Updated TaxonConcept Data set with data from the Encyclopedia of Life

Hi, I thought I would announce that I have a new TaxonConcept data set that includes millions of entries from an EoL NLP project. This was many about annotating the text corpus but the data set includes a lot of photos and additional data. IIt consists of 1,141,247 data objects:

Setting NGNIX to serve LOD Turtle.gz correctly

Hi I am trying to make the data set from the EoL Smithsonian NLP project available as simply as possible. This mainly was done for an NLP project but it includes photographs etc. and is pretty well interlinked with DBpedia and Uniprot. I have two kinds of things Taxa

Summary of OBO Ontologies Thread (my potentially flawed view)

To spare others from having to to through the entire OBO ontology thread, I thought it would be helpful to make a more digestible summary. I went to the page that the Hymenoptera Ontology Paper said was the site for the ontology. A Gross Anatomy Ontology for Hymenoptera

Re: How do OBO ontologies work on the LOD?

at 3:48 PM, Chris Mungall cjmung...@lbl.gov wrote: OBO-Format is a subset of OWL2-DL http://oboformat.org Cheers Chris On Feb 22, 2012, at 9:50 AM, Peter DeVries wrote: Hi Alan, *We use OWL and the Virtuoso endpoint you are using doesn't understand it.* Isn't it more accurate

Re: How do OBO ontologies work on the LOD?

concern? Respectfully, - Pete On Thu, Feb 23, 2012 at 10:09 AM, Chris Mungall cjmung...@lbl.gov wrote: On Feb 23, 2012, at 9:40 AM, Peter DeVries wrote: Hi Chris, http://oboformat.googlecode.com/svn/trunk/doc/obo-syntax.html#5 *On completions this section will define the semantics

Re: How do OBO ontologies work on the LOD?

will ask that this be added to Ontobee and the computers can use that. -Alan On Thu, Feb 23, 2012 at 3:40 PM, Kingsley Idehen kide...@openlinksw.comwrote: On 2/23/12 1:32 PM, Peter DeVries wrote: However, I think testing using the Vapour Validator is easier to understand. This might

Re: How do OBO ontologies work on the LOD?

, Feb 22, 2012 at 2:55 AM, Peter DeVries pete.devr...@gmail.comwrote: Hi Alan, Here is an example from the Hymenoptera Anatomy Ontology http://obofoundry.org/cgi-bin/detail.cgi?id=hymenoptera_anatomy Example via my endpoint http://lsd.taxonconcept.org/describe/?url=http://purl.obolibrary.org

Re: How do OBO ontologies work on the LOD?

at this: http://www.ncbi.nlm.nih.gov/pubmed/21388572 The implementation of the OBO to OWL mapping work is part of official Gene Ontology project. Juan Sequeda +1-575-SEQ-UEDA www.juansequeda.com On Mon, Feb 20, 2012 at 7:46 PM, Peter DeVries pete.devr...@gmail.comwrote: How do OBO type ontologies

Re: Modeling Taxonomic Classifications in a World where a given Species can have many Classifications

, 2012 at 3:39 PM, Peter DeVries pete.devr...@gmail.comwrote: Hi Jerven, Thank you for your response. Your reasoning makes sense to me and I like the move to skos:broader and skos:narrower. The problem that I have with subClassing is that some groups have made sameAs links between *txn

Re: Modeling Taxonomic Classifications in a World where a given Species can have many Classifications

, Jerven Bolleman On Jan 25, 2012, at 11:27 PM, Peter DeVries wrote: Hi, I have been trying to figure out the best way to deal with the following problem. There are entities that we see as species. (some argue if they are real things or simply an artificial human construct.) I

Recommendations for Documenting EoL.org Content Partners

Hi All, If you were to recommend how to markup the content providers listed on this page how would you do it? http://eol.org/content_partners Would you use SIOC, DOAP or some other vocabulary? What some would like is the ability to cite a content partner using just a URI. For example:

