December 2005 - tdwg-tag - lists.tdwg.org

Re: Topic 3: GUIDs for Taxon Names and Taxon Concepts
by Roderic Page 12 Dec '05

12 Dec '05

Luckily, the "Wayback Machine" at the Internet Archive (http://web.archive.org) has a copy, which you can get here: http://web.archive.org/web/20010215174320/http:// www.environment.gov.au/marine/manuals_reports/standards/general/ chapman.html . I found this page by Googling on the title of the essay, finding what looked like the broken link you mentioned, then putting the link into the Wayback machine. This nicely illustrates the issue of digital curation, which I think this community will need to think seriously about. Regards Rod On 12 Dec 2005, at 21:59, Arthur Chapman wrote: > I agree with Rod here > > If we try and build IP rights into a GUID we will get absolutely no > where. GUIDs are meant to be machine to machine and aren't meant to > be human readable or human intelligent. There are better ways to > handle IP /Access constraints/ Conditions of Use, etc. through > Metadata (at both the Dataset level and record level if necessary), > but these shouldn't be handles through GUIDs. > > The use of Creative Commons is not inconsistent with Dublin Core, it > is not necessarily one or the other - Creative Commons can fit neatly > inside Dublin Core. > > About 10 years ago I wrote a paper on "Intellectual Property Rights in > a Digital World" that covered some of these issues. Unfortunately, it > was electronic and the Government Department that owned the web site > later decided it was not important and deleted it in a revamp of the > Web site! If anyone still has a copy, could they please send it to > me, as I no longer have a copy myself. If I can get a copy, I will > make it available as I believe it is still relevant. > > Arthur Chapman > >> From Roderic Page <r.page(a)BIO.GLA.AC.UK> on 12 Dec 2005: > >> A quick comment: >> >>> >>> 6. Would there be any social or technical roadblocks to replacing >>> these identifiers with a single identifier that was guaranteed to be >>> unique? >>> >>> Yes. We are the creators and maintainers of both nomenclatural and >>> taxonomic data. We would be unhappy about any resolution mechanism >>> that didn't acknowldge our IP in that process. For example, if the >>> LSID contained another organisation's namespace when we were the >>> originators/editors of that entity. >> >> Leaving aside the awful term "Intellectual Property" -- which should >> be >>> >> avoided like the plague (see >> http://www.gnu.org/philosophy/not-ipr.xhtml ) -- this strikes me as an >> issue handled by metadata, not the GUID itself. For example, there are >> vocabularies such as Dublin Core (http://www.dublincore.org/), or even >> better, Creative Commons (http://creativecommons.org/) which can >> handle >>> >> these issues. I'd strongly favour the later, as Creative Commons >> licenses are designed to be computer-readable, and hence can be >> handled >>> >> automatically. If a license has to be read by a human, we're shooting >> ourselves in the foot. >> >> I understand that people want credit for their hard work, but this >> shouldn't get in the way of a workable system. Imagine if everybody >> submitting a sequence to GenBank insisted on their organisation's >> namespace being in the GenBank accession number! It would be a utter >> mess. In the same way, with DOIs even the mighty Elsevier don't mind >> that the DOI has nothing that (explicitly) identifies them as the >> source. >> >> Please let us not let "Intellectual Property" get in the way of a >> sensible solution. To my mind "IP" is one of the biggest obstacles in >> the way of biodiversity informatics achieving its potential. >> >> Regards >> >> Rod >> >> >> ---------------------------------------------------------------------- >> --> >> ---------------------------------------- >> Professor Roderic D. M. Page >> Editor, Systematic Biology >> DEEB, IBLS >> Graham Kerr Building >> University of Glasgow >> Glasgow G12 8QP >> United Kingdom >> >> Phone: +44 141 330 4778 >> Fax: +44 141 330 2792 >> email: r.page(a)bio.gla.ac.uk >> web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html >> reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html >> >> Subscribe to Systematic Biology through the Society of Systematic >> Biologists Website: http://systematicbiology.org >> Search for taxon names at >> http://darwin.zoology.gla.ac.uk/~rpage/portal/ >> Find out what we know about a species at http://ispecies.org >> > > ------------------------------------------------------------------------ ---------------------------------------- Professor Roderic D. M. Page Editor, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page(a)bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org Search for taxon names at http://darwin.zoology.gla.ac.uk/~rpage/portal/ Find out what we know about a species at http://ispecies.org ___________________________________________________________ To help you stay safe and secure online, we've developed the all new Yahoo! Security Centre. http://uk.security.yahoo.com

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Re: Topic 3: GUIDs for Taxon Names and Taxon Concepts
by Roderic Page 12 Dec '05

12 Dec '05

A quick comment: > > 6. Would there be any social or technical roadblocks to replacing > these identifiers with a single identifier that was guaranteed to be > unique? > > Yes. We are the creators and maintainers of both nomenclatural and > taxonomic data. We would be unhappy about any resolution mechanism > that didn't acknowldge our IP in that process. For example, if the > LSID contained another organisation's namespace when we were the > originators/editors of that entity. Leaving aside the awful term "Intellectual Property" -- which should be avoided like the plague (see http://www.gnu.org/philosophy/not-ipr.xhtml ) -- this strikes me as an issue handled by metadata, not the GUID itself. For example, there are vocabularies such as Dublin Core (http://www.dublincore.org/), or even better, Creative Commons (http://creativecommons.org/) which can handle these issues. I'd strongly favour the later, as Creative Commons licenses are designed to be computer-readable, and hence can be handled automatically. If a license has to be read by a human, we're shooting ourselves in the foot. I understand that people want credit for their hard work, but this shouldn't get in the way of a workable system. Imagine if everybody submitting a sequence to GenBank insisted on their organisation's namespace being in the GenBank accession number! It would be a utter mess. In the same way, with DOIs even the mighty Elsevier don't mind that the DOI has nothing that (explicitly) identifies them as the source. Please let us not let "Intellectual Property" get in the way of a sensible solution. To my mind "IP" is one of the biggest obstacles in the way of biodiversity informatics achieving its potential. Regards Rod ------------------------------------------------------------------------ ---------------------------------------- Professor Roderic D. M. Page Editor, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page(a)bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org Search for taxon names at http://darwin.zoology.gla.ac.uk/~rpage/portal/ Find out what we know about a species at http://ispecies.org

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Re: Topic 3: GUIDs for Taxon Names and Taxon Concepts
by Arthur Chapman 12 Dec '05

12 Dec '05

I agree with Rod here If we try and build IP rights into a GUID we will get absolutely no where. GUIDs are meant to be machine to machine and aren't meant to be human readable or human intelligent. There are better ways to handle IP /Access constraints/ Conditions of Use, etc. through Metadata (at both the Dataset level and record level if necessary), but these shouldn't be handles through GUIDs. The use of Creative Commons is not inconsistent with Dublin Core, it is not necessarily one or the other - Creative Commons can fit neatly inside Dublin Core. About 10 years ago I wrote a paper on "Intellectual Property Rights in a Digital World" that covered some of these issues. Unfortunately, it was electronic and the Government Department that owned the web site later decided it was not important and deleted it in a revamp of the Web site! If anyone still has a copy, could they please send it to me, as I no longer have a copy myself. If I can get a copy, I will make it available as I believe it is still relevant. Arthur Chapman >>>From Roderic Page <r.page(a)BIO.GLA.AC.UK> on 12 Dec 2005: > A quick comment: > > > > > 6. Would there be any social or technical roadblocks to replacing > > these identifiers with a single identifier that was guaranteed to be > > unique? > > > > Yes. We are the creators and maintainers of both nomenclatural and > > taxonomic data. We would be unhappy about any resolution mechanism > > that didn't acknowldge our IP in that process. For example, if the > > LSID contained another organisation's namespace when we were the > > originators/editors of that entity. > > Leaving aside the awful term "Intellectual Property" -- which should be > > > avoided like the plague (see > http://www.gnu.org/philosophy/not-ipr.xhtml ) -- this strikes me as an > issue handled by metadata, not the GUID itself. For example, there are > vocabularies such as Dublin Core (http://www.dublincore.org/), or even > better, Creative Commons (http://creativecommons.org/) which can handle > > > these issues. I'd strongly favour the later, as Creative Commons > licenses are designed to be computer-readable, and hence can be handled > > > automatically. If a license has to be read by a human, we're shooting > ourselves in the foot. > > I understand that people want credit for their hard work, but this > shouldn't get in the way of a workable system. Imagine if everybody > submitting a sequence to GenBank insisted on their organisation's > namespace being in the GenBank accession number! It would be a utter > mess. In the same way, with DOIs even the mighty Elsevier don't mind > that the DOI has nothing that (explicitly) identifies them as the > source. > > Please let us not let "Intellectual Property" get in the way of a > sensible solution. To my mind "IP" is one of the biggest obstacles in > the way of biodiversity informatics achieving its potential. > > Regards > > Rod > > > ------------------------------------------------------------------------> > ---------------------------------------- > Professor Roderic D. M. Page > Editor, Systematic Biology > DEEB, IBLS > Graham Kerr Building > University of Glasgow > Glasgow G12 8QP > United Kingdom > > Phone: +44 141 330 4778 > Fax: +44 141 330 2792 > email: r.page(a)bio.gla.ac.uk > web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html > reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html > > Subscribe to Systematic Biology through the Society of Systematic > Biologists Website: http://systematicbiology.org > Search for taxon names at http://darwin.zoology.gla.ac.uk/~rpage/portal/ > Find out what we know about a species at http://ispecies.org >

