April 2009 - tdwg-tag - lists.tdwg.org

TaxonOccurrence non-standard (Spinning off from something Peter DeVries mentioned)
by Roger Hyam 02 May '09

02 May '09

Hi Peter, The TaxonOccurrence standard is not actually a standard. It is part of the vocabulary that was put together two years ago and maps well to DwC. Meanwhile, as Markus points out, DwC has gone its own way. The whole TDWG ontology needs some clarification and sorting out and as Bob points out this is now done on a voluntary basis. I am working on the TaxonName and TaxonConcept vocabularies because I need to use them. I hope I will provide what Markus requests (good return type definitions for GUIDs) but I will only do it for taxon names and concepts because that is all I am working on. I hope to take this to a stage where it is solid, documented and standardizable. This will entail doing some stuff on the way the TDWG ontology/ vocabulary is presented but really it is not my department to do that alone. This is very important for TDWG (as Markus points out). What really needs to happen is for people who need things to happen in the ontology to role up their sleeves and make them happen. For occurrence stuff I recommend you join forces with John Wieczorek. All the best, Roger

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LSIDs: web based (HTTP) resolvers and web crawlers
by Nicola Nicolson 01 May '09

01 May '09

Hi, Further to my last design question re LSID HTTP proxies (thanks for the responses), I wanted to raise the issue of HTTP LSID proxies and crawlers, in particular the crawl delay part of the robots exclusion protocol. I'll outline a situation we had recently: The GBIF portal and ZipCodeZoo site both inclde IPNI LSIDs in the pages. These are presented in their proxied form using the TDWG LSID resolver (eg http://lsid.tdwg.org/urn:lsid:ipni.org:names:783030-1) Using the TDWG resolver to access the data for an IPNI LSID does not issue any kind of HTTP redirect, instead the web resolver uses the LSID resolution steps to get the data and presents it in its own response (ie returning a HTTP 200 OK response). The problem happens when one of these sites that includes proxied IPNI LSIDs is crawled by a search engine. The proxied links appear to belong to tdwg.org, so whatever crawl delay is agreed between TDWG and the crawler in question is used. The crawler has no knowledge that behind the scenes the TDWG resolver is hitting ipni.org. We (ipni.org) have agreed our own crawl limits with Google and the other major search engines using directives in robots.txt and directly agreed limits with Google (who don't use the robots.txt directly). On a couple of occasions in the past we have had to deny access to the TDWG LSID resolver as it has been responsible for far more traffic than we can support (up to 10 times the crawl limits we have agreed with search engine bots) - this due to the pages on the GBIF portal and / or zipcodezoo being crawled by a search engine, which in turn triggers a high volume of requests from TDWG to IPNI. The crawler itself has no knowledge that it is in effect accessing data held at ipni.org rather than tdwg.org as the HTTP response is HTTP 200. One of Rod's emails recently mentioned that we need a resolver to act like a tinyurl or bit.ly. I have pasted below the HTTP headers for an HTTP request to the TDWG LSID resolver, and to tinyurl / bit.ly. To the end user it looks as though tdwg.org is the true location of the LSID resource, whereas with the tinyurl and bitly both just redirect traffic. I'm just posting this for discussion really - if we are to mandate use of a web based HTTP resolver/proxies, it should really issue 30* redirects so that established crawl delays between producer and consumer will be used. The alternative would be for the HTTP resolver to read and process the directives in robots.txt, but this would be difficult to implement as it is not in itself a crawler, just a gateway. I'm sure that if proxied forms of LSIDs become more prevalent this problem will become more widespread, so now - with the on-going attempt to define what services a GUID resolver should provide - might be a good time to plan how to fix this. cheers, Nicky [nn00kg@kvstage01 ~]$ curl -I http://lsid.tdwg.org/urn:lsid:ipni.org:names:783030-1 HTTP/1.1 200 OK Via: 1.1 KISA01 Connection: close Proxy-Connection: close Date: Mon, 27 Apr 2009 11:41:55 GMT Content-Type: application/xml Server: Apache/2.2.3 (CentOS) [nn00kg@kvstage01 ~]$ curl -I http://tinyurl.com/czkquy HTTP/1.1 301 Moved Permanently Via: 1.1 KISA01 Connection: close Proxy-Connection: close Date: Mon, 27 Apr 2009 12:16:38 GMT Location: http://www.ipni.org/ipni/plantNameByVersion.do?id=783030-1&version=1.4&outp… Content-type: text/html Server: TinyURL/1.6 X-Powered-By: PHP/5.2.9 [nn00kg@kvstage01 ~]$ curl -I http://bit.ly/KO1Ko HTTP/1.1 301 Moved Permanently Via: 1.1 KISA01 Connection: Keep-Alive Proxy-Connection: Keep-Alive Content-Length: 287 Date: Mon, 27 Apr 2009 12:19:48 GMT Location: http://www.ipni.org/ipni/plantNameByVersion.do?id=783030-1&version=1.4&outp… Content-Type: text/html;charset=utf-8 Server: nginx/0.7.42 Allow: GET, HEAD, POST - Nicola Nicolson - Science Applications Development, - Royal Botanic Gardens, Kew, - Richmond, Surrey, TW9 3AB, UK - email: n.nicolson(a)rbgkew.org.uk - phone: 020-8332-5766

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Re: [tdwg-tag] darwin core terms inside tdwg ontology
by Roger Hyam 27 Apr '09

27 Apr '09

I am posting this for Bryan as his message seems to have bounced. I leave our comments in as they are informative re identifiers. Roger Begin forwarded message: > From: "P. Bryan Heidorn" <pheidorn(a)illinois.edu> > Date: 27 April 2009 14:36:31 BST > To: Roger Hyam <roger(a)hyam.net> > Subject: Re: Auto-discard notification > > No, I did not know it bounced. Can you forward for me while I figure > it out? Univ of Illinois changed its domain which might be the > problem... case in point for the need for stable identifiers that > are not university domain names! > > Thanks, > Bryan > -- > -------------------------------------------------------------------- > P. Bryan Heidorn > Graduate School of Library and Information Science > University of Illinois at Urbana-Champaign > pheidorn(a)illinois.edu > http://www.uiuc.edu/goto/heidorn > > > > On Apr 27, 2009, at 4:36 AM, Roger Hyam wrote: > >> Hi Bryan, >> >> Did you know this one bounced? Did it get through eventually? >> >> Roger >> >> >> Begin forwarded message: >> >>> From: tdwg-tag-bounces(a)lists.tdwg.org >>> Date: 25 April 2009 15:04:03 BST >>> To: tdwg-tag-owner(a)lists.tdwg.org >>> Subject: Auto-discard notification >>> >>> The attached message has been automatically discarded. >>> From: "P. Bryan Heidorn" <pheidorn(a)illinois.edu> >>> Date: 25 April 2009 15:03:33 BST >>> To: Technical Architecture Group mailing list <tdwg-tag(a)lists.tdwg.org >>> > >>> Cc: Stan Blum <sblum(a)calacademy.org>, exec(a)tdwg.org, Kevin >>> Richards <RichardsK(a)landcareresearch.co.nz> >>> Subject: Re: [tdwg-tag] darwin core terms inside tdwg ontology >>> >>> >>> Some taxon concept/name is always part of a Darwin Core record and >>> in the loose constraints of DwC that can just be a name string but >>> (typing back to the dreaded LSID/GUID argument) it could be a term >>> that is "defined" within the broader taxon concept world. This can >>> of course be _optional_ and when used might just be a string plus >>> a reference to the other standard where it is defined. So you can >>> just say "Quercus alba" or say Quercus alba plus a taxonomic >>> identifier that would lead to the particular concept of Quercus >>> alba you mean in this case with relationships to synonyms, >>> historical usage etc, but none of those relationships are in the >>> DwC record. >>> >>> A user of a collection of such records could then decide if the >>> string "Quercus alba" is a sufficient qualifier for the task at >>> hand or if a particular circumscription resolved by the taxonomic >>> reference is required. For example, if you are really interested >>> in all oaks you could build a parser that reads the records and >>> decides that the word "Quercus" means oak or you could choose to >>> use the taxonomic LSID/QUID to have the computer go to a taxonomic >>> resolution service that would be able to answer if or if not this >>> is a Quercus. >>> >>> The same type of mechanism could be used for locality. >>> >>> Any of this requires just an optional side element on fields >>> identifying two things. It need not be a globally accepted >>> standard if there are two components. One component that is an >>> identifier and another identifying the resolution context. That >>> context could be the "Backwoods Arboretum Shop and Taxonomic >>> Authority Database (BASTARD)" that defines everything by its >>> historical woodworking use or the context can be a TDWG approved >>> taxonomic resolution service respected by systematists (but not >>> necessarily wood workers or conservationists). >>> >>> -------------------------------------------------------------------- >>> P. Bryan Heidorn, Program Director >>> Division of Biological Infrastructure Rm. 615 N >>> National Science Foundation >>> 4201 Wilson Blvd. >>> Arlington VA 22230 >>> (703) 292-8470 >>> pheidorn(a)nsf.gov >>> >>> >>> >>> >>> On Apr 25, 2009, at 2:52 AM, Kevin Richards wrote: >>> >>>> I see the ontology as a model of ALL (hopefully, eventually all) >>>> the data in our domain of biodiversity informatics. >>>> I would love to see it as a standard (at the least it might give >>>> it a bit more clout). >>>> I agree that the ontology is