- tdwg-content - lists.tdwg.org

New term resolution: georeferencedDate
by John Wieczorek 05 Jul '11

05 Jul '11

Darwin Core Issues 82: http://goo.gl/XhxM The fact that this term is missing from the Darwin Core is an oversight. The term has been in use in Georeferencing Best Practices since 2001. Open Issues: Determine if there is any objection to adding this term to the Darwin Core.

1 0

New term resolution: alive/dead status
by John Wieczorek 05 Jul '11

05 Jul '11

Darwin Core Issue 91: http://goo.gl/jmk16 This issue has undergone public commentary. Open Issues: Though the term is well-described in the issue tracker and there is evidence of a real-world need for it, public commentary failed to produce a consensus, nor a complete proposal for a new term, nor demand from more than one "independent" source. This issue will be closed.

1 0

DarwinCore breaks my RDF
by Peter DeVries 04 Jul '11

04 Jul '11

Hi, I ran into a problem with the sig.ma service after incorporating some DarwinCore terms. This now prevents my RDF from being analyzed or it seems viewed via Sig.ma What is the cause? If you take this URI http://rs.tdwg.org/dwc/terms/index.htm#acceptedNameUsageID Plug it into the Vapour validator http://validator.linkeddata.org/vapour You get he following error. Vapour was unable to complete the request due to the following exception: ForbiddenAddress: forbidden request from 96.42.27.164 to http://rs.tdwg.org/dwc/terms/index.htm#acceptedNameUsageID (resolves to IP 192.38.28.106), internal IP addresses are forbidden Complete traceback: File "/home/wwwidi/vapour/src/vapour/cup/webclient.py", line 117, in GET recipes.checkRecipes(store, resourcesToCheck, validatorOptions) File "../../vapour/teapot/recipes.py", line 34, in checkRecipes checkWithoutAcceptHeader(graph, resource, validatorOptions) File "../../vapour/teapot/recipes.py", line 49, in checkWithoutAcceptHeader runScenario(graph, resource, scenarioDescription, requestedContentType, validatorOptions, "GET") File "../../vapour/teapot/recipes.py", line 82, in runScenario (rootTestSubject, httpResponse) = followRedirects(graph, "dereferencing " + resource['description'], resource['uri'], requestedContentType, httpMethod, validatorOptions) File "../../vapour/teapot/httpdialog.py", line 22, in followRedirects r = simpleRequest(graph, url, accept, redirectsCount, None, method, options) File "../../vapour/teapot/httpdialog.py", line 62, in simpleRequest raise ForbiddenAddress(str(ip), url, options.client) The particular section and terms seem to be these from http://lod.taxonconcept.org/ses/v6n7p.rdf  <dwc_terms:acceptedNameUsageID rdf:resource=" http://gni.globalnames.org/name_strings/772d5162-f5aa-596c-98e0-a1c6c5a29bb9 "/> <dwc_terms:acceptedNameUsage>Puma concolor (Linnaeus 1771)</dwc_terms:acceptedNameUsage> <dwc_terms:originalNameUsageID rdf:resource=" http://gni.globalnames.org/name_strings/35da7f30-25ff-5111-ab29-1a4f9988ef51 "/> <dwc_terms:originalNameUsage>Felis concolor Linnaeus 1771</dwc_terms:originalNameUsage> <dwc_terms:vernacularName>Cougar</dwc_terms:vernacularName> Please Fix, otherwise I will need to remove any DarwinCore from my RDF. Thanks, - 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 --------------------------------------------------------------------------------------

2 2

Darwin Core pending terms resolution
by John Wieczorek 29 Jun '11

29 Jun '11

Dear all, I am preparing to resolve outstanding issues with new terms that have been proposed for the Darwin Core following the procedure outlined in the Darwin Core Namespace Policy (http://rs.tdwg.org/dwc/terms/namespace/index.htm#classesofchanges) section 3.4. The list of terms under consideration include the following, the original proposals for which can be found in the Darwin Core Issue Tracker (http://code.google.com/p/darwincore/issues/list) DigitalStillImage (type vocabulary) Individual (class) and individualRemarks dcterms:source alive/dead status yearOfPublication geo:lat and geo:lng georeferencedDate The process for ratification calls for a 30-day public comment period. I will create separate threads explaining the current status for each of the terms or term combinations listed above so that the commentary can be tracked for each. Terms that pass the 30 days with consensus (which will be measured by a lack of dissenting opinion) will be entered into the Darwin Core vocabulary and I will make adjustments to the documentation, schemas, and canonical RDF representation of the standard. Terms that remain controversial will remain in the commentary stage until another semi-annual review can be undertaken. Questions or concerns about this process are welcome. John

2 2

Software available for LSID resolution, Linked Data, OAI-PMH [SEC=UNCLASSIFIED]
by Paul Murray 28 Jun '11