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[tdwg-tapir] Schema modification: r353 - trunk/protocol/examples
by tdwg-tapir＠lists.tdwg.org 07 Dec '05

07 Dec '05

Author: javier Date: 2005-12-07 22:34:29 +0100 (Wed, 07 Dec 2005) New Revision: 353 Added: trunk/protocol/examples/capabilities_request.xml trunk/protocol/examples/capabilities_response.xml trunk/protocol/examples/inventory_request.xml trunk/protocol/examples/inventory_response.xml trunk/protocol/examples/metadata_request.xml trunk/protocol/examples/metadata_response.xml trunk/protocol/examples/ping_request.xml trunk/protocol/examples/ping_response.xml Log: Added: trunk/protocol/examples/capabilities_request.xml =================================================================== --- trunk/protocol/examples/capabilities_request.xml 2005-12-01 12:00:36 UTC (rev 352) +++ trunk/protocol/examples/capabilities_request.xml 2005-12-07 21:34:29 UTC (rev 353) @@ -0,0 +1,10 @@ +<?xml version="1.0" encoding="UTF-8"?> +<request xmlns="http://www.tdwg.org/schemas/tapir/datasource/1.0" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://www.tdwg.org/schemas/tapir/datasource/1.0 http://ww2.biocase.org/svn/tapir/trunk/protocol/tapir.xsd"> + <header> + <source accesspoint="http://url_from_client" sendtime="2005-11-11T12:23:56.023+01:00"> + </source> + </header> + <capabilities/> +</request> \ No newline at end of file Added: trunk/protocol/examples/capabilities_response.xml =================================================================== --- trunk/protocol/examples/capabilities_response.xml 2005-12-01 12:00:36 UTC (rev 352) +++ trunk/protocol/examples/capabilities_response.xml 2005-12-07 21:34:29 UTC (rev 353) @@ -0,0 +1,96 @@ +<?xml version="1.0" encoding="UTF-8"?> +<response xmlns="http://www.tdwg.org/schemas/tapir/datasource/1.0" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://www.tdwg.org/schemas/tapir/datasource/1.0 + http://ww2.biocase.org/svn/tapir/trunk/protocol/tapir.xsd"> + <header> + <source accesspoint="http://accesspoint_url" sendtime="2005-11-11T12:23:56.023+01:00"> + <software name="TAPIR_Implementation" version="1.0"/> + </source> + </header> + <capabilities> + <operations> + <ping/> + <metadata/> + <capabilities/> + <search> + <queryTemplates> + <queryTemplate location="http://url_to_querytemplate"/> + </queryTemplates> + <customOutputModels accepted="false"/> + <variables> + <environment> + <lastUpdate/> + <timestamp/> + <datasourceName/> + <date/> + <metadata/> + <accessPoint/> + <custom/> + </environment> + </variables> + </search> + </operations> + <operators> + <expression> + <concept/> + <literal/> + <parameter/> + <variable/> + <arithmetic> + <div/> + <mul/> + <add/> + <custom/> + </arithmetic> + </expression> + <boolean> + <logical> + <or/> + <not/> + <custom/> + <and/> + <custom/> + </logical> + <comparative> + <like/> + <lessThanOrEquals/> + <lessThan/> + <isNull/> + <in/> + <greaterThanOrEquals/> + <greaterThan/> + <equals/> + <custom/> + </comparative> + </boolean> + </operators> + <concepts> + <conceptNameServers> + <primaryConceptNameServer location="http://url_to_primary_concept_server"/> + <secondaryConceptNameServer location="http://url_to_secondary_concept_server"/> + </conceptNameServers> + <schema namespace="http://www.tdwg.org/schemas/abcd/1.2" + location="http://www.bgbm.org/TDWG/CODATA/Schema/ABCD-1.20.xsd"> + <mappedConcept + id="/DataSets/DataSet/DatasetDerivations/DatasetDerivation/DateSupplied" + searchable="true"/> + <mappedConcept + id="/DataSets/DataSet/DatasetDerivations/DatasetDerivation/Description" + searchable="true"/> + </schema> + <schema namespace="http://digir.net/schema/conceptual/darwin/extension/curatorial/1.0" + location="http://digir.net/schema/conceptual/darwin/extension/curatorial/1.0/curatori…"> + <mappedConcept id="/CatalogNumberNumeric" searchable="true"/> + <mappedConcept id="/IdentifiedBy" searchable="true"/> + </schema> + </concepts> + <settings> + <minQueryTermLength>2</minQueryTermLength> + <maxElementLevels>20</maxElementLevels> + <maxResponseSize>500</maxResponseSize> + <maxElementRepetitions>10</maxElementRepetitions> + <maxResponseTags>500</maxResponseTags> + </settings> + </capabilities> +</response> Added: trunk/protocol/examples/inventory_request.xml =================================================================== --- trunk/protocol/examples/inventory_request.xml 2005-12-01 12:00:36 UTC (rev 352) +++ trunk/protocol/examples/inventory_request.xml 2005-12-07 21:34:29 UTC (rev 353) @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<request xmlns="http://www.tdwg.org/schemas/tapir/datasource/1.0" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://www.tdwg.org/schemas/tapir/datasource/1.0 http://ww2.biocase.org/svn/tapir/trunk/protocol/tapir.xsd"> + <header> + <source accesspoint="http://url_from_client" sendtime="2005-11-11T12:23:56.023+01:00"> + </source> + </header> + <inventory count="false" limit="100" start="0"> + <concepts> + <concept id="http://digir.net/schema/conceptual/darwin/2003/1.0#/Country"/> + <concept id="http://digir.net/schema/conceptual/darwin/2003/1.0#/Genus"/> + </concepts> + </inventory> +</request> Added: trunk/protocol/examples/inventory_response.xml =================================================================== --- trunk/protocol/examples/inventory_response.xml 2005-12-01 12:00:36 UTC (rev 352) +++ trunk/protocol/examples/inventory_response.xml 2005-12-07 21:34:29 UTC (rev 353) @@ -0,0 +1,26 @@ +<?xml version="1.0" encoding="UTF-8"?