<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Some responses inline<br>
<br>
Ramona Walls wrote:<br>
...<br>
If the <br>
<blockquote
cite="mid:CAJYF1k73mkkC9T3bT3dWYxnBDQR1CSXk5-Rp4-anPopB8=u1uQ@mail.gmail.com"
type="cite">
<div dir="ltr">
<div><br>
>> 3. TDWG should deliver a basic ontology in the form
of a<br>
>> graph of key relationships between the most significant<br>
>> conceptual entities in our world (TaxonName, TaxonConcept,<br>
>> Identification, Collection, Specimen, Locality, Agent, ?)<br>
<br>
The BCO could serve as this basic ontology for TDWG. Some additional
classes would be needed, and maybe those could come from the TDWG
ontology (but I would need to look into that). </div>
</div>
</blockquote>
The status of the TDWG ontology is probably too uncertain for this.
The original intention was that parts of the ontology would become bona
fide TDWG standards, but this never happened and the TDWG ontology is
not being actively maintained. The Vocabulary Management Group report
[1] discusses the status of the TDWG ontology and makes some
recommendations. We'll see whether anything follows from those
recommendations.<br>
<blockquote
cite="mid:CAJYF1k73mkkC9T3bT3dWYxnBDQR1CSXk5-Rp4-anPopB8=u1uQ@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>The BCO is intended to serve a broader need than just linking
Darwin Core archives, but it is a simple matter to make a subset that
would serve the specific needs of TDWG. The advantage of using BCO is
that it is designed to be compatible with other kinds of life science
ontologies and data, which makes it more flexible and more likely that
it will fulfill unforseen future needs. I (along with co-authors) plan
to give some more background on this approach in a talk at TDWG in a
few weeks. I am not ruling out DSW as a potential solution, either. My
main concerns with DSW are 1) it is tightly coupled to the Darwin Core
and therefor inherits some of the limitations of the Darwin Core. 2)
many of the classes and relations are application specific, and
therefor not interpretable outside the context of the application. I am
looking forward to learning more about DSW at the upcoming TDWG
meeting, where I expect there will be lengthy discussions of the
relative merits of DSW versus BCO. Both ontologies will be presented in
the same session.<br>
</div>
</div>
</blockquote>
It is my belief that the design of BCO and DSW allows them to
accomplish different kinds of things. I also hope there is some time
to talk about this, although the session is scheduled on the last day
of the conference, so I'm not sure how much time there will be left for
a discussion to take place. <br>
<blockquote
cite="mid:CAJYF1k73mkkC9T3bT3dWYxnBDQR1CSXk5-Rp4-anPopB8=u1uQ@mail.gmail.com"
type="cite">
<div dir="ltr">
<div><br>
>> 7. Every Darwin Core term should be documented to be<br>
>> tightly associated with a single, fixed class in the
ontology<br>
>> (e.g. scientificName and specificEpithet are ALWAYS
considered to<br>
>> be properties of a TaxonName whether or not that TaxonName
object<br>
</div>
<div>>> is clearly referenced or separated out)<br>
<br>
</div>
<div>What I see as one of the fundamental problems with DwC is that
the bulk of the terms are properties. That means that when data
suppliers enter data in a spread sheet, they are entering literals or
URIs that are the objects of these properties. Having hundreds of
properties that are unique to DwC </div>
</div>
</blockquote>
about 167 unique to DwC, not hundreds<br>
<blockquote
cite="mid:CAJYF1k73mkkC9T3bT3dWYxnBDQR1CSXk5-Rp4-anPopB8=u1uQ@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>seriously limits the interoperability of DwC tagged data sets
(as I mentioned in response to point 4). I think a better solution
would be to create ontology classes for most of the DwC terms (along
with a few properties), and then create data annotations that are
instances of those classes. That is a much more common way of
organizing ontology-annotated data and would allow reasoners to work
over the data. However, this would be a fundamental change to the
nature of the Darwin Core.<br>
</div>
</div>
</blockquote>
When you say the "many class" approach is more common, it depends on
what circles you are circulating in. It is certainly more common in
the OBO ontology world. But I'm not sure that is true for TDWG in
general in which this is an old discussion (see Roger Hyam/Bob Morris's
commentary at [2], also possibly [3] and the thread that follows).<br>
<br>
Steve
<div dir="ltr">
<div>
<div>
<div><br>
</div>
</div>
</div>
</div>
[1] <a class="moz-txt-link-freetext" href="http://www.gbif.org/resources/2246">http://www.gbif.org/resources/2246</a><br>
[2] <a class="moz-txt-link-freetext" href="http://wiki.tdwg.org/twiki/bin/view/TAG/SubclassOrNot">http://wiki.tdwg.org/twiki/bin/view/TAG/SubclassOrNot</a> Note
particularly the comment "...The TDWG ontology's principal role is not
modeling the entire domain to permit inference but allowing the mark up
of data so that it will flow between applications as freely as
possible. It has to be something that is easy to map into multiple
technologies and something that people can agree on rapidly. This
strongly suggests that the tagging approach should be taken wherever
possible. First agree on the basic semantic units and model the rest of
the semantics with tagging. Only subclass when absolutely necessary.
..." Also note comments about OWL inference.<br>
[3] <a class="moz-txt-link-freetext" href="http://lists.tdwg.org/pipermail/tdwg-content/2011-May/002393.html">http://lists.tdwg.org/pipermail/tdwg-content/2011-May/002393.html</a>
in which I get educated by Bob Morris and Hilmar Lapp (typical)<br>
<br>
<br>
<blockquote
cite="mid:CAJYF1k73mkkC9T3bT3dWYxnBDQR1CSXk5-Rp4-anPopB8=u1uQ@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>
<div>
<div>Ramona<br clear="all">
</div>
<div>
<div>
<div class="gmail_extra">
<div>
<div dir="ltr">------------------------------------------------------<br>
Ramona L. Walls, Ph.D.<br>
Scientific Analyst, The iPlant Collaborative, University of Arizona<br>
Laboratory Research Associate, New York Botanical Garden</div>
</div>
<br>
<br>
<div class="gmail_quote">On Mon, Oct 14, 2013 at 3:00 AM, <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:tdwg-content-request@lists.tdwg.org" target="_blank">tdwg-content-request@lists.tdwg.org</a>></span>
wrote:<br>
<blockquote class="gmail_quote"
style="border-left: 1px solid rgb(204, 204, 204); margin: 0px 0px 0px 0.8ex; padding-left: 1ex;">Send
tdwg-content mailing list submissions to<br>
<a moz-do-not-send="true"
href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a moz-do-not-send="true"
href="http://lists.tdwg.org/mailman/listinfo/tdwg-content"
target="_blank">http://lists.tdwg.org/mailman/listinfo/tdwg-content</a><br>
or, via email, send a message with subject or body 'help' to<br>
<a moz-do-not-send="true"
href="mailto:tdwg-content-request@lists.tdwg.org">tdwg-content-request@lists.tdwg.org</a><br>
<br>
You can reach the person managing the list at<br>
<a moz-do-not-send="true"
href="mailto:tdwg-content-owner@lists.tdwg.org">tdwg-content-owner@lists.tdwg.org</a><br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of tdwg-content digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. Re: A plea around basisOfRecord (Was: Proposed new Darwin<br>
Core terms - abundance, abundanceAsPercent) (Steve Baskauf)<br>
2. Re: A plea around basisOfRecord (Was: Proposed new Darwin<br>
Core terms - abundance, abundanceAsPercent) (Steve Baskauf)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Sun, 13 Oct 2013 17:13:58 -0500<br>
From: Steve Baskauf <<a moz-do-not-send="true"
href="mailto:steve.baskauf@vanderbilt.edu">steve.baskauf@vanderbilt.edu</a>><br>
Subject: Re: [tdwg-content] A plea around basisOfRecord (Was: Proposed<br>
new Darwin Core terms - abundance, abundanceAsPercent)<br>
To: Robert Guralnick <<a moz-do-not-send="true"
href="mailto:Robert.Guralnick@colorado.edu">Robert.Guralnick@colorado.edu</a>><br>
Cc: TDWG Content Mailing List <<a moz-do-not-send="true"
href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a>><br>
Message-ID: <<a moz-do-not-send="true"
href="mailto:525B1B26.1010806@vanderbilt.edu">525B1B26.1010806@vanderbilt.edu</a>><br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
Sorry, I don't agree at all.<br>
<br>
The core Darwin-SW classes include only Darwin Core classes and the two<br>
proposed DwC classes (Organism and CollectionObject a.k.a.<br>
dsw:IndividualOrganism and dsw:Evidence) which underwent 30 day public<br>
comment period [1] and were submitted to the Executive which recommended<br>
further consideration by the RDF Task Group and the community at large.<br>
The Documenting Darwin Core sessions at the TDWG meeting will pick up<br>
these and other open issues for further discussion and hopefully move<br>
them towards closure one way or the other. If the two proposed classes<br>
are at some point accepted for inclusion in DwC, Darwin-SW will use the<br>
new classes and deprecate dsw:IndividualOrganism and dsw:Evidence,<br>
leaving only Darwin Core classes as the core classes in Darwin-SW.<br>
<br>
It is NOT my view that Darwin-SW is unable to handle current needs for<br>
linking resources effectively. If anyone wants to know why I say that,<br>
