[tdwg-content] A plea around basisOfRecord (Was: Proposed new Darwin Core terms - abundance, abundanceAsPercent)
Steve Baskauf
steve.baskauf at vanderbilt.edu
Mon Oct 14 00:13:58 CEST 2013
Sorry, I don't agree at all.
The core Darwin-SW classes include only Darwin Core classes and the two
proposed DwC classes (Organism and CollectionObject a.k.a.
dsw:IndividualOrganism and dsw:Evidence) which underwent 30 day public
comment period [1] and were submitted to the Executive which recommended
further consideration by the RDF Task Group and the community at large.
The Documenting Darwin Core sessions at the TDWG meeting will pick up
these and other open issues for further discussion and hopefully move
them towards closure one way or the other. If the two proposed classes
are at some point accepted for inclusion in DwC, Darwin-SW will use the
new classes and deprecate dsw:IndividualOrganism and dsw:Evidence,
leaving only Darwin Core classes as the core classes in Darwin-SW.
It is NOT my view that Darwin-SW is unable to handle current needs for
linking resources effectively. If anyone wants to know why I say that,
come to our talk in the Friday 9AM session on Ontologies and Formal
Models at the meeting. We will show how real SPARQL queries on
Darwin-SW-based data can address important competency questions
involving diverse linked resources. Or see me any time during the
meeting earlier in the week and I'll be happy to give you a personal
demonstration not limited to 9 minutes.
Steve
[1]
http://lists.tdwg.org/pipermail/tdwg-content/2011-September/002727.html
see also open issue https://code.google.com/p/darwincore/issues/detail?id=69
Robert Guralnick wrote:
>
> Rod --- There are a couple different conceptions of
> interrelationships between Darwin Core "classes", including the Darwin
> Core Semantic Web effort led by Steve Baskauf and Cam Web, and the
> BiSciCol project. Darwin Core SW is
> here: https://code.google.com/p/darwin-sw/ and the BiSciCol "take" is
> here: http://biscicol.blogspot.com/2013_03_01_archive.html. The
> Darwin Core SW version includes new classes not in Darwin Core, while
> BiSciCol uses only existing class terms and a very simple set of
> predicates.
>
> I think in many people's view, including those of the authors of the
> above (although I hate speaking for them), neither DW-SW or
> DW-BiSciCol may be really able to handle the current needs for linking
> resources together effectively. There has been a major effort to
> refocus away from jury-rigging Darwin Core to try to serve in a more
> semantic framework and pushing towards other solutions that align
> biodiversity standards more with the OBO Foundry
> (http://www.obofoundry.org/). The Biocollections Ontology
> (BCO; https://code.google.com/p/bco/) represents (what I hope) is a
> clear rethinking of the challenge that does connect back to the Darwin
> Core.
>
> Best, Rob
>
>
>
> On Sun, Oct 13, 2013 at 1:52 PM, Roderic Page <r.page at bio.gla.ac.uk
> <mailto:r.page at bio.gla.ac.uk>> wrote:
>
> I've always been somewhat puzzled by the disconnect between the
> TDWG LSID ontology
> (e.g., http://rs.tdwg.org/ontology/voc/TaxonConcept ) which has a
> rich set of classes and links between those classes, and Darwin
> Core
> (e.g., http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm )
> which overlaps with this vocabulary and, in my opinion, does a
> worse job in some areas, notably taxon names and concepts. Maybe
> the LSID vocabulary suffered from the limited uptake of LSIDs
> (apart from the nomenclators and Catalogue of Life) or from the
> complexity of dealing with RDF, but it seems that much of the
> essential work was done when Roger Hyam created that ontology.
>
> What might help is a way to visualise the TDWG LSID ontology in
> terms of the interconnections between the different classes. I'm
> not aware of such a visualisation (nor of an equivalent one for
> the Darwin Core classes).
>
> In any event, it seems odd to have two distinct ontologies that
> are both in use, and which overlap so significantly.
>
> Regards
>
> Rod
> On 13 Oct 2013, at 16:12, Donald Hobern [GBIF] wrote:
>
>> It’s been a couple of weeks but I said I’d try to write something
>> about a more general concern I have around the way we use
>> basisOfRecord and dcterms:type to hold values like occurrence,
>> event and materialSample. This is something that has concerned
>> me for years and that, I worry, is making everything we all do
>> much messier than it need be.
>>
>> I believe that the way we have come to use Darwin Core
>> basisOfRecord is confused and unhelpful. I really wish we used
>> Darwin Core like this:
>>
>> 1. basisOfRecord should be used ONLY to indicate the type
>> of evidence that lies behind a record – a key aspect of whether
>> the record is likely to be useful for different purposes
>> 2. basisOfRecord values should be taken from a hierarchical
>> vocabulary with three main branches:
>> a. “specimens” (i.e. biological material that can be
>> reviewed), with a hierarchy of subordinate values such as
>> “pinnedSpecimen”, “herbariumSheet”, etc.
>> b. derived, non-biological evidence (not sure what name),
>> with a hierarchy of subordinate values such as “dnaSequence”,
>> “soundRecording”, “stillImage”, etc.
