YOKOFAKUN: SPARQL for solubility/RDF: my notebook

In a recent thread on FriendFeed , I've transformed Jean-Claude's Bradley's data about the solubility of some compounds into RDF.

The original data set looks like this:

The RDF version looks like this:

<!DOCTYPE rdf:RDF [
          <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#">
          <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#">
          <!ENTITY doap "http://usefulinc.com/ns/doap#">
          <!ENTITY foaf "http://xmlns.com/foaf/0.1/">
          <!ENTITY dc "http://purl.org/dc/elements/1.1/">
          <!ENTITY chem "http://blueobelisk.sourceforge.net/chemistryblogs/">
          ]>
<rdf:RDF
        xmlns:rdf="&rdf;"
        xmlns:dc="&dc;"
        xmlns:rdfs="&rdfs;"
        xmlns:doap="&doap;"
        xmlns:foaf="&foaf;"
        xmlns:chem="&chem;"
        >
<!--=== PERSONS ============================================================== -->
<foaf:Person rdf:about="http://www.chemistry.drexel.edu/people/bradley/bradley.asp">
        <foaf:name>Jean-Claude Bradley</foaf:name>
        <foaf:nick>jcbradley</foaf:nick>
        <foaf:sha1_sum>b68f7dca9555a1cfe1ad18c6d2be0db6e552d678</foaf:sha1_sum>
        <foaf:holdsAccount>
                <foaf:OnlineAccount>
                        <foaf:accountServiceHomepage rdf:resource="http://www.linkedin.com/"/>
                        <foaf:accountProfilePage rdf:resource="http://www.linkedin.com/in/jcbradley"/>
                </foaf:OnlineAccount>
        </foaf:holdsAccount>
</foaf:Person>

<!--=== PROJECT ============================================================== -->
<doap:Project rdf:ID="SolubilityProject">
        <doap:name>Solubility</doap:name>
        <doap:homepage rdf:resource="http://spreadsheets.google.com/ccc?key=plwwufp30hfq0udnEmRD1aQ" />
        <doap:shortdesc xml:lang="en">Solubility</doap:shortdesc>
        <doap:shortdesc xml:lang="fr">Solubilité</doap:shortdesc>
        <doap:description xml:lang="en">Solubility</doap:description>
        <doap:description xml:lang="fr">Solubilité</doap:description>
</doap:Project>
<!--=== Compound ============================================================== -->

<chem:Compound rdf:about="http://commons.wikimedia.org/wiki/Image:D-Mannitol_structure.png">
        <chem:name>D-Manitol</chem:name>
        <chem:image rdf:resource="http://upload.wikimedia.org/wikipedia/commons/b/bb/D-Mannitol_structure.png"/>
        <chem:smiles>O[C@H]([C@H](O)CO)[C@H](O)[C@H](O)CO</chem:smiles>
</chem:Compound>

<chem:Compound rdf:about="http://en.wikipedia.org/wiki/Ethanol">
        <chem:name>Ethanol</chem:name>
        <chem:image rdf:resource="http://upload.wikimedia.org/wikipedia/commons/6/6f/Ethanol_flat_structure.png"/>
        <chem:smiles>OCC</chem:smiles>
</chem:Compound>

<chem:Compound rdf:about="http://en.wikipedia.org/wiki/Sodium_chloride">
        <chem:name>Sodium chloride</chem:name>
        <chem:image rdf:resource="http://upload.wikimedia.org/wikipedia/commons/e/e9/Sodium-chloride-3D-ionic.png"/>
        <chem:smiles>[Na+].[Cl-]</chem:smiles>
</chem:Compound>

<!--=== Experiment ============================================================== -->
<chem:Experiment rdf:about="http://usefulchem.wikispaces.com/exp207">
        <dc:name>Hello, I'm Experiment 207</dc:name>
        <chem:project rdf:resource="#SolubilityProject"/>
</chem:Experiment>

<chem:Experiment rdf:about="http://usefulchem.wikispaces.com/exp1">
        <dc:name>Hello, I'm Experiment 1</dc:name>
        <chem:project rdf:resource="#SolubilityProject"/>
</chem:Experiment>

<!--=== Sample ============================================================== -->
<chem:Sample rdf:about="sample:11">
        <dc:name>Hello, I'm Sample 11</dc:name>
</chem:Sample>
<chem:Sample rdf:about="sample:3">
        <dc:name>Hello, I'm Sample 3</dc:name>
</chem:Sample>
<chem:Sample rdf:about="sample:12">
        <dc:name>Hello, I'm Sample 12</dc:name>
</chem:Sample>
<!--=== Experimental Data ============================================================== -->
<chem:ExperimentalData >
        <dc:date>2008-01-01</dc:date>
        <chem:author rdf:resource="http://www.chemistry.drexel.edu/people/bradley/bradley.asp"/>
        <chem:solute rdf:resource="http://commons.wikimedia.org/wiki/Image:D-Mannitol_structure.png"/>
        <chem:solvent rdf:resource="http://en.wikipedia.org/wiki/Ethanol"/>
        <chem:experiment-id rdf:resource="http://usefulchem.wikispaces.com/exp207"/>
        <chem:sample rdf:resource="sample:11"/>
        <chem:concentration rdf:datatype="chem:Molar">0.00</chem:concentration>
</chem:ExperimentalData>