> +<response xmlns="http://www.tdwg.org/schemas/tapir/datasource/1.0" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://www.tdwg.org/schemas/tapir/datasource/1.0 http://ww2.biocase.org/svn/tapir/trunk/protocol/tapir.xsd"> + <header> + <source accesspoint="http://accesspoint_url" sendtime="2005-11-11T12:23:56.023+01:00"> + <software name="TAPIR_Implementation" version="1.0"/> + </source> + </header> + <inventory> + <concepts> + <concept id="http://digir.net/schema/conceptual/darwin/2003/1.0#/Country"/> + <concept id="http://digir.net/schema/conceptual/darwin/2003/1.0#/Genus"/> + </concepts> + <record> + <value>AUSTRALIA</value> + <value>Calicium</value> + </record> + <record> + <value>AUSTRALIA</value> + <value>Fellhanera</value> + </record> + <summary start="1" totalReturned="2" totalMatched="15" next="3"/> + </inventory> +</response> + Added: trunk/protocol/examples/metadata_request.xml =================================================================== --- trunk/protocol/examples/metadata_request.xml 2005-12-01 12:00:36 UTC (rev 352) +++ trunk/protocol/examples/metadata_request.xml 2005-12-07 21:34:29 UTC (rev 353) @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> + +<request xmlns="http://www.tdwg.org/schemas/tapir/datasource/1.0" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://www.tdwg.org/schemas/tapir/datasource/1.0 http://ww2.biocase.org/svn/tapir/trunk/protocol/tapir.xsd"> + <header> + <source accesspoint="http://url_from_client" sendtime="2005-11-11T12:23:56.023+01:00"> + </source> + </header> + <metadata/> +</request> Added: trunk/protocol/examples/metadata_response.xml =================================================================== --- trunk/protocol/examples/metadata_response.xml 2005-12-01 12:00:36 UTC (rev 352) +++ trunk/protocol/examples/metadata_response.xml 2005-12-07 21:34:29 UTC (rev 353) @@ -0,0 +1,30 @@ +<?xml version="1.0" encoding="UTF-8"?> + +<response xmlns="http://www.tdwg.org/schemas/tapir/datasource/1.0" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://www.tdwg.org/schemas/tapir/datasource/1.0 http://ww2.biocase.org/svn/tapir/trunk/protocol/tapir.xsd"> + <header> + <source accesspoint="http://accesspoint_url" sendtime="2005-11-11T12:23:56.023+01:00"> + <software name="TAPIR_Implementation" version="1.0"/> + </source> + </header> + <metadata> + <label>Example Data Provider</label> + <accesspoint>http://accesspoint_url</accesspoint> + <relatedEntities> + <entity> + <name>TAPIR working group</name> + <contact> + <name>Frank Sinatra</name> + <email>f.sinatra(a)tapir.com</email> + <role>system administrator</role> + </contact> + <role>Hosting Provider</role> + </entity> + </relatedEntities> + </metadata> +</response> + Added: trunk/protocol/examples/ping_request.xml =================================================================== --- trunk/protocol/examples/ping_request.xml 2005-12-01 12:00:36 UTC (rev 352) +++ trunk/protocol/examples/ping_request.xml 2005-12-07 21:34:29 UTC (rev 353) @@ -0,0 +1,17 @@ +<?xml version="1.0" encoding="UTF-8"?> + +<request xmlns="http://www.tdwg.org/schemas/tapir/datasource/1.0" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://www.tdwg.org/schemas/tapir/datasource/1.0 http://ww2.biocase.org/svn/tapir/trunk/protocol/tapir.xsd"> + <header> + <source accesspoint="http://url_from_client" sendtime="2005-11-11T12:23:56.023+01:00"> + <software name="TAPIR_Implementation" version="1.0"/> + </source> + <destination>http://accesspoint_url</destination> + </header> + <ping></ping> +</request> + Added: trunk/protocol/examples/ping_response.xml =================================================================== --- trunk/protocol/examples/ping_response.xml 2005-12-01 12:00:36 UTC (rev 352) +++ trunk/protocol/examples/ping_response.xml 2005-12-07 21:34:29 UTC (rev 353) @@ -0,0 +1,13 @@ +<?xml version="1.0" encoding="UTF-8"?> + +<response xmlns="http://www.tdwg.org/schemas/tapir/datasource/1.0" + xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://www.tdwg.org/schemas/tapir/datasource/1.0 http://ww2.biocase.org/svn/tapir/trunk/protocol/tapir.xsd"> + <header> + <source accesspoint="http://accesspoint_url" sendtime="2005-11-11T12:23:57.023+01:00"></source> + </header> + <pong/> +</response> +