>> c. asserted observations with no revisitable evidence other
>> than the authority of the observer
>> 3. TDWG should deliver a basic ontology in the form of a
>> graph of key relationships between the most significant
>> conceptual entities in our world (TaxonName, TaxonConcept,
>> Identification, Collection, Specimen, Locality, Agent, …)
>> 4. This ontology should not attempt to map all the
>> complexity of biodiversity-related data – just provide the
>> high-level map and key relationships (TaxonConcept hasName
>> TaxonName, Specimen heldIn Collection, etc.) – it should leave
>> definition of other properties as a separate, open-ended activity
>> for the community
>> 5. This ontology should be reviewed at regular intervals
>> and versioned as necessary to address critical gaps – provided
>> that backwards compatibility is maintained (splitting a class
>> into multiple consitituent classes probably won’t break anything,
>> so start simple)
>> 6. The Darwin Core vocabulary should be published as a
>> flat, open-ended list of terms with clear definitions that can be
>> freely combined as columns in denormalised records
>> 7. Every Darwin Core term should be documented to be
>> tightly associated with a single, fixed class in the ontology
>> (e.g. scientificName and specificEpithet are ALWAYS considered to
>> be properties of a TaxonName whether or not that TaxonName object
>> is clearly referenced or separated out)
>> 8. Every data publisher should be encouraged to share all
>> relevant data elements in their source data in the most
>> convenient normalised or denormalised form, provided they use the
>> recognised Darwin Core properties for elements that match the
>> definition for those terms, and provided they give some metadata
>> for other elements. Possible forms include:
>> a. A completely hierarchical, ABCD-like, XML representation
>> b. A completely flat denormalised, simple-DwC-like, CVS
>> representation, if the data includes no elements with higher
>> cardinality
>> c. A set of flat, relational, CVS representations, as with
>> Darwin Core Archive star schemas, but with freedom to have more
>> complex graphed relationships as needed
>> 9. Each table of CVS data in 8b and 8c is a view that
>> corresponds to a linear subgraph of the TDWG ontology, identified
>> by the classes of the DwC properties used – this allows us to
>> infer the “shape” of the data in terms of the ontology
>> 10. If we do this, we do not need to worry about whether a
>> record is a checklist record, an event, an occurrence, a material
>> sample or whatever else, although we could use the dcterms: type
>> property, or some new property, to hold this detail as a further
>> clue to intent and possible use for the record
>>
>> Here is an example. In today’s terms, what sort of DwC record is
>> this? Do I really have to replace “recordId” with “eventId”,
>> “occurrenceId” or similar? And which should I choose?
>>
>> *recordId, decimalLatitude, decimalLongitude,
>> coordinatePrecision, eventDate, scientificName, individualCount*
>>
>> I think it is clear that this record tells us that there was a
>> recording event at a particular time and place where someone or
>> some process recorded a given number of individual organisms
>> which were identified as representatives of a taxon concept with
>> a name corresponding to the supplied scientific name. In other
>> words this gives us some properties from a subgraph that might
>> include, say, instances of TDWG Event, Locality, Date,
>> Occurrence, Identification, TaxonConcept and TaxonName classes.
>> None of these is specifically referenced but we can unambiguously
>> fold the flat record onto the ontology. We can moreover then use
>> the combination of supplied elements to decide whether this
>> record would be of interest to GBIF, a national information
>> facility, a tool cataloguing uses of scientific names, etc. The
>> same will also apply if multiple CVS tables are provided as in 8c.
>>
>> I have thought about this for a long time and cannot yet think of
>> an area in which this would not work efficiently – and
>> unambiguously – for all concerned. There are some cases where
>> multiple instances of the same ontology class would be referenced
>> within a single record, which may mean more care is needed by the
>> publisher (e.g. if an insect specimen record includes a reference
>> to a host plant). There may be cases where automated review of
>> the data indicates that there are impossible combinations or
>> ambiguities that the publisher must resolve. However I believe
>> we could use this approach to generalise all mobilisation and
>> consumption of biodiversity data (including all the things we
>> have addressed under ABCD, SDD, TCS, Plinian Core, etc.) and to
>> make it genuinely possible for any data holder to share all the
>> data they have in a form that makes sense to them, while allowing
>> others to consume these data intelligently.
>>
>> Right now, I think our confused use of basisOfRecord is almost
>> the only thing that stops us from exploring this. We have
>> blurred the question of the evidence for a record, with the
>> question of the “shape” of the record as a subgraph. These are
>> different things. Separating them will allow us to get away from
>> some of our unresolvable debates and open up the doors to much
>> simpler data sharing and reuse.
>>
>> Thanks,
>>
>> 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 <tel:%2B45%203532%201471> Mob: +45 2875 1471
>> <tel:%2B45%202875%201471> Fax: +45 2875 1480
>> <tel:%2B45%202875%201480>
>> ----------------------------------------------------------------------
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>
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> Institute of Biodiversity, Animal Health and Comparative Medicine
> College of Medical, Veterinary and Life Sciences
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QQ, UK
>
> Email: r.page at bio.gla.ac.uk <mailto:r.page at bio.gla.ac.uk>
> Tel: +44 141 330 4778 <tel:%2B44%20141%20330%204778>
> Fax: +44 141 330 2792 <tel:%2B44%20141%20330%202792>
> Skype: rdmpage
> Facebook: http://www.facebook.com/rdmpage
> LinkedIn: http://uk.linkedin.com/in/rdmpage
> Twitter: http://twitter.com/rdmpage
> Blog: http://iphylo.blogspot.com
> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> Wikipedia: http://en.wikipedia.org/wiki/Roderic_D._M._Page
> Citations:
> http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
> <http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ>
> ORCID: http://orcid.org/0000-0002-7101-9767
>
>
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>
--
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
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office: 2128 Stevenson Center
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If you fax, please phone or email so that I will know to look for it.
http://bioimages.vanderbilt.edu
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