<chem:ExperimentalData>
        <dc:date>2008-02-01</dc:date>
        <chem:author rdf:resource="http://www.chemistry.drexel.edu/people/bradley/bradley.asp"/>
        <chem:solute rdf:resource="http://en.wikipedia.org/wiki/Sodium_chloride"/>
        <chem:solvent rdf:resource="http://en.wikipedia.org/wiki/Ethanol"/>
        <chem:experiment-id rdf:resource="http://onschallenge.wikispaces.com/JennyHale-1"/>
        <chem:sample rdf:resource="sample:3"/>
        <chem:concentration rdf:datatype="chem:Molar">0.00</chem:concentration>
</chem:ExperimentalData>

<chem:ExperimentalData>
        <dc:date>2008-03-01</dc:date>
        <chem:author rdf:resource="http://www.chemistry.drexel.edu/people/bradley/bradley.asp"/>
        <chem:solute rdf:resource="http://en.wikipedia.org/wiki/Sodium_chloride"/>
        <chem:solvent rdf:resource="http://en.wikipedia.org/wiki/Ethanol"/>
        <chem:experiment-id rdf:resource="http://usefulchem.wikispaces.com/exp207"/>
        <chem:sample rdf:resource="sample:12"/>
        <chem:concentration rdf:datatype="chem:Molar">0.00</chem:concentration>
</chem:ExperimentalData>

</rdf:RDF>

Here I describe how I used SPARQL to retrieve Jean-Claude's original data set from this RDF file.
I've downloaded ARQ , the SPARQL engine, from http://jena.sourceforge.net/ARQ/.
Here are a few queries:

listing all the chem:Compound

query

PREFIX rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX doap: <http://usefulinc.com/ns/doap#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX dc:   <http://purl.org/dc/elements/1.1/>
PREFIX chem: <http://blueobelisk.sourceforge.net/chemistryblogs/>

SELECT ?x
{
    ?x  
}

Running the query

sparql -query jeter.rq --data=solubility.rdf

Result

----------------------------------------------------------------------
| x                                                                  |
======================================================================
| <http://en.wikipedia.org/wiki/Sodium_chloride>                     |
| <http://en.wikipedia.org/wiki/Ethanol>                             |
| <http://commons.wikimedia.org/wiki/Image:D-Mannitol_structure.png> |
----------------------------------------------------------------------

The same query but using prefixes

query

PREFIX rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX doap: <http://usefulinc.com/ns/doap#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX dc:   <http://purl.org/dc/elements/1.1/>
PREFIX chem: <http://blueobelisk.sourceforge.net/chemistryblogs/>

SELECT ?x
{
    ?x rdf:type chem:Compound
}

result

----------------------------------------------------------------------
| x                                                                  |
======================================================================
| <http://en.wikipedia.org/wiki/Sodium_chloride>                     |
| <http://en.wikipedia.org/wiki/Ethanol>                             |
| <http://commons.wikimedia.org/wiki/Image:D-Mannitol_structure.png> |
----------------------------------------------------------------------

Listing the compounds , their names, their 'smiles'

query

PREFIX rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX doap: <http://usefulinc.com/ns/doap#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX dc:   <http://purl.org/dc/elements/1.1/>
PREFIX chem: <http://blueobelisk.sourceforge.net/chemistryblogs/>

SELECT ?compound ?compoundName ?compoundSmiles
{
    ?compound rdf:type chem:Compound .
    ?compound chem:name ?compoundName .
    ?compound chem:smiles ?compoundSmiles .
}

result

-----------------------------------------------------------------------------------------------------------------------------------
| compound                                                           | compoundName      | compoundSmiles                         |
===================================================================================================================================
| <http://en.wikipedia.org/wiki/Sodium_chloride>                     | "Sodium chloride" | "[Na+].[Cl-]"                          |
| <http://en.wikipedia.org/wiki/Ethanol>                             | "Ethanol"         | "OCC"                                  |
|  | "D-Manitol"       | "O[C@H]([C@H](O)CO)[C@H](O)[C@H](O)CO" |
-----------------------------------------------------------------------------------------------------------------------------------

The same, but only the compounds with a name containing "OL"

query

PREFIX rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX doap: <http://usefulinc.com/ns/doap#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX dc:   <http://purl.org/dc/elements/1.1/>
PREFIX chem: <http://blueobelisk.sourceforge.net/chemistryblogs/>

