Hi Joel,

In the next day or so I will upload my TDWG talk to SlideShare, it explains some of this.

**But remember this was just an experiment to see if it would work.***

The main advantage of creating URI's for commonly used things is that then you can browse the connections between them and have them be the subjects of triples.

See http://bit.ly/hTJkWz

It also allows you to connect additional information to a person or thing that has a URI.

See attached png 

In an ideal world, I might have done something like this.

http://notarealsite.org/genus_epithet

So a semantic web service would look up http://notarealsite.org/Puma_concolor

Retrieve http://notarealsite.org/Puma_concolor.rdf

Which would give you:

1) list of what databases have that name

2) and what various kingdoms or Name Rules the different names fall under (Plant, Animal etc)

   For example: "This is both a plant and an animal name"

3) What are the current valid names for each of the species listed. => The list of related names you listed in your email.

=> Puma concolor (Linnaeus 1771)

I think this would be very useful since a number of data sources only list the genus and specific epithet.

* For instance the index that is at the back of the Entomology Society of America Annual Meeting Booklet

There are a couple of hurdles however.

1) What is the valid form of the name? Is there a machine that knows this or will this need to be partially curated by humans?
    In some cases the "valid" name is not clear.

2) Even though there are ~20 million names, there are probably some valid names that are not in the GNI.
    This is why I would encourage everyone to upload their names.

If these exist as URI's you get the following abilities

<gni_namestring:001> isSynonymOf <gni_namestring:002> etc.

Not that literals cannot be "subjects" of the subject-predicate-object triple.

Also, as current configured names like Callithrix melanura (É. Geoffroy 1812) and Callithrix melanura (E. Geoffroy 1812) are seen as different.

* Also the É. will have to be properly escaped to be part of a valid URL.

So a simple text search might not find them.

So in summary if we are going to get past everyone marking up their own name list in excel and then trying to merge them, we will need some architecture than
can scale to millions of names and allow different groups to make assertions about the relationships between those names.



Searching TaxonConcept.org:

For now you have two options for searching for names. (I am mainly concentrating on the RDF representation right now)

You can use google "Puma concolor site:lod.taxonconcept.org" *Google seems to prefer the .rdf version even though my sitemap specifies the .html.

Or use the Knowledge Base http://lsd.taxonconcept.org/fct/

I think I sent out a list of all the species collected at the BioBlitz, with their matching species concept ID.

Did you not get this? I think it on the Google site.


> iv. In what sense do you see Darwin Core as being deficient as a semantic web representation?

You agreed previously that some of the fields that currently use Literals would be more efficiently and unambiguously represented as URI's.

I would characterize DarwinCore as "not optimal" rather than deficient.

There is no reason we can't still use the DarwinCore for what it is good for, but it does not work very well for SPARQL queries and the LOD.

For instance, a search of occurrences of this Callithrix melanura (É. Geoffroy 1812) will not return occurrences with Callithrix melanura (E. Geoffroy 1812).

Respectfully,

- Pete



On Tue, Jan 18, 2011 at 1:42 PM, joel sachs <jsachs@csee.umbc.edu> wrote:
Pete -

I'm glad you're doing cool things with the data. A few comments/answers/questions ...

i. The quests for consistently used canonical URIs, and consistently used canonical names are both, for now, somewhat quixotic, and I'm not sure one is more so than the other. GNA/GNI seems to be pursuing both. Is that a fair assessment?

ii. I used opaque taxon concept URIs where they were readily available. Laziness motivated me to also use transparent identifiers for
a. making sure each taxonConcept had an rdf:resource as an identifier, and
b. asserting membership in the various rdfs:classes that I defined. But laziness has its drawbacks, and you point out a few of them. I think best practice when using either names or transparent URIs as identifiers would be to first run them through a spell checker and normalizer that would produce consistent usage of upper and lowe case characters, and probably drop authorship. Of course, this would produce some false positives when doing any sort of querying. But using UUIDs produces false negatives since they're not in common use. If we (as a community) follow through on the enthusiasm for creating competency cases that we showed in the Fall, it would be interesting to consider each case from the question of what's worse - false positives or false negatives. In any event, false positives can be weeded out by using the full scientific names and contextual information in the record, whereas false negatives may never be discovered.

BTW, does anyone know a good spell checker for scientific names?

iii. Mapping names to opaque URIs doesn't resolve the problems you raise below. Will the identifer for
Carpodacus mexicanus
be the same as the identifier for
Carpodacus mexicanus (Statius Muller, 1776)?

How about
Arabis laevigata (Muhl. ex Willd.) Poir.
vs.
Arabis laevigata ?

If yes, then why noy just use normalized names as identifiers? If no, then we'll get false negatives in the sorts of SPARQL queries that I gave at

http://www.csee.umbc.edu/~jsachs/occurrences/queries/

BTW, is there a lookup service for taxonconcept.org identifiers (i.e. give a list of names, get a list of identifiers)?

iv. In what sense do you see Darwin Core as being deficient as a semantic web representation?

