[tdwg-tag] [Lgtg] Re LSID-GUID

Tue Nov 17 03:46:43 CET 2009

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
------------------------------------------------------------
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