SELECT ?compound ?compoundName ?compoundSmiles
{
    ?compound rdf:type chem:Compound .
    ?compound chem:name ?compoundName .
    ?compound chem:smiles ?compoundSmiles .
    FILTER regex(?compoundName, "ol", "i")
}

result

------------------------------------------------------------------------------------------------------------------------------
| compound                                                           | compoundName | compoundSmiles                         |
==============================================================================================================================
| <http://en.wikipedia.org/wiki/Ethanol>                             | "Ethanol"    | "OCC"                                  |
| <http://commons.wikimedia.org/wiki/Image:D-Mannitol_structure.png> | "D-Manitol"  | "O[C@H]([C@H](O)CO)[C@H](O)[C@H](O)CO" |
------------------------------------------------------------------------------------------------------------------------------

the same, but add the 'chem:description', if any

query

PREFIX rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX doap: <http://usefulinc.com/ns/doap#>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX dc:   <http://purl.org/dc/elements/1.1/>
PREFIX chem: <http://blueobelisk.sourceforge.net/chemistryblogs/>

SELECT ?compound ?compoundName ?compoundSmiles ?description
{
    ?compound rdf:type chem:Compound .
    ?compound chem:name ?compoundName .
    ?compound chem:smiles ?compoundSmiles .
    FILTER regex(?compoundName, "ol", "i")
    OPTIONAL { ?compound chem:description ?description }

}

result

--------------------------------------------------------------------------------------------------------------------------------------------
| compound                                                           | compoundName | compoundSmiles                         | description |
============================================================================================================================================
| <http://en.wikipedia.org/wiki/Ethanol>                             | "Ethanol"    | "OCC"                                  |             |
| <http://commons.wikimedia.org/wiki/Image:D-Mannitol_structure.png> | "D-Manitol"  | "O[C@H]([C@H](O)CO)[C@H](O)[C@H](O)CO" |             |
--------------------------------------------------------------------------------------------------------------------------------------------

retrieving Jean-Claude's data

The query

PREFIX dc:   <http://purl.org/dc/elements/1.1/>
PREFIX chem: <http://blueobelisk.sourceforge.net/chemistryblogs/>

SELECT
    ?exp
    ?sample
    ?solvent ?solventName ?solventSmiles
    ?solute ?soluteName ?soluteSmiles
    ?conc
   
{
    ?solvent rdf:type chem:Compound .
    ?solvent chem:name ?solventName .
    ?solvent chem:smiles ?solventSmiles .

    ?solute rdf:type chem:Compound .
    ?solute chem:name ?soluteName .
    ?solute chem:smiles ?soluteSmiles .

   ?expData rdf:type chem:ExperimentalData .
   ?expData chem:solute ?solute .
   ?expData chem:solvent ?solvent .
   ?expData chem:concentration ?conc .
   ?expData chem:experiment-id ?exp .
   ?expData chem:sample ?sample .
}

result

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
| exp                                              | sample      | solvent                                | solventName | solventSmiles | solute                                                             | soluteName        | soluteSmiles                           | conc                 |
==================================================================================================================================================================================================================================================================================================
| <http://usefulchem.wikispaces.com/exp207>        | <sample:12> | <http://en.wikipedia.org/wiki/Ethanol> | "Ethanol"   | "OCC"         | <http://en.wikipedia.org/wiki/Sodium_chloride>                     | "Sodium chloride" | "[Na+].[Cl-]"                          | "0.00"^^<chem:Molar> |
| <http://onschallenge.wikispaces.com/JennyHale-1> | <sample:3>  | <http://en.wikipedia.org/wiki/Ethanol> | "Ethanol"   | "OCC"         | <http://en.wikipedia.org/wiki/Sodium_chloride>                     | "Sodium chloride" | "[Na+].[Cl-]"                          | "0.00"^^<chem:Molar> |
| <http://usefulchem.wikispaces.com/exp207>        | <sample:11> | <http://en.wikipedia.org/wiki/Ethanol> | "Ethanol"   | "OCC"         | <http://commons.wikimedia.org/wiki/Image:D-Mannitol_structure.png> | "D-Manitol"       | "O[C@H]([C@H](O)CO)[C@H](O)[C@H](O)CO" | "0.00"^^<chem:Molar> |
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

That's it

Pierre

4 comments:

Egon WillighagenWednesday, 12 November, 2008
There is information in the RDF that is not in the spreadsheet... did you compile it manually?
Pierre LindenbaumWednesday, 12 November, 2008
Egon, yes that was just a test to learn sparql.
Egon WillighagenWednesday, 12 November, 2008
OK, fine.

Writing some Jena code to convert the CSV into RDF. Will upload to GitHub...
Egon WillighagenMonday, 12 January, 2009
Pierre, on GitHub I have uploaded a slightly alternative route to get to wikipedia links: dbpedia.org.

11 November 2008

SPARQL for solubility/RDF: my notebook

listing all the chem:Compound

query

Running the query

Result

The same query but using prefixes

query

result

Listing the compounds , their names, their 'smiles'

query

result

The same, but only the compounds with a name containing "OL"

query

result

the same, but add the 'chem:description', if any

query

result

retrieving Jean-Claude's data

The query

result

4 comments: