[tdwg-content] A plea around basisOfRecord (Was: Proposed new Darwin Core terms - abundance, abundanceAsPercent)
Steve Baskauf
steve.baskauf at vanderbilt.edu
Tue Oct 15 15:55:25 CEST 2013
Donald,
With respect to your second paragraph, the proposed Darwin Core RDF
Guide [1] purposefully avoids getting entangled in issues of defining
exactly what the Darwin Core classes are and how they are related to
each other. To put it in other words, it does not define object
properties connecting the main Darwin Core classes. The guide restricts
itself to spelling out how users can express Darwin Core properties from
the main vocabulary as RDF in a consistent way.
Creating properties to describe the normalized relationships is an
important task, but is left to another layer that could be built on top
of the Guide and which requires additional consensus building as to how
those relationships should be modeled. Alternatively, there could be
several models and procedures could be established for converting from
one to the other. But the guide stays out of this and sticks with the
basics (as you say, avoids getting distracted).
Steve
[1] http://code.google.com/p/tdwg-rdf/wiki/DwcRdf
Donald Hobern [GBIF] wrote:
>
> Thanks, Steve.
>
>
>
> Taking this back to the concerns, I raised at the beginning, I think
> my concern can best be expressed by the fact that the rdf:type for
> many published records is not easily defined (or at least leads to
> arguments about whether some of the available data elements can
> properly apply to an object of that class). I think the majority of
> our records are best seen as a denormalised view of a join between
> instances of different classes rather than as an instance of a class.
>
>
>
> Your comments in your other messages about on-going TDWG work on
> ontologies are much appreciated. I would like to see that work
> carrying through to accepted recommendations and for the main Darwin
> Core vocabulary for the time being not to get distracted by whether
> the associated records are Events, Occurrences, MaterialSamples or
> whatever.
>
>
>
> Thanks again.
>
>
> Donald
>
>
>
> ----------------------------------------------------------------------
>
> Donald Hobern - GBIF Director - dhobern at gbif.org
> <mailto:dhobern at gbif.org>
>
> Global Biodiversity Information Facility http://www.gbif.org/
>
> GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
>
> Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480
>
> ----------------------------------------------------------------------
>
>
>
> *From:* Steve Baskauf [mailto:steve.baskauf at vanderbilt.edu]
> *Sent:* Monday, October 14, 2013 12:45 AM
> *To:* Donald Hobern [GBIF]
> *Cc:* 'Richard Pyle'; 'TDWG Content Mailing List'; 'Chuck Miller'
> *Subject:* Re: [tdwg-content] A plea around basisOfRecord (Was:
> Proposed new Darwin Core terms - abundance, abundanceAsPercent)
>
>
>
> Donald,
>
> With regards to the uncertainty about the meaning of
> dwc:basisOfRecord, the proposed Darwin Core RDF Guide attempts to
> inject clarity into the situation. It does so in two ways:
>
> 1. It allows dwc:basisOfRecord to be used with literal (text) values
> to allow existing implementations to expose whatever values they
> currently have for that term. However, it specifies that rdf:type
> should be used exclusively as the property for specifying
> URI-reference values intended to indicate the type of the subject
> resource. [1] There is some ambiguity about what the subject is of a
> dwc:basisOrRecord property (the resource, or the record about the
> resource?). However, there is no similar ambiguity about rdf:type
> which always serves to indicate the class of which the subject
> resource is an instance.
>
> 2. It specifies that classes in the Darwin Core Type vocabulary
> namespace (dwctype: = http://rs.tdwg.org/dwc/dwctype/ ) should be used
> for typing resources in the biodiversity domain rather than any
> corresponding classes in the main Darwin Core namespace (dwc: =
> http://rs.tdwg.org/dwc/terms/ ). [2] In other words, if given the
> choice between dwc:Occurrence and dwctype:Occurrence, use
> dwctype:Occurrence. The guide proposes to add to the type vocabulary
> any classes which exist in the dwc: namespace and not in the dwctype:
> namespace (e.g. dwc:Identification). The intention is that the DwC
> type vocabulary would be what it's name suggests: the vocabulary for
> describing types. There are some issues involving the current
> definitions in the type vocabulary, which I won't go into in this
> email. As Rich said earlier, this is a topic for one of the
> Documenting Darwin Core sessions at the meeting.
>
> Although these guidelines would hold force specifically for RDF
> implementations, this is a convention that could be followed in other
> implementations.
>
> Steve
>
> [1]
> http://code.google.com/p/tdwg-rdf/wiki/DwcRdfGuideProposal#2.3.1.4_Other_predicates_used_to_indicate_type
> [2]
> http://code.google.com/p/tdwg-rdf/wiki/DwcRdfGuideProposal#2.3.1.5_Classes_to_be_used_for_type_declarations_of_resources_de
>
> Donald Hobern [GBIF] wrote:
>
> Thanks, Rich.
>
>
>
> Very pleased to see this. With this encouragement, I'll say just a
> little bit more about why I think this is a critical need.
>
>
>
> I see the model I describe as the perfect real-world realisation of
> most of the key components in the GBIO Framework
> (http://www.biodiversityinformatics.org/), as follows:
>
>
>
> Everyone zips up whatever data they have from each resource
> (databases, field instruments, sequencers, data extracted from
> literature, checklists, whatever) into a DwC Archive using whatever
> DwC elements they can for data elements and describing other elements
> not currently recognised in DwC (the GBIO DATA layer)
>
> These archives should be placed in repositories that offer basic
> services (DOIs, annotation services, etc.) (the GBIO CULTURE layer)
>
> Harvesters assess the contents of each archive and determine what
> views can be supported from the supplied elements (occurrence records
> for GBIF, name usage records, species interactions, etc.) and
> catalogue these views in relevant discovery indexes (GBIF, Catalogue
> of Life, TraitBank, etc.) (the GBIO EVIDENCE layer)
>
> Users can at any time annotate elements in the archives to provide
> mappings for (potentially more recently defined) DwC or other
> properties, opening up new options for reuse
>
>
>
> Donald
>
>
>
> ----------------------------------------------------------------------
>
> Donald Hobern - GBIF Director - dhobern at gbif.org
> <mailto:dhobern at gbif.org>
>
> Global Biodiversity Information Facility http://www.gbif.org/
>
> GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
>
> Tel: +45 3532 1471 Mob: +45 2875 1471 Fax: +45 2875 1480
>
> ----------------------------------------------------------------------
>
>
>
> -----Original Message-----
> From: Richard Pyle [mailto:deepreef at bishopmuseum.org]
> Sent: Sunday, October 13, 2013 6:49 PM
> To: 'Donald Hobern [GBIF]'; 'TDWG Content Mailing List'
> Cc: 'Chuck Miller'
> Subject: RE: [tdwg-content] A plea around basisOfRecord (Was: Proposed
> new Darwin Core terms - abundance, abundanceAsPercent)
>
>
>
> Hi Donald,
>
>
>
> MANY thanks for this! And you are certainly not alone in your
> concerns about these issues. In fact, we have planned a Symposium for
> "Documenting DarwinCore"
>
> (https://mbgserv18.mobot.org/ocs/index.php/tdwg/2013/schedConf/trackPolicies
>
> #track11), and one of the four sessions (Session 3, to be precise) of
> the symposium focuses exactly on this issue of
> basisOfRecord/dcterms:type/etc.
>
>
>
> Another session (Session 2) will focus on proposed and
> perhaps-to-be-proposed new classes (Individual, MaterialSample,
> Evidence), and will start out with a series graphs illustrating the
> existing high-level ontology and possible alternative high-level
> ontologies, as you indicate in your items 3 & 4.
>
>
>
> Aloha,
>
> Rich
>
>
>
> --
> Steven J. Baskauf, Ph.D., Senior Lecturer
> Vanderbilt University Dept. of Biological Sciences
>
> postal mail address:
> PMB 351634
> Nashville, TN 37235-1634, U.S.A.
>
> delivery address:
> 2125 Stevenson Center
> 1161 21st Ave., S.
> Nashville, TN 37235
>
> office: 2128 Stevenson Center
> phone: (615) 343-4582, fax: (615) 322-4942
> If you fax, please phone or email so that I will know to look for it.
> http://bioimages.vanderbilt.edu
--
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
postal mail address:
PMB 351634
Nashville, TN 37235-1634, U.S.A.
delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235
office: 2128 Stevenson Center
phone: (615) 343-4582, fax: (615) 322-4942
If you fax, please phone or email so that I will know to look for it.
http://bioimages.vanderbilt.edu
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