Re: [sbml-annot] Annotation

[Nicolas Le N. <n.l...@gm...>]

On 17/12/13 09:48, Brett G. Olivier wrote:

> As you know this is a very topical issue within the
> constraint based modelling community. One interesting observation was
> that people weren't so worried about the RDF as such but being forced to
> use a URN/URL identifier - irrespective of whether this was in RDF or an
> XML key-value pair (although this may be a particular FBC issue)

I am a bit lost by the way this discussion is going, and I smell a red herring. I believe that there are a few intermediary steps between using undefined human readable notes and using cross-references to external resources, aligned with nested levels of semantic autonomy and complexity:

What is needed is a computer-readable annotation. That means information stored in the "annotation" element, in an XML format defined in its own namespace. An example of that is the system developed for the Yeast jamboree model for adding InChIs *at the demand of Manchester* people.
http://sbml.org/Community/Wiki/Known_SBML_annotations
The same approach could be used for many more example.

One step further in "standardisation" would be to extend the SBML controlled annotation within the context of FBC. By that I mean one could  conceive a few XML elements that are defined in FBC as standard. They would be identified by the FBC XML namespace.

Finally, there is the complete RDF way, which mean each subject, predicate, object have to be identified. For that, it is clear that external vocabularies are handy. NOTE THAT INCHIS AND INCHI KEYS ARE NOW IN THE REGISTRY
http://www.ebi.ac.uk/miriam/main/collections/MIR:00000383
http://www.ebi.ac.uk/miriam/main/collections/MIR:00000387

They are flagged as "dirty" because they really are not unambiguous identifiers. But if you want to use them in identifiers.org URI, you can.

> Personally, I am not too worried where the annotation happens, although
> I really like the type of approach that you advocate with dictionaries
> and that strict MathML 4.0 uses with OpenMath content dictionaries.
> However, this framework should happen in finite time, it should be
> flexible enough to handle a range of data-types and should be coupled to
> a process such that communities can develop their own identifier
> resources (in a non-intimidating way).
>
> Why this is particularly important (and may simply also be due to my
> ignorance) is that no ontology or set of ontologies can hold all
> meta-ainformation that anyone might want to ever annotate a model or
> model component with ... before they decide to do it.

I am not sure I get you. Do-you mean someone is annotating a model, and comes up with some info s/he wants to add to the model, but did not anticipate? That is by definition food for notes. What good would be to coin up some vocabulary on the spot if nobody is able to parse/understand?

> <brett>ducks and runs for cover</brett>
>
> On 16/12/13 21:43, Neil Swainston wrote:
>> Hi Team Annot,
>>
>> Is anyone still here?!? And if so, did annotations ever get discussed at COMBINE in Paris?
>>
>> I sent Brett and Pedro the following presentation to be gone through in my absence (I was on holiday, see slide 10) but I didn’t hear anything further.
>>
>> https://www.dropbox.com/s/bls85iwe1vfwnw4/Annotation%20with%20RDF.ppt
>>
>> My basic premise was that, while the previous Annotation proposal that we proposed a couple of years ago perhaps spiralled a little into the world of fantasy, the basic premise of updating the SBML annotation facility to take advantage of more features of RDF is a good one.
>>
>> The usual response to claims such as this is to either a) suggest that I am a semantic web / RDF evangelist; and / or b) make some comment that RDF is too complex to support.
>>
>> I personally don’t care less about RDF as such - I’m only interested in it in so far as that we’ve started to use it (since Core annotations were proposed) and to me it makes sense to continue rather than start again from scratch.
>>
>> The second claim - that RDF is too complex - is as bogus as claiming that XML is too complex. Like XML, RDF is not meant to be written directly but accessed through a third-party reader/writer, like libxml, Xerces, or (in the case of RDF) Apache Jena.
>>
>> The reason that I’m interested in this, is that there are a lot of things added to SBML (primarily as notes) which could be represented more formally as annotations with a minimum of extra work. There are examples aplenty in Recon2, path2models and others, but a simple example of annotating a metabolite with charge and inchi string is shown in the linked presentation.
>>
>> To illustrate how easy it is to implement this with an existing RDF library (Apache Jena), a very simple example of a prototype is available here:
>>
>> https://dl.dropboxusercontent.com/u/8980329/sbml-annotation.zip
>>
>> This in Java / JSBML, but C++ RDF parsers are also available.
>>
>> Finally, there’s also been a question about the overhead involved in supporting "all of RDF”. This certainly isn’t my intention. We can limit what we support by defining an RDF Vocabulary, which means that we control which predicates would be permissible in SBML annotations. It would work as a more formalised version of the current Biomodels qualifiers. An example of an RDF Vocabulary is Dublin Core, which we use already.
>>
>> I’m pretty sure that this could be implemented fairly quickly if there’s need for this. Some features of this overlap with the proposals for the FBC package, but to me at least it would seem questionable to implement many different methods of annotating elements in different extension packages.
>>
>> Cheers,
>>
>> Neil.
>>
>> Neil Swainston, PhD
>> Research Fellow
>>
>> Manchester Institute of Biotechnology
>> University of Manchester
>> Manchester M1 7DN
>> United Kingdom
>>
>>
>>
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-- 
Nicolas LE NOVERE, Babraham Institute, Babraham Campus Cambridge, CB22 3AT
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