Re: [tdwg-tag] SourceForge LSID project websites broken - role for TDWG?
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@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@lists.tdwg.org [mailto:tdwg-tag-bounces@lists.tdwg.org] On Behalf Of tdwg-tag-request@lists.tdwg.org Sent: 11 April 2009 12:00 To: tdwg-tag@lists.tdwg.org Subject: tdwg-tag Digest, Vol 36, Issue 17
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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@mac.com Subject: [tdwg-tag] FYI: SharedNames To: Technical Architecture Group mailing list tdwg-tag@lists.tdwg.org Message-ID: 690607AB-627E-4B9B-8168-4C412F81FE68@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@netspace.net.au Subject: Re: [tdwg-tag] SourceForge LSID project websites broken - role for TDWG? To: "'Roderic Page'" r.page@bio.gla.ac.uk Cc: 'Technical Architecture Group mailing list' tdwg-tag@lists.tdwg.org Message-ID: 002101c9ba38$8e3c2110$aab46330$@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@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
------------------------------
_______________________________________________ tdwg-tag mailing list tdwg-tag@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tag
End of tdwg-tag Digest, Vol 36, Issue 17 ****************************************
OK, here's what I think GBIF (or somebody, anybody) should do. Set up a proxy that handles ANY GUID, and add services such as those http://bit.ly have (e.g., http://bit.ly/info/3R6apo ). Wouldn't this be cool! Think about it, we get resolvable apps plus potentially the killer app for biodiversity informatics in one.
Rod
On 15 Apr 2009, at 09:58, Eamonn O Tuama (GBIF) wrote:
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@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@lists.tdwg.org [mailto:tdwg-tag-bounces@lists.tdwg.org] On Behalf Of tdwg-tag-request@lists.tdwg.org Sent: 11 April 2009 12:00 To: tdwg-tag@lists.tdwg.org Subject: tdwg-tag Digest, Vol 36, Issue 17
Send tdwg-tag mailing list submissions to tdwg-tag@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@lists.tdwg.org
You can reach the person managing the list at tdwg-tag-owner@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:
- FYI: SharedNames (Roger Hyam)
- 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@mac.com Subject: [tdwg-tag] FYI: SharedNames To: Technical Architecture Group mailing list tdwg-tag@lists.tdwg.org Message-ID: 690607AB-627E-4B9B-8168-4C412F81FE68@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@netspace.net.au Subject: Re: [tdwg-tag] SourceForge LSID project websites broken - role for TDWG? To: "'Roderic Page'" r.page@bio.gla.ac.uk Cc: 'Technical Architecture Group mailing list' tdwg-tag@lists.tdwg.org Message-ID: 002101c9ba38$8e3c2110$aab46330$@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@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
tdwg-tag mailing list tdwg-tag@lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tag
End of tdwg-tag Digest, Vol 36, Issue 17
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
I've put a preprint of a manuscript entitled "bioGUID: resolving, discovering, and minting identifiers for biodiversity informatics" online at Nature Precedings: http://hdl.handle.net/10101/npre.2009.3079.1
The manuscript covers some of the issues discussed in this thread.
Irony alert:
1. The manuscript has a handle (hdl:10101/npre.2009.3079.1) as it's GUID
2. As I write, http://precedings.nature.com is down
Regards
Rod
--------------------------------------------------------- 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
participants (2)
-
Eamonn O Tuama (GBIF) -
Roderic Page