[tdwg-tag] [Lgtg] Re LSID-GUID
Roderic Page
r.page at bio.gla.ac.uk
Tue Nov 17 09:36:07 CET 2009
Dear Pete,
I pretty much said all I want to say in my previous email. I'm also
conscious that members of the TDWG-TAG and LSID-GUID mailing lists
probably don't need their inboxes being filled up with this
discussion. I feel it's best to agree to disagree and move on.
Regards
Rod
On 17 Nov 2009, at 02:46, Peter DeVries wrote:
> Dear Rod,
>
> I am confused. You seem to be expressing the same arguments against
> and deep skepticism about the Linked Data approach that you did when
> I was advocating it nearly a year ago.
>
> So do you an advocate it or not?
>
> I started the GeoSpecies project (originally GeoBug) because their
> was no identifier system for a species as opposed to a name. Many at
> the time argued that the name is the species concept and some still
> seem to. The NCBI taxon ID's only work for those species for which
> sequences were available.
>
> I had been requesting something like this from TDWG since 2006.
> There is also a good paper that talks about some of these issues by
> Kennedy,
>
> but there was no usable identifier system for a species as opposed
> to a particular name. Numerous people on tdwg and taxocom argued
> that there was no need for one.
>
> There was also nothing available that followed linked data principles.
>
> I am sure that BioRDF would contain the metadata that you would like
> but it is not readily available. I have mapped most of my
> identifiers by hand.
>
> You have argued that you needed to convince the GBIF and EOL people
> about the merits of linked data but I have been in discussions with
> them for a long time about this and they are familiar with linked
> data and have expressed interest. If their is any reluctance, it
> seems to be about whether or not they want to really expose their
> data.
>
> I have been in discussions with EOL and GBIF personnel about ways to
> do this via meetings, email and twitter.
>
> Of course the GeoSpecies project is incomplete and imperfect. When I
> first started I was encouraged by the linked data community to add
> more taxa improve the hierarchy. I post a new version members of the
> linked data community look at it, discover mistakes and make
> suggestions. Somethings I am able to fix easily some things have to
> wait until I have time for a periodic fundamental
> rewrite of the application. In effect, it functions as a test bed to
> see how to best represent this kind of information as linked data.
>
> Unlike the linked data community you seem to waffle between
> dismissing the entire idea of linked data or dismissing my efforts
> as not being that of a major player. The merits of a particular
> conceptualization is intrinsic to itself, not dependent on the
> status or size of the conceptualizer. What seems to be completely
> absent from your efforts is any real attempt to see where a
> particular version succeeds or fails or any kind of constructive
> criticism.
>
> Did you make the Bio2RDF group aware of the deficiencies that you
> found in their project?
>
> By your standard we would have had to develop multiple perfect 4D
> microscopes, or been some "major player" who created software and
> techniques for multiple labeled confocal images for our efforts to
> have been meaningful,
>
> You also tout several off your services as the solution to bridging
> linked data and LSIDs, but the real world experience is that they do
> not work.
>
> They have just as many real world problems as many of the efforts
> you criticize.
>
> I was somewhat confused about the meeting. How many North American
> TDWG members are their and how many people were nominated by these
> TDWG members?
>
> In summary, over the last year and in your most recent note you seem
> to dismiss my efforts 1) because you don't have faith in linked data
> or 2) because I am not a "major player".
>
> These arguments are both inconsistent and spurious.
>
> The fact is what you proposed to do already exists in GeoSpecies,
> what is missing are resources to link to at GBIF and the EOL. There
> were already discussions on how GBIF and EOL might expose at least
> some of their data to the LOD and plans to integrate GeoSpecies like
> functionality into the GNA.
>
> Had I not already had experience with your numerous spurious
> dismissals of projects in development including the EOL, Bio2RDF and
> GeoSpecies I would have interpreted recent events as a fluke rather
> than a pattern.
>
> What is it about the need to oversell your own solutions while
> denigrating the efforts of others?
>
> - Pete
>
>
>
>
>
>
>
>
>
> On Mon, Nov 16, 2009 at 4:50 PM, Roderic Page <r.page at bio.gla.ac.uk>
> wrote:
> Dear Peter,
>
> I feel your latest email needs a response.
>
> I drew the diagram that appeared in the report (http://iphylo.blogspot.com/2009/08/gbif-and-linked-data.html
> ) that showed how GBIF data could relate to other major players in
> this area, specifically ones around the table at the time, or people
> who had been involved in the LSID discussions. That was the focus. I
> didn't include all potential or actual linked data providers. Some
> of these I regard as poorly developed. For example, http://
> bio2rdf.org is focussed (like most genomic RDF efforts) on proteins,
> and doesn't include any metadata about sequence sources (country,
> voucher, specimen, host) that would be central to efforts to link
> GBIF to GenBank. Until bio2rdf deals with this it seems of little
> direct relevance.
