[sbml-annot] Examples of annotation in OWL

[Allyson L. <a.l...@ne...>]

Hi all,

I've been asked to make up a basic example of how we might do things in the
annot package if we allowed OWL rather than just RDF. As OWL can be saved as
RDF/XML, people who aren't interested in the annotation, or who are just
interested in using a plain RDF parser can manage. We could still say in the
proposal that any RDF is allowed, but then further specify (if we so decide)
that MIRIAM annotations and other SBML-backed annotations are described
using OWL, thus allowing things like negation.

I'm not saying that we have to use OWL, or that we have to use these
structures (and I have deliberately left the example minimalist, without
much reference to the higher functions of OWL), but it would leave the door
open for more complex statements in future, without losing the RDF structure
many are familiar with.

Happy to go with the general consensus, of course. Just thought I'd put this
out there. By the way, I am sure there are other ways to do the examples,
and there might be other ways to do the negation. Please feel free to put
your own examples out, and definitely please comment on these.

Attachments can be viewed in a normal text editor (they're very simple) or
opened in Protege, where you get more of an idea of the shape of an OWL
file.
miriam-test.owl is the first example, and miriam-test-negation.owl is that
example converted into a negation.

Here are the examples. First, a simple bqb "is" qualifier. In SBML it looks
like this (this entry is BIOMD0000000001):

                    <rdf:RDF xmlns:rdf="
http://www.w3.org/1999/02/22-rdf-syntax-ns#"
                             xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:dcterms="http://purl.org/dc/terms/"
                             xmlns:vCard="
http://www.w3.org/2001/vcard-rdf/3.0#"
                             xmlns:bqbiol="
http://biomodels.net/biology-qualifiers/"
                             xmlns:bqmodel="
http://biomodels.net/model-qualifiers/">
                        <rdf:Description rdf:about="#_000002">
                             <bqbiol:is>
                                <rdf:Bag>
                                    <rdf:li
rdf:resource="urn:miriam:obo.go:GO%3A0031594"/>
                                </rdf:Bag>
                            </bqbiol:is>
                        </rdf:Description>
                    </rdf:RDF>

In the above example, we have the standard rdf:RDF element, which uses the
bqbiol namespace and the bqmodel namespace.

For a simple example (and based on how it's done in MFO to make life easier
for me - http://cisban-silico.cs.ncl.ac.uk/MFO/), the OWL equivalent of the
above annotation is below. In *bold* is the only major change to the
internals of the rdf:RDF element - the rest of the changes are "xmlns"
changes in the rdf:RDF tag:
<rdf:RDF xmlns="http://www.sbml.org/sbml/level2/sbmll2v4/"
     xml:base="http://www.sbml.org/sbml/level2/sbmll2v4/"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:sbmll2v4="http://www.sbml.org/sbml/level2/sbmll2v4/">
    <owl:Ontology rdf:about="http://www.sbml.org/sbml/level2/sbmll2v4/"/>
*<owl:NamedIndividual rdf:about="#_000002">
        <rdf:type rdf:resource="&sbmll2v4;MiriamAnnotation"/>
        <bqbIs
rdf:datatype="&xsd;string">urn:miriam:obo.go:GO%3A0031594</bqbIs>
    </owl:NamedIndividual>*
</rdf:RDF>


Some notes on this example:

   1. Not sure we'd need to name the ontology or not, so may not need the
   <owl:Ontology> element each time - certainly don't need it for simple RDF
   parsing.
   2. In this example, we are treating the sbml element as an
   individual/instance of the class MiriamAnnotation. This may or may not be
   the right decision - it could be an anonymous individual or could be a
   class, for example.
   3. Also, I'm ot sure *just* the metaid could go in the rdf:about field,
   though we do it in the SBML rdf annotation itself right now. Would need more
   experienced people for RDF or OWL to answer that. Otherwise, the rdf:about
   could point to a URI based on the model number and the metaid (e.g.
   http://www.sbml.org/sbml/level2/sbmll2v4/BIOMD0000000001_000002")


The above OWL example isn't quite the full story: the xmlns that I have
labelled sbmll2v4 would need to have, at a minimum, the following
declarations in it, as they are used in the example:

<!-- Definition of the datatype property bqb Is -->
<owl:DatatypeProperty rdf:about="&sbmll2v4;bqbIs">
        <rdfs:range rdf:resource="&xsd;string"/>
    </owl:DatatypeProperty>

<!-- The class for which the example above is an instance of -->
<owl:Class rdf:about="&sbmll2v4;MiriamAnnotation"/>

As an aside, in MFO everything is converted to OWL, so the Species class is
linked to the MiriamAnnotation class, which links through to the various bq
qualifiers. We wouldn't need to do all of that here, as we only want the
annotation in OWL.

As negation seems such a hot topic, below is the extra lines required for
the original example in order to add a second go term as a bqb is *not*.
These lines would be added within the same rdf:RDF element in the annotation
section:
    *<rdf:Description>
        <rdf:type rdf:resource="&owl;NegativePropertyAssertion"/>
        <owl:targetValue>urn:miriam:obo.go:GO%3A0031595</owl:targetValue>
        <owl:sourceIndividual rdf:resource="&sbmll2v4;_000002"/>
        <owl:assertionProperty rdf:resource="&sbmll2v4;bqbIs"/>
    </rdf:Description>*


Remember, the examples are also attached to be viewed in their completeness
either in an editor or in Protege.

It's a first bash, anyway. Enjoy!

-- 
Allyson Lister

Please note the new email address of all...@ne...,
although the old email address will still work.

Newcastle University, http://www.ncl.ac.uk
http://themindwobbles.wordpress.com