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Producing a global taxon register (was: ITIS TSNID to uBio NamebankIDs mapping)
by Tony.Rees＠csiro.au 05 Jun '11

05 Jun '11

Hi all (jumping in with some trepidation...) It's good to hear some ramp-up may be coming of activity in the GNUB space (congratulations, Rich et al.). My main concern, however is that it does not solve my particular problem - which is in a nutshell, given "any" cited taxonomic name, what can we tell about it - with regard to its classification, nomenclatural and taxonomic/synonym status, and certain attributes (initially for my use case, simple geologic time - is it extant or not - and simple habitat classification - is it marine or not - though of course infinitely expandable from there). To me the vision of GNUB is too grand - to index all usages of all names in all sources - and the vision of GNI is too limited - to index the names but not actually record/harmonise/verify/manage (in a structured way) any associated information. I'm after something in between - what I have tentatively previously called HCAL - a hierarchical catalogue of all life (presuming that at least one "management" hierarchy is incorporated) - or maybe just a GTR - global taxon register. Sort of, waiting for the Catalogue of Life and/or ITIS to be complete, for both extant and fossil taxa, and also incorporate selected "taxon attributes" as above. (This is the space into which my IRMNG database is cast as a preliminary/"working for now" solution, but obviously without the significant resourcing / community cooperation required to build and sustain the thing for the long term). So my question is, how can such a product emerge from ongoing developments in GN* space, or other... Over to the experts, Best - Tony ________________________________________ From: tdwg-content-bounces(a)lists.tdwg.org [tdwg-content-bounces(a)lists.tdwg.org] On Behalf Of Richard Pyle [deepreef(a)bishopmuseum.org] Sent: Saturday, 4 June 2011 8:48 AM To: tdwg-content(a)lists.tdwg.org Subject: Re: [tdwg-content] ITIS TSNID to uBio NamebankIDs mapping Working backwards through this thread... I hadn't read Dima's post until just now, and I see that at least a couple of his points (i.e., #2, #5, #6) apply to exposing the UUIDs externally. However, I think that a simple protocol (such as replacing spaces with "_", and avoiding characters that look the same but are different -- such as the Cyrillic 'a') could go a long way to mitigating those problems. On the other hand, it really depends on what the identifier is for. The string "Danaus_plexippus_(Linnaeus_1758)" may be more friendly to our eyes, but "A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523" is definitely more friendly to a computer (Dima's points 1, 3 & 4, among others). My feeling is that the push for GUIDs is more about enabling computer-computer conversations, than it is about enabling human-human or human-computer interactions; and therefore we should not get bogged down in the "ugliness" of the identifiers. In the context of electronic data services, the "ugliness" potential of the "Danaus_plexippus_(Linnaeus_1758)" approach to identifiers is far greater than the ugliness potential of "A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523", when it comes to interlinking electronic biodiversity data. It is nothing for a computer to render relevant metadata of the object identified by "A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523" into "Danaus plexippus (Linnaeus_1758)" on a computer screen or piece of paper for human-eyeball consumption. But there are many pitfalls (some noted by Dima) for a computer to unambiguously resolve "Danaus_plexippus_(Linnaeus_1758)" back to a meaningful data object. I guess my revised point is: GNI (and uBio/NameBank) are essentially the only taxonomic databases out there where a human-friendly persistent/actionable identifier of the sort being discussed is even plausible as an option. It may not even be wise in this context (as per Dima's points), but it *might* be, depending on the need for a human-friendly identifier. Maybe the simplest thing to do would be to not regard "http://gni.globalnames.org/name_strings/Danaus_plexippus_(Linnaeus_1758)" as an identifier per se, but rather as a protocol for a web service. In other words, if you append a text string to the root URL "http://gni.globalnames.org/name_strings/", GNI would run that text string against its index and return whatever metadata based on a text-string match. This is not