come to our talk in the Friday 9AM session on Ontologies and Formal<br>
Models at the meeting. We will show how real SPARQL queries on<br>
Darwin-SW-based data can address important competency questions<br>
involving diverse linked resources. Or see me any time during the<br>
meeting earlier in the week and I'll be happy to give you a personal<br>
demonstration not limited to 9 minutes.<br>
<br>
Steve<br>
<br>
[1]<br>
<a moz-do-not-send="true"
href="http://lists.tdwg.org/pipermail/tdwg-content/2011-September/002727.html"
target="_blank">http://lists.tdwg.org/pipermail/tdwg-content/2011-September/002727.html</a><br>
see also open issue <a moz-do-not-send="true"
href="https://code.google.com/p/darwincore/issues/detail?id=69"
target="_blank">https://code.google.com/p/darwincore/issues/detail?id=69</a><br>
<br>
<br>
<br>
<br>
Robert Guralnick wrote:<br>
><br>
> Rod --- There are a couple different conceptions of<br>
> interrelationships between Darwin Core "classes", including the
Darwin<br>
> Core Semantic Web effort led by Steve Baskauf and Cam Web, and the<br>
> BiSciCol project. Darwin Core SW is<br>
> here: <a moz-do-not-send="true"
href="https://code.google.com/p/darwin-sw/" target="_blank">https://code.google.com/p/darwin-sw/</a>
and the BiSciCol "take" is<br>
> here: <a moz-do-not-send="true"
href="http://biscicol.blogspot.com/2013_03_01_archive.html"
target="_blank">http://biscicol.blogspot.com/2013_03_01_archive.html</a>.
The<br>
> Darwin Core SW version includes new classes not in Darwin Core,
while<br>
> BiSciCol uses only existing class terms and a very simple set of<br>
> predicates.<br>
><br>
> I think in many people's view, including those of the authors of
the<br>
> above (although I hate speaking for them), neither DW-SW or<br>
> DW-BiSciCol may be really able to handle the current needs for
linking<br>
> resources together effectively. There has been a major effort to<br>
> refocus away from jury-rigging Darwin Core to try to serve in a
more<br>
> semantic framework and pushing towards other solutions that align<br>
> biodiversity standards more with the OBO Foundry<br>
> (<a moz-do-not-send="true" href="http://www.obofoundry.org/"
target="_blank">http://www.obofoundry.org/</a>). The Biocollections
Ontology<br>
> (BCO; <a moz-do-not-send="true"
href="https://code.google.com/p/bco/" target="_blank">https://code.google.com/p/bco/</a>)
represents (what I hope) is a<br>
> clear rethinking of the challenge that does connect back to the
Darwin<br>
> Core.<br>
><br>
> Best, Rob<br>
><br>
><br>
><br>
> On Sun, Oct 13, 2013 at 1:52 PM, Roderic Page <<a
moz-do-not-send="true" href="mailto:r.page@bio.gla.ac.uk">r.page@bio.gla.ac.uk</a><br>
> <mailto:<a moz-do-not-send="true"
href="mailto:r.page@bio.gla.ac.uk">r.page@bio.gla.ac.uk</a>>>
wrote:<br>
><br>
> I've always been somewhat puzzled by the disconnect between the<br>
> TDWG LSID ontology<br>
> (e.g., <a moz-do-not-send="true"
href="http://rs.tdwg.org/ontology/voc/TaxonConcept" target="_blank">http://rs.tdwg.org/ontology/voc/TaxonConcept</a>
) which has a<br>
> rich set of classes and links between those classes, and Darwin<br>
> Core<br>
> (e.g., <a moz-do-not-send="true"
href="http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm"
target="_blank">http://rs.tdwg.org/dwc/terms/type-vocabulary/index.htm</a>
)<br>
> which overlaps with this vocabulary and, in my opinion, does a<br>
> worse job in some areas, notably taxon names and concepts.
Maybe<br>
> the LSID vocabulary suffered from the limited uptake of LSIDs<br>
> (apart from the nomenclators and Catalogue of Life) or from the<br>
> complexity of dealing with RDF, but it seems that much of the<br>
> essential work was done when Roger Hyam created that ontology.<br>
><br>
> What might help is a way to visualise the TDWG LSID ontology in<br>
> terms of the interconnections between the different classes.
I'm<br>
> not aware of such a visualisation (nor of an equivalent one for<br>
> the Darwin Core classes).<br>
><br>
> In any event, it seems odd to have two distinct ontologies that<br>
> are both in use, and which overlap so significantly.<br>
><br>
> Regards<br>
><br>
> Rod<br>
> On 13 Oct 2013, at 16:12, Donald Hobern [GBIF] wrote:<br>
><br>
>> It?s been a couple of weeks but I said I?d try to write
something<br>
>> about a more general concern I have around the way we use<br>
>> basisOfRecord and dcterms:type to hold values like
occurrence,<br>
>> event and materialSample. This is something that has
concerned<br>
>> me for years and that, I worry, is making everything we
all do<br>
>> much messier than it need be.<br>
>><br>
>> I believe that the way we have come to use Darwin Core<br>
>> basisOfRecord is confused and unhelpful. I really wish we
used<br>
>> Darwin Core like this:<br>
>><br>
>> 1. basisOfRecord should be used ONLY to indicate the
type<br>
>> of evidence that lies behind a record ? a key aspect of
whether<br>
>> the record is likely to be useful for different purposes<br>
>> 2. basisOfRecord values should be taken from a
hierarchical<br>
>> vocabulary with three main branches:<br>
>> a. ?specimens? (i.e. biological material that can be<br>
>> reviewed), with a hierarchy of subordinate values such as<br>
>> ?pinnedSpecimen?, ?herbariumSheet?, etc.<br>
>> b. derived, non-biological evidence (not sure what
name),<br>
>> with a hierarchy of subordinate values such as
?dnaSequence?,<br>
>> ?soundRecording?, ?stillImage?, etc.<br>
>> c. asserted observations with no revisitable
evidence other<br>
>> than the authority of the observer<br>
>> 3. TDWG should deliver a basic ontology in the form
of a<br>
>> graph of key relationships between the most significant<br>
>> conceptual entities in our world (TaxonName, TaxonConcept,<br>
>> Identification, Collection, Specimen, Locality, Agent, ?)<br>
>> 4. This ontology should not attempt to map all the<br>
>> complexity of biodiversity-related data ? just provide the<br>
>> high-level map and key relationships (TaxonConcept hasName<br>
>> TaxonName, Specimen heldIn Collection, etc.) ? it should
leave<br>
>> definition of other properties as a separate, open-ended
activity<br>
>> for the community<br>
>> 5. This ontology should be reviewed at regular
intervals<br>
>> and versioned as necessary to address critical gaps ?
provided<br>
>> that backwards compatibility is maintained (splitting a
class<br>
>> into multiple consitituent classes probably won?t break
anything,<br>
>> so start simple)<br>
>> 6. The Darwin Core vocabulary should be published as
a<br>
>> flat, open-ended list of terms with clear definitions that
can be<br>
>> freely combined as columns in denormalised records<br>
>> 7. Every Darwin Core term should be documented to be<br>
>> tightly associated with a single, fixed class in the
ontology<br>
>> (e.g. scientificName and specificEpithet are ALWAYS
considered to<br>
>> be properties of a TaxonName whether or not that TaxonName
object<br>
>> is clearly referenced or separated out)<br>
>> 8. Every data publisher should be encouraged to
share all<br>
>> relevant data elements in their source data in the most<br>
>> convenient normalised or denormalised form, provided they
use the<br>
>> recognised Darwin Core properties for elements that match
the<br>
>> definition for those terms, and provided they give some
metadata<br>
>> for other elements. Possible forms include:<br>
>> a. A completely hierarchical, ABCD-like, XML
representation<br>
>> b. A completely flat denormalised, simple-DwC-like,
CVS<br>
>> representation, if the data includes no elements with
higher<br>
>> cardinality<br>
>> c. A set of flat, relational, CVS representations,
as with<br>
>> Darwin Core Archive star schemas, but with freedom to have
more<br>
>> complex graphed relationships as needed<br>
>> 9. Each table of CVS data in 8b and 8c is a view that<br>
>> corresponds to a linear subgraph of the TDWG ontology,
identified<br>
>> by the classes of the DwC properties used ? this allows us
to<br>
>> infer the ?shape? of the data in terms of the ontology<br>
>> 10. If we do this, we do not need to worry about whether
a<br>
>> record is a checklist record, an event, an occurrence, a
material<br>