Re: Recommendations for Documenting EoL.org Content Partners

/content_partners/159 Bernard 2012/1/18 Peter DeVries pete.devr...@gmail.com Hi All, If you were to recommend how to markup the content providers listed on this page how would you do it? http://eol.org/content_partners Would you use SIOC, DOAP or some other vocabulary? What some would like

Role of RDFa in OWL classes, Systems that create URI's classes but allow regular humans to add information about those classes, alternative classifications

Hi All, I is is my understanding that if we want to setup a web resource that defines owl classes you can't use RDFa markup. For instance, if I wanted to mint an owl class for the taxon group Mammalia, I would need to do that in one of the following ways. 1) An OWL ontology created with

Re: Role of RDFa in OWL classes, Systems that create URI's classes but allow regular humans to add information about those classes, alternative classifications

-assoc.comwrote: On Jan 12, 2012, at 1:08 PM, Peter DeVries wrote: Hi All, I is is my understanding that if we want to setup a web resource that defines owl classes you can't use RDFa markup. RDFa can markup pretty much any RDF, but you might not always be able to use the shortcuts

Re: The truth about SPARQL Endpoint availability

I think this is great, but I am wondering if there should be some way of differentiating between the original endpoint and third-party endpoints. The GeoSpecies/TaxonConcept endpoint is the same, but there are other third-party endpoints. I don't understand why the statistics for the

Re: URI Comparisons: RFC 2616 vs. RDF

Hi Martin, I have URI's where case is important only at the terminal identifier. (HTML URI's in this example) http://lod.taxonconcept.org/ses/v6n7p.html http://lod.taxonconcept.org/ses/v6n7p.htmlshould be different than http://lod.taxonconcept.org/ses/v6N7p.html Am I correct in thinking that

Request for Feedback and Suggestions on a vocabulary that extends geo into an Area with a radius in meters and uses the new ietf.org geo URI

There was an earlier discussion on the pedantic list about how to markup a geo:Point with an error measure. The biodiversity informatics community has a similar problem with how to annotate a species observation with some measure of extent plus error. In addition to the error from the GPS

Re: Is it best practices to use a rdfs:seeAlso link to a potentially multimegabyte PDF?, existing predicate for linking to PDF?

Thanks to everyone. I fixed the issues with wdrs:describedby, used dcterms:hasFormat to link to the PDF the #OriginalDescription section now shows. txn:SpeciesOriginalDescription rdf:about= http://lod.taxonconcept.org/ses/v6n7p#OriginalDescription; !-- Ideally, this should link to a resource in

Is it best practices to use a rdfs:seeAlso link to a potentially multimegabyte PDF?, existing predicate for linking to PDF?

I was wondering if there is an existing predicate for linking to a PDF file? I would like to incorporate a link between bibliographic reference description and a URL to the location of a PDF of that document. I had minted a predicate txn:hasPDFVersion, as demonstrated in this RDF snippet. (Part

Invitation to connect on LinkedIn

LinkedIn I'd like to add you to my professional network on LinkedIn. - Peter Peter DeVries Ph.D. Dissertator at Department of Entomology, University of Wisconsin Madison, Wisconsin Area Confirm that you know Peter DeVries https://www.linkedin.com/e/-6t5m3-ghnv04ot-59/isd

Re: isDefinedBy and isDescribedBy, Tale of two missing predicates

I was wondering if an example might help me understand this better. I have currently been linking between entities and the RDF that describes them using foaf:topic and foaf:page If I understand this correctly, I would continue to use foaf:topic to point from the RDF page to the entities it

Re: Correct Usage of rdfs:idDefinedBy in Vocabulary Specifications with a Hash-based URI Pattern

Just to be clear, what should I be doing for my *txn* vocab? http://lod.taxonconcept.org/ontology/txn.owl * The code below is partly the way it is because of how Protege seems to want it. rdf:RDF xmlns=ontology2;txn.owl# xml:base=ontology2;txn.owl