28 Jun '11

We have uploaded to google code the software currently being used at biodiversity.org.au to serve up LSID metadata, linked-data objects identified by URI, and reply to OAI-PMH requests. The code is available here: svn checkout http://ala-nsl.googlecode.com/svn/service-layer/trunk service-layer or svn checkout https://ala-nsl.googlecode.com/svn/service-layer/trunk service-layer (I find that http doesn't work for me - something to do with authenticating to google code through the corporate firewall) The system is our "quick, get something working" interim solution for creating a web presence for our data, pending a full National Species List application. It is a suite of XSQL source files that are loaded into an instance of the eXist XML database (exist.sourceforge.net) Using it is a matter of * acquiring a domain name that you wish to use for your LSID authority and hosting the software * generating dumps of your data as XML * identifying your XML elements with lsids * writing XSL style shhets to convert your XML into the various output formats that you wish to support. As this system imposes few constraints on the underlying XML, you do not need to "massage" your data into some specific format. Being small and self-contained, it could be a useful way of exposing small data sets peculiar to some space - although it accommodates millions of records perfectly well at our installation. The payoff is that system does correctly implement the LSID standard (etc). This can be seen by navigating to http://lsid.tdwg.org/summary/urn:lsid:biodiversity.org.au:apni.taxon:54321 As you see - the software at tdwg has no difficulty talking to our resolver and fetching the data from it. Likewise, linked data is implemented - although HEAD requests are not getting through correctly and so the first test on this page fails. http://validator.linkeddata.org/vapour?vocabUri=http%3A%2F%2Fbiodiversity.o… Nevertheless: uriburner, zeitgeist and so on manage to retrieve and process the data from our URIs correctly. Caveats: * The system is not tested with LSIDs with versions. I believe that the usual use for versioned LSIDs is for serving up data (eg: media) rather than metadata, and that is not the focus of this bit of software. * The system requires some configuration, both internally and at the web server. Most particularly, we needed to perform mappings at our reverse proxy to get URIs passed though to the correct targets behind out firewall. * The script that loads the executable XSQL into eXist is a unix script which works on Solaris and on OSX. The repository does not include an equivalent windows command file. * You will almost certainly need to write at least some XSLT to get the output you want. The repository comes with a demo dataset. * There is minimal documentation, I'm afraid. The READMEs point you at our confluence page, but there's not much there in relation to getting this bit of software going. * The system does not magically vanish all the issues with regard to RDF and XML vocabularies and the like. Conforming to standards is a matter of generating and loading conformant XML, or tweaking your XSLT. If you have received this transmission in error please notify us immediately by return e-mail and delete all copies. If this e-mail or any attachments have been sent to you in error, that error does not constitute waiver of any confidentiality, privilege or copyright in respect of information in the e-mail or attachments. Please consider the environment before printing this email.

1 0

RFC 4122 as motivation, was Re: Why UUIDs alone are not adequate as GUIDs
by Bob Morris 09 Jun '11

09 Jun '11

For better or worse, the TDWG Applicability Statement for GUID's, and most of the TDWG community, uses "GUID" in a generic sense, not conformant to RFC 4122 which declares "GUID" and "UUID" to be equivalent terms. Also, according to http://www.rfc-editor.org, ---which by STD 1 always contains the current status of any RFC---it seems that RFC 4122 has never advanced past "Proposed Standard" in the 6 years since it was proposed. So, however one reads RFC 4122 on the question of "*ONE* GUID" (meaning in the 4122 context "*ONE* UUID"), at best "*ONE* GUID" is a proposal, not a standard in the sense of IETF. Not even a Draft Standard. Finally, FWIW, the author of http://en.wikipedia.org/wiki/Universally_unique_identifier seems to not take "Unique" to mean at most one per resource: "The intent of UUIDs is to enable distributed systems to uniquely identify information without significant central coordination. Thus, anyone can create a UUID and use it to identify something with reasonable confidence that the identifier will never be unintentionally used by anyone for anything else. Information labeled with UUIDs can therefore be later combined into a single database without needing to resolve name conflicts." I find nothing in the above, nor in RFC 4122 that prohibits multiple UUIDs for the same resource, counterproductive as that might be. The TDWG GUID Applicability standard, however, needs some cleaning on related points, since it has some internally confusing narrative on this issue. On balance, it comes out implicitly in favor of a single UUID (or any other kind of "GUID") for each resource, issued only by the resource provider; but explicitly permits multiple schemes for identifying a resource. Bob Morris On Wed, Jun 8, 2011 at 10:56 PM, Paul Murray <pmurray(a)anbg.gov.au> wrote: > > On 08/06/2011, at 8:05 AM, Steve Baskauf wrote: > > ... I think it's foolish to regard all of these different > resolution mechanisms as distinct "identifiers". There is *ONE* GUID. It > is: A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523. There are ten different ways to > make it actionable. It therefore meets the recommendations of the > applicability statement. > > The problem is that when you create an HTTP URI out of a UUID, you are > creating an identifier whether you think you are or not. > > Jumping in again, but perhaps RFC 4122 might help a little here. > A GUID (or UUID) is a set of 128 bits, 16 octets, 32 hex digits, 5 inches of > punched paper tape. However you choose to write or express it, there is > indeed "*ONE* GUID". > A URI is not a GUID. This: > http://example.org/A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523 > is a different URI to this > http://my.organisation.org/A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523 > is a different URI to this: > http://example.org/A9F435E08ED746DDBAB4EA8E5BF41523 > Furthermore, these uris have nothing whatever to do with the guid - apart > from the fact that it's obvious to we humans that they do. > Fortunately, there is a standard for expressing a guid/uuid as a URI, and it > is the "uuid" urn namespace, defined in RFC-4122. Thus: > urn:uuid:A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523 > is a URI that - according to a w3c standard - corresponds to the 128-bit > guid. This: > urn:uuid:A9F435E08ED746DDBAB4EA8E5BF41523 > is *not valid* - it doesn't conform to the schema. There is one unique (case > insensitive) uuid urn for any guid, and a defined equivalence between them. > These are not "cool uris", but guids are inherently uncool so that's to be > expected. > If you want to use GUIDs for identifiers and need equivalent URIs (for use > in RDF and the semweb), then urn:uuid:<the guid> might be a good way to go. > > If you have received this transmission in error please notify us immediately > by return e-mail and delete all copies. If this e-mail or any attachments > have been sent to you in error, that error does not constitute waiver of any > confidentiality, privilege or copyright in respect of information in the > e-mail or attachments. Please consider the environment before printing this > email. > > _______________________________________________ > tdwg-content mailing list > tdwg-content(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-content > > -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 IT Staff Filtered Push Project Department of Organismal and Evolutionary Biology Harvard University email: morris.bob(a)gmail.com web: http://efg.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile)

3 3

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

09 Jun '11

Hi Steve (and Dave), [NB: After having composed the email below, just before sending it, I re-read your initial email more carefully and realized that you said you already had the ITIS TSNs, and were looking to add the NamebankIDs! Doh! Well, in case you (or anyone else) is interested in methods of matching names to get TSNs, I'll go ahead and send this anyway. But do note the comments below about the ITIS "versions" and ongoing overhaul of the vascular plant data in ITIS!!! -Dave] I noticed this just before leaving work last week, and was out yesterday, but I wanted to chime in on this. I'm glad the uBio tools are meeting your needs (they do have some cool stuff!), but it should be noted that those tools are using a static snapshot of ITIS data from January 2009, and we have added about 50,000 additional scientific names, and updated tens of thousands of names beyond that (most of that in the last 6 months, as the frequency of loads dropped off in 2009-2010 due to technical issues). I also want to note that ITIS is right in the middle of a full update of the vascular plant data in ITIS, and we're loading updated families on a monthly basis... and at long last we are tackling all the leftover issues from several bulk loads from USDA PLANTS data that left unreconciled bits of ITIS' older vascular plant data in various confusing states... so it is a VAST improvement that is underway. There are several options for bouncing your names off the current version of ITIS. One is to automate a matching process using the live ITIS data, based on the existing ITIS Web Services. I am CC'ing Alan Hampson, our IT fellow who built the Web Services ( http://www.itis.gov/web_service.html ), in case you'd like to follow up with him on that option. The advantage is that once you have a process in place it is completely self-serve and can always utilize the current ITIS data. If you have the resources to do this I think it would be greatly to your advantage to use this approach. You can explore some ideas for client software to use the services at: http://www.itis.gov/ws_develop.html And for more information on ITIS web services try http://www.itis.gov/ws_description.html http://www.itis.gov/ITISWebService.xml The ability to flag multiply-matched names (as you noted) should probably be considered, so that appropriate manual steps can be taken. This solution will allow you to take advantage of subsequent updates to ITIS with a minimum of additional effort, and given that the plant data are in the middle of a major overhaul, this bears consideration! Another possibility is to grab a full snapshot of the ITIS data, and load it into a database so you can do what you wish. The obvious drawback is that it goes out of date, as with the ITIS snapshot uBio is currently using. But it puts you in the driver's seat re what to do & getting new versions of ITIS. Some general information about the full exports is in the following page, although conspicuously absent is any mention of the MySQL version which (assuming you have the free MySQL properly installed & configured) can be loaded with just a few clicks or a few command lines (depending on your platform): http://www.itis.gov/ftp_download.html And the current ITIS data are all here for downloading: http://www.itis.gov/downloads/ A third option, which I note with some trepidation, is the old "Compare Nomenclature/Taxonomy" function on the ITIS site: http://www.itis.gov/taxmatch_ftp.html This is a VERY old function that we do plan on replacing (timeframe not yet certain), and it is vulnerable to timeouts, etc., which is why it notes to limit the number of names per pass. But with smaller chunks of names it does work quite well. The caveat is that I would make sure to choose the 4th option in Step 4, as it is at least aware (unlike the 3 other options) of multiply-matched name cases, and lists them separately at the bottom of the report. Just a bare listing of the scientific names, with the word "name" at the top, saved as plain text, is all that is needed for input. A final option would be to ask someone at ITIS to handle the matching for you (leaving you to decide re the multiply-matched names). This might be simple from your end, but is suboptimal as it leaves you in the same position as you are now should you want or need to compare names again in the future (whether due to acquiring new names in your system, or wanting to check against a later updated version of ITIS), and it pulls someone here (probably me) off of the push to get more updates into ITIS. But in a pinch, I'm certainly willing to try to help you, should it come down to that! I would just ask that you seriously consider the web services option (in particular) or the others above first. I hope this helps some. If you have already run all your matches against the old "ITIS" data via uBio then you might consider re-running (against the current ITIS data) at least the leftover names that you did not yet get matched. Let us know if you have questions (the itiswebmaster(a)itis.gov address goes to myself and Alan and several others, so that might be the best bet for a follow-up unless you have a question specifically for me). Regards, Dave David Nicolson Data Development Coordinator, Integrated Taxonomic Information System Biologist, USGS Core Science Systems, Biological Informatics Program nicolsod(a)si.edu Office 202-633-2149 Fax 202-786-2934 http://www.itis.gov/ http://www.cbif.gc.ca/itis/ "Nihil sumas necesse est..." -----Original Message----- Date: Fri, 20 May 2011 05:42:03 -0500 From: Steve Baskauf <steve.baskauf(a)vanderbilt.edu> Subject: Re: [tdwg-content] ITIS TSNID to uBio NamebankIDs mapping To: "David Remsen (GBIF)" <dremsen(a)gbif.org> Cc: "tdwg-content(a)lists.tdwg.org" <tdwg-content(a)lists.tdwg.org> Message-ID: <4DD6457B.2080204(a)vanderbilt.edu> Content-Type: text/plain; charset="iso-8859-1" Thanks, all, for the responses. The "Compare to ITIS" function does just what I want. I did a test run of 1000 names and it worked like a charm. I will need to do a little massaging because sometimes two or more ITIS IDs come back for each uBio ID. But I can handle that. Steve David Remsen (GBIF) wrote: > Steve > > Have you tried this? > http://www.ubio.org/clients/ITIS/index.php > > or this? > http://www.ubio.org/services/mapper/index2.php > > All this ubio talk makes me think we were on to something. Worth a thought about adopting the new stnadrds and tools and making it really smooth. > > DR > > > On 20 May 2011, at 04:46, Steve Baskauf wrote: > > >> I have generated a csv spreadsheet of about 39 000 plant names for the >> U.S. which has the ITIS TSNIDs for the names in a column. I would like >> to have the uBio Namebank IDs in another column of the table. I have >> been looking them up on the uBio website by typing in the names as I >> need to know the IDs, but after doing about 300 of them, I'm getting >> tired of it. Does anybody have a clever idea of a way to get the other >> 38 000 Namebank IDs without looking them up. I'm sure that it would be >> possible to find this out because uBio gets names from ITIS. However, I >> haven't seen any clues about how to do it in an automated fashion. I'm >> guessing that there might be some way to use the uBio web services, but >> if so, it isn't obvious and I probably don't have the skills to carry it >> out anyway. >> >> Any ideas? >> Steve >> >> -- >> Steven J. Baskauf, Ph.D., Senior Lecturer >> Vanderbilt University Dept. of Biological Sciences >> >> postal mail address: >> VU Station B 351634 >> Nashville, TN 37235-1634, U.S.A. >> >> delivery address: >> 2125 Stevenson Center >> 1161 21st Ave., S. >> Nashville, TN 37235 >> >> office: 2128 Stevenson Center >> phone: (615) 343-4582, fax: (615) 343-6707 >> http://bioimages.vanderbilt.edu >> >> _______________________________________________ >> tdwg-content mailing list >> tdwg-content(a)lists.tdwg.org >> http://lists.tdwg.org/mailman/listinfo/tdwg-content >> >> > > . > > -- Steven J. Baskauf, Ph.D., Senior Lecturer Vanderbilt University Dept. of Biological Sciences postal mail address: VU Station B 351634 Nashville, TN 37235-1634, U.S.A. delivery address: 2125 Stevenson Center 1161 21st Ave., S. Nashville, TN 37235 office: 2128 Stevenson Center phone: (615) 343-4582, fax: (615) 343-6707 http://bioimages.vanderbilt.edu _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

16 52

Re: [tdwg-content] Why UUIDs alone are not adequate as GUIDs, was Re: ITIS TSNID to uBio NamebankIDs mapping
by Chuck Miller 09 Jun '11

09 Jun '11

Yes, ratified following the official TDWG process. Ratified is the final status of a proposed standard that has followed the process all the way through and has become "official". This process replaced the deprecated "member voting" formerly conducted at the annual meeting. Chuck -----Original Message----- From: tdwg-content-bounces(a)lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Kevin Richards Sent: Wednesday, June 08, 2011 4:16 PM To: Richard Pyle; 'Steve Baskauf' Cc: tdwg-content(a)lists.tdwg.org Subject: Re: [tdwg-content] Why UUIDs alone are not adequate as GUIDs, was Re: ITIS TSNID to uBio NamebankIDs mapping Answering your question about whether the GUID applicability statements are "ratified" standards... To be honest, I am not sure of the difference between an un-ratified standard and a ratified standard. My impression was that we have done all we need to with the applicability statements in the standards process, so perhaps they are ratified?? An email from 22 February (ironic date - the date of our devastating earthquake) about the applicability statements: "The TDWG Executive Committee has approved the Life Sciences Identifiers Applicability Statement (LSID_AS) and the Globally Unique Identifiers (GUID_AS) Applicability Statement as new TDWG standards. The Executive committee acknowledges Kevin Richards of Landcare New Zealand as author of the GUID Applicability Statement. Likewise, Kevin Richards, Ricardo Pereira (TDWG Infrastructure Project), Donald Hobern (Atlas of Living Australia), Roger Hyam (TDWG Infrastructure Project), Lee Belbin (TDWG Infrastructure Project) and Stan Blum (California Academy of Sciences) as co-authors of the LSID Applicability Statement. The committee also greatly appreciated the patience and perseverance of Ben Richardson of the Department of Environment and Conservation of Western Australia who was the Review Manager for these standards. The process, as can be seen from the institutional associations, was in this case longer than all would have liked, but we hope that the standards will prove useful to the Biodiversity Informatics community. We would also thank all those who were involved as formal or public reviewers of these standards. Your input was greatly appreciated and was in various ways, incorporated into the final standards. These standards can be downloaded from http://www.tdwg.org/standards/150/download/. Chuck Miller TDWG Chair On behalf of the TDWG Executive Committee" Kevin -----Original Message----- From: tdwg-content-bounces(a)lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org] On Behalf Of Richard Pyle Sent: Thursday, 9 June 2011 8:46 a.m. To: 'Steve Baskauf' Cc: tdwg-content(a)lists.tdwg.org Subject: Re: [tdwg-content] Why UUIDs alone are not adequate as GUIDs, was Re: ITIS TSNID to uBio NamebankIDs mapping Hi Steve, First of all, I owe you (and the list at large) a sincere apology for my excessively long and largely discombobulated email. I was distracted by many things, and I ended up writing it in chunks over the course of a full day. You were very clear on who you were responding to in each section, but I probably lost track of that because of the discontinuous mode of my response. Another problem is that I converted my reply to plain text, and that caused me to lose track in a few places whom I was responding to. Again, my sincere apologies. > For the purposes of clarity, any time I say "GUID" here, I intend it > in the sense of the TDWG GUID Applicability Statement. OK thanks. That became clear as I responded, but somehow I didn't pick up on that when I first started responding. But even the TDWG GUID Applicability Statement (TGAS) is not perfectly clear or consistent in its use of the term GUID. In some cases, the term implies self-actionability; in other cases, it says what to do when GUIDs are not self-actionable. > In the GBIF "Adoption of Persistent Identifiers for Biodiversity > Informatics" document > (http://www2.gbif.org/Persistent-Identifiers.pdf) > the term "persistent actionable identifiers" is used instead of GUID, > but in the interest of brevity I'll use GUID. OK, fair enough. The GBIF document was the most recent one I contributed to, so I was thinking in those terms for using the qualified "persistent actionable identifiers" language in contrast to "GUID"; but I'm perfectly happy using the term "GUID" now that we have it (reasonably) well-defined. > Thanks for taking the time to explain more about how GNUB will work. > I am anxious to see it come to fruition and to use it. I'm hoping that by late summer we'll have it functioning with several core services, and perhaps you and others on this list can help test those services and provide suggestions for new services. Before that can be a productive use of everyone's time, though, we need to hammer out some technical documentation. As I am writing this from my hotel room at Disney's Caribbean Beach Resort in Orlando (while my family naps after a long flight in preparation for some serious Magic Kingdom action tonight), I'm not really in a position to delve into this in too much detail right now. But I'll take a stab at it. > First a word about the TDWG GUID Applicability Statement. > You were expressing some reservations about calling it a "standard". > If you go to http://www.tdwg.org/standards/, you will find it listed > under "Current Standards". My reservations were mostly about calling it a "ratified standard". I honestly don't know if it is or isn't, but I don't rememeber a vote on it (like there was for TCS and for the "ratified" DwC). Perhaps Kevin Richards or someone else at TDWG can clarify (for both of us). > So an understanding of the "appropriate" way to apply something like a > UUID must be inferred from the general statements and examples about > UUIDs, by "reading between the lines" by considering how general > recommendations about GUIDs would impact the handling of UUIDs, and by > analogy to how LSIDs (another non-HTTP URI-based GUID) are handled. Perhaps instead of reading between the lines, the discussion surrounding the drafting of the "TGAS" is available online somewhere. That would include details about the thinking behind the final wording. > So based on this, you are correct to call a UUID a GUID. However, the > part that I disagree with is: > > ... I think it's foolish to regard all of these different resolution > mechanisms as distinct "identifiers". There is *ONE* GUID. It > is: A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523. There are ten different > ways to make it actionable. It therefore meets the recommendations of > the applicability statement. You are not alone in disagreeing with me on this. > The problem is that when you create an HTTP URI out of a UUID, you are > creating an identifier whether you think you are or not. Fair enough; but by that definition & logic, *every* HTTP URI (sensu the "Contemporary View" explained at http://www.w3.org/TR/uri-clarification/; i.e., inclusive of things we sometimes call URN or URL) is an identifier. But I think that goes well beyond the scope of the discussion we're having here about GUIDs. > I suppose as a matter of semantics, you could say "I don't intend for > the ten ways I showed of making my UUID actionable to be GUIDs", but > if I encounter one of them, how am I supposed to know that? That is *exactly* the point I was trying to get at in my earlier message. Right now, everything that resolves via HTTP GET must be treated as a GUID. But it's not guaranteed to be persistent (thinking again in terms of the more explicit "persistent actionable identifiers"). I think our community can do better than that. The problem is not the resolution -- I can (and intend to) persist all ten service syntax forms, so they will all fit the TGAS recommendation as GUIDs. But that doesn't do you any good if you're trying to compare cited objects in two different datasets that each happened to use different syntax for the resolution mechanism. A little more context might be helpful here. Those ten different mechanisms to resolve ZooBank identifiers existed before the drafting of the TGAS document. I assumed, at the time I established them, that everyone would see as clearly as I do that the need for identification is different from the need for "resolution" (=actionability). So strong was the opposition to what seemed obvious to me, that I followed my normal pattern in such cases, which is to assume that I was wrong. But the unsettling part is that the more carefully I thought about it, the more obvious it became that I was right, and the opposing viewpoint was wrong (despite the inherent assumption by various big-name web luminaries, who I otherwise hold enormous respect for). So, through the early TDWG/GBIF discussions, and both TDWG/GBIF GUID workshops, and the drafting of the various TDWG and GBIF documents, I stubbornly maintained this perspective (that identification and resolution should not be conflated). I believe that it was my stubbornness that accounts for the acknowledgement of the distinction between identification and resolution in TGAS and other documents. Now, the easy way out would be to throw in the towel and terminate 9 of those resolution services, and make everyone happy with a single ZooBank URI that can be actioned via HTTP GET. But to do so instills in me the same sort of lack of conviction that I would feel if I confessed to a crime I did not commit just because it was the easy way out. On this issue, I'm not ready to do that, because it is so glaringly obvious to me that we *must* maintain a distinction between identification and resolution. > You may not think that an HTTP proxied non-HTTP URI GUID (e.g. an HTTP > proxied UUID) is a GUID, but anyone who is interested in describing > the properties of the identified resource in RDF (which should be > everyone, GUID A.S. > recommendation 10) will think so. Not everyone. But I concede that most would. And this is what I want to fix. Another part of the TGAS that I quoted was this part (p 11): "For non-self-resolving GUIDs, such as UUIDs, resolution of that GUID via the HTTP protocol’s GET method (the standard method by which a resource is retrieved on the web) must be implemented. This ensures that the data for the object being identified can be obtained from the provider of that GUID with tools that a majority of Internet users and developers already understand and use." This, I believe, is one of the paragraphs inserted because of my insistence that the roles of identification and actionability be distinguished. Nothing in that statement -- or anywhere else in the TGAS that I am aware of -- suggests that HTTP-proxied "non-self-resolving GUIDs" themselves represent distinct GUIDs. Nor does it say that multiple mechanisms for establishing that HTTP-proxied actionability function represent a violation of Recommendation 4. > The GUID A.S. does not contain any RDF examples (unfortunately) but > the LSID Applicability Statement talks in detail about how LSIDs should be used in RDF. > Recommendation 29 of the LSID A.S. states that "objects must be > identified by an LSID in its standard form using the rdf:about > attribute". You can do this with an LSID because it is a urn (subset > of the more generic URI) and therefore a describable thing in RDF. > However, a UUID cannot be used similarly in an rdf:about attribute > because it is not any kind of URI. It is just a globally unique string. Right -- which is exactly why ZooBank identifiers are presented publicly as LSIDs (with proper resolution mechanisms), rather than simply as UUIDs. But that doesn't change the fact that the UUID is the "real" identifier, and is simply "wrapped" in LSID-compliant resolution metadata. But I will say that I also regard the LSID as a bona-fide "identifier" in and of itself, because that's how the LSID spec is written. So I (grudgingly) admit that our minting of LSIDs commits us to treating the full-context LSID as though it is a distinct identifier from the UUID that it encapsulates. However, I don't think this applies to all the flavors of HTTP proxying, because there is no spec (that I am aware of) that says "all HTTP URIs should be treated as though they are GUIDs" -- even though, by some definitions, they technically are. > Recommendation 31 says "All references to objects identified by LSIDs > using the rdf:resource attribute must use a proxy version of the LSID." Right, and this is where I think I dropped the ball on ZooBank LSID resolution. At the moment, resolving a ZooBank LSID directly (e.g., via Rod Page's LSID tester, or TDWG's LSID resolver service) retruns the proper RDF (thanks to Kevin Richards, who set that service up). However, the HTTP proxy version returns HTTP by default. I needed to do this because I didn't (and still don't) know enough about applying style sheets to RDF to render them in a human-friendly form. I spoke with Rob Whitton about this last week, and he will have this fixed soon. > Recommendation 30 says that the description of all objects identified > by an LSID must contain an owl:sameAs, owl:equivalentProperty or > owl:equivalentClass statement expressing the equivalence beteen the object identifier in its standard form and its proxy version. Ahh!! OK, this may be the fatal bullet to my argument. But let me explain a bit further: The "true" GUID for a ZooBank record is the UUID. The standard form of presenting this UUID to the public is as an LSID. I'm happy with saying that the LSID *is* the TDWG-context GUID for the record (calling the UUID the "true" GUID is just a semantic technicality that has no real bearing in the context of TDWG standards). The standard http proxy for ZooBank LSIDs is "http://zoobank.org/[LSID]" -- that is, the LSID appended to a "http://zoobank.org" prefix. I have no argument with the Recommendation 30 that says there should be an owl:sameAs, owl:equivalentProperty or owl:equivalentClass statement expressing the equivalence between the LSID and its proxy version. But I do have an argument against the notion that *any* web service that can resolve the LSID into its constituent metadata (whether HTTP, RDF, or whatever) must be treated as a distinct GUID, with a similar need for the owl:sameAs [etc.] statement. Perhaps this, ultimately, is the crux of our argument. > I don't think you were seriously suggesting that all 12 of the > identifiers on the list would actually be used in "real life". You > were making a point about how a UUID could be made actionable. In part yes. But what I was really saying is that it's silly to think of all of those different metadata resolution services as distinct GUIDs (even though in the broad sense, all HTTP URIs are technically GUIDs). Also, it depends on what you mean by "used in real life". They should certainly not be used in "real life" as identifiers of the sort you gave examples for. But they may well be "used" in other real-life contexts. > But my point is that you simply cannot meet the requirements of the > GUID A.S. with ONLY a UUID. We may quibbling about semantics here. I never said that the TGAS was met with ONLY a UUID. My point was, the UUID *is* the identifier, and it can meet the TGAS requirements and recommendations *provided* that there is an appropriate HTTP GET resolution service for it, and provided that the UUID is exposed externally only in the context of the relevant resolution metadata. In other words, I *COMPLETELY* agree with you (and have tried to make this clear all along) that one would never see something like "<dc:identifier>A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523</dc:identifier>" in an RDF (or other similar) document. But I do believe that something like "<dc:identifier>http://zoobank.org/A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523</dc:identifier>" *would* be compliant. > You MUST have an HTTP proxied version of it in order to "do the right thing" > (i.e. GUID A.S. rec 10) and provide metadata in the form of RDF serialized as XML. Yes, exactly. > That HTTP proxied version isn't just going to be seen as a "resolution mechanism". But my point is that it *should* be. In other words, our community should rise to that level of sophistication, because it would, I am quite certain, benefit us in the long run. > If you and GNUB are going to participate in BiSciCol as I understand > it to be developing (and I believe that you are), you will HAVE to > have an HTTP URI version of your UUIDs and in that context the raw > UUID will be relatively irrelevant. Of course! And if you ever thought otherwise, then obviously I am not expressing myself well. Maybe part of our argument is that you are focused on implementation, and I am speaking more on principle. I thought I made it clear in my first post on this thread that a UUID by itself is not actionable (recall my example of walking through the park and discovering a UUID written on a slip of paper), and therefore not, by itself, functional as a persistent actionable identifier (sensu TDWG/GBIF). My only point in all of this is that identification and resolution are two separate functions, and we should be sophisticated enough to recognize the distinction. I don't know if it's feasible, but I think one way that it could be made feasible comes back to my suggestion of a registry of resolution services. This is not going backward; it's going forward. However, our community may have its hands full with just implementing the things we most need to implement, and may not have the luxury of time and resources to implement a standard acknowledgement of the distinction between resolution services and object identification -- by my contention is that we ignore that distinction at our peril. > My point is that you should decide on just one of these HTTP URIs and > use that as your identifier when you communicate with the outside > world. That is already the case (has been the case ever since July 2007, when Kevin Richards set up our LSID resolution service). > My preference would be "http://zoobank.org/A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523" > as the shortest and least complex one that would do everything that > needs to get done. Well, for various reasons we went with the LSID version: "http://zoobank.org/urn:lsid:zoobank.org:act:A9F435E0-8ED7-46DD-BAB4-EA8E5BF…" Or, as RDF in accordance with the LSID spec: http://zoobank.org/authority/metadata/?lsid=urn:lsid:zoobank.org:act:A9F435… > I guess that there isn't problem with the other nine existing, but > from my point of view there is nothing but harm to be done by exposing > them to the outside world. I guess that depends on what you mean by "exposing" them. In my mind, they are already "exposed" because they work. However, I don't think anyone would (or should) embed them in semantic documents as though they were TDWG-style GUIDs. HOWEVER, the point I was originally making is that if we could (rightly) recognize the different roles of identification and resolution, then we wouldn't have a problem. You could very easily use your preferred "short" version of "http://zoobank.org/A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523", and reasoning service would have no difficulty recognizing it as identifying the same object as urn:lsid:zoobank.org:act:A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523, or http://zoobank.org/urn:lsid:zoobank.org:act:A9F435E0-8ED7-46DD-BAB4-EA8E5BF…. I realize there is no elegant way to do this using existing RDF syntax, which is why this is *really* a much more fundamental argument than just TDWG-space. But in my extremely naïve way of representing it, it might look something like: <rdf:Description rdf:about="http://zoobank.org/A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523"> <dc:identifier>A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523</dc:identifier> <xxx:resolutionService>http://zoobank.org/</xxx:resolutionService> ...which would have no trouble combining with a document that had something like this: <rdf:Description rdf:about="http://zoobank.org/?uuid=A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523"> <dc:identifier>A9F435E0-8ED7-46DD-BAB4-EA8E5BF41523</dc:identifier> <xxx:resolutionService>http://zoobank.org/?uuid=</xxx:resolutionService> > The other point which I was trying to make is: why would you choose to > expose to the outside world an identifier that only does part of the > desirable things that we want (i.e. my list of 8 desirable attributes > of a GUID), when you could use a modification of that identifier that would do everything you want? I would *never* "choose" to do that. However, I may very well be stuck with that due to insufficient resources and expertise. *That* is what I intend to fix now that I (finally) have both resources and expertise. > But with virtually no additional cost (15 minutes of time from > somebody who knows how to create a single 3 kB XSLT file) Ah....if only I had 15 minutes of such a person's time before now! :-) > I would assert the same thing about LSIDs. Why would you create in > identifier that is part of (what seems to me to be universally > recognized as) a dead technology when you could create a simpler HTTP > URI that would do the same thing and potentially more? The answer to that is much easier, and should be self-evident when you consider what I already mentioned previously: that the service was established in the summer of 2007. At that time, LSID was absolutely NOT dead, and indeed was actively being promoted by both TDWG and GBIF. This was the outcome of the two GUID workshops those organizations sponsored. There certainly were detractors to LSIDs back then, making the same arguments they are making now. To the extent that LSIDs are currently perceived as "dead" by some, is due largely to the self-fulfilling prophecy of those detractors. But in any case, regardless of whether LSIDs really are dead or not, and regardless of why that may be so (if it is so), there were very good reasons why ZooBank went with LSIDs. And while I realize that the four years since then are a veritable EON in IT contexts, keep in mind that ZooBank has to think in terms of centuries. In that context, the HTTP protocol is not guaranteed to be persistent, and things like DOI are pretty-much downright ephemeral. In fact, this is exactly why I went with UUIDs in the first place. As long as electronic data are stored in binary form, 128 bits will have mathematical stability. *That's* why I realized that UUIDs were the only defensible choice for the "real" identifier, and is the identifier that ZooBank will persist. The choice of LSID as a resolution protocol was, as already stated, influenced by the thinking of our community at the time. *My* thinking at the time was that the only thing with any real plausibility of ICZN-scale longevity was binary data encoding (even that may not withstand more than a few decades), so I embraced UUIDs (which is to say, I embraced 128-bit identity). Everything else (LSID protocol, HTTP protocol, etc.) could be regarded as no more than the "resolution mechanism du joir". Perhaps this starts to explain why I keep emphasizing the distinction between identity and metadata resolution. The ZooBank registry has to think in terms of long-term identity, and assume that resolution mechanisms will continue to change as the technological wind blows. > In the case of uBio and Biodiversity Collections Index, they were set > up when LSIDs were believed to be the "Next Big Thing". Actually, all of us were implementing them at the same time. I think IPNI was one of the first; BCI came later. This all emerged from the two TDWG/GBIF GUID workshops. > That did not turn out to be the case, so those organizations are stuck > with painful HTTP URIs like > "http://biocol.org/urn:lsid:biocol.org:col:35115" and > "http://www.ubio.org/authority/metadata.php?lsid=urn:lsid:ubio.org:namebank:…" > when they could have had "http://biocol.org/35115" > and "http://www.ubio.org/9479554". I would say "lesson learned" - Ha! Hardly! We are only just now beginning to start learning lessons. Let's revisit this conversation again in a couple of decades and see how many more lessons are yet in store for us. In any case, my family just woke up from their nap, so I'll have to look at the rest of your message later, after some time with Mickey and the gang. Aloha, Rich Richard L. Pyle, PhD Database Coordinator for Natural Sciences Associate Zoologist in Ichthyology Dive Safety Officer Department of Natural Sciences, Bishop Museum 1525 Bernice St., Honolulu, HI 96817 Ph: (808)848-4115, Fax: (808)847-8252 email: deepreef(a)bishopmuseum.org http://hbs.bishopmuseum.org/staff/pylerichard.html _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content 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 _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

1 0

Proposal to reconcile Current DarwinCore with Possible Fully Semantic Representations
by Peter DeVries 08 Jun '11

08 Jun '11

Hi, I was thinking that we are a bit stuck on current vs. new representations and the idea whether a potential semantic version should be fully decidable or if an executable version would be more appropriate. There is also the issue of the various data restrictions that are entailed in different data sets. I created the diagram below that I hope will illustrate the following idea. End users format their data in DarwinCore. GBIF or some other group would need to clean and normalize this data. They could then output this data in various forms. 1) One based on a fully decidable model 2) One based on an executable model 3) One based on an executable model that would be open and public This would require some sort of data fuzzying and I was thinking that replacing the actual GPS records with a URI that represents the 10km x 10km region of the earth. The size of 10km x 10km is flexible, it just needs to be some standard size and represented by a URI Here is the URI to the diagram http://www.taxonconcept.org/storage/images/DarwinSWProposal.png 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 --------------------------------------------------------------------------------------

1 0

DwC Occurrence [SEC=UNCLASSIFIED]
by Paul Murray 07 Jun '11

07 Jun '11

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

7 18