Sorry,<div><br></div><div>I meant <a href="http://www.freebase.com/view/en/puma">http://www.freebase.com/view/en/puma</a>. </div><div><br></div><div>Sort of , I have an "all different in my people ontology.</div><div>
<br></div><div>DBpedia has the same link with freebase. I wonder if that freebase URI has changed recently.</div><div><br></div><div>- Pete</div><div><br></div><div><br><br><div class="gmail_quote">On Tue, May 17, 2011 at 5:17 PM, Jim Croft <span dir="ltr"><<a href="mailto:jim.croft@gmail.com">jim.croft@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">hmmm... a <a href="http://www.freebase.com/view/en/cougar" target="_blank">http://www.freebase.com/view/en/cougar</a> seems to be an<br>
'armoured fighting vehicle'...<br>
<br>
which might be part of the point you are making... wondering if<br>
NotEvenRemotelyTheSameAs is a valid relationship type... ;)<br>
<br>
jim<br>
<div><div></div><div class="h5"><br>
On Wed, May 18, 2011 at 8:00 AM, Peter DeVries <<a href="mailto:pete.devries@gmail.com">pete.devries@gmail.com</a>> wrote:<br>
> Hi Matt,<br>
> It took me a while to ponder your question. There is a long answer which<br>
> complex and easily misinterpreted and there is a shorter answer.<br>
> For now I think the "shorter" answer set in a historical context is best.<br>
> The best use of my abilities seems to be recognizing a "ability gap" and<br>
> figuring out a technical solution or tool to address it.<br>
> The most visible of these were involving microscopy and visualization tools<br>
> to make complex ideas understandable.<br>
> My interest in the species problem dates back to when I had the opportunity<br>
> to talk with E.O. WIlson in 1991/1992.<br>
> At that time he said that if you have a knack for computers we need all this<br>
> information in databases so it is accessible.<br>
> *One of his former Ph.D. students is on my committee.<br>
> Years later I had the opportunity to work on questions like this and started<br>
> to think about how to connect all these disparate facts about species<br>
> together in a usable queryable knowledge base.<br>
> I noticed that several groups and individuals were marking up data sets<br>
> including observations with different scientific names even though they were<br>
> clearly meaning the same "species".<br>
> * These groups would agree that they were communicating about the same<br>
> species, but not always agree on the name<br>
> This prevents large scale data integration and analysis which in part is<br>
> described here: <a href="http://about.geospecies.org/" target="_blank">http://about.geospecies.org/</a><br>
> With the advent of the web, and the the semantic web in particular, this<br>
> "database" could be global and almost infinitely scalable.<br>
> I started lobbying TDWG starting in 2006 for two things:<br>
> 1) A GUID for the "species" that was not tied to a particular name string<br>
> 2) A system that followed semantic web best practices which LSID etc. do<br>
> not.<br>
> Since my TDWG efforts were not successful, I started GeoSpecies and based on<br>
> comments from a semantic web expert modified these somewhat into what is now<br>
> TaxonConcept.org<br>
> The TCS is an xml standard for transmitting information about a taxon<br>
> concepts that I think maps best to a "name use concept." (Rich's TNU's)<br>
> The TaxonConcepts are identified with semantic web GUIDs that follow<br>
> semantic web best practices and resolve to an informative documents.<br>
> In their current form these documents are not ideal because they do not do a<br>
> good enough job clearing up what would be the best concept match for a given<br>
> individual or specimen.<br>
> They do however have most of the plumbing for this in that they allow<br>
> semantic web links to name uses, specimens, occurrence records, images, DNA,<br>
> authors and publications including the original description.<br>
> They also link to similar entities that are on the semantic web, most<br>
> notably DBpedia, Uniprot, Freebase, Bio2RDF etc.<br>
> This linking may not seem valuable to a humans, is valuable for machines<br>
> that need to determine what entities are similar and what entities are<br>
> different.<br>
> This also increases the "findability" of these other data sets.<br>
> I see my current set of about 105,000 species as an example set that people<br>
> can use to try out these models.<br>
> In their final form these should be authored by editors that determine what<br>
> specimens and other data are good examples of instances of these concepts.<br>
> The editors will be linked via a URI so it is easy to track attribution.<br>
> The final concepts do not have to be in one place, they could be distributed<br>
> but to avoid the kinds of nomenclatural differences that have occurred<br>
> between zoology / botany etc it would be best to have one code base for now.<br>
> They don't have to have the same underlying stack, which now is based on<br>
> Ruby on Rails, but could be ported to anything.<br>
> What they do need is a common structure and a common understanding as to<br>
> what each attribute means and how it can be appropriately used.<br>
> For some use cases it is appropriate to consider the following the same<br>
> "thing"<br>
> <a href="http://lod.taxonconcept.org/ses/v6n7p#Species" target="_blank">http://lod.taxonconcept.org/ses/v6n7p#Species</a><br>
> <a href="http://purl.uniprot.org/taxonomy/9696" target="_blank">http://purl.uniprot.org/taxonomy/9696</a><br>
> <a href="http://www.freebase.com/view/en/cougar" target="_blank">http://www.freebase.com/view/en/cougar</a><br>
> <a href="http://sw.opencyc.org/concept/Mx4rvVj5o5wpEbGdrcN5Y29ycA" target="_blank">http://sw.opencyc.org/concept/Mx4rvVj5o5wpEbGdrcN5Y29ycA</a><br>
> <a href="http://www.bbc.co.uk/nature/species/Cougar#species" target="_blank">http://www.bbc.co.uk/nature/species/Cougar#species</a><br>
><br>
> For other use cases, this sameAs is not appropriate.<br>
> Wikipedia is very valuable, but if someone changes the article title then<br>
> the URI changes in DBpedia.<br>
> Uniprot and Bio2RDF are useful in that they link to lots of related data but<br>
> they don't really give you any information about what specimens are<br>
> instances of that concept and they only have those species which have NCBI<br>
> ID's.<br>
> What I want is a set of GUID's that resolve to a human readable HTML page<br>
> and an RDF representation that people can use to "tag" their data.<br>
> For instance:<br>
> I am going to assert that what I have under the microscope is an instance of<br>
> the concept described on this page. I do not tie this assertion to a<br>
> particular name or classification hierarchy.<br>
> Because it makes no sense to replicate the functionality of the Encyclopedia<br>
> of Life etc., I am mainly concentrating on the RDF representations and<br>
> testing if they behave as expected in SPARQL queries.<br>
> * The HTML pages are not really pretty or as informative as the RDF or as<br>
> the concept as viewed in the knowledge base.<br>
> I have been working with the Encyclopedia of Life and GNI groups for a while<br>
> exploring how these may or may not be useful to them.<br>
> During my visited Woods Hole I said that I have no interest in building and<br>
> empire I just want to build a solution and would like to partner with them<br>
> and GBIF.<br>
> Although I remain active on TDWG I find the most valuable suggestions seem<br>
> to come from the LOD community since we seem to have a common goal - that is<br>
> creating something that works in a reasonable amount of time.<br>
> Also, in the LOD cloud every linked data set increases the value of all the<br>
> other data sets.<br>
> This is probably more than your question required, but it provides some<br>
> explanation as to what these are and why I have implemented them in the way<br>
> I have.<br>
> Respectfully,<br>
> - Pete<br>
><br>
><br>
> On Fri, May 13, 2011 at 4:14 PM, Matt Jones <<a href="mailto:jones@nceas.ucsb.edu">jones@nceas.ucsb.edu</a>> wrote:<br>
>><br>
>> Hi Peter,<br>
>> Does your idea of #ObjectiveSpeciesModel correspond 1:1 with the TCS<br>
>> standard's idea of a Nominal Concept (i.e., <TaxonConcept type="nominal">) ?<br>
>> Can you outline how your concept types differ from TCS concept types?<br>
>> Thanks,<br>
>> Matt<br>
>> On Fri, May 13, 2011 at 12:41 PM, Peter DeVries <<a href="mailto:pete.devries@gmail.com">pete.devries@gmail.com</a>><br>
>> wrote:<br>
>>><br>
>>> Hi Nico,<br>
>>> Thanks for posting this.<br>
>>> I have something in the concept model to indicate the basis for the<br>
>>> species concept.<br>
>>> For now I have three types. An individual species concept can have a<br>
>>> combination of one, two or all three<br>
>>> In the RDF they look like this<br>
>>> <txn:speciesConceptBasedOn<br>
>>> rdf:resource="<a href="http://lod.taxonconcept.org/ontology/txn.owl#ObjectiveSpeciesModel" target="_blank">http://lod.taxonconcept.org/ontology/txn.owl#ObjectiveSpeciesModel</a>"/><br>
>>><br>
>>> The first is what I call the #ObjectiveSpeciesModel - this indicates that<br>
>>> it is a species concept because we say it is.<br>
>>> All the species concepts are at least an #ObjectiveSpeciesModel<br>
>>> *This is in part a way to handle things like the domestic cat which you<br>
>>> want to be seen as different from the African Wildcat.<br>
>>> There are also tags for<br>
>>> txn:PhylogeneticSpeciesModel<br>
>>> txn:BiologicalSpeciesModel<br>
>>> For now I don't have these other models set in the example data, but<br>
>>> fields are in the database and the code for that an editor could state the<br>
>>> basis for the model.<br>
>>> I can think of a couple of different ways to handle the issue of<br>
>>> alternative species concepts.<br>
>>> * Note that the identifications as proposed by DarwinCore don't seem to<br>
>>> indicate what kind of model the identifications were based on.<br>
>>> So it is not clear to me if a straight DarwinCore data set would allow<br>
>>> the analysis above.<br>
>>> Instead of having multiple different statements like<br>
>>> txn:occurrenceHasSpeciesConcept <> in the record for each occurrence<br>
>>> one could use different predicates to link to different kinds of species<br>
>>> concepts.<br>
>>> txn:occurrenceHasUniprotConcept =><br>
>>> <<a href="http://purl.uniprot.org/taxonomy/9696" target="_blank">http://purl.uniprot.org/taxonomy/9696</a>><br>
>>> This would allow someone to query for the occurrences<br>
>>> of <<a href="http://purl.uniprot.org/taxonomy/9696" target="_blank">http://purl.uniprot.org/taxonomy/9696</a>><br>
>>> That said, it is not clear to me what people mean by different<br>
>>> identifications.<br>
>>> Is the intent to have identifications with different homotypic synonyms<br>
>>> to be an identification of the same thing or not?<br>
>>> The way it works now in many data sets is that Felis concolor, Puma<br>
>>> concolor and Puma conncolor are treated as identifications of different<br>
>>> things.<br>
>>> This is another way of saying is the namestring the concept?<br>
>>> My understanding of the eBird project is that it allows citizen<br>
>>> scientists to contribute their own observations. This creates a much larger<br>
>>> data set for analysis etc.<br>
>>> They have a created a curated list of species and a ~6 letter code for<br>
>>> each. This serves as a guide for observers on how to encode their<br>
>>> observations.<br>
>>> I think their progress would be inhibited, the occurrence coding<br>
>>> inconsistant, and contributors frustrated, if they have a list that included<br>
>>> many overlapping species concepts.<br>
>>> Thanks again for you comments,<br>
>>> - Pete<br>
>>><br>
>>> On Fri, May 13, 2011 at 3:05 AM, Nico Franz <<a href="mailto:nico.franz@upr.edu">nico.franz@upr.edu</a>> wrote:<br>
>>>><br>
>>>> Hello Pete (et al.):<br>
>>>><br>
>>>> For bird, Town Peterson at KU and colleagues have published these<br>
>>>> papers showing how alternative bird taxonomies affect the ranking of<br>
>>>> conservation priorities.<br>
>>>><br>
>>>><br>
>>>> <a href="http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/PN_CB_1999.pdf" target="_blank">http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/PN_CB_1999.pdf</a><br>
>>>><br>
>>>> <a href="http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/NP_BN_2004.pdf" target="_blank">http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/NP_BN_2004.pdf</a><br>
>>>><br>
>>>> <a href="http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/P_BCI_2006.pdf" target="_blank">http://specify5.specifysoftware.org/Informatics/bios/biostownpeterson/P_BCI_2006.pdf</a><br>
>>>><br>
>>>> Here's the abstract of the 1999 paper:<br>
>>>><br>
>>>> Analysis of geographic concentrations of endemic taxa is often used to<br>
>>>> determine priorities for conservation<br>
>>>> action; nevertheless, assumptions inherent in the taxonomic authority<br>
>>>> list used as the basis for<br>
>>>> analysis are not always considered. We analyzed foci of avian endemism<br>
>>>> in Mexico under two alternate species<br>
>>>> concepts. Under the biological species concept, 101 bird species are<br>
>>>> endemic to Mexico and are concentrated<br>
>>>> in the mountains of the western and southern portions of the country.<br>
>>>> Under the phylogenetic species<br>
>>>> concept, however, total endemic species rises to 249, which are<br>
>>>> concentrated in the mountains and lowlands<br>
>>>> of western Mexico. Twenty-four narrow endemic biological species are<br>
>>>> concentrated on offshore islands, but<br>
>>>> 97 narrow endemic phylogenetic species show a concentration in the<br>
>>>> Transvolcanic Belt of the mainland and<br>
>>>> on several offshore islands. Our study demonstrates that conservation<br>
>>>> priorities based on concentrations of<br>
>>>> endemic taxa depend critically on the particular taxonomic authority<br>
>>>> employed and that biodiversity evaluations<br>
>>>> need to be developed in collaboration or consultation with practicing<br>
>>>> systematic specialists.<br>
>>>><br>
>>>> There was a debate recently on Taxacom that was started and<br>
>>>> subsequently neatly summarized by Fabian Haas. The topic was "let's<br>
>>>> summarize reasons why 'donors' seem to not fund taxonomy". One point from<br>
>>>> the summary was this:<br>
>>>><br>
>>>> 3) Taxonomy is over-accurate for most applications<br>
>>>><br>
>>>> Most (not all) decisions in e.g. modelling and conservation are done and<br>
>>>> can be done without complete knowledge of taxa. As it is, decisions for<br>
>>>> conservation areas are often based on flagship species (e.g. elephants), on<br>
>>>> taxa which have an excellent research background, e.g. birds (IBAs), on<br>
>>>> availability of land (e.g. land with a high Tsetse burden), importance as<br>
>>>> corridor and other factors, but never on a complete view on an all<br>
>>>> biodiversity in a specific area. Even if an inventory existed, it would be<br>
>>>> an illusion that we could collect data on ecological requirements and<br>
>>>> population dynamics for most of the species necessary for informed<br>
>>>> decisions. A complete inventory does not seem to provide an advantage for<br>
>>>> conservation.<br>
>>>><br>
>>>> I personally think there's some truth to that. I also think that,<br>
>>>> while it's understandable that an accurate representation of the (sometimes)<br>
>>>> fleetingness of taxonomic consensus it not a priority for applied ecological<br>
>>>> projects, if taxonomists themselves don't find better ways to document and<br>
>>>> link these alternatives perspectives, then it's not the best science we can<br>
>>>> do. That would be fine too if adopted outright as a pragmatic stance.<br>
>>>><br>
>>>> Regards,<br>
>>>><br>
>>>> Nico<br>
>>>><br>
>>>><br>
>>>> On 5/13/2011 1:08 AM, Peter DeVries wrote:<br>
>>>><br>
>>>> I thought that I would also mention that in addition to The Plants List,<br>
>>>> the eBird project also uses on overlapping concepts in its bird list (it<br>
>>>> does have concepts for common hybrids)<br>
>>>> What is clear to me is that you cannot create graphs like these if every<br>
>>>> observation can have X number of species (especially those that overlapping<br>
>>>> ) without any indication which is is the most appropriate one.<br>
>>>> eBird Occurrence Maps Northern Cardinal<br>
>>>> <a href="http://ebird.org/content/ebird/about/occurrence-maps/northern-cardinal" target="_blank">http://ebird.org/content/ebird/about/occurrence-maps/northern-cardinal</a><br>
>>>><br>
>>>> NCBI is also similar.<br>
>>>> Perhaps a member of the consensus committee can comment?<br>
>>>> -- Pete<br>
>>>><br>
>>>> ------------------------------------------------------------------------------------<br>
>>>> Pete DeVries<br>
>>>> Department of Entomology<br>
>>>> University of Wisconsin - Madison<br>
>>>> 445 Russell Laboratories<br>
>>>> 1630 Linden Drive<br>
>>>> Madison, WI 53706<br>
>>>> Email: <a href="mailto:pdevries@wisc.edu">pdevries@wisc.edu</a><br>
>>>> TaxonConcept & GeoSpecies Knowledge Bases<br>
>>>> A Semantic Web, Linked Open Data Project<br>
>>>><br>
>>>> --------------------------------------------------------------------------------------<br>
>>>><br>
>>>> _______________________________________________<br>
>>>> tdwg-content mailing list<br>
>>>> <a href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a><br>
>>>> <a href="http://lists.tdwg.org/mailman/listinfo/tdwg-content" target="_blank">http://lists.tdwg.org/mailman/listinfo/tdwg-content</a><br>
>>>><br>
>>>><br>
>>>> _______________________________________________<br>
>>>> tdwg-content mailing list<br>
>>>> <a href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a><br>
>>>> <a 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>
>>> --<br>
>>><br>
>>> ------------------------------------------------------------------------------------<br>
>>> Pete DeVries<br>
>>> Department of Entomology<br>
>>> University of Wisconsin - Madison<br>
>>> 445 Russell Laboratories<br>
>>> 1630 Linden Drive<br>
>>> Madison, WI 53706<br>
>>> Email: <a href="mailto:pdevries@wisc.edu">pdevries@wisc.edu</a><br>
>>> TaxonConcept & GeoSpecies Knowledge Bases<br>
>>> A Semantic Web, Linked Open Data Project<br>
>>><br>
>>> --------------------------------------------------------------------------------------<br>
>>><br>
>>> _______________________________________________<br>
>>> tdwg-content mailing list<br>
>>> <a href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a><br>
>>> <a 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>
><br>
> --<br>
> ------------------------------------------------------------------------------------<br>
> Pete DeVries<br>
> Department of Entomology<br>
> University of Wisconsin - Madison<br>
> 445 Russell Laboratories<br>
> 1630 Linden Drive<br>
> Madison, WI 53706<br>
> Email: <a href="mailto:pdevries@wisc.edu">pdevries@wisc.edu</a><br>
> TaxonConcept & GeoSpecies Knowledge Bases<br>
> A Semantic Web, Linked Open Data Project<br>
> --------------------------------------------------------------------------------------<br>
><br>
> _______________________________________________<br>
> tdwg-content mailing list<br>
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> <a 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>
<br>
</div></div>--<br>
_________________<br>
Jim Croft ~ <a href="mailto:jim.croft@gmail.com">jim.croft@gmail.com</a> ~ <a href="tel:%2B61-2-62509499" value="+61262509499">+61-2-62509499</a> ~ <a href="http://about.me/jrc" target="_blank">http://about.me/jrc</a><br>
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of doubtful sanity.'<br>
- Robert Frost, poet (1874-1963)<br>
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</blockquote></div><br><br clear="all"><br>-- <br>
------------------------------------------------------------------------------------<br>Pete DeVries<br>Department of Entomology<br>University of Wisconsin - Madison<br>445 Russell Laboratories<br>1630 Linden Drive<br>Madison, WI 53706<br>
Email: <a href="mailto:pdevries@wisc.edu" target="_blank">pdevries@wisc.edu</a><br><a href="http://www.taxonconcept.org/" target="_blank">TaxonConcept</a> & <a href="http://about.geospecies.org/" target="_blank">GeoSpecies</a> Knowledge Bases<br>
A Semantic Web, <a href="http://linkeddata.org/" target="_blank">Linked Open Data</a> Project<br>--------------------------------------------------------------------------------------<br>
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