Re: Summary for Extending geo for Areas with a Radius, Test Vocabulary and Sample RDF

Thanks Kingsley, Once I saw it in URIburner, I understood :-) Thanks! - Pete On Tue, Oct 12, 2010 at 11:26 AM, Kingsley Idehen kide...@openlinksw.comwrote: On 10/11/10 4:54 PM, Peter DeVries wrote: Thanks very much Kingsley, I thought I should better check that I have interpreted you

Re: Best Way to Extend the Geo Vocabulary to include an error or extent radius in meters

standard vocabulary like geonames to indicate the county or state the observation was made. Thanks Again, - Pete On Mon, Oct 11, 2010 at 9:47 AM, Paul Houle ontolo...@gmail.com wrote: On Thu, Oct 7, 2010 at 5:28 PM, Peter DeVries pete.devr...@gmail.comwrote: Hi LOD'ers, There was some

Summary for Extending geo for Areas with a Radius, Test Vocabulary and Sample RDF

After reviewing the feedback I created a test vocabulary and RDF file. The test vocabulary is in it's own namespace and called dwc_area. It is here: http://lod.taxonconcept.org/ontology/dwc_area.owl The HTML Document is here http://lod.taxonconcept.org/ontology/dwc_area_doc/index.html (For some

Re: Summary for Extending geo for Areas with a Radius, Test Vocabulary and Sample RDF

/foaf/0.1/topic rdfs:isDefinedBy http://xmlns.com/foaf/0.1/ Thanks :-) - Pete On Mon, Oct 11, 2010 at 3:09 PM, Kingsley Idehen kide...@openlinksw.comwrote: On 10/11/10 2:52 PM, Peter DeVries wrote: After reviewing the feedback I created a test vocabulary and RDF file. The test

Best Way to Extend the Geo Vocabulary to include an error or extent radius in meters

Hi LOD'ers, There was some discussion about ways to record species observations using the geo vocabulary at a recent biodiversity informatics meeting. Some see the advantages of using the geo standard, but we really need to have a way to incorporate and error or extent in meters. What would be

Re: Best Way to Extend the Geo Vocabulary to include an error or extent radius in meters

Thanks Bernard, I will try that! :-) - Pete On Thu, Oct 7, 2010 at 4:54 PM, Bernard Vatant bernard.vat...@mondeca.comwrote: Hi Peter Something like the example below, but I suspect that this might not make it a real geo:Point? barely. The old maths teacher in me frowns at points having

Re: TaxonConcept Interlinking SPARQL Query, Results and questions about interpretation

google search for a given scientific name brings up all sorts of poorly matched images and I suspect that the same might happen with linked data. Thanks Again, - Pete On Sat, Sep 18, 2010 at 1:42 PM, Richard Cyganiak rich...@cyganiak.dewrote: Peter, On 17 Sep 2010, at 20:48, Peter DeVries wrote

Updated TaxonConcept Knowledge Base, some changes / additions with explanations :-)

I have updated the TaxonConcept Knowledge Base data set. There are some changes that are worth mentioning. There is an additional download file mentioned in the void and sitemap.xml.gz called *se_states.rdf.gz* sc:dataDumpLocationhttp://lod.taxonconcept.org/txn_base.rdf.gz

Re: Way to generate LOD cloud diagram Interlinking Stats from the Virtuoso OpenSource SPARQL endpoint named graphs?

match and then will run the query you sent to get the latest info. Thanks! - Pete On Thu, Sep 9, 2010 at 10:39 AM, Richard Cyganiak rich...@cyganiak.dewrote: Peter, On 9 Sep 2010, at 02:54, Peter DeVries wrote: I was wondering if anyone has figured out a way to generate the LOD interlinking

Re: Way to generate LOD cloud diagram Interlinking Stats from the Virtuoso OpenSource SPARQL endpoint named graphs?

ocs.geospecies.org sws.geonames.org 39 - Pete On Thu, Sep 9, 2010 at 4:18 PM, Peter DeVries pete.devr...@gmail.comwrote: Hi Richard, You appear to be correct about versions. The public site is running the ubuntu package which is a little order. I have a private instance that is running

Re: Next version of the LOD cloud diagram. Please provide input, so that your dataset is included.

