September 2010 - tdwg-content

Why the Linked Data Approach Makes Sense For Biodiversity Informatics
by Peter DeVries 30 Sep '10

30 Sep '10

I got a question tonight at TDWG about the advantages of the Linked Data approach. I described one of the main advantages in this blog post. http://www.taxonconcept.org/taxonconcept-blog/2010/8/5/why-linked-open-data… As with the BHL example, it often makes more sense to link to related data curated maintained by a group which has that area as their primary concern. The alternative is to spend resources replicating and curating data that is outside the main focus of your work. A related benefit is that the value of both linked resources is enhanced. I am not a biographer, and there are often very good articles about significant taxonomic authors on Wikipedia. The value of both DBpedia and TaxonConcept are increased when I correctly link between a species concept and a DBpedia resource describing a taxon author. For many of the taxa, you can go from a URI of a taxonomic author to lots of additional information related to the taxa he or she described. Respectfully, - Pete ---------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies Knowledge Base <http://lod.geospecies.org/> About the GeoSpecies Knowledge Base <http://about.geospecies.org/> ------------------------------------------------------------ _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

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Species Concept to GNI Namestring Linking - Initial Experiments
by Peter DeVries 29 Sep '10

29 Sep '10

In preparation for the Nomina session on Thursday. Here are some things to look at for the session titled "Exploring Semantic Web Technologies for Global Names Architecture Name Resolution" Dima and I have figured out a way to expose the name strings in the GNI to the Semantic Web. At this point it is really about exploring ways in which distributed data projects can link to entities in the GNI. In these experiments we have been exploring the mapping of names strings to species concepts. For the most part these should work with different kinds of species concepts but for now this experiment is using the TaxonConcept.org concepts. The html version for humans of the relevant species concept is < http://lod.taxonconcept.org/ses/v6n7p.html> The RDF version for computers of the relevant species concept is < http://lod.taxonconcept.org/ses/v6n7p.rdf> The initial stages were fairly basic. This concept has some association with the following name strings in the GNI. There was no real effort to determine the nature of these relationships until very recently. I marked up an RDF file that makes the following relationship assertions about how a concept is related to a particular name string. The GBIF site mentioned a movement toward databasing names in the following plain text form *Puma concolor (Linnaeus 1771)* * * * Italics can be added in web views etc. For the sake of argument, lets say that the preferred from is like that above with no comma between the author and date. This particular string could them be mapped to slight variations that are correctly formed and mean the same thing. This particular string could also be mapped to common misspellings etc of the same name. Those various alternatives form a lexical group. Similarly, the synonym *Felis concolor Linnaeus 1771* also has a list of essentially correct strings of characters and common malformed variants. This would be a second lexical group. So the concept represented by this page and URI can then be related to these name variants and a linkage is formed between the entities in the TaxonConcept Dataset and the GNI dataset. These relationships can be represented in the N3 form which some humans find easier to interpret than the alternative RDF/XML form. Note that these predicates have the "URI" suffix to differentiate between those predicates that expect URI object and and similar predicates that expect a literal object. Subject Predicate Object <http://lod.taxonconcept.org/ses/v6n7p#Species> txn:hasAcceptedScientificNameURI < http://gni.globalnames.org/name_strings/772d5162-f5aa-596c-98e0-a1c6c5a29bb9 > <http://lod.taxonconcept.org/ses/v6n7p#Species> txn:hasSynonymNameURI < http://gni.globalnames.org/name_strings/35da7f30-25ff-5111-ab29-1a4f9988ef51 > <http://lod.taxonconcept.org/ses/v6n7p#Species> txn:hasBasionymNameURI < http://gni.globalnames.org/name_strings/35da7f30-25ff-5111-ab29-1a4f9988ef51 > Rather than rely on inferencing I also make the reverse relationship Subject Predicate Object < http://gni.globalnames.org/name_strings/772d5162-f5aa-596c-98e0-a1c6c5a29bb9> txn:isAcceptedScientificNameURI_Of < http://lod.taxonconcept.org/ses/v6n7p#Species> < http://gni.globalnames.org/name_strings/35da7f30-25ff-5111-ab29-1a4f9988ef51> txn:isAcceptedScientificNameURI_Of < http://lod.taxonconcept.org/ses/v6n7p#Species> < http://gni.globalnames.org/name_strings/35da7f30-25ff-5111-ab29-1a4f9988ef51> txn:isBasionymNameURI_Of < http://lod.taxonconcept.org/ses/v6n7p#Species> These same statements are made in RDF/XML in the following RDF < http://lod.taxonconcept.org/tdwg_nomina.rdf > When exposed to the Linked Open Data Cloud those statements are associated with both the species concept and the GNI namestrings. In my own quad store you can see that they appear in this view of the species concept: < http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org… > Not that relevant statements from other databases also appear - demonstrating one of the key advantages of the Linked Data approach. The nomina RDF and other information is part of this view even though it was not part of the basic species concept RDF above. The same concept is viewable on the cloud via the prettier Sig.ma service. < http://sig.ma/search?pid=9421eef0751cff0694b481d744607c98 > Note Sig.ma service also resolves the GNI namestring URI and exposed the rdf:label associated with that URI. - Pete ---------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies Knowledge Base <http://lod.geospecies.org/> About the GeoSpecies Knowledge Base <http://about.geospecies.org/> ------------------------------------------------------------ _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