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Re: [tdwg-tapir] Logs from existing services
by "Döring, Markus" 07 Dec '05

07 Dec '05

Roger, I am logging full requests since a couple of weeks. They are intermixed with Species2000 requests which look quite different, but I created an archive for you to download: http://ww3.bgbm.org/tmp/requests-2005.tar.gz Enjoy, Markus -----Ursprüngliche Nachricht----- Von: tdwg-tapir-bounces(a)lists.tdwg.org [mailto:tdwg-tapir-bounces@lists.tdwg.org] Im Auftrag von Roger Hyam Gesendet: Dienstag, 6. Dezember 2005 13:49 An: tdwg-tapir(a)lists.tdwg.org Betreff: [tdwg-tapir] Logs from existing services Hi Everyone, I have mentioned this before in another context but now I am coming to the same place from a different direction. I am building scenarios and use cases for the standards architecture and it would be good to see how current standards are used. Does anyone have any logs of the kinds of queries and responses that are actually being asked of BioCase and DiGIR providers? Or can anyone suggest who I could approach to get examples of logs? Many thanks, Roger -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 ------------------------------------- _______________________________________________ tdwg-tapir mailing list tdwg-tapir(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tapir_lists.tdwg.org

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[tdwg-tapir] Logs from existing services
by Roger Hyam 07 Dec '05

07 Dec '05

Hi Everyone, I have mentioned this before in another context but now I am coming to the same place from a different direction. I am building scenarios and use cases for the standards architecture and it would be good to see how current standards are used. Does anyone have any logs of the kinds of queries and responses that are actually being asked of BioCase and DiGIR providers? Or can anyone suggest who I could approach to get examples of logs? Many thanks, Roger -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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info URI scheme
by Matt Jones 06 Dec '05