Regards -
Joel.



On Thu, 13 Jan 2011, Peter DeVries wrote:

Thanks Joel,

Here is one of the BioBlitz Occurrence Records marked up with Darwin Core

http://lsd.taxonconcept.org/describe/?url=http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_5&sid=217&urilookup=1

Here is one of the TaxonConcept Records marked up in the txn vocabulary
http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9%23Occurrence

Some people have trouble with how the %23 above is escaped in their email,
they might like this bit.ly bundle
better.<http://lsd.taxonconcept.org/describe/?url=http://ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9%23Occurrence>
<http://lsd.taxonconcept.org/about/html/http/ocs.taxonconcept.org/ocs/f522444a-2dd9-400e-be59-47213ef38cb9%01Occurrence>
http://bit.ly/hZdUpP


<http://bit.ly/hZdUpP>Also an issue to discuss is that identifications are
to both a name and a concept so

Should these should be the same dwc:taxonConcepts

http://spire.umbc.edu/ethan/Apis_mellifera
http://spire.umbc.edu/ethan/Apis_Mellifera
==> http://bit.ly/g1zzJC (Apis mellifera se:z9oqP)

http://spire.umbc.edu/ethan/Ascelpius_syruaca
http://spire.umbc.edu/ethan/Asclepias_syriaca
==> HTML page http://lod.taxonconcept.org/ses/tTEIq.html Concept View
Bit.ly http://bit.ly/dJHJqj

http://spire.umbc.edu/ethan/Aster_nova-belgii
http://spire.umbc.edu/ethan/Aster_nova-gelgii

http://spire.umbc.edu/ethan/Baccharis_halimifolia
http://spire.umbc.edu/ethan/Baccharis_halimifolia_L.

http://spire.umbc.edu/ethan/Bartonia_virginia
http://spire.umbc.edu/ethan/Bartonia_virginica

http://spire.umbc.edu/ethan/Branta_canadensis
http://spire.umbc.edu/ethan/Branta_canadensis_(Linnaeus,_1758)

http://spire.umbc.edu/ethan/Carex_pennsylvanica
http://spire.umbc.edu/ethan/Carex_pensylvanica

http://spire.umbc.edu/ethan/Cyperus_esculantus
http://spire.umbc.edu/ethan/Cyperus_Esculantus
http://spire.umbc.edu/ethan/Cyperus_esculentus
http://spire.umbc.edu/ethan/Cyperus_esculentus_L.

http://spire.umbc.edu/ethan/Carpodacus_mexicanus
http://spire.umbc.edu/ethan/Carpodacus_mexicanus_(Statius_Muller,_1776)

>From the taxonconcepts their should be a link to the various name strings.

vs. modeling the namestring as the concept.

Also I think that DarwinCore is good for somethings but maybe not as a
semantic web representation.

Respectfully,

- Pete


On Thu, Jan 13, 2011 at 6:53 AM, joel sachs <jsachs@csee.umbc.edu> wrote:

Pete,
Thanks - I corrected the geo properties.
Joel.




On Wed, 12 Jan 2011, Peter DeVries wrote:

 Hi Joel,

Cool :-)

I just loaded this into my SPARQL endpoint.

In the named graph
urn:org:linkedopenspeciesdata:dataspace:tdwg2010bioblitz

It consists of 19,990 Triples

Here is one of the dwc:taxonConceptID entries.

*About: http://spire.umbc.edu/ethan/Ampelopsis_brevipedunculata*

http://lsd.taxonconcept.org/describe/?url=http://spire.umbc.edu/ethan/Ampelopsis_brevipedunculata

*About: http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1627*
<
http://lsd.taxonconcept.org/describe/?url=http://spire.umbc.edu/ethan/Ampelopsis_brevipedunculata


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
This
should give you an a count of occurrences.

SELECT count(*) WHERE {?s a <http://rs.tdwg.org/dwc/terms/#Occurrence>};

= 1882

SELECT count(*) WHERE {?s a <http://rs.tdwg.org/dwc/terms/#taxonConceptID
};

This should give you a list of occurrences


http://lsd.taxonconcept.org/describe/?url=http://rs.tdwg.org/dwc/terms/%23Occurrence

If this did not come through your email system try the bit.ly.

http://bit.ly/g9BcoL

I tried the following that should have given me a google map of all the
occurrences but it did not result in the map.

DESCRIBE ?x WHERE {
 ?x <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <
http://rs.tdwg.org/dwc/terms/#Occurrence>.
}

I looked that the RDF and I think I see the problem.

In the RDF

<geo:latitude>
41.53
</geo:latitude>

<geo:longitude>
-70.67
</geo:longitude>

Should be

<geo:lat>
41.53
</geo:lat>

<geo:long>
-70.67
</geo:long>

See http://www.w3.org/2003/01/geo/

I did the following query to get a list of all the dwc:taxonConceptID's
and
have attached them as a .txt file.

select distinct ?o WHERE {?s <
http://rs.tdwg.org/dwc/terms/#taxonConceptID>
?o}

Pretty neat :-)

There are some things that I will get back to Joel on.

Here is where you can manually enter a SPARQL query. Click on "Advanced"
for
the entry window.

http://lsd.taxonconcept.org/isparql/

Respectfully,

- Pete



On Wed, Jan 12, 2011 at 5:55 PM, joel sachs <jsachs@csee.umbc.edu> wrote:

 Hi Everyone,

I've posted rdf of the bioblitz data. It's at
http://www.cs.umbc.edu/~jsachs/occurrences/TechnoBioblitzOccurrences.rdf.

Individual occurrences can be retrieved via
http://www.cs.umbc.edu/~jsachs/occurrences/[occurrence_id]<http://www.cs.umbc.edu/~jsachs/occurrences/%5Boccurrence_id%5D>

e.g. http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1835

Individual identifications can be retrieved via
http://www.cs.umbc.edu/~jsachs/identifications/[identification_id]<http://www.cs.umbc.edu/~jsachs/identifications/%5Bidentification_id%5D>

e.g.
http://www.cs.umbc.edu/~jsachs/identifications/tdwg2010bioblitz_1835_id_1

The scripts behind this are on the kludgy side, so reports of errors and
abnormalities will be warmly welcomed.

Implicit in each of the following notes is the question "Is this a good
way to do it?":

1. The data is "normalized" w.r.t. identification. "Normalized" is in
quotes because I mean it in the sense that Steve Baskauf was using in his
Fall 2010 series of posts. His meaning of the term makes sense to me, but
many people (e.g. the OBO folks), take "normalized ontology" to mean
"disentangled" (i.e. no multiple inheritance.)
As an example, here's an occurrence with two crowdsourced determinations:
http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644

2. I used sequential integers for observation and identification IDs; in
practice, a mechanism needs to be in place to prevent two people from
assigning the same id to their respective identifications.

3. My answer to Cam Webb's Question #1 from
http://lists.tdwg.org/pipermail/tdwg-content/2010-October/001720.html
is "both". In other words, just as "Joel Sachs" is both me and also my
name, so
http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1668 is both
an occurrence and an occurrence_id, expressed as:
---
<dwc:Occurrence
rdf:about="
http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644">
<dwc:occurrenceID>
http://www.cs.umbc.edu/~jsachs/occurrences/tdwg2010bioblitz_1644
</dwc:occurrenceID>
<blah blah blah/>
</dwc:Occurrence>
---

4. I was surprised to see that the Darwin Core Identification class has
no
"occurrenceID" or "specimenID" term. How is one supposed to tie an
identification to an observation (assuming the identification is not
in-lined, of course)? DeVries and Baskauf each mint their own terms for
doing this (txn:identificationHasOccurrence, and
sernec:basedOnOccurrence,
respectively); I used dwc:occurrenceID as if it were a record level term.

5. We had scope for multiple taxonConceptID columns in the Fusion table,
and assigned lsids where possible. I also mean to work with Pete to
assign
GUIDs from taxoncocept.org. In addition, I assigned ethan taxon concept
ids, which look like this:
http:.//spire.umbc.edu/ethan/Coffea_arabica

In their argument over opaque vs. transparent taxonCoceptIDs, I was
sympathetic to both Pete's and Gregor's arguments. Ultimately, if the
tooling exists to always display the rdfs:labels every time I'm loooking
at a list of opaqueIDs, then transparent IDs are unnecessary. But, for
now, it's really helpful to look at an ID and know what it's referring
to.

(For species names not in the spire database, the rdf returned by
http:.//spire.umbc.edu/ethan/$name
is simply an rdfs:seeAlso to
http://http://gni.globalnames.org/name_strings?search_term=$name)

6. It was easy to assert membership in RDF classes corresponding to
various Cape Cod categories of concern - invasive species, threatenened
species, indicators, etc. You can see these classes at
http://spire.umbc.edu/ontologies/lists (Information of where these lists
come from is included as rdfs:comments. I'll add further documentation,
e.g. links to eml files.)

Note that "ThingOfConcern" is defined as the superclass of all the other
classes in the collection. The idea here is that people can create their
own "ThingOfConcern" class, and then query for observations that are of
concern to them. You can see sample sparql queries at
http://www.csee.umbc.edu/~jsachs/occurrences/queries/sample.txt


As an aside, I think we, as a community, should come up with a
biodiversity benchmark suite of rdf data and corresponding sparql
queries,
that can be
used to test the suitability and scalability of semantic web knowledge
bases. I'll take this up in a future post (unless someone beats me to
it).

Comments, questions, and better ideas are welcome.

Thanks -
Joel.

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--
---------------------------------------------------------------
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/>
------------------------------------------------------------




--
---------------------------------------------------------------
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/>
------------------------------------------------------------




--
---------------------------------------------------------------
Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
TaxonConcept Knowledge Base / GeoSpecies Knowledge Base
About the GeoSpecies Knowledge Base
------------------------------------------------------------