[tdwg-content] opposing anything that comes from outside a small click was Re: If you need something for referring to a population, then it is probably best to do it as a related class
Steve Baskauf
steve.baskauf at vanderbilt.edu
Sun May 1 17:11:47 CEST 2011
Comments inline
Peter DeVries wrote:
> I was expressing my disappointment about how this process operates,
> not disappointment in you or your efforts.
OK, cool. I am excited about the possibility that there can be
productive discussion about how to move forward on something that will
work for LOD.
>
> A while back I posted several messages with examples showing that the
> current DarwinCore, while good for it's current use, is not well
> suited for the Semantic Web.
>
> I proposed that we work on something that might be better suited for
> that use while data providers continued to use the DarwinCore.
>
> There seemed to be no consensus that this was the thing to do, or that
> anyone else agreed with my proposal.
Well, I think you are right that there may not have been a consensus on
exactly what to do, but I think there might have been a consensus that
SOMETHING should be done. See "Do we need an RDF
version/guide/representation of Darwin Core?" at the bottom of the
"http://code.google.com/p/darwin-sw/wiki/Rationale" wiki page. I
suppose that I may disagree with you somewhat that the current DwC is
not well-suited for the semantic web. I think that most of the terms
that are there currently could be used for data properties. The problem
is that there are a lot of missing object properties and the
dwc:xxxxxxID terms are too ambiguous to use for that. So I would assert
that DwC really needs an extension rather than a replacement. Of course
I could be wrong...
>
> It is not clear how TDWG decisions are made. There seem to be
> discussions and debate, not voting or clear consensus on the email list.
I think that you won't necessarily get disagreement on this. The fact
that proposals for DwC additions have been there for as long as a year
without an up or down vote is an indication that the process isn't very
efficient. I think you were at a session at TDWG where this problem
(i.e. the functioning of the TDWG Technical Architecture Group) was
discussed.
It was suggested in
http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001591.html and
http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001653.html
that a Task Group be chartered to work on this. Cam and I didn't follow
that route for several reasons. Cam's in the jungle of Borneo and I have
no funding, and work and family constraints that make it difficult for
me to attend meetings. Also, we are both pretty much novices at this
and are "learning by doing". I, in particular, wouldn't feel
comfortable chairing a Task Group if I didn't think I could follow
through with the commitment. So maybe it was bad to come up with DSW
outside of a Task Group. But it was something we needed for our own
work in a relatively short period of time and development by committee
is usually a very slow process. So rightly or wrongly we just did it.
Maybe it is time for a Task Group. But I think somebody else may have
to shoulder that responsibility.
>
> What does seem to happen is some mysterious entity, /that I like to
> call the TDWG Illuminati/, seems decide what the "consensus" is.
>
> So apparently there was consensus that we should investigate a more
> semantic version of the DarwinCore and the minting a separate set of
> URI"s was blessed by the Illuminati.
I don't understand what you mean. Are you talking about DSW? If so, it
wasn't "blessed" by anybody. Last fall Cam suggested we try having a go
at it and at first I didn't think it was realistic, but then he
convinced me that it would be fun and that we could do it over the
Internet. So off we went. It was entirely our project and idea and we
didn't ask for or get a blessing from anybody in TDWG or anywhere else.
So we will take full responsibility (and blame if necessary) for it. At
this point, we are interested in knowing how many bullets it can take
and still keep standing. So load up and fire away. Our feelings are
not easily hurt.
I really don't like conspiracy theories because there is never any way
to convince the people who are proposing them that they are not true.
What I see in the situation (from list posts) is a number of people
"playing around" with RDF, LOD, and semantic web stuff to try to see
what they can do with it. I think this is really a necessary step
before trying to do anything more concrete. I don't think you will
disagree with that, you are doing the same thing yourself. I don't
think there is any kind of consensus at all about what should happen,
just maybe that "something" should happen. I'm only getting that from
the list posts, given that I don't really have direct connections with
other TDWG people (except for one BiSciCol meeting and that's not an
official TDWG thing).
>
> What I don't understand is this: Is there is any real difference
> between examples that start with "txn" are any "dsw"
No. You are completely right about this, to the extent that you intend
for your txn classes to mean the same thing as what Cam and I mean with
the dsw classes. Actually there are only two dsw classes,
IndividualOrganism and Token. The rest are either dwc or dcterms
classes that we imported. If you classes are the same as the
dwc/dcterms/dsw classes, then it makes absolutely no difference whether
the string "txn:identificationOfIndividual" or "dsw:identifies" is used
to describe the relationships. Our choices were mostly based on liking
names that were short and which expressed the relationship clearly. But
they were arbitrary and we could have just as easily used your names (if
we were sure that you intended for your classes to be equivalent to
dwc/dcterms classes).