06 Dec '05

Hi, I want to bring to your attention the "info" URI scheme that I came across today. This URI is intended to be used for non-dereferenceable identifiers. I wrote up a wiki page giving some details: http://wiki.gbif.org/guidwiki/wikka.php?wakka=Info Here's a couple of example "info" URIs: info:lccn/2002022641 info:doi/10.1000.10/123456 Personally I feel that the total separation from any dereferencing scheme is a liability, but the authors of the info scheme feel that it is a strength. Just thought I would throw it into the mix for reference purposes. Interesting reading at a minimum. Matt PS Donald and Ricardo -- I couldn't add a link to the front page of the wiki as I seem to no longer have write access there. Maybe you could? -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Matt Jones Ph: 907-789-0496 jones(a)nceas.ucsb.edu SIP #: 1-747-626-7082 National Center for Ecological Analysis and Synthesis (NCEAS) UC Santa Barbara http://www.nceas.ucsb.edu/ecoinformatics ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Re: [tdwg-tapir] TaxonAPI
by "Döring, Markus" 05 Dec '05

05 Dec '05

Roger, actually the caller knows exactly the filter, cause he knows the URL pointing to the template defining the parameters. And there he can easily check what kind of operator it is - unary,binary, unbounded. Markus -----Ursprüngliche Nachricht----- Von: tdwg-tapir-bounces(a)lists.tdwg.org [mailto:tdwg-tapir-bounces@lists.tdwg.org] Im Auftrag von Roger Hyam Gesendet: Freitag, 2. Dezember 2005 16:36 An: Döring, Markus Cc: tdwg-tapir(a)lists.tdwg.org Betreff: Re: [tdwg-tapir] TaxonAPI Hi Markus, I can see that but what I don't get is how "id=tr123672&id=df678923&id=jk8912494" maps into the filter. If the filter contains a " WHERE x IN (id) " then it would be quite easy to see what to do with multiple values but if the filter contained a "WHERE x = id" then I what should the implementation do? Throw an error I guess. The caller would have to know that a parameter of a filter could be multi valued or not. I suppose this is fine because the caller has to know other stuff as well. Roger Döring, Markus wrote: > Roger, I dont think there is a problem in pasing multiple values for the same parameter name. Like for multi select boxes in html you can pass the same parameter several times with different value. Et voila, the IN operator has several arguments. > > For example: > http://short.com/TapirLite.cgi?op=search&id=tr123672&id=df678923&id=jk > 8912494 > > markus > > > -----Ursprüngliche Nachricht----- > Von: Roger Hyam [mailto:roger@tdwg.org] > Gesendet: Donnerstag, 1. Dezember 2005 15:11 > An: Döring, Markus > Cc: Renato De Giovanni; tdwg-tapir(a)lists.tdwg.org > Betreff: Re: [tdwg-tapir] TaxonAPI > > > The place where we need to pass the array of string is in passing a set of IDs to retrieve multiple objects so there is no need for a likeAny operator I don't think. An In operator does the job. What is difficult is how we pass in the values in a URL. Perhaps there should be a requirement for multiple occurrences of the same parameter to be concatenated together in some useful ways - to build and IN. > > Parameters other than the IDs for these calls are just ANDed together. > > When I stipulates the passing of an array like that it was because I envisaged a client crawling a resource. The client would typically retrieve an object (or objects) then want to get a set of related objects. Being able to pass a list saves making multiple calls. > > It may be kinder to the publisher to only get one object by id at a time. It would be easier to implement and would entail less work per call but more calls. > > Simplicity would dictate change the API not to have arrays like this. > > I'll have a think about it next time I look at the API. It may be easier to change the API than Tapir but I am not clear how one would pass a list of parameters to a Tapir IN at the moment anyhow. > > Roger > > > > Döring, Markus wrote: > > Renato & Roger, > would it make sense to have a new unbound "likeAny" operator that works like an IN but does a like instead of an equals behind the scenes? > > Then you could just pass an array of string arguments for like or equal comparisons just with the same GET paramter name. E.g. > TapirLite.cgi?op=search&name=Abies*&name=Pinus*&name=Picea* > > Markus > > > -----Ursprüngliche Nachricht----- > Von: tdwg-tapir-bounces(a)lists.tdwg.org [mailto:tdwg-tapir-bounces@lists.tdwg.org] Im Auftrag von Renato De Giovanni > Gesendet: Mittwoch, 30. November 2005 17:54 > An: tdwg-tapir(a)lists.tdwg.org > Betreff: Re: [tdwg-tapir] TaxonAPI > > Hi Roger, > > I looked at the API and apparently it seems to be consistent with the TapirLite idea, although there are still lots of things that I still need to learn about the TCS world. > > The only thing is that you frequently define parameter types as "Array of Strings", and we don't have that notion in the protocol. > As far as I know, the only way to do this with the current parameterised Tapir filters is to limit the parameter to a single string value (and then make several requests), or define a filter with several conditions referencing different string parameters (like name1, name2, etc) all joined by ORs. > > Another possibility would be to change the "in" operator and make it accept not only literal values but also a parameter that could be expanded according to the number of associated values. It looks more elegant but needs a small change in the protocol (and additional notes in the specification). > > Regards, > -- > Renato > > On 28 Nov 2005 at 10:54, Roger Hyam wrote: > > > > Hi Everyone, > > I have been doing some work on a TaxonAPI. This is a high/low > definition of the kind of thing I believe people publishing taxonomic > data need to produce and people consuming it need to eat based on the > work I have been involved in on TCS. > > It is framed as if it were a web service type of thing but I imagine > that each of the method calls mentioned could equate to a Tapir > template of some kind. I imagine a template containing a parameterized > filter (not sure if those exist anymore). > > This is still work in progress as I need to define the list of > parameters more closely and sort the greater than/less than issue for > dates and a few other bits. Plus no one has seen it to comment on! > > You can read more about it here: > > http://www.tdwg.hyam.net/twiki/bin/view/TIP/TaxonAPI > > I would be most grateful for your comments. > > How does this fit with Tapir? > > Roger > > > > > _______________________________________________ > tdwg-tapir mailing list > tdwg-tapir(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tapir_lists.tdwg.org > > > _______________________________________________ > tdwg-tapir mailing list > tdwg-tapir(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tapir_lists.tdwg.org > > > > > > -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 ------------------------------------- _______________________________________________ tdwg-tapir mailing list tdwg-tapir(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tapir_lists.tdwg.org