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Potential predicates to relate species concepts to GNI namestring URI's
by Peter DeVries 28 Sep '10

28 Sep '10

I was working toward creating some consensus on a vocabulary on how to relate the namestrings in the Global Names Index to some sort of species concept. The goal is to have a vocabulary that works with a number of different "types" of species concept. It was suggested to me that I just go ahead and make one. Here is what I am proposing and hope to demonstrate at the Nomina section on Thursday at TDWG. One of the first things to decide is what should be the "best" form of a scientific name string. After looking through the GBIF info it seems that the following form which has no comma between the author and year might be preferred form. For example Puma concolor (Linnaeus 1771) The other various forms of the "same" name can then be related to each other using semantic web predicates in addition to the relationship between a name string and species concept. Using this as a model, I thought the following triple structure might work well to map the concept to Accepted, Synonym etc. Since the GNI namestrings are in the form of URI's they can serve as both subjects and objects. Literals can not be used as subjects. I use the form hasAcceptedScientificNameURI to distinguish between the URI form and the the literal form txn:hasAcceptedScientificName. I was a little reluctant to do this within the txn namespace since it might be something for the TDWG vocabulary. GUID Forms <concept> txn:hasAcceptedScientificNameURI < http://gni.globalnames.org/name_strings/772d5162-f5aa-596c-98e0-a1c6c5a29bb9 > <concept> txn:hasSynonymNameURI < http://gni.globalnames.org/name_strings/35da7f30-25ff-5111-ab29-1a4f9988ef51 > <concept> txn:hasBasionymNameURI < http://gni.globalnames.org/name_strings/35da7f30-25ff-5111-ab29-1a4f9988ef51 > < http://gni.globalnames.org/name_strings/772d5162-f5aa-596c-98e0-a1c6c5a29bb9> txn:isAcceptedScientificNameURI_Of <concept> < http://gni.globalnames.org/name_strings/35da7f30-25ff-5111-ab29-1a4f9988ef51> txn:isAcceptedScientificNameURI_Of <concept> < http://gni.globalnames.org/name_strings/35da7f30-25ff-5111-ab29-1a4f9988ef51> txn:isBasionymNameURI_Of <concept> Humans, note that the RDF representation of these GNI namestring information can be seen by adding ".rdf" to the end of the URI. Semantic Web applications already understand the distinction between the html and rdf representations. For example http://gni.globalnames.org/name_strings/772d5162-f5aa-596c-98e0-a1c6c5a29bb… It is also important to discuss and make a decision about the Domain and Range for each of these predicates. txn:hasAcceptedScientificNameURI Domain - Some sort of TaxonConcept but may be best to leave the Domain unspecified except that it should be a URI. Range - Some sort of Namestring represented in RDF. Within a typical browser, the RDF form of the URI It might make some sense to have a range that follows some standard RDF representation, but they do not necessarily have to be namestrings in the GNI. I was thinking that those RDF representations that follow a specific structure could be seen as instances of the class "NameString" If these are namestrings provided only by the GNI, then they might be in a modeled as instances of the class "GNI_NameString" ========== Literal