mutually exclusive with an "identifier" in the form of "http://gni.globalnames.org/name_strings/A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523", that would less ambiguously resolve a known record in GNI. At this point, the line between "identifier" and "service" gets fuzzy, of course. But the analogy is true in ZooBank: The persistent "Identifer" looks like this: A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523 One way that this identifier can be represented as an *actionable* identifier is this: urn:lsid:zoobank.org:act:A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523 Another "actionable" form of the identifier might be this: http://zoobank.org/urn:lsid:zoobank.org:act:A9F435E0-8ED7-46DD-BAB4-EA8E5BF… or this: http://zoobank.org/A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523 or even this(?): http://lsid.tdwg.org/urn:lsid:zoobank.org:act:A9F435E0-8ED7-46DD-BAB4-EA8E5… (all of which work, by the way) However, the following are examples of what I would think of as *services*: http://www.google.com/search?q=Danaus+plexippus+(Linnaeus+1758) http://lsid.tdwg.org/summary/urn:lsid:zoobank.org:act:A9F435E0-8ED7-46DD-BA… http://darwin.zoology.gla.ac.uk/~rpage/lsid/tester/?q=urn:lsid:zoobank.org:… But really, from the perspective of the end-user, does it matter if it's an identifier or a service? Ultimately, they ask the questions, and the answers appear on their computer screens. Aloha, Rich > -----Original Message----- > From: tdwg-content-bounces(a)lists.tdwg.org [mailto:tdwg-content- > bounces(a)lists.tdwg.org] On Behalf Of Dmitry Mozzherin > Sent: Friday, June 03, 2011 4:34 AM > To: David Remsen (GBIF) > Cc: tdwg-content(a)lists.tdwg.org; Dmitry Mozzherin; Orrell, Thomas; Alan J > Hampson; Nicolson, David; Gerald Guala > Subject: Re: [tdwg-content] ITIS TSNID to uBio NamebankIDs mapping > > In my opinion UUIDs have a few advantages over strings -- > > 1. It is uuid, so it will work with uuid tools (current and future ones) > 2. It is less ambiguous -- For example -- what is the difference between Betulа and > Betula for your eyes? (one of them has a Cyrillic 'a') > 3. Database wise it is faster to search because it is just a 128bit number, while > a name is at least 245 byte varchar -- it makes searching much faster because > in relational databases the size of keys directly proportional to the search > speed > 4. UUID v. 5 > (http://en.wikipedia.org/wiki/Universally_unique_identifier) > allows to generate UUID algorithmically without looking up a database (no > need for network connection) > 5. Links like http://gni.globalnames.org/name_strings/Danaus_plexippus_(Linnaeus_1758) might be ambigous -- I can think of several ways I can represent name string > part in the url and they will all resolve to the same thing in GNI. > 6. Unescaped unicode characters in url containing literal name strings (people > will forget to escape them) will depend on an implementation of a url > resolver > > Saying this links like > http://gni.globalnames.org/name_strings/Danaus_plexippus_(Linnaeus_175 > 8) > are definitely attractive and is it good to have them as another way to access > a name! > My personal preference would be not use them as main identifier because > of the reasons 1, 2, 3 and 5. > > Dima > > > > > On Fri, Jun 3, 2011 at 7:59 AM, David Remsen (GBIF) <dremsen(a)gbif.org> > wrote: > > Why not use the name as the basis for the resolvable identifier > > instead of a uuid. Isnt there a 1:1 cardinality between the name and > > the uuid in the GNI? Doesnt that mean that > > > > http://gni.globalnames.org/name_strings/4ef223c4-0c3e-5e84-ace9- > 755c34 > > c601ec > > and > > > http://gni.globalnames.org/name_strings/Danaus_plexippus_(Linnaeus_175 > > 8) > > > > are equally unique? The latter is certainly more readable. In those > > cases where the namestring is a homonym like > > > > http://gni.globalnames.org/name_strings/Oenanthe > > > > couldn't you just return the addresses of the two globally unique > > forms of the name when you resolve it? > > > > http://gni.globalnames.org/name_strings/Oenanthe_Smith_1899 > > > > http://gni.globalnames.org/name_strings/Oenanthe_Jones_1900 > > > > Wouldn't those be as globally unique and easier to read and adjust to? > > Or am I missing something. I always wanted to do that with ubio IDs > > after a back and forth with Gregor Hagedorn and wished we hadn't > > exposed those integers. > > > > DR > > > >> Hi Steve, > >> > >> I don't have time to go through this in detail, and I can't speak for > >> the GNI, but I can tell you about how the GNI URI's work at least for now. > >> > >> A while back Dima Mozzherin and I were looking into how triples etc. > >> might be of use to the GNI. > >> > >> We needed a way to generate unique URI's for each name. > >> > >> We wanted to avoid having to keep these in sync and not require > >> everyone to look each ID up through some service. > >> > >> Dima came up with the following plan. We use the namestring as seed > >> to generate a unique UUID. > >> > >> Basically this is a shared algorithm which the GNI and TaxonConcept > >> both use. But it could be used by anyone. > >> > >> You feed the name string to the algorithm and it spits out a UUID. We > >> append then append that to a URI and web service so it is resolvable. > >> > >> So the name Danaus plexippus (Linnaeus 1758) => > >> 4ef223c4-0c3e-5e84-ace9-755c34c601ec > >> > >> So if the GNI and and another group have the same namestring they > >> have the same UUID. > >> > >> People can then can link their data set to the GNI with the following > >> URI > >> > >> http://gni.globalnames.org/name_strings/4ef223c4-0c3e-5e84-ace9- > 755c3 > >> 4c601ec > >> > >> RDF > >> http://gni.globalnames.org/name_strings/4ef223c4-0c3e-5e84-ace9- > 755c3 > >> 4c601ec.rdf > >> > >> <http://gni.globalnames.org/name_strings/4ef223c4-0c3e-5e84-ace9- > 755c > >> 34c601ec.rdf>If you think of your data set as one table and the GNI > >> as another, this URI serves as the foreign key that connects them > >> together. > >> > >> Some on the list don't like how these look, but there is a tremendous > >> advantage in not having to worry about syncing two large data sets > >> and determining if a given integer is already in use. > >> > >> Also Rod Page has written a recently about UUID's. > >> http://iphylo.blogspot.com/2011/05/zoobank-on-couchdb-uuids-replicati > >> on.html > >> > >> <http://iphylo.blogspot.com/2011/05/zoobank-on-couchdb-uuids- > replicat > >> ion.html>There may be a way to do something similar with bit.ly like > >> identifiers that are shorter (mCcSp), but I think it the general idea > >> is a good one. > >> > >> If you recall from my talk at TDWG, I was able to use these to make > >> statements that one namestring was a synonym etc. of another etc. > >> > >> The algorithm we use is written in Ruby but I could be ported to many > >> different languages since UUIDs are widely supported. > >> > >> Respectfully, > >> > >> - Pete > >> > >> > >> > >> On Thu, Jun 2, 2011 at 11:41 PM, Steven J. Baskauf < > >> steve.baskauf(a)vanderbilt.edu> wrote: > >> > >>> My email access has been sporadic since this thread developed, so > >>> at this point I'll respond to points made in several of the > >>> messages. > >>> > >>> First, I should note that there has been previous discussion on this > >>> list on a similar topic from > >>> http://lists.tdwg.org/pipermail/tdwg-content/2011-January/002231.htm > >>> lthrough > >>> http://lists.tdwg.org/pipermail/tdwg-content/2011- > January/002231.html. > >>> One can review what was said at that time rather quickly by starting > >>> on the first linked message and clicking on the "Next Message" link > >>> until you get to the end of the range I gave above. > >>> > >>> My reason for the request for information that started this thread > >>> was that I wanted to link to a URI that would anchor the name > >>> portion of a name/sensu pair (TNU or Taxon Concept a la TCS if you > >>> prefer) as in this RDF > >>> snippet: > >>> > >>> <tc:nameString>Quercus rubra L.</tc:nameString> > >>> <tc:hasName > >>> > rdf:about="http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio > .org:namebank:448439" > >>> <http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:n > >>> amebank:448439>/> > >>> > >>> > >>> At this point in the discussion, I'm not actually talking about > >>> creating a link to a taxon concept but rather to a taxon name, so > >>> some of the issues Pete raised don't apply here (e.g. what's the > >>> "right" name for a concept > >>> - > >>> the question here is simply what's a stable identifier for the name) . > >>> In > >>> principle, I could probably just provide the name string and be done > >>> with it. However, having some degree of faith that Smart, Computer > >>> Savvy People might some day be able to use the metadata returned by > >>> the URI (or perhaps metadata which they already have in a triple > >>> store onsite) to do cool things like knowing that my name is the > >>> same as an orthographic variant or that "Quercus rubra L." is > >>> basically