I was able to create a new OpenID and use that to update the documentation for the following entries: http://www.ckan.net/package/taxonconcept http://www.ckan.net/package/geospecies I have a number of links to GeoNames in GeoSpecies, but have not been able to get a count yet. This RDF will

Way to generate LOD cloud diagram Interlinking Stats from the Virtuoso OpenSource SPARQL endpoint named graphs?

I was wondering if anyone has figured out a way to generate the LOD interlinking (InLinks/OutLinks) stats from a Virtuoso OpenSource SPARQL Endpoint. The two named graphs I am most interested in are: urn:org:linkedopenspeciesdata:dataspace:taxonconcept *taxonconcept*

Re: Next version of the LOD cloud diagram. Please provide input, so that your dataset is included.

I am kind of annoyed by the CKAN site. 1) A lot of this information they are requesting are already provided by my void file, sitemap.xml and SPARQL Endpoint 2) My google openID does not seem to work on this site and their are no non-openid account setup alternative. 3) The TaxonConcept data set

Re: URI's for Geogrid like Resource

be reasoned. This sort of model for species range also seems to align well with conventional GIS vector and raster models. Cheers, -- Sean On Mon, Jun 14, 2010 at 10:30 PM, Peter DeVries pete.devr...@gmail.comwrote: Hi Søren, People will correct me if I am wrong but I think

Re: URI's for Geogrid like Resource

of saying Organism expectedIn geographicalArea - Pete On Fri, Jun 11, 2010 at 1:57 PM, Peter DeVries pete.devr...@gmail.comwrote: Hi Bernard, I was just looking through this spec yesterday. I am not sure. These would be have circles of uncertainty around them, so to cover the earth they would need

Re: Looking for use of skos mapping in the Linked Data Cloud

Hi Bernard, I have skos mapping in both TaxonConcept and GeoSpecies. See http://lod.taxonconcept.org/ses/mCcSp.rdf And http://lod.geospecies.org/ses/mCcSp.rdf Also EUNIS has skos mapping. It is RDFa See http://eunis.eea.europa.eu/species/90910 These should be in the cloud as they were

Re: Request for Feedback, Suggestions on TaxonConcept Species Concepts

. eunis:SpeciesSynonym rdf:about=http://eunis.eea.europa.eu/species/90910 skos:closeMatch rdf:resource= http://lod.taxonconcept.org/ses/mCcSp#Species/ rdfs:seeAlso rdf:resource=http://eunis.eea.europa.eu/species/90910/ /eunis:SpeciesSynonym - Pete On Sun, Jun 6, 2010 at 4:13 PM, Peter DeVries

Re: Request for Feedback, Suggestions on TaxonConcept Species Concepts

, - Pete On Sun, Jun 6, 2010 at 4:18 AM, Toby Inkster t...@g5n.co.uk wrote: On Fri, 4 Jun 2010 18:06:08 -0500 Peter DeVries pete.devr...@gmail.com wrote: I would appreciate feedback on these models and any suggestions for how they could be improved. :-) The following: @prefix txn

Re: Request for Feedback, Suggestions on TaxonConcept Species Concepts

18:06:08 -0500 Peter DeVries pete.devr...@gmail.com wrote: I would appreciate feedback on these models and any suggestions for how they could be improved. :-) The following: @prefix txn: http://lod.taxonconcept.org/ontology/txn.owl# . http://lod.taxonconcept.org/ses/mCcSp#Species