>
> Your geospecies work is another example of linked data, and in
> hindsight it's a pity that mention of geospecies dropped out of the
> report (a lot of stuff got dropped). However, I regard geospecies in
> much the same way as bio2rdf, an incomplete demonstration of what
> can be done. The real target of my diagram was the primary data
> providers, such as GBIF, IPNI, IndexFungorum, etc. Anybody can put
> RDF wrappers around existing databases (and generate a whole new
> series of URIs for those entities), and LOD is full of this (one
> could make a case that the LOD approach will fail in part because of
> this problem). What I'd like to see is the data providers themselves
> assume responsibility for providing this data. Ironically, for all
> their idiosyncrasies, LSIDs have played a part in this, as we now
> have native RDF being served by several key databases (albeit poorly
> linked).
>
> I wasn't responsible for the other part of the report you complain
> about, which concerned ambiguity of taxonomic names. However, you're
> going to have a hard time convincing anybody that the notion of a
> stable, unique identifier for a concept is original with you. This
> is precisely the model used by the NCBI taxonomic database, where
> Taxon IDs are stable even if the name changes.
>
> On a more personal note, I really take exception to the notion that
> somehow I've co-opted your ideas as my own, and that I'm engaged in
> an attempt "to create a paper trail that makes the proposal look
> like their own". I (and quite a few others) have been talking about
> the general problem of linking together biodiversity data for
> several years now. There's much vigourous discussion about ways to
> do this, some behind closed doors in workshops (some I've been at,
> many I've not), some very publicly (e.g., in blog comments). I've
> discussed this topic in papers from 2005 onwards, and numerous blog
> posts on http://iphylo.blogspot.com, as well as the defunct blogs http://semant.blogspot.com/
> and http://bioguid.blogspot.com/ . Pretty much everything I do,
> warts and all, is there for people to see. Furthermore, I'm actually
> rather sceptical that linked data approaches will work as well as
> people hope (see http://www.betaversion.org/~stefano/linotype/news/304/
> and http://www.betaversion.org/~stefano/linotype/news/351/ for some
> reasons ).
>
> You seem to feel that your efforts aren't given enough credit.
> Whatever the merits of that perception, attacking me isn't going to
> help. We've both got much better things to do with our time.
>
> Regards
>
> Rod
>
>
> On 16 Nov 2009, at 20:21, Peter DeVries wrote:
>
>> Dear Éamonn,
>>
>>
>> My goal of including the text about my ability to attend the LSID-
>> GUID task group was simply to address the earlier assertion that
>> the meeting
>> was open to anyone.
>>
>>
>> It my understanding that although I was nominated by one of the US
>> reps, I did not realize until after the fact that I was supposed to
>> send in
>> my C.V.. So part of this confusion was the result of an error on my
>> part.
>>
>>
>> You were kind enough to send me the pre-meeting documents which I
>> looked over. At the time it seemed that the goal of the meeting was
>> to coordinate and promote the use of LSID's. Also I noted that the
>> document did mention my work (see below). So I preceded,
>> unconcerned since what was proposed was only nominally related to
>> what I have been proposing at a number of talks and email
>> discussions, and it even mentioned my work.
>>
>> "Among the resources of obvious relevance to biodiversity are
>> DBpedia, PubMed, geonames, geospecies, and the RDF Book Mashup.
>>
>> "
>>
>>
>> When I saw the draft proposal it appeared as if the goals of the
>> meeting had changed since the original documents distributed a few
>> weeks before.
>>
>> What Rod Page was now advocating was almost identical to what I had
>> been advocating for over the last year. A proposal that I had
>> thought was going to be incorporated into the GNA. It also mirrored
>> what I had been doing with the GeoSpecies and TaxonConcept
>> projects, which are mentioned on the TDWG site as examples of the
>> TDWG vocabulary.
>>
>> So not only did mention of my work disappear in the next draft
>> revision, Rod Page appeared to be representing my proposal as his
>> own.
>>
>> Since this was already positioned to be part of the EOL-GBIF GNA, I
>> can't see any reason for them to be concerned about turf. As far as
>> I was concerned there had been several discussions about
>> incorporating my work into the GNA and that appears to be moving
>> forward.
>>
>> I can see how one person might be trying to create a paper trail
>> that makes the proposal look like their own. A pattern which I have
>> seen several times before and is well documented in the history of
>> science.
>>
>> I think the whole reason I was nominated for this group was because
>> of my existing work and proposals so it is strange that there is no
>> mention of it in the post meeting draft.
>>
>> Since it was already planned to be incorporated in the GNA, why
>> wouldn't it have been mentioned?
>>
>> Respectfully,
>>
>> - Pete
>>
>>
>>
>> On Mon, Nov 16, 2009 at 2:23 AM, Éamonn Ó Tuama <eotuama at gbif.org>
>> wrote:
>> Dear Peter,
>>
>>
>> The call to participate in the LGTG was open to everyone but,
>> unfortunately, for reasons already given to you and because of the
>> need to limit numbers to create a functional and effective work
>> group, and to be able to cover travel costs, the maximum number
>> that could actually participate in the workshop was limited. We
>> sought to get the inputs of those individuals who expressed
>> interest but were not selected for the core task group through
>> comments on drafts of the report and all your emails, along with
>> those from others, were shared with the group. There was no intent
>> to exclude any significant work – the final report was not meant to
>> be an exhaustive literature review of the current state of the
>> field – it needed to be kept concise – but I support Kevin’s
>> response (attached) and would be happy to see a reference to
>> GeoSpecies in the linked data section.
>>
>>
>> I think there will be plenty of opportunities for your
>> contributions as we move forward. The plan is to create a web site
>> for the report with facility to comment and suggest additional
>> materials. Expansion on some of the briefly mentioned use cases in
>> the report is one area, for example, that needs amplification.
>>
>>
>> Best regards,
>>
>>
>> Éamonn
>>
>>
>>
>> From: lgtg-bounces at lists.gbif.org [mailto:lgtg-
>> bounces at lists.gbif.org] On Behalf Of Peter DeVries
>> Sent: 15 November 2009 02:40
>> To: Technical Architecture Group mailing list; lgtg at lists.gbif.org
>> Subject: [Lgtg] Re LSID-GUID
>>
>>
>> I also thought I would also address this statement about the LSID-
>> GUID meeting
>>
>>
>> > The invitation to the LGTG workshop was open to everyone.
>>
>>
>> "Thank you for your expression of interest in participating in the
>> GBIF LSID-GUID Task Group. Due to the need to have a mix of skills/
>> experience and to try to maintain a geographical spread
>> (difficult), it did not prove possible to include you in the core
>> group (North America was over-represented in the nominations)"
>>
>>
>> I have no animosity toward GBIF for this, I have just become
>> increasingly concerned about a growing paper trail that is
>> amazingly similar to my own proposals but fails to mention my work.
>>
>>
>> It seems strange to me that of all the people involved in TDWG and
>> Linked Data discussions over the last year my efforts seem to be
>> being positioned as "invisible".
>>
>>
>> - Pete
>>
>>
>>
>>
>> ----------------------------------------------------------------
>> Pete DeVries
>> Department of Entomology
>> University of Wisconsin - Madison
>> 445 Russell Laboratories
>> 1630 Linden Drive
>> Madison, WI 53706
>> GeoSpecies Knowledge Base
>> About the GeoSpecies Knowledge Base
>> ------------------------------------------------------------
>>
>>
>>
>>
>> --
>> ----------------------------------------------------------------
>> Pete DeVries
>> Department of Entomology
>> University of Wisconsin - Madison
>> 445 Russell Laboratories
>> 1630 Linden Drive
>> Madison, WI 53706
>> GeoSpecies Knowledge Base
>> About the GeoSpecies Knowledge Base
>> ------------------------------------------------------------
>> _______________________________________________
>> tdwg-tag mailing list
>> tdwg-tag at lists.tdwg.org
>> http://lists.tdwg.org/mailman/listinfo/tdwg-tag
>
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> DEEB, FBLS
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QQ, UK
>
> Email: r.page at bio.gla.ac.uk
> Tel: +44 141 330 4778
> Fax: +44 141 330 2792
> AIM: rodpage1962 at 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
>
>
>
>
>
>
>
>
>
> --
> ----------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> GeoSpecies Knowledge Base
> About the GeoSpecies Knowledge Base
> ------------------------------------------------------------
---------------------------------------------------------
Roderic Page
Professor of Taxonomy
DEEB, FBLS
Graham Kerr Building
University of Glasgow
Glasgow G12 8QQ, UK
Email: r.page at bio.gla.ac.uk
Tel: +44 141 330 4778
Fax: +44 141 330 2792
AIM: rodpage1962 at 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
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