the same thing as "Quercus rubra", I would like to also > >>> provide a functional URI. > >>> > >>> As an end -user who isn't very interested in the technical issues > >>> involving names, I don't really care what URI I use. I would prefer > >>> for it to be widely recognized and for it to "work" (i.e. be > >>> resolvable). In the earlier > >>> (January) thread, there was discussion about existing identifiers. > >>> There > >>> were a number of posts, but in particular > >>> http://lists.tdwg.org/pipermail/tdwg-content/2011-January/002258.htm > >>> l > >>> http://lists.tdwg.org/pipermail/tdwg-content/2011-January/002259.htm > >>> ldiscussed the relative merits of ITIS and uBio ID numbers. My > >>> take-home message from this was that uBio represented the largest > >>> single set of names with assigned identifiers (see > >>> http://gni.globalnames.org/data_sourcescited in Pete's email) and > >>> that uBio metadata provides useful references. > >>> Hence my interest in referencing uBio ids as a URI. However, as a > >>> practical matter, the organizations that I share images with either > >>> want ITIS TSNs (EOL and Morphbank) or just names (Discover Life). > >>> Nobody is asking for uBio identifiers or any other identifier. > >>> > >>> I found Kevin's comment at > >>> http://lists.tdwg.org/pipermail/tdwg-content/2011-May/002486.html > >>> very > >>> thought-provoking: "My thoughts are that the most likely way this > >>> will be solved is by standard market type pressures - ie the best > >>> solution/IDs will be used the most and 'float' to the top." I'm not > >>> going to make a judgment about what is the "best" solution or ID. > >>> But I would say that in "computer" > >>> history, being the "best" doesn't necessarily mean that something > >>> will be used. Take for example, the FOAF vocabulary. What the heck > >>> is Friend of a Friend? I would venture to say that most of the > >>> people using the FOAF vocabulary don't know or care. The FOAF > >>> vocabulary was the one that people started to use and once that > >>> happened, people didn't switch even if there was something better. > >>> I'm not familiar with the history of other stuff like YouTube and > >>> Craig's List, but I would guess that they weren't necessarily "the > >>> best" systems - they were just the one that the most people started > >>> using first and once that happened, people didn't switch. I'm using > >>> ITIS IDs because they are easy to get and the people I communicate > >>> with want them. Whether they are the "best" or "done correctly" > >>> doesn't matter to me as much as the fact that that they are widely > >>> recognized and stable (and that thus far every name that I've looked > >>> for has been in their database). > >>> > >>> I think that one reason why this question has been on my mind is > >>> that I've been waiting for GNUB (Global Name Use Bank) to come out. > >>> I'm not really up on how it is going to work, but my impression is > >>> that it was going to be based on the Global Name Index (GNI) which > >>> was mentioned in that earlier January thread. At that point, the > >>> GNI names didn't have any identifiers that were exposed to the > >>> public as permanent GUIDs. I'm assuming that if GNUB refers to GNI > >>> names, they will have some kind of identifiers. So if that happens > >>> how is the GUID recommendation 8 going to be followed? As Kevin > >>> said in > >>> http://lists.tdwg.org/pipermail/tdwg-content/2011-June/002499.html > >>> "What I take from recommendation 8 of the GUID applicability guide > >>> ... is that if you DON'T already have a record in your own database > >>> for a taxon name/concept, then reuse an existing one. " What we > >>> have here with GNI is a situation where none of the records have > >>> identifiers. In my mind, the "best practice" according to > >>> recommendation 8 would be for the GNI to reuse existing identifiers > >>> where they exist and NOT make up new ones. This is a bit more > >>> complicated because the ITIS identifiers (which are in common > >>> use) > >>> don't have an http URI version that is resolvable, and while the > >>> uBio identifiers have a resolvable http URI, it's in the form of a > >>> proxied LSID, which I've already complained is very ugly. So I'd > >>> like to hear some ideas about how to have "reused" identifiers in > >>> the GNI. > >>> > >>> One thing that comes to my mind would be to have a "domain name" > >>> like "http://purl.org/gni/" <http://purl.org/gni/> or > >>> "http://purl.org/tn/"<http://purl.org/tn/>("tn" for "taxon name") > >>> and to follow it with a namespace/id combination similar to what is > >>> done with lsids. So for example "itis/19408" and "ubio/448439" > >>> could be appended, creating http://purl.org/gni/itis/19408and > >>> http://purl.org/gni/ubio/448439 for "Quercus rubra L." Both URIs > >>> could point to the same RDF and that RDF could indicate that the two > >>> identifiers are owl:sameAs . I realize from what Bob Morris has > >>> cautioned in the past that there are problems with owl:sameAs when > >>> the two things aren't actually the same thing (e.g. if the uBio ID > >>> refers to a name string only but the ITIS TSN refers to the name > >>> plus an "accepted" status and a relationship to parent taxa). > >>> However, if there were an understanding that the GNI only refers to > >>> name strings, then one could still refer to > >>> http://purl.org/gni/itis/19408 as an identifier for the name string > >>> of the thing (whatever it is) that is referred to by an ITIS TSN of > >>> 19408. I don't think there would be a problem saying that and the > >>> ubio ID were "owl:sameAs". Some kind of solution like this would > >>> allow people to easily generate a resolvable URI for a name if they > >>> were using ITIS TSNs or uBio IDs. If the name that one wanted to > >>> use was so obscure that it was one of the 9.5 million names that > >>> uBio has that ITIS doesn't have, then that name would only have the > >>> ubio version. I have no idea whether this would be a good idea or > >>> not, but I was really cringing to think about 19 million newly > >>> minted UUIDs appended to > >>> "http://gni.globalnames.org/"<http://gni.globalnames.org/>and > >>> figuring out how to connect those horrid things to the names and > >>> ITIS TSNs that I'm already using. I think that I said this before, > >>> but using the purl.org domain rather than one like > >>> http://gni.globalnames.org/ would in the future allow somebody else > >>> to take over management of providing the metadata when the GUIDs > are > >>> resolved without having to deal with issues of who "owns" the domain > >>> name. > >>> > >>> Steve > >>> > >>> > >>> > >>> Kevin Richards wrote: > >>> > >>> Pete, > >>> > >>> I'm not trying to say what you are doing is a waste of time/impossible. > >>> I > >>> actually think RDF + semantics are a good way forward, but this > >>> really implies that we need to rely on the semantics and linkages > >>> rather than having a SINGLE ID for a taxon name. (which is what I > >>> thought Steve was getting at). Each instance of a taxon name can > >>> have its own ID and then all these instances are connected via > >>> ontology defined semantic links. This seems more appropriate to me > >>> than insisting everyone uses the "Global Taxon Name ID X". > >>> > >>> > >>> > >>> In your example of *Aedes triseriatus* and *Ochlerotatus > >>> triseriatus* - these are two different names so they need two > >>> different IDs, they may be linked by a single taxon concept, but > >>> they are separate names. So which of these now 3 IDs do you expect > >>> people to use, and according to what source?? > >>> > >>> > >>> > >>> For example if we have a name, eg the Robin, Erithacus rubecula, > >>> mentioned > >>> in IT IS (TSN : 559964) and also in EOL (www.eol.org/pages/1051567) > >>> also > >>> in GBIF (http://data.gbif.org/species/21266780) also in avibase ( > >>> http://avibase.bsc-eoc.org/species.jsp?avibaseid=C809B2B90399A43D) > >>> which > >>> ID are you hoping people will use?? Would you put the IT IS ID in your > >>> own > >>> dataset as the ID for that name - unlikely. Or would it be better to > >>> link > >>> them up with semantic linkages. > >>> > >>> > >>> > >>> What I take from recommendation 8 of the GUID applicability guide (as > >>> Steve > >>> puts is "stop making up new identifiers when somebody else already has > >>> one > >>> for the thing you are talking about") is that if you DON'T already have > >>> a > >>> record in your own database for a taxon name/concept, then reuse an > >>> existing > >>> one. NOT ditch all your current IDs and adopt someone else's > >>> (especially > >>> hard considering it is so hard to work out which if the multitude of > >>> names > >>> ad concept IDs that directly relates to your taxon name). > >>> > >>> > >>> > >>> I am all for limiting the number of IDs for the "same" thing, but in > >>> some > >>> cases it is more useful to build linkages than force this tight > >>> integration > >>> of data and IDs. Especially for taxon names and concepts, where it