The BridgeDb DataSource Ontology

This example uses the BridgeDb DataSource Ontology, created by BridgeDb developers from Manchester University (Christian, Stian, and Alasdair). The ontology covers describing data sources of identifiers, a technology outlined in the BridgeDb paper by Martijn (see below) as well as terms from the Open PHACTS Dataset Descriptions for the Open Pharmacological Space by Alasdair et al.

Because I needed to put this online for Open PHACTS (BTW, the project won a big award!) and our previous solution did not work well enough anymore. You may also see the HTML of the result first. You may also want to verify it really is HTML: here is the HTML5 validation report. Also, you may be interested in what the ontology in RDF looks like: here is the extracted RDF for the ontology. Now follow the HTML+RDFa snippets. First, the ontology details (actually, I have it split up):

<div about="http://vocabularies.bridgedb.org/ops#"
     typeof="owl:Ontology">
  <h1>The <span property="rdfs:label">BridgeDb DataSource Ontology</span>
    (version <span property="owl:versionInfo">2.1.0</span>)</h1>
  <p>
    This page describes the BridgeDb ontology. Make sure to visit our
    <a property="rdfs:seeAlso" href="http://www.bridgedb.org/">homepage</a> too!
  </p>
</div>
<p about="http://vocabularies.bridgedb.org/ops#">
  The OWL ontology can be extracted
  <a property="owl:versionIRI"
     href="http://www.w3.org/2012/pyRdfa/extract?uri=http://vocabularies.bridgedb.org/ops#">here</a>.
  The Open PHACTS specification on
  <a property="rdf:seeAlso"
    href="http://www.openphacts.org/specs/2013/WD-datadesc-20130912/#bridgedb"
  >Dataset Descriptions</a> is also useful.
</p>

This is the last time I show the custom color coding, but for a first time it is useful. In red are basically the predicates, where @about indicates a new resource is started, @typeof defines the rdf:type, and @property indicates all other predicates. The blue and green blobs are literals and object resources, respectively. If you work this out, you get this OWL code (more or less):

bridgedb: a owl:Ontology;
  rdfs:label "BridgeDb DataSource Ontology"@en;
  rdf:seeAlso
    <http://www.openphacts.org/specs/2013/WD-datadesc-20130912/#bridgedb>;
  rdfs:seeAlso <http://www.bridgedb.org/>;
  owl:versionIRI
    <http://www.w3.org/2012/pyRdfa/extract?uri=http://vocabularies.bridgedb.org/ops#>;
  owl:versionInfo "2.1.0"@en .

An OWL class

Defining OWL classes are using the same approach: define the resource it is @about, define the @typeOf and giving is properties. BTW, note that I added a @id so that ontology terms can be looked up using the HTML # functionality. For example:

<div id="DataSource"
  about="http://vocabularies.bridgedb.org/ops#DataSource"
  typeof="owl:Class">
  <h3 property="rdfs:label">Data Source</h3>
  <p property="dc:description">A resource that defines
    identifiers for some biological entity, like a gene,
    protein, or metabolite.</p>
</div>

An OWL object property

Defining an OWL data property is pretty much the same, but note that we can arbitrary add additional things, making use of <span>, <div>, and <p> elements. The following example also defines the rdfs:domain and rdfs:range:

<div id="aboutOrganism"
  about="http://vocabularies.bridgedb.org/ops#aboutOrganism"
  typeof="owl:ObjectProperty">
  <h3 property="rdfs:label">About Organism</h3>
  <p><span property="dc:description">Organism for all entities
    with identifiers from this datasource.</span>
    This property has
    <a property="rdfs:domain"
      href="http://vocabularies.bridgedb.org/ops#DataSource">DataSource</a>
    as domain and
    <a property="rdfs:range"
      href="http://vocabularies.bridgedb.org/ops#Organism">Organism</a>
    as range.</p>
</div>

So, now anyone can host an OWL ontology with dereferencable terms: to remove confusion, I have used the full URLs of the terms in @about attributes.