Forms txn:hasAcceptedScientificName "Ochlerotatus triseriatus (Say 1823)" txn:hasAcceptedScientificName "Aedes triseriatus (Say 1823)" txn:hasBasionymName "Culex triseriatus Say 1823" GUID Forms <concept> txn:hasAcceptedScientificNameURI < http://gni.globalnames.org/name_strings/3f418cbf-358a-5174-ade1-25ae846a219e > <concept> txn:hasAcceptedScientificNameURI < http://gni.globalnames.org/name_strings/e9f5e126-5cdb-52bf-9050-349df4a9dd18 > <concept> txn:hasBasionymNameURI < http://gni.globalnames.org/name_strings/6ce63b2c-58be-5335-826b-622b7b4bc328 > < http://gni.globalnames.org/name_strings/3f418cbf-358a-5174-ade1-25ae846a219e> txn:isAcceptedScientificNameURI_Of <concept> < http://gni.globalnames.org/name_strings/e9f5e126-5cdb-52bf-9050-349df4a9dd18> txn:isAcceptedScientificNameURI_Of <concept> < http://gni.globalnames.org/name_strings/3f418cbf-358a-5174-ade1-25ae846a219e> txn:isBasionymNameURI_Of <concept> ========== Do we want to also include information like that described below. In some cases, each of the databases have their own version of the "Accepted Name" This would allow one to determine which DB's have different "Accepted" names <concept> txn:hasCOL2010_ScientificNameURI <> <concept> txn:hasNCBI_ScientificNameURI <> <concept> txn:hasITIS_ScientificNameURI <> <concept> txn:hasGBIF_ScientificNameURI <> Tracking the Catalog of Life LSID's over time. Since there is a new COL LSID each year, you will need to create some mapping between these. <concept> txn:hasCol2009LSID <urn:lsid:catalogueoflife.org: taxon:24e7d624-60a7-102d-be47-00304854f810:ac2009> <concept> txn:hasCol2010LSID <urn:lsid:catalogueoflife.org: taxon:24e7d624-60a7-102d-be47-00304854f810:ac2010> These LSID will work within VIrtuoso only because this quadstore has written extensions that allow them. LSID's themselves are not really true LOD identifiers. Most semantic web tools do not know how to deal with these. The relationships between these "properly formed" Accepted Names, Synonyms, Basionyms can then be represented with additional predicates depending on the relationship between the concept and the namestring. I have choosen to not emphasize what kind of taxon concept we are using since these should be usable with many "kinds" of taxon concepts. The advantage of representing these namestrings as URI's is that once loaded into a triplestore / quadstore one will be able to see and query what namestrings are related to a specific concept and what namestrings are related to various concepts. Unless their is some disagreement, I plan to modify my ontology and upload the example triples to the cloud so the namestring relationships are viewable in SIndice etc by the time of the Nomina meeting on Thursday. Respectively, - Pete -- ---------------------------------------------------------------- Pete DeVries Department of Entomology University of Wisconsin - Madison 445 Russell Laboratories 1630 Linden Drive Madison, WI 53706 TaxonConcept Knowledge Base <http://www.taxonconcept.org/> / GeoSpecies Knowledge Base <http://lod.geospecies.org/> About the GeoSpecies Knowledge Base <http://about.geospecies.org/> ------------------------------------------------------------ _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

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stake in the ground for an Annotation ontology
by Bob Morris 26 Sep '10