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Re: Two Scenarios
by Peter Dawyndt 03 Dec '05

03 Dec '05

Dear Arthur, tracing the transfer of biological specimen among collections on different locations and - by extension - tracking all the downstream information that has been collected on a given specimen by different people provides many scenarios that can be neatly resolved by using a solid UID/ontology framework. Here's a use-case that shows you some examples in the microbial domain (among others) that comes pretty close to the two scenarios that you were drawing Over 500 collections around the world (bacteria, archaea, filamentous fungi, yeast) have been registered at the World Data Centre for Microorganisms (http://lmg.ugent.be/~pdawyndt/maps/world_collections.html), which is the data center of the World Federation of Culture Collections. The StrainInfo.net portal system (http://www.straininfo.net) enables simple navigation through all collections from a single entry point (access to the portal is currently restricted, use 'guest' as login and 'straininfo' as password). For each specimen (eg. try "LMG 6923", a bacterial specimen), the portal system offers the following services to the user: 1. a list of cultures of the same specimen in other collections around the world. Multiple resolution is provided to the related entry in the online catalogs of the culture collections, providing further background information on the specimen 2. a complete history of the specimen, showing its transfer among different collections ever since its original isolation (http://lmg.ugent.be/~pdawyndt/maps/history.pdf) 3. a list of sequences in EMBL/GenBank/DDBJ. Remark that the public sequence databases score poorly in their support of searching sequences for a given specimen 4. a list of literature references of studies that use the given specimen 5. geographic distribution of the collections where the given specimen can be ordered All these services and the information system that goes behind the StrainInfo.net portal strongly build on unique identifiers and a extensive network of object-relationships. To keep pace with updated information sources, the information system perpetually finds new objects (and automatically assigns unique identifiers to them if they are not in place; i.e. accumulative learning) and discovers all sorts relationships between these objects (built on top of the unique identifiers). This requires an expert system that is tightly coupled to an extensible domain-related ontology (what is what, and how should it be recognized in the light of synonymy, homology, syntactical variation). The good thing is that all of this complexity remains pretty much hidden for the end-user. Hopefully, this sketches somewhat the possibilities of the GUID/ontology frameworks that are envisioned in this mailing list Cheers, Peter Further reading: Dawyndt P, Vancanneyt M, De Meyer H, Swings J. Knowledge Accumulation and Resolution of Data Inconsistencies during the Integration of Microbial Information Sources. IEEE Transactions on Knowledge and Data Engineering, 17(8), pp. 1111-1126, 2005. Romano P, Dawyndt P, Piersigilli F, Swings J. Improving interoperability between microbial information and sequence databases. BMC Bioinformaticsi, 6(4), S23, 2005. doi:10.1186/1471-2105-6-S4-S23. ----------------------------------------------------------- Dr. Peter Dawyndt Laboratory of Microbiology Ghent University Ledeganckstraat 35 B-9000 Gent, Belgie Tel.: (32)9.264.51.32 Fax.: (32)9.264.50.92 KERMIT -- Research Unit "Knowledge-based Systems" Ghent University Coupure links 653 B-9000 Gent, Belgie Tel.: (32)9.264.60.18 Email: Peter.Dawyndt(a)UGent.be -----------------------------------------------------------