is > >>> complex to define if you are even talking about the "same" thing or not. > >>> > >>> > >>> > >>> Kevin > >>> > >>> > >>> > >>> *From:* Peter DeVries > >>> [mailto:pete.devries@gmail.com<pete.devries(a)gmail.com>] > >>> > >>> *Sent:* Wednesday, 1 June 2011 12:38 p.m. > >>> *To:* Kevin Richards > >>> *Cc:* Steve Baskauf; tdwg-content(a)lists.tdwg.org; Gerald Guala; > >>> Nicolson, > >>> David; Alan J Hampson; Orrell, Thomas > >>> *Subject:* Re: [tdwg-content] ITIS TSNID to uBio NamebankIDs mapping > >>> > >>> > >>> > >>> Hi Kevin, > >>> > >>> > >>> > >>> I forgot one mention some other things that are different about my > >>> project. > >>> > >>> > >>> > >>> You can write a simple SPARQL query to get a list of all the > >>> TaxonConcept's > >>> that have ITIS ids, or all those that have ITIS and NCBI ID's etc. > >>> > >>> > >>> > >>> You can do this on any SPARQL endpoint that hosts the data. > >>> > >>> > >>> > >>> You can download the entire data set and run the queries on your own > >>> endpoint. > >>> > >>> > >>> > >>> You can write a script that runs the query and downloads the ITIS > >>> numbers > >>> and exports them to CSV etc. > >>> > >>> > >>> > >>> - Pete > >>> > >>> > >>> > >>> On Tue, May 31, 2011 at 5:16 PM, Peter DeVries > <pete.devries(a)gmail.com> > >>> wrote: > >>> > >>> Hi Kevin, > >>> > >>> On Tue, May 31, 2011 at 3:27 PM, Kevin Richards < > >>> RichardsK(a)landcareresearch.co.nz> wrote: > >>> > >>> This is exactly why this problem still exists and will be very complex > >>> to > >>> solve - everyone says "we should have a single ID for a specific taxon > >>> name, > >>> there seems to be several IDs 'out there' that refer to the same taxon > >>> name, > >>> so Im going to create another ID to link them all up" - yet another ID > >>> that > >>> no one will particularly want to follow - you would have to get everyone > >>> to > >>> agree that your combinations/integration of taxon names is the best one > >>> and > >>> hope everyone follows it - unlikely in this domain. > >>> > >>> > >>> > >>> Isn't this kind of what the The Plant List, and eBird already do? > >>> > >>> > >>> > >>> A difference being that they tie these to a specific name and specific > >>> classification. > >>> > >>> > >>> > >>> The Plant list is not really even open so it is difficult to people to > >>> adopt it in mass. > >>> > >>> > >>> > >>> For instance, if I manage a herbarium, how do I easily reconcile my > >>> species > >>> list with the entities represented in the Plant List? > >>> > >>> > >>> > >>> eBird has millions of records which implies that they have been able to > >>> convince the observers in the field to adopt their system. You are > >>> correct > >>> in that there are probably a lot of taxonomists that don't like their > >>> list. > >>> > >>> It differs from many of the other classifications, but remember the > >>> system > >>> rewards them for not agreeing. Note the difference between the > microbial > >>> taxonomists and other taxonomists. In the case of the microbial > >>> > >>> workers, the system rewards them for solving problems not debating > >>> alternatives. Also, if a good idea comes out that will make it easier > >>> for > >>> the microbiologists to solve the problems they are rewarded for solving, > >>> they are less likely to care whose idea it is. > >>> > >>> > >>> > >>> Like the microbiologists, there are lots of biologists that work with > >>> species with the goal of addressing some non-taxonomic problem. > >>> > >>> > >>> > >>> They don't really care if the name is *Aedes triseriatus* or > >>> *Ochlerotatus > >>> triseriatus, *but they do care that the identifier that they connect > >>> their > >>> data to is stable. > >>> > >>> > >>> > >>> In regards to the issue of market forces,I suspect (but have no > >>> knowledge > >>> of) that there were probably decisions made in devising these lists that > >>> have more to do with appeasing certain personalities that creating best > >>> list. With the way this system rewards people it is likely that the > >>> "correct" version will float to the top only after that person has > >>> passed > >>> away. I don't have much faith that the best system will always float to > >>> the > >>> top, That has a lot to do with the personalities and how the system > >>> rewards > >>> are setup. Theoretically, it is possible for one strong personality or > >>> group > >>> to force others to adopt their less than optimal solution - at least > >>> this > >>> seems to happen in other environments. > >>> > >>> > >>> > >>> Also, there