Now, addressing the limitations of the current citation databases is technically simple, and purely blocked by social and commercial aspects. The Citation Typing Ontology by David Shotton defines the framework to define citation types, independent from any existing database. The semantic web technologies will take it from there, and allow aggregation etc.

There are some things to think about on how to use such citation networks, though. If we calculate the impact of the CDK project, we should combine citation counts to the website(s), papers, etc, after removal of duplicates, etc. The cito:cites does link to resources, and the CDK paper resources is not the same as the CDK website resource. But, we could define a Project Class, where both are foo:partOf. Then, we could define that the triple chain the:citingWork cito:cites the:CDKArticle foo:partOf the:CDKProject would imply the triple the:citingWork cito:cites the:CDKProject.

Typed Citations

Now, while writing up this blog, I realize that my fork of this morning, A BIBO Citation Typing Ontology, might actually be counter-productive in the long run, as I was only working out a solution to a simpler, but different problem, which the CiTO also addresses: a citation is not typed. When a paper does cite the CDK paper, we still do not know if it uses the CDK, or merely mentioned it as related-but-unused, or even refuted work.

Now, as I am leaning towards the Biobliography Ontology as RDF-based system for my references, and been using this already in the RDF store hosting the ChEMBL data, I forked the CiTO to define rdfs:domain and rdfs:range on bibo:Document. The CiTO 1.5 actually defines a large set of document types too, and I rather see BIBO reused.

This indeed has the downside that the bibocto:cites cannot be used for the above chaining, and this might bite me seriously later. Well, nothing wrong with a failing experiment, right? For now, it will serve my purpose: setting up a citation database for the CDK project papers.

The CDK citation database

So, here goes (it’s RDFa-enabled; check this RDF pulled out):

@prefix bibo: <http://purl.org/ontology/bibo/>.
@prefix bibocto: <http://github.com/egonw/bibo-cto/>.

<urn:doi:10.1186/1758-2946-2-1> a bibo:Article ;
  bibocto:cites <urn:doi:10.1021/ci025584y> .

I am not entirely happy about the error-prone XHTML+RDFa of the above example, and filed a question of better solution on SemanticOverflow.

While the above example merely defines the citation of Peter Ertl’s article to the CDK (whether that is valid or not… would he have cited the other paper perhaps?), the citation typing allows me to state how the CDK paper is cited. Now, Peter states:

It is also gratifying to see the advent of open source movement in cheminformatics on the Internet, as advocated for example by the Blue Obelisk Group (40) and witnessed by collaborative projects like Chemistry Development Kit CDK (41), Jmol (42), Bioclipse (43) and several others.

So, I think it is fair to state that:

<urn:doi:10.1186/1758-2946-2-1> bibocto:credits <urn:doi:10.1021/ci025584y> .

which is very much appreciated!

Then I read about SKOS, Simplified Knowledge Organisation System. Unlike OWL, SKOS is less strict on relations between concepts being marked up. Often these concepts are loosely bound, instead following a strict is_a hierarchy. ArMet is a Metabolomics knowledge system which does not have a strong hierarchy, and SKOS seemed to me to be the most suitable markup candidate. So, I SKOS-ified the ArMet specification, resulting in this rather simple document. The document is SKOS, but has an associated skos2html.xsl XSLT stylesheet, so that Firefox converts it to XHTML on the fly.

An entry looks like:

<skos:Concept rdf:about="GenotypeID">
  <skos:prefLabel>genotypeID</skos:prefLabel>

  <skos:definition>A unique identifier for the genotype.</skos:definition>
  <skos:broader rdf:about="GenotypeProperty"/>
</skos:Concept>

The full SKOS specification allows capturing much of what we want to do, including i18n via the label system, loos hierarchical relations via skos:broader, and the concepts of skos:Collection to aggregate concepts. Where needed, it allows borrowing from other languages. For example, to link concepts from MetWare to the original ArMet specification owl:sameAs can be used.