Request for Feedback, Suggestions on TaxonConcept Species Concepts

Hi Everyone, I am working on a new model for species concepts at TaxonConcept.org. These are an extension of my work on GeoSpecies, and are also designed to investigate mapping names to concepts as part of the Global Names Initiativehttp://gni.globalnames.org/ . The main difference between

Re: Request for Feedback, Suggestions on TaxonConcept Species Concepts

, instead of, say, dc:subject?) I look forward to using this dataset - Regards, Joel. On Fri, 4 Jun 2010, Peter DeVries wrote: Hi Everyone, I am working on a new model for species concepts at TaxonConcept.org. These are an extension of my work on GeoSpecies, and are also designed

Re: Request for Feedback, Suggestions on TaxonConcept Species Concepts

look forward to using this dataset - Regards, Joel. On Fri, 4 Jun 2010, Peter DeVries wrote: Hi Everyone, I am working on a new model for species concepts at TaxonConcept.org. These are an extension of my work on GeoSpecies, and are also designed to investigate mapping names to concepts

Re: Species Concept Mapping RDF fixes and question, should the species be represented as a class? Class SpeciesConcept = Class Species Cougar

If by reasoning you mean formal logic, and if you want to stay in OWL DL or some other computationally tractable RDF based language, I am inclined to guess that you will be forced to make this conclusion somewhat tautogical. In general you won't be able to use a single predicate, e.g.

Re: Species Concept Mapping RDF fixes and question, should the species be represented as a class? Class SpeciesConcept = Class Species Cougar

! - Pete On Tue, Dec 15, 2009 at 7:19 AM, Leigh Dodds leigh.do...@talis.com wrote: Hi Bob, 2009/12/4 Bob Morris morris@gmail.com: On Tue, Dec 1, 2009 at 10:14 PM, Peter DeVries pete.devr...@gmail.com wrote: ... In the end, for ecological observations, it is likely

Re: Lightweight RDF to Map Various Semantic Representations of Species

in the near future, so stay tuned. Cheers Bernard [1] http://blog.hubjects.com/2009/11/representation-as-translation.html 2009/11/30 Peter DeVries pete.devr...@gmail.com Hi LOD'ers :-) I am trying to work out some way to map the various semantic representations for a species

Species Concept Mapping RDF fixes and question, should the species be represented as a class? Class SpeciesConcept = Class Species Cougar

Hi LOD'ers, Richard Cyganiak was kind enough to suggest some fixes and changes, which you can see on the new version. http://rdf.taxonconcept.org/ses/v6n7p.rdf http://rdf.taxonconcept.org/ont/txn_doc/index.html http://rdf.taxonconcept.org/ont/void.rdf I also made another change which I would

Re: Species Concept Mapping RDF fixes and question, should the species be represented as a class? Class SpeciesConcept = Class Species Cougar

that will allow you to determine which concept is the best match for the captured specimen. * * At least that is what I would like to do. :-) - Pete On Tue, Dec 1, 2009 at 8:30 PM, Bob Morris morris@gmail.com wrote: On Tue, Dec 1, 2009 at 8:40 PM, Peter DeVries pete.devr...@gmail.com wrote: Hi

Lightweight RDF to Map Various Semantic Representations of Species

Hi LOD'ers :-) I am trying to work out some way to map the various semantic representations for a species, in conjunction with a friendly three letter organization. The goal of these documents is in part to improve findability of information about species. The hope is that they will also help

Re: Data linking to Geonames

Hi Bernard, I link to Geonames in both my species, observation and location RDF. At this point in time, the links in the species RDF make up the bulk of the interlinking. I am about to update my data, but here is a preview of the linking for each species RDF (one of 15,863) that will be online

Updated GeoSpecies Data Set 1,765,790 Triples

I have updated the GeoSpecies data set. You can read about it here: http://about.geospecies.org/ You can browse it here: http://lod.geospecies.org/ The RDF dump can be obtained here: Here is the new RDF dump http://lod.geospecies.org/geospecies.rdf.tar.gz (1,765,790 Triples) The data set