>
> Haven't I said all along that my stuff could be moved into the DarwinCore?
I guess maybe you said that at some point, but I think I either forgot
it or missed it. I have thought of your examples as an alternative to
Darwin Core - I think primarily because you often choose term names that
aren't the same as those used in DwC.
>
> The reason I created txn was that my efforts at advocating for a
> markup that followed Linked Open Data best practices was going nowhere.
I wouldn't say nowhere. I think that because of people's lack of
familiarity with RDF, involvement in other projects, and general
busy-ness movement towards involvement in LOD is very slow but it is
there. There have been a number of people talking about it. As I said
in the other message that I just sent, I think that the large scale and
complexity of txn is an impediment to people understanding it. I'm not
saying that as a criticism, I just think that it is true. I also think
that it is not a safe assumption that because people don't post to the
list that it means that people are ignoring what you are doing. Some
people may feel insecure about posting and others just may be "lurking"
and don't have anything to say. I for one have read and considered
every post that you have ever written and even though you never got much
in the way of responses on your geo: suggestions, I know that there is
at least one group who has seriously looked at it as a viable way to
express location information.
>
> I needed URI's that resolved correctly.
>
> The issue relating to my TaxonConcepts are complicated, the specifics
> will need to come at a later date.
>
> However, I take issue with the idea that Taxon = name use when you
> consider the actual practice of the vast majority of biologists and
> the actual data sets that are available.
>
> If NCBI, eBird, BOLD, or any data from of the countless field and lab
> observations were tagged with a "sensu" or "secundum" then you might
> have an argument.
I think there is widespread agreement that people don't do this, but I
think there is considerable sentiment that they should. And so any
system we build should be designed to make it easy for people to do this.
>
> So the consensus in the larger biological community is that this is
> not how information about species is tagged.
>
> The goal of my TaxonConcepts is provide machine / human interpretable
> species concepts so that different biologists can more reliably and
> repeatedly determine which concept is the most appropriate "tag" for
> the individual organism they are looking at in a microscope or through
> binoculars.
>
> A tag that can remain stable to changes in nomenclature like that seen
> seen with Aedes / Ochlerotatus.
>
> A first step in this process is to connect that species to the many
> name variants with which it is associated.
I don't fundamentally disagree with most of what you say here. What you
are trying to do is useful and important. What I am saying is that the
way that the term "taxon concept" has been used in the literature, in
previous TDWG standards (e.g. the TCS schema), and the the nascent TDWG
ontology does not seem to be the same thing that you are calling "taxon
concept". Perhaps there needs to be a different term for what you are
doing.
The meaning of "Taxon", especially as it applies to the dwc:Taxon class
is much more obscure. If one ferrets out information from the hundreds
of tdwg-content postings, you pretty much come up with
http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001703.html and
http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001814.html
which seems to indicate that the people who created DwC intended for
instances of the dwc:Taxon class to be taxon name usages (TNUs) which I
take to be a more broadly defined entity that includes the more narrowly
defined tc:TaxonConcept. It would be nice if it were stated explicitly
on the DwC wiki that this is the case (if it actually is). In the tdwg
ontology, tc:Taxon is defined to be an equivalent class to
tc:TaxonConcept. Whether that means that tc:Taxon is exactly the same
as dwc:Taxon is not clear, but from the standpoint of DSW, we have
defined them to be the same thing. I think we can do that because
Darwin Core terms don't have very strict definitions. (By the way, this
is all summarized at http://code.google.com/p/darwin-sw/wiki/ClassTaxon)
>
> A second step is to link the concept to closely related concepts,
> identifiers and other existing documentation on the web.
>
> Some of these concepts include links to the original description,
> etype pages, BOLD barcodes etc. They have the ability to be linked to
> the type and other specimens.
Again, an awesome and cool thing which I support wholeheartedly. I just
think it doesn't fit the standard definition of "taxon concept". That
isn't a conspiracy of any Illuminati. It means that people have
published work saying that's what it means. It's kind of like the in
the legal system where people follow precedents even if they aren't what
those people would have done in the absence of previous cases.
>
> They have been looked at very carefully my leaders in the Linked Open
> Data community and the GeoSpecies / TaxonConcept are seen as one of
> the better designed LOD data sets.
I do not have the experience to judge this, but I'll take your word for
it. The challenge here is to come up with something that will make both
people inside and outside the biodiversity informatics community happy
(or as happy as is possible). If you only make one group or the other
happy, then you don't have something that will bridge both groups. So
despite whatever problems there might be in the TDWG community, that's
the community that we have. People who don't have experience with a
technology need to be led by the hand and shown why the technology that
is proposed will do something that they actually need. That probably
won't happen fast.
That's my "two cents worth" (translate into your local currency :-).
Steve
>
> In general, SPARQL queries on a local or LOD endpoint work as expected.
>
> Are they perfect? No.
>
> Respectfully,
>
> - Pete
>
> On Fri, Apr 29, 2011 at 9:46 PM, Steve Baskauf
> <steve.baskauf at vanderbilt.edu <mailto:steve.baskauf at vanderbilt.edu>>
> wrote:
>
> Hi Pete,
> I want to respond to your message in two parts. It may take me
> some time to write a response to the second part (i.e. questions
> about your suggestion) so it may not come right away. But I also
> wanted to comment about the first part, that is:
>
> Peter DeVries wrote:
>
> I am still somewhat puzzled why TDWG seems so opposed to
> adopting anything that comes from outside a small click?
>
> I'm not exactly sure if this is directed at Cam and me (in the
> context of darwin-sw), or to others. If it is directed at me,
> then you can read my response. If not, then you can ignore it.
> First of all, I'd like to say that I greatly respect the work that
> you've done on trying to promote the use of LOD in the TDWG
> community. I have read every one of your posts and have tried to
> understand all of them to the extent that I'm able. I think we
> referenced your posts over 20 times at
> http://code.google.com/p/darwin-sw/wiki/TdwgContentEmailSummary,
> cited your taxon concept examples at
> http://code.google.com/p/darwin-sw/wiki/ClassTaxon and included
> your model in the analysis of previous models at
> http://code.google.com/p/darwin-sw/wiki/RelationshipToExistingModels.
> Your suggestion of using the geo: scheme was included in the
> discussion of the Location class at
> http://code.google.com/p/darwin-sw/wiki/ClassLocation . I would
> say that at least half of what I know about RDF comes from looking
> at your examples and trying to understand what you have done. I
> am therefore very grateful for the work that you have done and
> your enthusiasm for bringing creative ideas into the community.
> So why did Cam and I create Darwin-SW instead of just using your
> ontologies at taxonconcept.org <http://taxonconcept.org> ? There
> are several reasons, some of which are alluded to at
> http://code.google.com/p/darwin-sw/wiki/RelationshipToExistingModels
> . But to be succinct (OK, maybe not that succinct), I'll state
> them here:
>
> 1. Darwin Core is a ratified TDWG standard. It therefore
> qualifies as a "well-known" vocabulary. If I refer to
> dwc:recordedBy as a property, people in the biodiversity
> informatics community will know what it means. If I refer to
> dwc:Identification, it will also be known in our community. For
> this reason, Cam and I wanted as much as possible to build
> Darwin-SW on Darwin Core rather than using terms that we or any
> other individual minted.
> 2. Cam and I wanted the Darwin-SW ontology to (as much as
> possible) reflect the community consensus on what classes meant
> and and how they were related to each other. Of course, the
> problem is knowing what that consensus was. After the hundreds of
> emails that were posted on the tdwg-content list from September
> 2010 to the present, I feel like I have a much better
> understanding of what the consensus is than I did before (where
> there IS a consensus, of course). I have spent more hours than I
> care to remember trying to read, re-read, and understand the
> various emails that were sent and then asking annoying questions
> until somebody was patient enough to explain things to me. Most
> of those explanations are referenced on the class wiki pages. So
> I don't consider the ideas embodied in Darwin-SW to be "our" ideas
> - they are the ideas we absorbed from the community, including
> you. (If you want to see "my" actual ideas, look at the examples
> in my Biodiversity Informatics article. I don't really think that
> they are really that good any more.) The outlook of DSW also
> recognizes historical precedents such as the ACS model. As cool
> and clever as taxonconcept.org <http://taxonconcept.org> is, it
> fundamentally represents Pete DeVries' ideas. That means that it
> will readily be accepted by you, but the community may be less apt
> to buy into it if it doesn't embody community concepts. It may
> turn out that Darwin-SW does NOT actually represent the community
> consensus (as we hope it does), or is stupid, or doesn't work. In
> those cases, it will get shot down and somebody else will pick up
> the task of trying to figure out what the community consensus is
> about how things should be represented in RDF. I should note that
> I don't think the discussion last Oct/Nov was limited to a clique
> of TDWG architects. I was an active participant and I certainly
> don't qualify as a TDWG insider, having only been to one TDWG
> meeting for less than 24 hours and knowing almost no other TDWG
> contributors personally.
> 3. There are a couple of structural things about taxonconcept.org
> <http://taxonconcept.org> terms and classes that I have questions
> about and I'll raise them in my second email to come after this
> one. But I think that one of the most problematic things about
> taxonconcept.org <http://taxonconcept.org> for me is the way that
> you describe taxon concepts. I hate to even bring up the subject
> because it's taken me months just to try to understand what people
> mean when they are talking about a taxon concept and I don't want
> to unleash another hundred emails about the minutae of taxon
> concepts, which people on this list love to talk about. So
> suffice it to say that the sense that I've gotten from the many
> posts on the subject is that most people see a Taxon Concept (= =
> Taxon and similar to a "taxon name use") as the combination of a
> taxon name and a "sensu" or "secundum" (accordingTo) reference.
> That's how it is modeled in the TCS model, which is another
> ratified TDWG standard. That's also how it's modeled in the
> unfinished TDWG ontology, which despite its unfinished state is
> nonetheless is actually being used by some people to describe
> taxon concepts (see
> http://code.google.com/p/darwin-sw/wiki/ClassTaxon for links to
> some examples). When I look at how you model taxon concepts such
> as in http://lod.taxonconcept.org/ses/v6n7p.rdf which describes
> the species concept http://lod.taxonconcept.org/ses/v6n7p#Species
> , there are a lot of metadata about the scientific name, related
> name strings, URIs that represent similar resources, connections
> to the original description, etc. But I don't see any
> sensu/secundum reference or a property that links to one. So
> although http://lod.taxonconcept.org/ses/v6n7p#Species is a cool
> thing that links to a lot of useful information about Puma
> concolor, it doesn't seem to be the same thing as what everybody
> else is calling a taxon concept. If I were to link to your
> "species concepts", you and I might know what that meant, but
> nobody else would. That is in contrast to a tc:Taxon (= =
> tc:TaxonConcept) instance which is defined by reference to the TCS
> model and I would therefore consider "well known" (and is what we
> DO reference in DSW).
> So I think that in some sense, my reluctance to adopt individually
> "minted" classes and properties comes from the reason why I'm
> interested in RDF in the first place. I'm actually NOT very
> interested in using RDF to do reasoning in the "Semantic Web"
> sense - I guess I'm still a bit of a skeptic about how likely it
> is that anybody will be able to find out anything useful by doing
> reasoning on RDF that they suck in from the cloud, particularly if
> lots of people are using their own minted properties and if
> different people intend for the classes they use to rdf:type
> things to mean different things and have different properties.
> What I AM interested in is figuring out a way to make it possible
> for people to have a consistent understanding of the meaning of
> metadata that they discover when they resolve GUIDs. I think that
> will be increasingly important when projects like BiSciCol get
> rolling. The only way that I see this as possible is to base
> properties primarily on vocabularies that a lot of institutions
> already "understand" and are using, like Darwin Core.
> That doesn't mean that people will ONLY use Darwin Core. I have
> already heard plenty of talk on this list about using other
> vocabularies such as geo:, skos:, and foaf: (with some cautions
> from Bob). John Wieczorek, the architect of the Darwin Core
> standard, proposed adding geo: terms to DwC (see
> http://code.google.com/p/darwincore/issues/detail?id=82). There
> are also at least four people on this list that I know are
> interested in trying to make sure that DwC can interface with the
> OBOE ontology. So I don't think it is fair to say that "TDWG" is
> opposed to adopting things outside its clique. I just think that
> people are cautious about supporting things that they are not
> familiar with (or perhaps don't understand) and in a lot of cases
> just don't have the time (or aren't willing to take the time) to
> figure out something new.
> So I hope that you aren't discouraged that people are slow to jump
> on the LOD bandwagon. I think that more people will be interested
> in supporting it when they start seeing tangible applications
> within our community and that's already starting to happen.
> Unfortunately, since you are so far ahead of the rest of us in
> your understanding of how the LOD world works, I think that you
> are probably doomed to be one of the ones pulling the wagon! :-)
> I look forward (as I have in the past) to hearing more of your
> innovative ideas.
>
> Steve
>
> --
> Steven J. Baskauf, Ph.D., Senior Lecturer
> Vanderbilt University Dept. of Biological Sciences
>
> postal mail address:
> VU Station B 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 <tel:%28615%29%20343-4582>, fax: (615)
> 343-6707 <tel:%28615%29%20343-6707>
> http://bioimages.vanderbilt.edu
>
>
>
>
> --
> ------------------------------------------------------------------------------------
> Pete DeVries
> Department of Entomology
> University of Wisconsin - Madison
> 445 Russell Laboratories
> 1630 Linden Drive
> Madison, WI 53706
> Email: pdevries at wisc.edu <mailto:pdevries at wisc.edu>
> TaxonConcept <http://www.taxonconcept.org/> & GeoSpecies
> <http://about.geospecies.org/> Knowledge Bases
> A Semantic Web, Linked Open Data <http://linkeddata.org/> Project
> --------------------------------------------------------------------------------------
--
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
postal mail address:
VU Station B 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) 343-6707
http://bioimages.vanderbilt.edu
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