approach would be that one is indicating that the particular Occurrence is an instance of a class that consists of all Occurrences of the species Bororia selene. That seems to be what the intention is. But this seems to be a case of creating many subclasses rather than having a general class and assigning it properties that help one to understand the nature of the instance of that class. It requires the creation of a class for every species on the planet. Instead of there being a relatively small number of classes that includes the basic kinds of resources (Occurrence, individual, Identification, taxon concept) there is a class for occurrences of every kind of taxon concept. Actually, there are several classes for every instance of taxon concept, because you are recommending that the "lightweight tag" approach be used for other types of things as well, such as individuals and (in your suggestion below, populations). There isn't anything intrinsically "wrong" with this approach, but with my bias toward preferring "well known" types/classes it just seems like a lot to expect consuming applications to "understand" what amounts to potentially millions of classes that this method would introduce. >> >> I also don't quite understand what a txn:SpeciesOccurrenceTag is exactly. In the RDF that defines the txn:SpeciesOccurrenceTag instance for Bororia selene (http://lod.taxonconcept.org/ses/ICmLC#Occurrence) the dcterms:description says that it "allow species occurrences to be modeled as instances of SpeciesOccurrenceTag". But that doesn't seem to be what is actually occurring. When the Occurrence instance http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9#Occurr… is described, it is not typed as the lightweight tag (which IS a txn:SpeciesOccurrenceTag because of the implicit typing caused by the XML container element name). The lightweight tag URI is the object of the txn:occurrenceHasSpeciesOccurrenceTag property, but that doesn't make the Occurrence an instance of SpeciesOcurrenceTag as would be the case (I think) if the lightweight tag URI were the object of a rdf:type property. Anyway, I'm confused about this. >> >> The other issue that I would raise with this approach is that it brings up the same issue that I raised in the other email that I wrote. It essentially puts a burden of anticipating the results of a query onto the metadata provider. If one follows the model of allowing multiple Identifications for an organism, then it is possible that someone somewhere else might apply their own Identification instance to the individual represented in the Occurrence. As was the case in my earlier example, for txn:occurrenceHasSpeciesOccurrenceTag to be useful as a thing to be queried, the metadata provider would need to somehow know that this additional Identification had been made, and then create another txn:occurrenceHasSpeciesOccurrenceTag property for the Occurrence instance. This seems to somewhat at odds with the benefit that the Linked Data world has in allowing resources to be created by people all over the cloud and then linked rather than expecting a centralized authority to do everything. >> >> Anyway, maybe you can explain what is going on so that I can understand it better and maybe explain why this approach is better than just creating a few classes and describing their instances by descriptive properties. >> >> Steve >> >> >> Peter DeVries wrote: >>> >>> I am still somewhat puzzled why TDWG seems so opposed to adopting anything that comes from outside a small click? >>> >>> I was thinking that it would be best to create a separate class that can be used for populations of a species. >>> >>> This would require adding an additional tag to the TaxonConcept Species Concept Model, which currently includes several tags like entities >>> >>> http://lod.taxonconcept.org/ses/mCcSp#Species <- The Species Concept for the Cougar >>> >>> See http://lod.taxonconcept.org/ses/v6n7p.html HTML >>> http://lod.taxonconcept.org/ses/v6n7p.rdf RDF >>> http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org… Knowledge Base View (http://bit.ly bit.ly/gMFqR1 >>> >>> The model mints URI's for the following related entities. See RDF. or KB View >>> >>> http://lod.taxonconcept.org/ses/mCcSp#Image - An image of a Cougar >>> http://lod.taxonconcept.org/ses/mCcSp#Occurrence - An occurrence of a Cougar >>> http://lod.taxonconcept.org/ses/mCcSp#Individual - An individual Cougar >>> http://lod.taxonconcept.org/ses/mCcSp#Taxonomy - A Basic Taxonomy for the Cougar, one alternative among many potential classifications >>> http://lod.taxonconcept.org/ses/mCcSp#NCBI_Taxonomy - The NCBI Taxonomy for Cougar, or starting at the lowest available clade >>> http://lod.taxonconcept.org/ses/mCcSp#OriginalDescription - The Original Description of the Cougar, ideally with links to the PDF or BHL URI. >>> >>> >>> Here is how a subset of these would relate to the new #Population Tag and related semantic entities. >>> >>> >>> This tag is used an individual organism that that is an instance of the species concept pecies concept RDF. >>> This allows you to refer to a individual cougar in a way that is separate from the concept of cougar and retains links to other data relating to that species concept. >>> >>> >>> <txn:SpeciesIndividualTag rdf:about="http://lod.taxonconcept.org/ses/v6n7p#Individual"> >>> <dcterms:title>A Tag for individuals of the species concept Puma concolor se:v6n7p</dcterms:title> >>> <skos:prefLabel>A Tag-like resource that is used to label individuals of the species concept Puma concolor se:v6n7p</skos:prefLabel> >>> <dcterms:identifier>http://lod.taxonconcept.org/ses/v6n7p#Individual</dcterms:identifier> >>> <dcterms:description>A lightweight tag that can be used to label individuals of this species. These allow individual organisms to be modeled as instances of SpeciesIndividualTag</dcterms:description> >>> <dcterms:isPartOf rdf:resource="http://lod.taxonconcept.org/ses/v6n7p#Species"/> >>> <wdrs:describedby rdf:resource="http://lod.taxonconcept.org/ses/v6n7p.rdf"/> >>> </txn:SpeciesIndividualTag> >>> >>> Add a tag for a species population to the species concept RDF. >>> This allows you to refer to a population of cougars in a way that is separate for an individual cougar and retains links to other data relating to that species concept. >>> >>> <txn:SpeciesPopulationTag rdf:about="http://lod.taxonconcept.org/ses/v6n7p#Population"> >>> <dcterms:title>A Tag for populations of the species concept Puma concolor se:v6n7p</dcterms:title> >>> <skos:prefLabel>A Tag-like resource that is used to label populations of the species concept Puma concolor se:v6n7p</skos:prefLabel> >>> <dcterms:identifier>http://lod.taxonconcept.org/ses/v6n7p#Population</dcterms:identifier> >>> <dcterms:description>A lightweight tag that can be used to label populations of this species. These allow populations of a species to be modeled as instances of SpeciesIndividualTag</dcterms:description> >>> <dcterms:isPartOf rdf:resource="http://lod.taxonconcept.org/ses/v6n7p#Species"/> >>> <wdrs:describedby rdf:resource="http://lod.taxonconcept.org/ses/v6n7p.rdf"/> >>> </txn:SpeciesPopulationTag> >>> >>> >>> This is the RDF for a population, it has as one of it's parts an individual organism. >>> It is typed to indicate that it refers to a population of Cougars. >>> >>> <owl:Class rdf:about="http://lod.taxonconcept.org/pops/NorthAmericanCougarPopulation"> >>> <rdf:type rdf:resource="http://lod.taxonconcept.org/ses/v6n7p#Population"/> >>> <skos:prefLabel>The population of North American Cougars Puma concolor se:v6n7 </skos:prefLabel> >>> <dcterms:hasPart rdf:resource="http://ocs.taxonconcept.org/ocs/51cd124d-78c5-40aa-a7ff-2e3f58ca6ade#Indivi…"/> >>> <wdrs:describedby rdf:resource="http://lod.taxonconcept.org/pops/NorthAmericanCougarPopulation.rdf"/> >>> </owl:Class> >>> >>> Respectfully, >>> >>> - 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 & GeoSpecies Knowledge Bases >>> >>> A Semantic Web, Linked Open Data Project >>> >>> --------------------------------------------------------------------------------------- >>> >>> >> >> -- >> 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 >> >> >> >> >> -- >> ------------------------------------------------------------------------------------ >> Pete DeVries >> Department of Entomology >> University of Wisconsin - Madison >> 445 Russell Laboratories >> 1630 Linden Drive >> Madison, WI 53706 >> Email: pdevries(a)wisc.edu >> TaxonConcept & GeoSpecies Knowledge Bases >> A Semantic Web, Linked Open Data Project >> -------------------------------------------------------------------------------------- > > -- > 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 > > > > > -- > ------------------------------------------------------------------------------------ > Pete DeVries > Department of Entomology > University of Wisconsin - Madison > 445 Russell Laboratories > 1630 Linden Drive > Madison, WI 53706 > Email: pdevries(a)wisc.edu > TaxonConcept & GeoSpecies Knowledge Bases > A Semantic Web, Linked Open Data Project > -------------------------------------------------------------------------------------- > > -- > 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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If you need something for referring to a population, then it is probably best to do it as a related class
by Peter DeVries 09 May '11

09 May '11

I am still somewhat puzzled why TDWG seems so opposed to adopting anything that comes from outside a small click? I was thinking that it would be best to create a separate class that can be used for populations of a species. This would require adding an additional tag to the TaxonConcept Species Concept Model, which currently includes several tags like entities http://lod.taxonconcept.org/ses/mCcSp#Species <- The Species Concept for the Cougar See http://lod.taxonconcept.org/ses/v6n7p.html HTML http://lod.taxonconcept.org/ses/v6n7p.rdf RDF http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org… Base View (http://bit.ly bit.ly/gMFqR1 The model mints URI's for the following related entities. See RDF. or KB View http://lod.taxonconcept.org/ses/mCcSp#Image - An image of a Cougar http://lod.taxonconcept.org/ses/mCcSp#Occurrence - An occurrence of a Cougar http://lod.taxonconcept.org/ses/mCcSp#Individual - An individual Cougar http://lod.taxonconcept.org/ses/mCcSp#Taxonomy - A Basic Taxonomy for the Cougar, one alternative among many potential classifications http://lod.taxonconcept.org/ses/mCcSp#NCBI_Taxonomy - The NCBI Taxonomy for Cougar, or starting at the lowest available clade http://lod.taxonconcept.org/ses/mCcSp#OriginalDescription - The Original Description of the Cougar, ideally with links to the PDF or BHL URI. Here is how a subset of these would relate to the new #Population Tag and related semantic entities. This tag is used an individual organism that that is an instance of the species concept pecies concept RDF. This allows you to refer to a individual cougar in a way that is separate from the concept of cougar and retains links to other data relating to that species concept. <txn:SpeciesIndividualTag rdf:about=" http://lod.taxonconcept.org/ses/v6n7p#Individual"> <dcterms:title>A Tag for individuals of the species concept Puma concolor se:v6n7p</dcterms:title> <skos:prefLabel>A Tag-like resource that is used to label individuals of the species concept Puma concolor se:v6n7p</skos:prefLabel> <dcterms:identifier>http://lod.taxonconcept.org/ses/v6n7p#Individual </dcterms:identifier> <dcterms:description>A lightweight tag that can be used to label individuals of this species. These allow individual organisms to be modeled as instances of SpeciesIndividualTag</dcterms:description> <dcterms:isPartOf rdf:resource=" http://lod.taxonconcept.org/ses/v6n7p#Species"/> <wdrs:describedby rdf:resource=" http://lod.taxonconcept.org/ses/v6n7p.rdf"/> </txn:SpeciesIndividualTag> Add a tag for a species population to the species concept RDF. This allows you to refer to a population of cougars in a way that is separate for an individual cougar and retains links to other data relating to that species concept. <txn:SpeciesPopulationTag rdf:about=" http://lod.taxonconcept.org/ses/v6n7p#Population"> <dcterms:title>A Tag for populations of the species concept Puma concolor se:v6n7p</dcterms:title> <skos:prefLabel>A Tag-like resource that is used to label populations of the species concept Puma concolor se:v6n7p</skos:prefLabel> <dcterms:identifier>http://lod.taxonconcept.org/ses/v6n7p#Population </dcterms:identifier> <dcterms:description>A lightweight tag that can be used to label populations of this species. These allow populations of a species to be modeled as instances of SpeciesIndividualTag</dcterms:description> <dcterms:isPartOf rdf:resource=" http://lod.taxonconcept.org/ses/v6n7p#Species"/> <wdrs:describedby rdf:resource=" http://lod.taxonconcept.org/ses/v6n7p.rdf"/> </txn:SpeciesPopulationTag> This is the RDF for a population, it has as one of it's parts an individual organism. It is typed to indicate that it refers to a population of Cougars. <owl:Class rdf:about=" http://lod.taxonconcept.org/pops/NorthAmericanCougarPopulation"> <rdf:type rdf:resource="http://lod.taxonconcept.org/ses/v6n7p#Population "/> <skos:prefLabel>The population of North American Cougars Puma concolor se:v6n7 </skos:prefLabel> <dcterms:hasPart rdf:resource=" http://ocs.taxonconcept.org/ocs/51cd124d-78c5-40aa-a7ff-2e3f58ca6ade#Indivi… "/> <wdrs:describedby rdf:resource=" http://lod.taxonconcept.org/pops/NorthAmericanCougarPopulation.rdf"/> </owl:Class> Respectfully, - 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://lod.geospecies.org/> Knowledge Bases A Semantic Web, Linked Open Data <http://linkeddata.org/> Project ---------------------------------------------------------------------------------------

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Updated TDWG BioBlitz SPARQL Example
by Peter DeVries 06 May '11

06 May '11

*Updated TDWG BioBlitz SPARQL Example* I have a link to a bit.ly bundle for the query and screenshots. http://bit.ly/l7LWuF <http://bit.ly/l7LWuF>* It is possible that the LOD cache will be updating to the new version when you read this, so if the live query does not work the bundle has screen shots that will. The query text is below. Note it is set to return just 500 records. Depending on the time of day etc. I had some issues with Pivot so I set the limit to 500 rather than 1005. Attributes like time:month and time:dayOfYear are useful for browsing the data for patterns (maybe not in this BioBlitz example) Also, I limit the records to those from the BioBlitz using the predicate dcterms:isPartOf 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 foaf: <http://xmlns.com/foaf/0.1/> PREFIX cc: <http://creativecommons.org/ns#> PREFIX time: <http://www.w3.org/2006/time#> PREFIX geo: <http://www.w3.org/2003/01/geo/wgs84_pos#> select distinct ?s, ?o as ?image, ?kingdom, ?phylum, ?class, ?order, ?family, ?genus, ?sciname, ?cname, ?month, ?observer, ?lat, ?long where { ?s rdf:type txn:Occurrence. ?s dcterms:isPartOf < http://lod.taxonconcept.org/ontology/txn.owl#TDWG2010_BioBlitz>. ?s txn:kingdom ?kingdom. ?s txn:phylum ?phylum. ?s txn:class ?class. ?s txn:order ?order. ?s txn:family ?family. ?s txn:genus ?genus. ?s txn:hasScientificName ?sciname. ?s time:month ?month. ?s cc:attributionName ?observer. optional {?s foaf:depiction ?o. ?s txn:commonName ?cname. ?s geo:lat ?lat. ?s geo:long ?long. }. } limit 500 The live SPARQL Pivot Query http://t.co/RNTLGL9 via LOD cache CLOUD The live SPARQL No Pivot Query (my endpoint - just a table, but all observations) http://bit.ly/mPd8vi Here are some direct links, there are more on bit.ly Observations viewed by Kingdom http://assets.taxonconcept.org/ss/UpdatedTDWGBioBlitzByKingdom_1024x564.png Donald's Observations http://assets.taxonconcept.org/ss/DonaldHobernTDWG2010Observations_1024x564… Cyndy's Observations http://assets.taxonconcept.org/ss/CyndyParrTDWG2010Observations_1024x564.png Why not the Wood Frog? It must have not been in the first 500 records but it is here http://ocs.taxonconcept.org/ocs/fbdc4c11-25d4-4f47-91b8-99c649b9f0b9.html Also I changed the observation and species RDF a little to make some queries easier. There is a plant that was identified as *Luzula banksiana, ( http://lod.taxonconcept.org/ses/py5ST.html) *but I think this a New Zealand plant? Is it cultivated in the US? See http://ocs.taxonconcept.org/ocs/index.html <http://assets.taxonconcept.org/ss/UpdatedTDWGBioBlitzByKingdom_1024x564.png> -- 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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