Re: Updated GeoSpecies Data Set

Hi Daniel, I am in the process of updating the GeoSpecies data set and have added your species to the database. I will send you a note when this new version is live. In the meantime, you might like to look over these sparql query examples. http://about.geospecies.org/sparql.xhtml

Re: Updated GeoSpecies Data Set

You should be able to submit the data to GBIF using their xml format. In my next update your species with author names will be linked to the GBIF id DBpedia Resource NCBI id - get you to bio2rdf resource and some others like Wikispecies. I have this done on the development machine, but I still

Example Queries of GeoSpecies Data Set

Here are some example SPARQL queries of the current GeoSpecies Data Set. They should work on your local triple store or, on the LOD once the new data set is updated. Note the difference between *geospecies:isExpectedIn* (could be expected in area even if unlikely) and

Updated GeoSpecies Data Set

I have fixed a number of issues and improved LOD linkages for the GeoSpecies data set. You can read about it here: http://about.geospecies.org/ http://about.geospecies.org/You can browse it here: http://lod.geospecies.org/ http://lod.geospecies.org/The RDF dump can be obtained here: Here is

New Version of the Geospecies Knowledge Base Data Set

I have a new version of the GeoSpecies Knowledge Base Dataset at: http://lod.geospecies.org/ You can download the new data dump at: http://lod.geospecies.org/geospecies.rdf.tar.tz It is either in the LOD could or will be soon. The major differences between this version are: 1) Shorter

What is the current thinking about how to tie a concept or tag to a webpage via LinkedData?

I was wondering what the current thinking is on ontologies that tie a concept or tag to a web page? I was thinking of creating links between species entities and webpages that are about that species. For instance the species entity *Puma concolor v6n7p *represented with this uri*:* * *

Re: Example RDF linking species concepts to photo gallery RDF, Suggestions or Comments Appreciated

to make two predicates? Thanks! - Pete On Fri, May 8, 2009 at 2:48 AM, Dan Brickley dan...@danbri.org wrote: On 8/5/09 09:14, Toby A Inkster wrote: On 8 May 2009, at 01:30, Peter DeVries wrote: With the except of the predicates speciesHasGallery, galleryHasSpecies. In http

How to represent different types of web pages and rdf resources?

I have been wondering about how to best represent different types of web pages or rdf resources. I think it is useful to represent some pages like Wikipedia pages as subclasses of foaf:document. This is because I would like to be able to easily query for the Wikipedia pages for a taxon without

Example RDF linking species concepts to photo gallery RDF, Suggestions or Comments Appreciated

I thought I would try marking up some RDF that links species concepts to a gallery of photo's of that species. Kingsley suggested I create links from my photo's to my species concepts using a photo gallery rdf for each species. The RDF was done by hand, but I created the uri so that it could be

Differences in thinking between TDWG and LinkedData groups about data sharing / integration

This paragraph below seems to encapsulate the differences in thinking between the linkeddata community and some of the TDWG people on how to best share biodiversity data. *The notion of a fabric of resources that are individually described, queried, and resolved may seem unmanageable or like

Uniprot Taxonomy rdfs:seeAlso vs. foaf:isPrimaryTopicOf

I was working with OpenLink Data Explorer, and I noticed the following in the uniprot taxonomy records See http://linkeddata.uriburner.com/about/html/http://purl.uniprot.org/taxonomy/7162 rdfs:seeAlso * http://en.wikipedia.org/wiki/Aedes *

Re: Updated GeoSpecies Knowledge Base, would welcome comments or suggestions

Hi Giovanni, I updated the site and data set. I fixed the sitemap file so it should work now. http://species.geospecies.org/sitemap.gz It mainly shows the rdf data dump location: http://rdf.geospecies.org/geospecies.rdf.tar.gz Also you should be able to crawl the data starting with this file: