Hi Joel,<div><br></div><div>Cool :-)</div><div><br></div><div>I just loaded this into my SPARQL endpoint.</div><div><br></div><div>In the named graph <font class="Apple-style-span" face="'courier new', monospace">urn:org:linkedopenspeciesdata:dataspace:tdwg2010bioblitz</font></div>
<div><br></div><div>It consists of 19,990 Triples</div><div><br></div><div>Here is one of the dwc:taxonConceptID entries.</div><div><br></div><div><b>About: <a href="http://spire.umbc.edu/ethan/Ampelopsis_brevipedunculata">http://spire.umbc.edu/ethan/Ampelopsis_brevipedunculata</a></b></div>
<div><a href="http://lsd.taxonconcept.org/describe/?url=http://spire.umbc.edu/ethan/Ampelopsis_brevipedunculata">http://lsd.taxonconcept.org/describe/?url=http://spire.umbc.edu/ethan/Ampelopsis_brevipedunculata</a></div><div>
<br></div><div><b>About: <a href="http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1627">http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1627</a></b></div><div><a href="http://lsd.taxonconcept.org/describe/?url=http://spire.umbc.edu/ethan/Ampelopsis_brevipedunculata"></a><a href="http://lsd.taxonconcept.org/describe/?url=http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1627">http://lsd.taxonconcept.org/describe/?url=http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1627</a></div>
<div><br></div><div><br></div><div><a href="http://lsd.taxonconcept.org/describe/?url=http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1627"></a>This should give you an a count of occurrences.</div><div><br></div>
<div><div><font class="Apple-style-span" face="'courier new', monospace">SELECT count(*) WHERE {?s a <<a href="http://rs.tdwg.org/dwc/terms/#Occurrence">http://rs.tdwg.org/dwc/terms/#Occurrence</a>>};</font></div>
<div><br></div><div>= 1882</div><div><br></div><div><meta charset="utf-8"><span class="Apple-style-span" style="font-family: 'courier new', monospace; ">SELECT count(*) WHERE {?s a <<a href="http://rs.tdwg.org/dwc/terms/#taxonConceptID">http://rs.tdwg.org/dwc/terms/#taxonConceptID</a>>};</span></div>
<div><br></div><div>This should give you a list of occurrences</div><div><br></div><div><a href="http://lsd.taxonconcept.org/describe/?url=http://rs.tdwg.org/dwc/terms/%23Occurrence">http://lsd.taxonconcept.org/describe/?url=http://rs.tdwg.org/dwc/terms/%23Occurrence</a><br>
</div><div><br></div><div>If this did not come through your email system try the <a href="http://bit.ly">bit.ly</a>.</div><div><br></div><div><a href="http://bit.ly/g9BcoL">http://bit.ly/g9BcoL</a><br></div><div><br></div>
<div>I tried the following that should have given me a google map of all the occurrences but it did not result in the map.</div><div><br></div><div><div><font class="Apple-style-span" face="'courier new', monospace">DESCRIBE ?x WHERE { </font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"> ?x <<a href="http://www.w3.org/1999/02/22-rdf-syntax-ns#type">http://www.w3.org/1999/02/22-rdf-syntax-ns#type</a>> <<a href="http://rs.tdwg.org/dwc/terms/#Occurrence">http://rs.tdwg.org/dwc/terms/#Occurrence</a>>.</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">}</font></div></div><div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'trebuchet ms', sans-serif">I looked that the RDF and I think I see the problem.</font></div>
<div><br></div><div>In the RDF </div><div><br></div><div><div><font class="Apple-style-span" face="'courier new', monospace"><geo:latitude></font></div><div><font class="Apple-style-span" face="'courier new', monospace">41.53</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"></geo:latitude></font></div><div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace"><geo:longitude></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">-70.67</font></div><div><font class="Apple-style-span" face="'courier new', monospace"></geo:longitude></font></div></div><div><br>
</div><div>Should be</div><div><br></div><div><meta charset="utf-8"><div><font class="Apple-style-span" face="'courier new', monospace"><geo:lat></font></div><div><font class="Apple-style-span" face="'courier new', monospace">41.53</font></div>
<div><font class="Apple-style-span" face="'courier new', monospace"></geo:lat></font></div><div><font class="Apple-style-span" face="'courier new', monospace"><br></font></div><div><font class="Apple-style-span" face="'courier new', monospace"><geo:long></font></div>
<div><font class="Apple-style-span" face="'courier new', monospace">-70.67</font></div><div><font class="Apple-style-span" face="'courier new', monospace"></geo:long></font></div></div><div><br></div>
<div>See <a href="http://www.w3.org/2003/01/geo/">http://www.w3.org/2003/01/geo/</a></div><div><br></div><div>I did the following query to get a list of all the dwc:taxonConceptID's and have attached them as a .txt file.</div>
<div><br></div><div><font class="Apple-style-span" face="'courier new', monospace">select distinct ?o WHERE {?s <<a href="http://rs.tdwg.org/dwc/terms/#taxonConceptID">http://rs.tdwg.org/dwc/terms/#taxonConceptID</a>> ?o}</font></div>
<div><br></div><div>Pretty neat :-)</div><div><br></div><div>There are some things that I will get back to Joel on.</div><div><br></div><div>Here is where you can manually enter a SPARQL query. Click on "Advanced" for the entry window.</div>
<div><br></div><div><a href="http://lsd.taxonconcept.org/isparql/">http://lsd.taxonconcept.org/isparql/</a><br></div><div><br></div><div>Respectfully,</div><div><br></div><div>- Pete</div><div><br></div><div><br></div><br>
<div class="gmail_quote">On Wed, Jan 12, 2011 at 5:55 PM, joel sachs <span dir="ltr"><<a href="mailto:jsachs@csee.umbc.edu">jsachs@csee.umbc.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi Everyone,<br>
<br>
I've posted rdf of the bioblitz data. It's at<br>
<a href="http://www.cs.umbc.edu/~jsachs/occurrences/TechnoBioblitzOccurrences.rdf" target="_blank">http://www.cs.umbc.edu/~jsachs/occurrences/TechnoBioblitzOccurrences.rdf</a> .<br>
<br>
Individual occurrences can be retrieved via<br>
<a href="http://www.cs.umbc.edu/~jsachs/occurrences/[occurrence_id]" target="_blank">http://www.cs.umbc.edu/~jsachs/occurrences/[occurrence_id]</a><br>
e.g. <a href="http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1835" target="_blank">http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1835</a><br>
<br>
Individual identifications can be retrieved via<br>
<a href="http://www.cs.umbc.edu/~jsachs/identifications/[identification_id]" target="_blank">http://www.cs.umbc.edu/~jsachs/identifications/[identification_id]</a><br>
e.g.<br>
<a href="http://www.cs.umbc.edu/~jsachs/identifications/tdwg2010bioblitz_1835_id_1" target="_blank">http://www.cs.umbc.edu/~jsachs/identifications/tdwg2010bioblitz_1835_id_1</a><br>
<br>
The scripts behind this are on the kludgy side, so reports of errors and<br>
abnormalities will be warmly welcomed.<br>
<br>
Implicit in each of the following notes is the question "Is this a good<br>
way to do it?":<br>
<br>
1. The data is "normalized" w.r.t. identification. "Normalized" is in<br>
quotes because I mean it in the sense that Steve Baskauf was using in his<br>
Fall 2010 series of posts. His meaning of the term makes sense to me, but<br>
many people (e.g. the OBO folks), take "normalized ontology" to mean<br>
"disentangled" (i.e. no multiple inheritance.)<br>
As an example, here's an occurrence with two crowdsourced determinations:<br>
<a href="http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644" target="_blank">http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644</a><br>
<br>
2. I used sequential integers for observation and identification IDs; in<br>
practice, a mechanism needs to be in place to prevent two people from<br>
assigning the same id to their respective identifications.<br>
<br>
3. My answer to Cam Webb's Question #1 from<br>
<a href="http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001720.html" target="_blank">http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001720.html</a><br>
is "both". In other words, just as "Joel Sachs" is both me and also my<br>
name, so<br>
<a href="http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1668" target="_blank">http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1668</a> is both<br>
an occurrence and an occurrence_id, expressed as:<br>
---<br>
<dwc:Occurrence<br>
rdf:about="<a href="http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644" target="_blank">http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644</a>"><br>
<dwc:occurrenceID><br>
<a href="http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644" target="_blank">http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644</a><br>
</dwc:occurrenceID><br>
<blah blah blah/><br>
</dwc:Occurrence><br>
---<br>
<br>
4. I was surprised to see that the Darwin Core Identification class has no<br>
"occurrenceID" or "specimenID" term. How is one supposed to tie an<br>
identification to an observation (assuming the identification is not<br>
in-lined, of course)? DeVries and Baskauf each mint their own terms for<br>
doing this (txn:identificationHasOccurrence, and sernec:basedOnOccurrence,<br>
respectively); I used dwc:occurrenceID as if it were a record level term.<br>
<br>
5. We had scope for multiple taxonConceptID columns in the Fusion table,<br>
and assigned lsids where possible. I also mean to work with Pete to assign<br>
GUIDs from <a href="http://taxoncocept.org" target="_blank">taxoncocept.org</a>. In addition, I assigned ethan taxon concept<br>
ids, which look like this:<br>
http:.//<a href="http://spire.umbc.edu/ethan/Coffea_arabica" target="_blank">spire.umbc.edu/ethan/Coffea_arabica</a><br>
<br>
In their argument over opaque vs. transparent taxonCoceptIDs, I was<br>
sympathetic to both Pete's and Gregor's arguments. Ultimately, if the<br>
tooling exists to always display the rdfs:labels every time I'm loooking<br>
at a list of opaqueIDs, then transparent IDs are unnecessary. But, for<br>
now, it's really helpful to look at an ID and know what it's referring to.<br>
<br>
(For species names not in the spire database, the rdf returned by<br>
http:.//<a href="http://spire.umbc.edu/ethan/$name" target="_blank">spire.umbc.edu/ethan/$name</a><br>
is simply an rdfs:seeAlso to<br>
http://<a href="http://gni.globalnames.org/name_strings?search_term=$name" target="_blank">http://gni.globalnames.org/name_strings?search_term=$name</a>)<br>
<br>
6. It was easy to assert membership in RDF classes corresponding to<br>
various Cape Cod categories of concern - invasive species, threatenened<br>
species, indicators, etc. You can see these classes at<br>
<a href="http://spire.umbc.edu/ontologies/lists" target="_blank">http://spire.umbc.edu/ontologies/lists</a> (Information of where these lists<br>
come from is included as rdfs:comments. I'll add further documentation,<br>
e.g. links to eml files.)<br>
<br>
Note that "ThingOfConcern" is defined as the superclass of all the other<br>
classes in the collection. The idea here is that people can create their<br>
own "ThingOfConcern" class, and then query for observations that are of<br>
concern to them. You can see sample sparql queries at<br>
<a href="http://www.csee.umbc.edu/~jsachs/occurrences/queries/sample.txt" target="_blank">http://www.csee.umbc.edu/~jsachs/occurrences/queries/sample.txt</a><br>
<br>
<br>
As an aside, I think we, as a community, should come up with a<br>
biodiversity benchmark suite of rdf data and corresponding sparql queries, that can be<br>
used to test the suitability and scalability of semantic web knowledge<br>
bases. I'll take this up in a future post (unless someone beats me to it).<br>
<br>
Comments, questions, and better ideas are welcome.<br>
<br>
Thanks -<br>
Joel.<br>
<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><a href="http://www.taxonconcept.org/" target="_blank">TaxonConcept Knowledge Base</a> / <a href="http://lod.geospecies.org/" target="_blank">GeoSpecies Knowledge Base</a><br><a href="http://about.geospecies.org/" target="_blank">About the GeoSpecies Knowledge Base</a><br>
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