26 Sep '10

At http://bdei2.cs.umb.edu/mw/AnnotationOntology will be found comments about (and diagrams, and links to a current version) of an evolving ontology for biodiversity data annotation. It will be put on the table for the new TDWG data annotation interest group. I'll talk about in last of the TDWG Thursday sessions on Annotation. -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: morris.bob(a)gmail.com web: http://bdei.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile) _______________________________________________ tdwg-content mailing list tdwg-content(a)lists.tdwg.org http://lists.tdwg.org/mailman/listinfo/tdwg-content

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[tdwg-phylo] TDWG mailing list consolidation
by Markus Döring (GBIF) 08 Sep '10

08 Sep '10

Dear members of the TDWG mailing list tdwg-phylo, TDWG has seen a proliferation of mailing lists over the years, most of which are inactive today. Traffic on most lists is rather little and usually limited to only a short period of time. As most lists also have very much the same subscribers, we are seeking to merge lists into just a few ones. The main 3 mailing lists we want to maintain in the future being: tdwg(a)lists.tdwg.org A list with very low traffic for official TDWG announcements from the executive committee http://lists.tdwg.org/mailman/listinfo/tdwg tdwg-content(a)lists.tdwg.org A list for all non technical discussions covering all TDWG working groups / standards http://lists.tdwg.org/mailman/listinfo/tdwg-content tdwg-tag(a)lists.tdwg.org The technical architecture group list that will host discussions about the technical details of standards http://lists.tdwg.org/mailman/listinfo/tdwg-tag Within the next days we will automatically add all subscribers of this list to tdwg and tdwg-content and will merge all existing archives of the mailing list tdwg-phylo into tdwg-content. The list tdwg-phylo will be closed and removed once the archives have been merged. Best wishes, Markus Döring

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[tdwg-lit] TDWG mailing list consolidation
by Markus Döring (GBIF) 08 Sep '10

08 Sep '10

Dear members of the TDWG mailing list tdwg-lit, TDWG has seen a proliferation of mailing lists over the years, most of which are inactive today. Traffic on most lists is rather little and usually limited to only a short period of time. As most lists also have very much the same subscribers, we are seeking to merge lists into just a few ones. The main 3 mailing lists we want to maintain in the future being: tdwg(a)lists.tdwg.org A list with very low traffic for official TDWG announcements from the executive committee http://lists.tdwg.org/mailman/listinfo/tdwg tdwg-content(a)lists.tdwg.org A list for all non technical discussions covering all TDWG working groups / standards http://lists.tdwg.org/mailman/listinfo/tdwg-content tdwg-tag(a)lists.tdwg.org The technical architecture group list that will host discussions about the technical details of standards http://lists.tdwg.org/mailman/listinfo/tdwg-tag Within the next days we will automatically add all subscribers of this list to tdwg and tdwg-content and will merge all existing archives of the mailing list tdwg-lit into tdwg-content. The list tdwg-lit will be closed and removed once the archives have been merged. Best wishes, Markus Döring

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Survey on biodiversity Knowledge Organization
by Bob Morris 08 Sep '10

08 Sep '10

Dear colleague, The team listed below is charged by the Global Biodiversity Information Facility (GBIF) with developing a position paper about its future needs for Knowledge Organization Systems (KOS), a rubric which includes thesauri, controlled vocabularies, ontologies, gazetteers, linked data, and other such resources. The paper will cover tools, impediments to deployment, training requirements, etc. After we draft it, the position paper will be put forth for a period of public comment before final recommendations to GBIF. In order to put together the position paper, we solicit your opinions, experiences, needs, and information on resources you already in place about Knowledge Organization for biodiversity research. Please go to http://surveymonkey.com/GBIFKOSurvey to participate in the survey. We especially value your input about points you feel the survey doesn’t cover. Please feel free to forward this invitation to mailing lists or colleagues you feel appropriate, hopefully to people who may not have seen it already. Thanks GBIF KOS position paper team Bob Morris, Convenor. Terry Catapano, Donald Hobern, Hilmar Lapp, Norman Morrison, Natasha Noy, Mark Schildhauer, Dave Thau September 7, 2010 -- Robert A. Morris Emeritus Professor of Computer Science UMASS-Boston 100 Morrissey Blvd Boston, MA 02125-3390 Associate, Harvard University Herbaria email: morris.bob(a)gmail.com web: http://bdei.cs.umb.edu/ web: http://etaxonomy.org/mw/FilteredPush http://www.cs.umb.edu/~ram phone (+1) 857 222 7992 (mobile)

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[tdwg-tnc] TDWG mailing list consolidation
by Markus Döring (GBIF) 08 Sep '10

08 Sep '10

Dear members of the TDWG mailing list tdwg-tnc, TDWG has seen a proliferation of mailing lists over the years, most of which are inactive today. Traffic on most lists is rather little and usually limited to only a short period of time. As most lists also have very much the same subscribers, we are seeking to merge lists into just a few ones. The main 3 mailing lists we want to maintain in the future being: tdwg(a)lists.tdwg.org A list with very low traffic for official TDWG announcements from the executive committee http://lists.tdwg.org/mailman/listinfo/tdwg tdwg-content(a)lists.tdwg.org A list for all non technical discussions covering all TDWG working groups / standards http://lists.tdwg.org/mailman/listinfo/tdwg-content tdwg-tag(a)lists.tdwg.org The technical architecture group list that will host discussions about the technical details of standards http://lists.tdwg.org/mailman/listinfo/tdwg-tag Within the next days we will automatically add all subscribers of this list to tdwg and tdwg-content and will merge all existing archives of the mailing list tdwg-tnc into tdwg-content. The list tdwg-tnc will be closed and removed once the archives have been merged. Best wishes, Markus Döring

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[tdwg-spm] TDWG mailing list consolidation
by Markus Döring (GBIF) 08 Sep '10

08 Sep '10

Dear members of the TDWG mailing list tdwg-spm, TDWG has seen a proliferation of mailing lists over the years, most of which are inactive today. Traffic on most lists is rather little and usually limited to only a short period of time. As most lists also have very much the same subscribers, we are seeking to merge lists into just a few ones. The main 3 mailing lists we want to maintain in the future being: tdwg(a)lists.tdwg.org A list with very low traffic for official TDWG announcements from the executive committee http://lists.tdwg.org/mailman/listinfo/tdwg tdwg-content(a)lists.tdwg.org A list for all non technical discussions covering all TDWG working groups / standards http://lists.tdwg.org/mailman/listinfo/tdwg-content tdwg-tag(a)lists.tdwg.org The technical architecture group list that will host discussions about the technical details of standards http://lists.tdwg.org/mailman/listinfo/tdwg-tag Within the next days we will automatically add all subscribers of this list to tdwg and tdwg-content and will merge all existing archives of the mailing list tdwg-spm into tdwg-content. The list tdwg-spm will be closed and removed once the archives have been merged. Best wishes, Markus Döring

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[tdwg-sdd] TDWG mailing list consolidation
by Markus Döring (GBIF) 08 Sep '10

08 Sep '10

Dear members of the TDWG mailing list tdwg-sdd, TDWG has seen a proliferation of mailing lists over the years, most of which are inactive today. Traffic on most lists is rather little and usually limited to only a short period of time. As most lists also have very much the same subscribers, we are seeking to merge lists into just a few ones. The main 3 mailing lists we want to maintain in the future being: tdwg(a)lists.tdwg.org A list with very low traffic for official TDWG announcements from the executive committee http://lists.tdwg.org/mailman/listinfo/tdwg tdwg-content(a)lists.tdwg.org A list for all non technical discussions covering all TDWG working groups / standards http://lists.tdwg.org/mailman/listinfo/tdwg-content tdwg-tag(a)lists.tdwg.org The technical architecture group list that will host discussions about the technical details of standards http://lists.tdwg.org/mailman/listinfo/tdwg-tag Within the next days we will automatically add all subscribers of this list to tdwg and tdwg-content and will merge all existing archives of the mailing list tdwg-sdd into tdwg-content. The list tdwg-sdd will be closed and removed once the archives have been merged. Best wishes, Markus Döring

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