useful to tie other TDWG schemas >>>> together, using it as a core/master model. I would be happy to >>>> see it used for ALL tasks within TDWG, but I understand the >>>> usefulnes of the more specific schemas/standards - horses for >>>> courses. >>>> >>>> If I understand Stan here, I agree with him about the dubious use >>>> of DwC for representing Taxon Concepts/Names. As far as I know, >>>> it was really intended as a transfer standard for observation >>>> records?? It contains very limited taxon information! It really >>>> is not a overly difficult job to use a more suitable schema/ >>>> ontology. I think the popularity of Darwin Core is due to its >>>> simplicity - and I wonder if what Roger is proposing will help >>>> with this - ie an XML implementation of the ontology as well as >>>> an RDF version. This will allow people to create very simple XML >>>> documents with reasonably simple/flat data, eg an xml document of >>>> TaxonName entities, with perhaps 6 or 7 or so key fields - even >>>> simpler than DwC. :-) >>>> >>>> Kevin >>>> >>>> From: tdwg-tag-bounces(a)lists.tdwg.org [tdwg-tag-bounces(a)lists.tdwg.org >>>> ] On Behalf Of Blum, Stan [sblum(a)calacademy.org] >>>> Sent: Saturday, 25 April 2009 6:12 a.m. >>>> To: Technical Architecture Group mailing list; exec(a)tdwg.org >>>> Subject: Re: [tdwg-tag] darwin core terms inside tdwg ontology >>>> >>>> From: tdwg-tag-bounces(a)lists.tdwg.org on behalf of John R. >>>> WIECZOREK >>>> Sent: Fri 2009-04-24 8:58 AM >>>> To: Roger Hyam >>>> Cc: Technical Architecture Group mailing list >>>> Subject: Re: [tdwg-tag] darwin core terms inside tdwg ontology >>>> >>>> Anything I should do on the DwC side in anticipation of harmony? >>>> >>>> http://rs.tdwg.org/dwc/terms/index.htm#theterms >>>> >>>> =========================================================== >>>> >>>> John, >>>> >>>> At some point, all or (most) of the DarwinCore terms need to be >>>> added to the TDWG ontology. >>>> >>>> But having said that, I also need to say that I'm uncomfortable >>>> with: >>>> >>>> 1) The current state of the TDWG ontology (primarily the naming >>>> conventions; lets just use terms names), and our understanding of >>>> the role it plays in TDWG and how it will be managed (entry of >>>> terms, integration of terms into the conceptual [is-a / has-a] >>>> relationships to other terms); and >>>> >>>> 2) the fact that the new DarwinCore straddles or overlaps the >>>> roles of an ontology and an application schema. >>>> >>>> I understood the past TAG roadmaps to indicate that we were >>>> adopting an approach in which the TDWG Ontology would be a >>>> repository for data concepts that are present in (or implied by) >>>> TDWG standards; and that real data transmission would be >>>> accomplished with application schemas. The ontology itself would >>>> not be a standard, but would be a tool that helps integrate >>>> standards. I thought our standards would be created to function >>>> as application schemas or components of application schemas (as >>>> in the DwC and its extensions). I am now pretty confused. I'd >>>> like to hear the rationale for combining taxonomic name/concept >>>> with organism occurrence. I haven't gone over all the existing >>>> docs, so apologies if I've missed that, but I think it's >>>> confusing that a (new) DarwinCore record could be either a >>>> taxonomic name or an organism occurrence, or maybe something >>>> else. Maybe I'm too attached to object orientation and just >>>> don't GET the semantic web, but it feels to me like we are >>>> stepping into squishy ground. >>>> >>>> Also, I the the DCMI maintenance procedures are also more >>>> appropriately applied to the ontology than a TDWG standard. The >>>> existing process for ratifying TDWG standards and the procedure >>>> in the DwC seem to be pretty explicitly in conflict; one can >>>> change the other cannot (without becoming another thing). >>>> >>>> Is anyone else having these same trepidations? I don't think >>>> I've been as much of a Rip Van Winkle as Jim Croft, but I clearly >>>> missed some important shifts. >>>> >>>> -Stan >>>> >>>> >>>> >>>> >>>> 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-tag mailing list >>>> tdwg-tag(a)lists.tdwg.org >>>> http://lists.tdwg.org/mailman/listinfo/tdwg-tag >>> >>> >>> >> >

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Differences in thinking between TDWG and LinkedData groups about data sharing / integration
by Peter DeVries 26 Apr '09

26 Apr '09

This paragraph below seems to encapsulate the differences in thinking between the linkeddata community and some of the TDWG people on how to best share biodiversity data. *"The notion of a fabric of resources that are individually described, queried, and resolved may seem unmanageable or like science fiction. For organizations that are used to large, manual, centralized efforts to standardize on everything, it may seem anarchic to allow resources to grow organically and be described by anyone. The same people would probably not believe the Web possible in the first place if there were not already ample proof of its success."* REST for Java developers, Part 4: The future is RESTful From http://www.javaworld.com/javaworld/jw-04-2009/jw-04-rest-series-4.html?page… I think that some people may have lost sight of the goal of making data available to improve the understanding of our natural world and hopefully better manage our natural resources. It does not seem that creating a distributed network of fiefdoms will help us achieve this goal. - Pete I was led to this article by @janzemanek on twitter. --------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 ------------------------------------------------------------

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GUID Persistence as Zen kōan
by Roger Hyam 24 Apr '09

24 Apr '09

For those of you who can take any more of it I have posted my thoughts on persistence of GUIDs to my blog. http://www.hyam.net/blog/archives/346 If you don't have the time or patience to read it the summary is: GUID Persistence == diddly squat Your comments are welcome. All the best, Roger

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Call for Nominations for a GBIF LSID-GUID Task Group
by Eamonn O Tuama (GBIF) 24 Apr '09

24 Apr '09

[Apologies for cross posting] Dear TDWG TAG Members, The Call for Nominations for a GBIF LSID-GUID Task Group is attached. Please observe the deadline of 10 May 2009 for nominating candidates. Kindly send your nominations directly to Éamonn Ó Tuama (eotuama(a)gbif.org) Best regards, Éamonn _______________________________________________ Éamonn Ó Tuama, M.Sc., Ph.D. ( <mailto:eotuama@gbif.org> eotuama(a)gbif.org) Senior Programme Officer, Inventory, Discovery, Access (IDA), Global Biodiversity Information Facility Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, DENMARK Phone: +45 3532 1494; Fax: +45 3532 1480

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Re: [tdwg-tag] SourceForge LSID project websites broken - role for TDWG?
by Donald.Hobern＠csiro.au 24 Apr '09

24 Apr '09

Thanks, Rod. http://bioguid.info/ and your precedings paper are both very nice work and very constructive. Best wishes, Donald Donald Hobern, Director, Atlas of Living Australia CSIRO Entomology, GPO Box 1700, Canberra, ACT 2601 Phone: (02) 62464352 Mobile: 0437990208 Email: Donald.Hobern(a)csiro.au Web: http://www.ala.org.au/

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Re: [tdwg-tag] SourceForge LSID project websites broken - role for TDWG?
by Eamonn O Tuama (GBIF) 23 Apr '09

23 Apr '09

Hi All, As one of the largest international organisations directly concerned with enabling a bioinformatics infrastructure for sustained data sharing, GBIF is very interested in exploring the possibility of becoming administrator for a redirection/resolver domain for biodiversity GUIDs regardless of the technologies that are ultimately deployed - whether LSIDs, DOIs, PURLS, etc., or, perhaps more realistically, a mixture of several. Many interesting arguments have been put forward in this sustained thread and, after internal consultation amongst the GBIF informatics team, we think that it is worth considering using established GBIF processes as a way to move to the implementation phase, at the same time helping inform GBIF's policy/strategy regarding GUIDs in general, and through GBIF, the wider community of practitioners grappling with challenging issues around biodiversity informatics. As mentioned previously, we will be making some resources available to convene a dedicated task group which will provide recommendations to GBIF on deployment of GUIDs on the GBIF network. The terms of reference for this group will be released within a week and we invite you to support the group either directly, by going forward for nomination - there will be a limited number of places in the core group -, or by participating in the broader consultation process that the group will employ. Our plan would be to have the group report back with their recommendations after about four months. This is considered the minimum timeframe that will allow meaningful engagement/consultation as feedback from the GBIF community and others is an essential component of the recommendations drafting process. I will inform the list once the call for participation and terms of reference have been released. Best regards, Éamonn _______________________________________________ Éamonn Ó Tuama, M.Sc., Ph.D. (eotuama(a)gbif.org) Senior Programme Officer, Inventory, Discovery, Access (IDA), Global Biodiversity Information Facility Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, DENMARK Phone: +45 3532 1494; Fax: +45 3532 1480 -----Original Message----- From: tdwg-tag-bounces(a)lists.tdwg.org [mailto:tdwg-tag-bounces@lists.tdwg.org] On Behalf Of tdwg-tag-request(a)lists.tdwg.org Sent: 11 April 2009 12:00 To: tdwg-tag(a)lists.tdwg.org Subject: tdwg-tag Digest, Vol 36, Issue 17 Send tdwg-tag mailing list submissions to tdwg-tag(a)lists.tdwg.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.tdwg.org/mailman/listinfo/tdwg-tag or, via email, send a message with subject or body 'help' to tdwg-tag-request(a)lists.tdwg.org You can reach the person managing the list at tdwg-tag-owner(a)lists.tdwg.org When replying, please edit your Subject line so it is more specific than "Re: Contents of tdwg-tag digest..." Today's Topics: 1. FYI: SharedNames (Roger Hyam) 2. Re: SourceForge LSID project websites broken - role for TDWG? (Lee Belbin) ---------------------------------------------------------------------- Message: 1 Date: Fri, 10 Apr 2009 12:55:50 +0100 From: Roger Hyam <rogerhyam(a)mac.com> Subject: [tdwg-tag] FYI: SharedNames To: Technical Architecture Group mailing list <tdwg-tag(a)lists.tdwg.org> Message-ID: <690607AB-627E-4B9B-8168-4C412F81FE68(a)mac.com> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes You may be interested in this project to set up PURLs for biomedical resources http://sharedname.org/page/Main_Page ------------------------------ Message: 2 Date: Sat, 11 Apr 2009 10:00:39 +1000 From: "Lee Belbin" <leebel(a)netspace.net.au> Subject: Re: [tdwg-tag] SourceForge LSID project websites broken - role for TDWG? To: "'Roderic Page'" <r.page(a)bio.gla.ac.uk> Cc: 'Technical Architecture Group mailing list' <tdwg-tag(a)lists.tdwg.org> Message-ID: <002101c9ba38$8e3c2110$aab46330$(a)net.au> Content-Type: text/plain; charset="us-ascii" Thanks Rod. Very constructive. Lee Lee Belbin TDWG Secretariat -----Original Message----- From: Roderic Page [mailto:r.page@bio.gla.ac.uk] Sent: Friday, 10 April 2009 1:30 AM To: Lee Belbin Cc: 'Technical Architecture Group mailing list' Subject: Re: [tdwg-tag] SourceForge LSID project websites broken - role for TDWG? In a rare attempt at being constructive, here are a few thoughts. LSIDs and linked data ================= If adoption of LSIDs proceeds, then we should make efforts to see that they play nicely with Linked Data efforts. For example, a HTTP resolver would need to support 303 redirects and content negotiation. This help avoid us creating our own ghetto, but still exploit whatever advantages LSIDs have. Roger set up something along these lines to handle Biological Collections Index (BioCol) LSIDs. There is a nice tool at http://validator.linkeddata.org/ to check whether a URI behaves as Linked Data tools expect. Sadly the proxied BioCol LSIDs (e.g., http://biocol.org/urn:lsid:biocol.org:col:15670 ) don't validate, but this should be easy to fix. The TDWG resolver similarly fails. I've implemented a simple resolver at bioGUID that returns either raw RDF or a clumsily formatted HTML version of the XML, but which passes the http://validator.linkeddata.org tests. An example URI is http://bioguid.info/urn:lsid:indexfungorum.org:names:213649 , which validates http://tinyurl.com/cgje5n So, my first recommendation is to ensure that a TDWG HTTP proxy passes http://validator.linkeddata.org/ . This means we can play with the Semantic Web crowd with LSIDs. Note that getting HTTP URIs to play with Linked Data is not trivial, so whatever technology we adopt we'll need clear guidelines as to how to use it. As an aside bioGUID can make DOIs play nice as well (they don't by default), and Kinglsey Idehen http://www.openlinksw.com/blog/ ~kidehen/ of OpenLink Software is supporting LSIDs in the Linked Data tools he's developing. Ontology ======= As part of my experiment to wikify taxonomic names, literature, etc., I've been playing with the TDWG vocabularies. I've a few grizzles, but in general they've been really useful, and I think these will be key (as Donald and Lee have emphasised). Service ====== Ironically one of the examples Lee listed when defending the TDWG's resolver (urn:lsid:gdb.org:GenomicSegment:GDB132938) seems to have disappeared (I think TDWG has a cached copy). This raises the ongoing problem of service availability. TDWG's resolver could help here, in that could be used to generate reports on service quality and notify providers when something's wrong. Whatever GUID technology adopted this will be an issue, and the challenge is to build tools and mechanisms to manage this. Funding ====== I've nothing useful to say here, other than to suggest that clearly the integration of biodiversity data sales pitch hasn't (yet?) succeeded. I think us techies get it, but we've not made that vision real or compelling. If we had, I think we'd have institutions falling over themselves to ensure the infrastructure exists and persists. Naive, I know, but we could ask why we haven't managed to convince those with the purse strings that this stuff matters. One quick and dirty way that might help is if the TDWG LSID resolver stored all the metadata in the LSIDs it resolves in a triple store and exposes a SPARQL query interface to that metadata. We could then start to look for interesting links between data. Regards Rod --------------------------------------------------------- Roderic Page Professor of Taxonomy DEEB, FBLS Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK Email: r.page(a)bio.gla.ac.uk Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rodpage1962(a)aim.com Facebook: http://www.facebook.com/profile.php?id=1112517192 Twitter: http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html ------------------------------ _______________________________________________ tdwg-tag mailing list tdwg-tag(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tag End of tdwg-tag Digest, Vol 36, Issue 17 ****************************************