are all sorts of ways that people can use the publication > >>> record to rewrite history. Simply cite the review paper that cites the > >>> original paper. Or don't cite it at all. > >>> > >>> > >>> > >>> I would have used only the ITIS TSN but if the name changes the ID > >>> changes. > >>> This isn't "wrong", it just does not solve my problem. > >>> > >>> > >>> > >>> * ITIS also should add the spiders from the World Spider Catalog. > >>> > >>> > >>> > >>> Another issue that I think has inhibited adoption of a common list is > >>> that > >>> people can't agree on a particular name or a particular classification. > >>> > >>> > >>> > >>> Since you can model a species concept as having many names and many > >>> classifications why not do so? > >>> > >>> > >>> > >>> If this idea was originally accepted, I would not have needed to create > >>> TaxonConcept.org. > >>> > >>> > >>> > >>> My plan has aways been to get something that works to solve some > >>> problems > >>> and then let some larger group take it over. > >>> > >>> > >>> > >>> In a sense, I am more like the microbiologists in that I am not being > >>> paid > >>> to solve this or debate this problem. > >>> > >>> > >>> > >>> I am doing it because I think something like this is needed, and it is > >>> an > >>> interesting and personally rewarding puzzle. > >>> > >>> > >>> > >>> - Pete > >>> > >>> > >>> > >>> > >>> > >>> > >>> My thoughts are that the most likely way this will be solve is by > >>> stnadard > >>> market type pressures - ie the best solution/IDs will be used the most > >>> and > >>> "float" to the top. It is easy to say that the global taxon name data > >>> is a > >>> mess, but if you think about it 30 years ago taxon name data were very > >>> disparate, duplicated, unconnected, many with NO IDs at all. So I > >>> beleive > >>> we are making progress and that we will continue to do so albeit at a > >>> fairly > >>> slow rate. > >>> > >>> Kevin > >>> > >>> > >>> > >>> "I agree. This was one of the reasons that I setup TaxonConcept the way > >>> I > >>> did. It attempts to connect both the LOD entities and the foreign key > >>> based > >>> entities." > >>> > >>> Please consider the environment before printing this email > >>> Warning: This electronic message together with any attachments is > >>> confidential. If you receive it in error: (i) you must not read, use, > >>> disclose, copy or retain it; (ii) please contact the sender immediately > >>> by > >>> reply email and then delete the emails. > >>> The views expressed in this email may not be those of Landcare > Research > >>> New > >>> Zealand Limited. http://www.landcareresearch.co.nz > >>> > >>> > >>> > >>> > >>> -- > >>> > >>> ------------------------------------------------------------------------------------ > >>> 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 > >>> > >>> -------------------------------------------------------------------------------------- > >>> > >>> > >>> > >>> > >>> -- > >>> > >>> ------------------------------------------------------------------------------------ > >>> 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 > >>> > >>> -------------------------------------------------------------------------------------- > >>> > >>> ------------------------------ > >>> Please consider the environment before printing this email > >>> Warning: This electronic message together with any attachments is > >>> confidential. If you receive it in error: (i) you must not read, use, > >>> disclose, copy or retain it; (ii) please contact the sender immediately > >>> by > >>> reply email and then delete the emails. > >>> The views expressed in this email may not be those of Landcare > Research > >>> New > >>> Zealand Limited. http://www.landcareresearch.co.nz > >>> > >>> > >>> -- > >>> 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) > >>> 343-6707http://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 <http://www.taxonconcept.org/> & > >> GeoSpecies<http://about.geospecies.org/> Knowledge > >> Bases > >> A Semantic Web, Linked Open Data <http://linkeddata.org/> Project > >> -------------------------------------------------------------------------------------- > >> _______________________________________________ > >> tdwg-content mailing list > >> tdwg-content(a)lists.tdwg.org > >> http://lists.tdwg.org/mailman/listinfo/tdwg-content > >> > > > > > > > > ---------------------------------------------------------------------------- > > 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 > > Skype: dremsen > > ---------------------------------------------------------------------------- > > > > > > > > _______________________________________________ > > 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 _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

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Updated Book, Provable Models vs. Executable Models and Use Cases
by Peter DeVries 04 Jun '11

04 Jun '11

A new edition of this book just came out. *Semantic Web for the Working Ontologist, Second Edition: Effective Modeling in RDFS and OWL* [Paperback] Dean Allemang, James Hendler http://www.amazon.com/Semantic-Web-Working-Ontologist-Second/dp/0123859654/ Starting on page 326 there is a good section on OWL subsets and Modeling Philosophy. It describes provable models (decidable) and executable models. There is a lot of good info in here, but I thought I would highlight these sentences. *"In fact, it is quite challenging to come up with a logical system that can represent anything useful that is also decidable" * also under Executable Models. *"A different motivation for modeling in the Semantic Web is to form an integrated picture of some sort of domain by federating information from multiple sources"* Individuals should really read the entire chapter and come to their own conclusions, but I think these are issues that people need to think about. To what extent can we design a system that actually is decidable? How are these models going to be used, what is their purpose, and what are some clear use cases? Here is the use case that started me down path of linked data and the semantic web. I am in location X,Y and have a specimen of family Z. What species of family Z are expected here and what are the characters that can be used to differentiate them? Give me a list of other resources that contain information about these species. 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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USDA Plants Growth Forms added to TaxonConcept Plants - Example SPARQL Queries
by Peter DeVries 03 Jun '11

03 Jun '11

I have a new update to my data set. It is not in the cloud yet but you can download it or run queries on my server. See http://www.taxonconcept.org/rdf_and_sitemap/ The USDA Plants data set has lists of plants expected in each county and state. I have marked up this data as triples for several states in the Midwest as well as Massachusetts and Texas. I have also marked up the data for each Wisconsin County. The USDA data set also has an attribute called "GrowthForm" I have these attributes marked up in this vocabulary OWL http://lod.taxonconcept.org/ontology/usda_plants.owl Doc http://lod.taxonconcept.org/ontology/usda_plants_doc/index.html Here are the Growth forms I have as triples. usda_plant:Growth_Habit_Tree usda_plant:Growth_Habit_Shrub usda_plant:Growth_Habit_Subshrub usda_plant:Growth_Habit_Forb_Herb usda_plant:Growth_Habit_Graminoid You can see this in this example from the Knowledge Base http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org… bit.ly http://bit.ly/locSNl You can now run the following kinds of queries: What plants with the USDA Growth Form Forb_Herb are expected in Door County WI. 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 door_county_wi: <http://sws.geonames.org/5250768/> PREFIX usda_plant: <http://lod.taxonconcept.org/ontology/usda_plants.owl#> select distinct ?s, ?o as ?image, ?col_class, ?sciname where { ?s rdf:type txn:SpeciesConcept. ?s rdf:type usda_plant:Growth_Habit_Forb_Herb. ?s txn:isExpectedIn door_county_wi:. ?s txn:inCoLClass ?col_class. ?s txn:hasScientificName ?sciname. optional {?s txn:thumbnail ?o.}. } ORDER BY ASC(?col_class) limit 650 This link is the query encoded in a URI < http://lsd.taxonconcept.org/isparql/view/?query=PREFIX%20txn%3A%20%20%3Chtt… > Since this does not always go though email, here is the bit.ly link http://bit.ly/j5PLzH <http://bit.ly/j5PLzH>Since the a number of the TDWG BioBlitz Species are included in the USDA Plants data set, those species concepts now have the USDA attributes attached. Since many of these related and now linked data sets exist under different names, it would have been difficult for this to work without some identifier like my species concepts. 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: 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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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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