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 ------------------------------------------------------------
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 Kevins 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@lists.gbif.org [mailto:lgtg-bounces@lists.gbif.org] On Behalf Of Peter DeVries Sent: 15 November 2009 02:40 To: Technical Architecture Group mailing list; lgtg@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 ------------------------------------------------------------
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@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@lists.gbif.org [mailto:lgtg-bounces@lists.gbif.org] *On Behalf Of *Peter DeVries *Sent:* 15 November 2009 02:40 *To:* Technical Architecture Group mailing list; lgtg@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
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@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@lists.gbif.org [mailto:lgtg- bounces@lists.gbif.org] On Behalf Of Peter DeVries Sent: 15 November 2009 02:40 To: Technical Architecture Group mailing list; lgtg@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@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@bio.gla.ac.uk Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rodpage1962@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
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@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@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@lists.gbif.org [mailto:lgtg-bounces@lists.gbif.org] *On Behalf Of *Peter DeVries *Sent:* 15 November 2009 02:40 *To:* Technical Architecture Group mailing list; lgtg@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@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@bio.gla.ac.uk Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rodpage1962@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
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@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@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@lists.gbif.org [mailto:lgtg- bounces@lists.gbif.org] On Behalf Of Peter DeVries Sent: 15 November 2009 02:40 To: Technical Architecture Group mailing list; lgtg@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
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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@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@bio.gla.ac.uk Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rodpage1962@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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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@bio.gla.ac.uk Tel: +44 141 330 4778 Fax: +44 141 330 2792 AIM: rodpage1962@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
Dear Rod,
1) At various times you have either dismissed the linked data approach or advocated it.
2) You dismiss my efforts based on your lack of faith in the linked data approach.
3) You later dismiss my efforts because I am not a "major player".
4) Then you advocate a linked data approach and a propose something which is nearly identical to what I have.
5) You have made a number of spurious criticisms of other initiatives which don't hold up under scrutiny, expecially when compared to your alternatives.
6) When an initiative make efforts to address your criticisms, you don't acknowledge the change, you simply criticize them for something else.
7) You are either unaware of your changing positions and spuriousness of your criticisms or you are aware and your comments are part of some sort of strategy.
I may be jumping to conclusions about your motivations, but these are the kinds of techniques others have used to instill "fear, uncertaintly, and doubt" among competing alternatives.
A motivation that is not based on what is in the best interest of the community as a whole.
Respectfully,
- Pete
participants (3)
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Peter DeVries -
Roderic Page -
Éamonn Ó Tuama