>> sample or whatever else, although we could use the
dcterms: type<br>
>> property, or some new property, to hold this detail as a
further<br>
>> clue to intent and possible use for the record<br>
>><br>
>> Here is an example. In today?s terms, what sort of DwC
record is<br>
>> this? Do I really have to replace ?recordId? with
?eventId?,<br>
>> ?occurrenceId? or similar? And which should I choose?<br>
>><br>
>> *recordId, decimalLatitude, decimalLongitude,<br>
>> coordinatePrecision, eventDate, scientificName,
individualCount*<br>
>><br>
>> I think it is clear that this record tells us that there
was a<br>
>> recording event at a particular time and place where
someone or<br>
>> some process recorded a given number of individual
organisms<br>
>> which were identified as representatives of a taxon
concept with<br>
>> a name corresponding to the supplied scientific name. In
other<br>
>> words this gives us some properties from a subgraph that
might<br>
>> include, say, instances of TDWG Event, Locality, Date,<br>
>> Occurrence, Identification, TaxonConcept and TaxonName
classes.<br>
>> None of these is specifically referenced but we can
unambiguously<br>
>> fold the flat record onto the ontology. We can moreover
then use<br>
>> the combination of supplied elements to decide whether this<br>
>> record would be of interest to GBIF, a national information<br>
>> facility, a tool cataloguing uses of scientific names,
etc. The<br>
>> same will also apply if multiple CVS tables are provided
as in 8c.<br>
>><br>
>> I have thought about this for a long time and cannot yet
think of<br>
>> an area in which this would not work efficiently ? and<br>
>> unambiguously ? for all concerned. There are some cases
where<br>
>> multiple instances of the same ontology class would be
referenced<br>
>> within a single record, which may mean more care is needed
by the<br>
>> publisher (e.g. if an insect specimen record includes a
reference<br>
>> to a host plant). There may be cases where automated
review of<br>
>> the data indicates that there are impossible combinations
or<br>
>> ambiguities that the publisher must resolve. However I
believe<br>
>> we could use this approach to generalise all mobilisation
and<br>
>> consumption of biodiversity data (including all the things
we<br>
>> have addressed under ABCD, SDD, TCS, Plinian Core, etc.)
and to<br>
>> make it genuinely possible for any data holder to share
all the<br>
>> data they have in a form that makes sense to them, while
allowing<br>
>> others to consume these data intelligently.<br>
>><br>
>> Right now, I think our confused use of basisOfRecord is
almost<br>
>> the only thing that stops us from exploring this. We have<br>
>> blurred the question of the evidence for a record, with the<br>
>> question of the ?shape? of the record as a subgraph.
These are<br>
>> different things. Separating them will allow us to get
away from<br>
>> some of our unresolvable debates and open up the doors to
much<br>
>> simpler data sharing and reuse.<br>
>><br>
>> Thanks,<br>
>><br>
>> Donald<br>
>><br>
>>
----------------------------------------------------------------------<br>
>> Donald Hobern - GBIF Director - <a moz-do-not-send="true"
href="mailto:dhobern@gbif.org">dhobern@gbif.org</a><br>
>> <mailto:<a moz-do-not-send="true"
href="mailto:dhobern@gbif.org">dhobern@gbif.org</a>><br>
>> Global Biodiversity Information Facility <a
moz-do-not-send="true" href="http://www.gbif.org/" target="_blank">http://www.gbif.org/</a><br>
>> GBIF Secretariat, Universitetsparken 15, DK-2100
Copenhagen ?,<br>
>> Denmark<br>
>> Tel: <a moz-do-not-send="true"
href="tel:%2B45%203532%201471" value="+4535321471">+45 3532 1471</a>
<tel:%2B45%203532%201471> Mob: <a moz-do-not-send="true"
href="tel:%2B45%202875%201471" value="+4528751471">+45 2875 1471</a><br>
>> <tel:%2B45%202875%201471> Fax: +45 2875 1480<br>
>> <tel:%2B45%202875%201480><br>
>>
----------------------------------------------------------------------<br>
>> _______________________________________________<br>
>> tdwg-content mailing list<br>
>> <a moz-do-not-send="true"
href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a>
<mailto:<a moz-do-not-send="true"
href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a>><br>
>> <a moz-do-not-send="true"
href="http://lists.tdwg.org/mailman/listinfo/tdwg-content"
target="_blank">http://lists.tdwg.org/mailman/listinfo/tdwg-content</a><br>
><br>
> ---------------------------------------------------------<br>
> Roderic Page<br>
> Professor of Taxonomy<br>
> Institute of Biodiversity, Animal Health and Comparative
Medicine<br>
> College of Medical, Veterinary and Life Sciences<br>
> Graham Kerr Building<br>
> University of Glasgow<br>
> Glasgow G12 8QQ, UK<br>
><br>
> Email: <a moz-do-not-send="true"
href="mailto:r.page@bio.gla.ac.uk">r.page@bio.gla.ac.uk</a> <mailto:<a
moz-do-not-send="true" href="mailto:r.page@bio.gla.ac.uk">r.page@bio.gla.ac.uk</a>><br>
> Tel: <a moz-do-not-send="true"
href="tel:%2B44%20141%20330%204778" value="+441413304778">+44 141 330
4778</a> <tel:%2B44%20141%20330%204778><br>
> Fax: <a moz-do-not-send="true"
href="tel:%2B44%20141%20330%202792" value="+441413302792">+44 141 330
2792</a> <tel:%2B44%20141%20330%202792><br>
> Skype: rdmpage<br>
> Facebook: <a moz-do-not-send="true"
href="http://www.facebook.com/rdmpage" target="_blank">http://www.facebook.com/rdmpage</a><br>
> LinkedIn: <a moz-do-not-send="true"
href="http://uk.linkedin.com/in/rdmpage" target="_blank">http://uk.linkedin.com/in/rdmpage</a><br>
> Twitter: <a moz-do-not-send="true"
href="http://twitter.com/rdmpage" target="_blank">http://twitter.com/rdmpage</a><br>
> Blog: <a moz-do-not-send="true"
href="http://iphylo.blogspot.com" target="_blank">http://iphylo.blogspot.com</a><br>
> Home page: <a moz-do-not-send="true"
href="http://taxonomy.zoology.gla.ac.uk/rod/rod.html" target="_blank">http://taxonomy.zoology.gla.ac.uk/rod/rod.html</a><br>
> Wikipedia: <a moz-do-not-send="true"
href="http://en.wikipedia.org/wiki/Roderic_D._M._Page" target="_blank">http://en.wikipedia.org/wiki/Roderic_D._M._Page</a><br>
> Citations:<br>
> <a moz-do-not-send="true"
href="http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ"
target="_blank">http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ</a><br>
> <<a moz-do-not-send="true"
href="http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ"
target="_blank">http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ</a>><br>
> ORCID: <a moz-do-not-send="true"
href="http://orcid.org/0000-0002-7101-9767" target="_blank">http://orcid.org/0000-0002-7101-9767</a><br>
><br>
><br>
> _______________________________________________<br>
> tdwg-content mailing list<br>
> <a moz-do-not-send="true"
href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a>
<mailto:<a moz-do-not-send="true"
href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a>><br>
> <a moz-do-not-send="true"
href="http://lists.tdwg.org/mailman/listinfo/tdwg-content"
target="_blank">http://lists.tdwg.org/mailman/listinfo/tdwg-content</a><br>
><br>
><br>
<br>
--<br>
Steven J. Baskauf, Ph.D., Senior Lecturer<br>
Vanderbilt University Dept. of Biological Sciences<br>
<br>
postal mail address:<br>
PMB 351634<br>
Nashville, TN 37235-1634, U.S.A.<br>
<br>
delivery address:<br>
2125 Stevenson Center<br>
1161 21st Ave., S.<br>
Nashville, TN 37235<br>
<br>
office: 2128 Stevenson Center<br>
phone: <a moz-do-not-send="true" href="tel:%28615%29%20343-4582"
value="+16153434582">(615) 343-4582</a>, fax: <a
moz-do-not-send="true" href="tel:%28615%29%20322-4942"
value="+16153224942">(615) 322-4942</a><br>
If you fax, please phone or email so that I will know to look for it.<br>
<a moz-do-not-send="true" href="http://bioimages.vanderbilt.edu"
target="_blank">http://bioimages.vanderbilt.edu</a><br>
<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a moz-do-not-send="true"
href="http://lists.tdwg.org/pipermail/tdwg-content/attachments/20131013/1c736d97/attachment-0001.html"
target="_blank">http://lists.tdwg.org/pipermail/tdwg-content/attachments/20131013/1c736d97/attachment-0001.html</a><br>
<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Sun, 13 Oct 2013 17:44:38 -0500<br>
From: Steve Baskauf <<a moz-do-not-send="true"
href="mailto:steve.baskauf@vanderbilt.edu">steve.baskauf@vanderbilt.edu</a>><br>
Subject: Re: [tdwg-content] A plea around basisOfRecord (Was: Proposed<br>
new Darwin Core terms - abundance, abundanceAsPercent)<br>
To: "Donald Hobern [GBIF]" <<a moz-do-not-send="true"
href="mailto:dhobern@gbif.org">dhobern@gbif.org</a>><br>
Cc: 'TDWG Content Mailing List' <<a moz-do-not-send="true"
href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a>>,
'Chuck<br>
Miller' <<a moz-do-not-send="true"
href="mailto:Chuck.Miller@mobot.org">Chuck.Miller@mobot.org</a>><br>
Message-ID: <<a moz-do-not-send="true"
href="mailto:525B2256.8060706@vanderbilt.edu">525B2256.8060706@vanderbilt.edu</a>><br>
Content-Type: text/plain; charset="iso-8859-1"<br>
<br>
Donald,<br>
<br>
With regards to the uncertainty about the meaning of dwc:basisOfRecord,<br>
the proposed Darwin Core RDF Guide attempts to inject clarity into the<br>
situation. It does so in two ways:<br>
<br>
1. It allows dwc:basisOfRecord to be used with literal (text) values to<br>
allow existing implementations to expose whatever values they currently<br>
have for that term. However, it specifies that rdf:type should be used<br>
exclusively as the property for specifying URI-reference values intended<br>
to indicate the type of the subject resource. [1] There is some<br>
ambiguity about what the subject is of a dwc:basisOrRecord property (the<br>
resource, or the record about the resource?). However, there is no<br>
similar ambiguity about rdf:type which always serves to indicate the<br>
class of which the subject resource is an instance.<br>
<br>
2. It specifies that classes in the Darwin Core Type vocabulary<br>
namespace (dwctype: = <a moz-do-not-send="true"
href="http://rs.tdwg.org/dwc/dwctype/" target="_blank">http://rs.tdwg.org/dwc/dwctype/</a>
) should be used<br>
for typing resources in the biodiversity domain rather than any<br>
corresponding classes in the main Darwin Core namespace (dwc: =<br>
<a moz-do-not-send="true" href="http://rs.tdwg.org/dwc/terms/"
target="_blank">http://rs.tdwg.org/dwc/terms/</a> ). [2] In other
words, if given the<br>
choice between dwc:Occurrence and dwctype:Occurrence, use<br>
dwctype:Occurrence. The guide proposes to add to the type vocabulary<br>
any classes which exist in the dwc: namespace and not in the dwctype:<br>
namespace (e.g. dwc:Identification). The intention is that the DwC type<br>
vocabulary would be what it's name suggests: the vocabulary for<br>
describing types. There are some issues involving the current<br>
definitions in the type vocabulary, which I won't go into in this<br>
email. As Rich said earlier, this is a topic for one of the Documenting<br>
Darwin Core sessions at the meeting.<br>
<br>
Although these guidelines would hold force specifically for RDF<br>
implementations, this is a convention that could be followed in other<br>
implementations.<br>
<br>
Steve<br>
<br>
[1]<br>
<a moz-do-not-send="true"
href="http://code.google.com/p/tdwg-rdf/wiki/DwcRdfGuideProposal#2.3.1.4_Other_predicates_used_to_indicate_type"
target="_blank">http://code.google.com/p/tdwg-rdf/wiki/DwcRdfGuideProposal#2.3.1.4_Other_predicates_used_to_indicate_type</a><br>
[2]<br>
<a moz-do-not-send="true"
href="http://code.google.com/p/tdwg-rdf/wiki/DwcRdfGuideProposal#2.3.1.5_Classes_to_be_used_for_type_declarations_of_resources_de"
target="_blank">http://code.google.com/p/tdwg-rdf/wiki/DwcRdfGuideProposal#2.3.1.5_Classes_to_be_used_for_type_declarations_of_resources_de</a><br>
<br>
Donald Hobern [GBIF] wrote:<br>
><br>
> Thanks, Rich.<br>
><br>
><br>
><br>
> Very pleased to see this. With this encouragement, I'll say just a<br>
> little bit more about why I think this is a critical need.<br>
><br>
><br>
><br>
> I see the model I describe as the perfect real-world realisation of<br>
> most of the key components in the GBIO Framework<br>
> (<a moz-do-not-send="true"
href="http://www.biodiversityinformatics.org/" target="_blank">http://www.biodiversityinformatics.org/</a>),
as follows:<br>
><br>
><br>
><br>
> 1. Everyone zips up whatever data they have from each
resource<br>
> (databases, field instruments, sequencers, data extracted from<br>
> literature, checklists, whatever) into a DwC Archive using whatever<br>
> DwC elements they can for data elements and describing other
elements<br>
> not currently recognised in DwC (the GBIO DATA layer)<br>
><br>
> 2. These archives should be placed in repositories that offer<br>
> basic services (DOIs, annotation services, etc.) (the GBIO CULTURE
layer)<br>
><br>
> 3. Harvesters assess the contents of each archive and
determine<br>
> what views can be supported from the supplied elements (occurrence<br>
> records for GBIF, name usage records, species interactions, etc.)
and<br>
> catalogue these views in relevant discovery indexes (GBIF,
Catalogue<br>
> of Life, TraitBank, etc.) (the GBIO EVIDENCE layer)<br>
><br>
> 4. Users can at any time annotate elements in the archives to<br>
> provide mappings for (potentially more recently defined) DwC or
other<br>
> properties, opening up new options for reuse<br>
><br>
><br>
><br>
> Donald<br>
><br>
><br>
><br>
>
----------------------------------------------------------------------<br>
><br>
> Donald Hobern - GBIF Director - <a moz-do-not-send="true"
href="mailto:dhobern@gbif.org">dhobern@gbif.org</a><br>
><br>
> Global Biodiversity Information Facility <a moz-do-not-send="true"
href="http://www.gbif.org/" target="_blank">http://www.gbif.org/</a><br>
><br>
> GBIF Secretariat, Universitetsparken 15, DK-2100 Copenhagen ?,
Denmark<br>
><br>
> Tel: <a moz-do-not-send="true" href="tel:%2B45%203532%201471"
value="+4535321471">+45 3532 1471</a> Mob: <a moz-do-not-send="true"
href="tel:%2B45%202875%201471" value="+4528751471">+45 2875 1471</a>
Fax: <a moz-do-not-send="true" href="tel:%2B45%202875%201480"
value="+4528751480">+45 2875 1480</a><br>
><br>
>
----------------------------------------------------------------------<br>
><br>
><br>
><br>
> -----Original Message-----<br>
> From: Richard Pyle [mailto:<a moz-do-not-send="true"
href="mailto:deepreef@bishopmuseum.org">deepreef@bishopmuseum.org</a>]<br>
> Sent: Sunday, October 13, 2013 6:49 PM<br>
> To: 'Donald Hobern [GBIF]'; 'TDWG Content Mailing List'<br>
> Cc: 'Chuck Miller'<br>
> Subject: RE: [tdwg-content] A plea around basisOfRecord (Was:
Proposed<br>
> new Darwin Core terms - abundance, abundanceAsPercent)<br>
><br>
><br>
><br>
> Hi Donald,<br>
><br>
><br>
><br>
> MANY thanks for this! And you are certainly not alone in your<br>
> concerns about these issues. In fact, we have planned a Symposium
for<br>
> "Documenting DarwinCore"<br>
><br>
> (<a moz-do-not-send="true"
href="https://mbgserv18.mobot.org/ocs/index.php/tdwg/2013/schedConf/trackPolicies"
target="_blank">https://mbgserv18.mobot.org/ocs/index.php/tdwg/2013/schedConf/trackPolicies</a><br>
><br>
> #track11), and one of the four sessions (Session 3, to be precise)
of<br>
> the symposium focuses exactly on this issue of<br>
> basisOfRecord/dcterms:type/etc.<br>
><br>
><br>
><br>
> Another session (Session 2) will focus on proposed and<br>
> perhaps-to-be-proposed new classes (Individual, MaterialSample,<br>
> Evidence), and will start out with a series graphs illustrating the<br>
> existing high-level ontology and possible alternative high-level<br>
> ontologies, as you indicate in your items 3 & 4.<br>
><br>
><br>
><br>
> Aloha,<br>
><br>
> Rich<br>
><br>
<br>
--<br>
Steven J. Baskauf, Ph.D., Senior Lecturer<br>
Vanderbilt University Dept. of Biological Sciences<br>
<br>
postal mail address:<br>
PMB 351634<br>
Nashville, TN 37235-1634, U.S.A.<br>
<br>
delivery address:<br>
2125 Stevenson Center<br>
1161 21st Ave., S.<br>
Nashville, TN 37235<br>
<br>
office: 2128 Stevenson Center<br>
phone: (615) 343-4582, fax: (615) 322-4942<br>
If you fax, please phone or email so that I will know to look for it.<br>
<a moz-do-not-send="true" href="http://bioimages.vanderbilt.edu"
target="_blank">http://bioimages.vanderbilt.edu</a><br>
<br>
-------------- next part --------------<br>
An HTML attachment was scrubbed...<br>
URL: <a moz-do-not-send="true"
href="http://lists.tdwg.org/pipermail/tdwg-content/attachments/20131013/786e836c/attachment-0001.html"
target="_blank">http://lists.tdwg.org/pipermail/tdwg-content/attachments/20131013/786e836c/attachment-0001.html</a><br>
<br>
------------------------------<br>
<br>
_______________________________________________<br>
tdwg-content mailing list<br>
<a moz-do-not-send="true" href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a><br>
<a moz-do-not-send="true"
href="http://lists.tdwg.org/mailman/listinfo/tdwg-content"
target="_blank">http://lists.tdwg.org/mailman/listinfo/tdwg-content</a><br>
<br>
<br>
End of tdwg-content Digest, Vol 54, Issue 11<br>
********************************************<br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
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.
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu">http://bioimages.vanderbilt.edu</a>
</pre>
</body>
</html>