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Re: [tdwg-tapir] TaxonAPI
by "Döring, Markus" 02 Dec '05

02 Dec '05

Roger, I dont think there is a problem in pasing multiple values for the same parameter name. Like for multi select boxes in html you can pass the same parameter several times with different value. Et voila, the IN operator has several arguments. For example: http://short.com/TapirLite.cgi?op=search&id=tr123672&id=df678923&id=jk89124… markus -----Ursprüngliche Nachricht----- Von: Roger Hyam [mailto:roger@tdwg.org] Gesendet: Donnerstag, 1. Dezember 2005 15:11 An: Döring, Markus Cc: Renato De Giovanni; tdwg-tapir(a)lists.tdwg.org Betreff: Re: [tdwg-tapir] TaxonAPI The place where we need to pass the array of string is in passing a set of IDs to retrieve multiple objects so there is no need for a likeAny operator I don't think. An In operator does the job. What is difficult is how we pass in the values in a URL. Perhaps there should be a requirement for multiple occurrences of the same parameter to be concatenated together in some useful ways - to build and IN. Parameters other than the IDs for these calls are just ANDed together. When I stipulates the passing of an array like that it was because I envisaged a client crawling a resource. The client would typically retrieve an object (or objects) then want to get a set of related objects. Being able to pass a list saves making multiple calls. It may be kinder to the publisher to only get one object by id at a time. It would be easier to implement and would entail less work per call but more calls. Simplicity would dictate change the API not to have arrays like this. I'll have a think about it next time I look at the API. It may be easier to change the API than Tapir but I am not clear how one would pass a list of parameters to a Tapir IN at the moment anyhow. Roger Döring, Markus wrote: Renato & Roger, would it make sense to have a new unbound "likeAny" operator that works like an IN but does a like instead of an equals behind the scenes? Then you could just pass an array of string arguments for like or equal comparisons just with the same GET paramter name. E.g. TapirLite.cgi?op=search&name=Abies*&name=Pinus*&name=Picea* Markus -----Ursprüngliche Nachricht----- Von: tdwg-tapir-bounces(a)lists.tdwg.org [mailto:tdwg-tapir-bounces@lists.tdwg.org] Im Auftrag von Renato De Giovanni Gesendet: Mittwoch, 30. November 2005 17:54 An: tdwg-tapir(a)lists.tdwg.org Betreff: Re: [tdwg-tapir] TaxonAPI Hi Roger, I looked at the API and apparently it seems to be consistent with the TapirLite idea, although there are still lots of things that I still need to learn about the TCS world. The only thing is that you frequently define parameter types as "Array of Strings", and we don't have that notion in the protocol. As far as I know, the only way to do this with the current parameterised Tapir filters is to limit the parameter to a single string value (and then make several requests), or define a filter with several conditions referencing different string parameters (like name1, name2, etc) all joined by ORs. Another possibility would be to change the "in" operator and make it accept not only literal values but also a parameter that could be expanded according to the number of associated values. It looks more elegant but needs a small change in the protocol (and additional notes in the specification). Regards, -- Renato On 28 Nov 2005 at 10:54, Roger Hyam wrote: Hi Everyone, I have been doing some work on a TaxonAPI. This is a high/low definition of the kind of thing I believe people publishing taxonomic data need to produce and people consuming it need to eat based on the work I have been involved in on TCS. It is framed as if it were a web service type of thing but I imagine that each of the method calls mentioned could equate to a Tapir template of some kind. I imagine a template containing a parameterized filter (not sure if those exist anymore). This is still work in progress as I need to define the list of parameters more closely and sort the greater than/less than issue for dates and a few other bits. Plus no one has seen it to comment on! You can read more about it here: http://www.tdwg.hyam.net/twiki/bin/view/TIP/TaxonAPI I would be most grateful for your comments. How does this fit with Tapir? Roger _______________________________________________ tdwg-tapir mailing list tdwg-tapir(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tapir_lists.tdwg.org _______________________________________________ tdwg-tapir mailing list tdwg-tapir(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-tapir_lists.tdwg.org -- ============================================== Roger Hyam ---------------------------------------------- Biodiversity Informatics Independent Web Development ---------------------------------------------- http://www.hyam.net roger(a)hyam.net ---------------------------------------------- 2 Janefield Rise, Lauder, TD2 6SP, UK. T: +44 (0)1578 722782 M: +44 (0)7890 341847 ==============================================

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