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LSID HTTP Proxy - design question
by Nicola Nicolson 22 Apr '09

22 Apr '09

Hi, I've been looking into setting up an HTTP proxy for the ipni.org LSIDs. I've read the usage recommendations at http://wiki.tdwg.org/twiki/bin/view/GUID/LsidHttpProxyUsageRecommendation but want to ask a question re the design of the proxy itself, ie: Should an HTTP proxy for LSIDs behave as: (1) a webapp that acts as an LSID "client" or (2) a mechanism to issue redirects to the metadata address as specified in the LSID authority WSDL The latter is simple - I can just set up a mod_rewrite rule so that http://lsid.ipni.org/[lsid] is redirected to the HTTP URL for the metadata for the specified LSID. This will of course only work for LSIDs for which ipni.org is the authority, but I think that is OK. If the former, I'll need to encode the resolution process: ie parse the LSID, extract the authority, do the DNS lookup, get the WSDL, construct the address etc, BUT it will mean that the HTTP LSID proxy is dependent upon correct functioning of the LSID infrastructure (DNS SRV records, authority WSDL etc). I guess the TDWG LSID proxy behaves this way, but that is to be expected as it can be used as an HTTP proxy for *any* LSID. In summary option (1) treats the proxied LSID as *an LSID*, the other really just treats it as a character string. Which is preferred? cheers, Nicky - Nicola Nicolson - Science Applications Development, - Royal Botanic Gardens, Kew, - Richmond, Surrey, TW9 3AB, UK - email: n.nicolson(a)rbgkew.org.uk - phone: 020-8332-5766

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Re: [tdwg-tag] SourceForge LSID project websites broken - role for TDWG?
by Lee Belbin 15 Apr '09

15 Apr '09

I can't hold off commenting on this discussion any longer. Apologies for the tome of accumulating thoughts. As noted, there are three aspects to recent discussions about GUIDs - the techie (easy?) bits, the social (harder?) bits and the funding/financial (hardest?) bits. I was at the two TDWG funded meetings to decide on an appropriate GUID for the biodiversity informatics community. The (wide-ranging) group decided to support LSIDs. A number of us subsequently rounded up a library of resources (http://wiki.tdwg.org/GUID/) and drafted quite a few documents (http://www.tdwg.org/activities/guid/documents/) including the LSID Applicability Statement (the application of an existing standard to our domain). Ricardo Pereira (among a host of other work) setup the SourceForge site (http://lsids.sourceforge.net/) and that is the ONLY TDWG LSID resource that is currently down. It is down because SourceForge changed their website provider configuration (with previous notice) that broke our setup, and we were not able to restore it - but we are working on it (minus Ricardo - which is why the delay). To quote Ricardo: "Important pieces of the LSID infrastructure were never off-line, not even for a minute in the last year or so. Examples: http://lsid.tdwg.org/ http://lsid.tdwg.org/summary/urn:lsid:ubio.org:namebank:11815 http://lsid.tdwg.org/summary/urn:lsid:ubio.org:classificationbank:1164063 http://lsid.tdwg.org/summary/urn:lsid:indexfungorum.org:names:213649 http://lsid.tdwg.org/summary/urn:lsid:gdb.org:GenomicSegment:GDB132938 http://lsid.tdwg.org/summary/urn:lsid:ipni.org:names:30000959-2 The actual LSID infrastructure, including the TDWG LSID resolver and the LSID authorities listed there have always been operational, as you can see from the links above. The open source community website that supports software developers involved in implementing LSID clients and resolvers also was never off-line: http://sourceforge.net/projects/lsids (open source collaboration site) http://sourceforge.net/project/showfiles.php?group_id=198923 (downloads) http://lsids.svn.sourceforge.net/viewvc/lsids/ (version control - subversion) http://sourceforge.net/mailarchive/forum.php?forum_name=lsid-developer (LSID developer forum)" As has been stated previously, the 'social' aspects involved in the uptake of standards is important. As Jim said, TDWG develops standards (not software or an implementation service). We assume end-users have the skills to use the standards or that companies such as ETI (that are thin on the ground) can provide a service. This has drawn criticism. It is not an easy call as we are already spread far too thinly. We have also previously missed addressing the needs of the managers of the people in TDWG (who hold the purse strings and who make decisions). I did commission 'executive summaries' of most of the TDWG 'standards' (including at least three on LSIDs) but I agree that we need to consider deployment before a new TDWG standard is released. One of my responsibilities as part of the TDWG Infrastructure Project (TIP) was to consider a funding model for TDWG. I found it amazing that an organization in TDWG's position has so few members. TDWG develops standards for sharing biodiversity information. Most of us know just how central that is (as has been stated) for work such as GBIF, CoL, EoL, ALA, EDIT, OBIS, ITIS....and all museums, herbaria etc (a hell of a huge community!!). In 'biodiversity', we are also talking about one of the planets key resources! When TIP started, TDWG had 23 individual members and 17 institutional members. Amazing isn't it!? Why? Maybe because of the small original overlap of let's call them 'biotypes' with Information Technologists? TDWG started as a club of IT inclined biotypes playing with databases. The explosion of IT has radically changed that. TDWG is still at a point where the biotypes can't easily understand the few (unbelievably valuable and overworked!) people with IT skills that TDWG had fortunately attracted. I know that some people have not joined TDWG because they see it as 'bureaucratic': To quote Rod Page and Nike "...Just do it...". I'm convinced that TIP's restructured TDWG has addressed that. Movement is now far more dependent on the individual than the committee - and we can't do better (or worse) than that. It was obvious to me that we needed to build TDWG membership before we look to Sugar Daddies or more handouts. With a substantial membership, we make a stronger case to potential supporters, and we can better spread the load. In 2008, we had 32 Individual members and 47 institutional members - better but still a very small percentage of the catchment of those who should be supporting TDWG in some form. In discussing financial models, I would like to single out GBIF's support of TDWG. TDWG has a special relationship with GBIF. TDWG does have an excess of servers that can be used for infrastructure such as mentioned (thanks to TIP). These servers are housed and supported by GBIF. We GREATLY appreciate this considerable support. How does all of this relate to the LSID discussion? 1. As an Australian media personality likes to say "It is better to have people inside the tent pissing out than outside pissing in." This on two counts. A decision was made to try and implement LSIDs. A lot of work has been done toward that goal. The LSID Applicability Statement forms a foundation for general GUID use. If we decide something is better, evolution should not be a major hassle. Donald, as the Chairman of TDWG also deserves our support (will anyone else out there take on the role?). Ben Richardson has taken on the role of Review Manager of the LSID Applicability Statement. When it goes to public review (hopefully soon), do what you can to make the document a useful foundation for future developments. Please be constructive. 2. Do what you can to assist TDWG to build the membership and to spread the (considerable) load. A hybrid financial model is a foregone conclusion. Full stop. We need a substantial membership to fund infrastructure support (as has been discussed). Medium to long-term funding support from external agencies to support infrastructure is almost impossible. We also need substantial additional funding for specific projects that probably can't get done without it. Right now we are desperate for an effective tool for building/discussing/maintaining a TDWG ontology. TDWG is going to be increasingly dependent on an effective ontology. Unless I'm blind, this project should be in good position to attract special funding. LSID (or other GUID) infrastructure looks equally important. Lee Lee Belbin TDWG Secretariat

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