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[cellml-discussion] Biological and other non-model citations in CellML metadata?


Chronological Thread 
  • From: lenov at ebi.ac.uk (Nicolas Le Novere)
  • Subject: [cellml-discussion] Biological and other non-model citations in CellML metadata?
  • Date: Sat, 31 Mar 2007 12:51:25 +0100 (BST)

> I misunderstand the scope of the property isDescribedBy. I also don't
> think reverse engineering URIs to obtain meaning is a good practice.

But ... you do not reverse engineer anything. The URI IS the meaning. In
the English dictionary, there is a word "publication", with a definition.
Well, in MIRIAM dictionary, this word is "http://www.pubmed.gov/";

> How do you say one URI means the same as another if the URI scheme
> changes? It seems you leave this up to the developer to make sure they
> accomodate both instead of letting rdfs take care of this.

The URI scheme should not change. In the rare case it changes, it is up to
us to provide a deprecation system so that the developer actually does not
feel the change at all.

>> If you create an element <bqs:PubMed_id> in your language, rather than
>> having a generic reference scheme, with a type PubMed defined elsewhere.
>
> I don't see what hardcoded means. Using properties that are defined in
> a shared schema or standard is a pretty basic premise of sharing
> information using RDF. How do you think RSS or dublin core works?

Exactly, and this is why we dumped first CellML metadata. When we started
with CellML metadata, we had bqs:PubMed_id, bqs:Medline_id and bqs:CAS_id

- PubMed and Medline are redundant (Medline actually gave up their id.
They use PubMed ones now)

- We could not refer to anything that was not in PubMed. This is the case
of MANY models.

We coul have asked you guys to develop a new version of CellML metadata
spec, with bqs:DOI. How long before we would asked another version with
bqs:arXiv? bqs:Scopus_id?

And this is only for bibliography.

By the way, Dublin Core does not work that well. I explored extensively
the usage of DC and it is an absolute mess. Everybody implement its own
usages and rules. Elements and their syntax change wildly from one place
to the other. At the end, this is the usual semantic web. Everybody export
the information alright, but barely anybody can read-it. I am not even
talking about interpreting it.

> our bqs namespace reflects OMG's Bibliographic Query Service
> specification - see http://www.omg.org/docs/dtc/01-04-05.pdf

I know BQS very well. It has been developed in the room next to mine for a
project that died before birth (because we massively gave up CORBA). It is
NOT a standard. It has been endorsed by the OMG because at that time the
EBI was a member, and because Martin Senger was the person writing many of
those things (he also wrote the specification of LSID)

>> >> The big advantage of externalising the type of metadata is that the
>> >> scheme is generic.
>
> What does generic mean? Standardised and used by everyone like a
> published schema would be?

No. Generic, because it can be applied to any kind of data. You do not
need to define specific scheme for each new data-type. Bibliography is
just a type of metadata like any other. No need to a special treatment.

>> > What do you mean by the 'type' of metadata?
>>
>> EC page, PubMed entry, DOI indexed document, UniProt entry, Gene
>> Ontology term etc.
>
> The type of metadata is externalized as soon as it is presented in a
> Schema and made public and adopted by the community.

That cannot work for several reasons.

First, the type of metadata evolves very rapidly. We already have 29 types
in MIRIMA resources, but I anticipate that number to grow very rapidly as
libSBML3 (that implement the RDF annotation scheme) is adopted by the
developers.

Second, the relevant metadata varies according to the community. An
obvious example is BQS. It used PubMed because it was developed at the EBI
by a software engineer who just did not know there was anything else than
PubMed in bibliography.

Third, who decide what "adopted" and "community" means? For instance we
have been struggling with that in SBML for years. We are just starting to
have a robust model of development, with a balance between democracy and
technical soundness. I think we actually have a pretty good system. But it
is not trivial. (In case there is a misunderstanding here: SBML and MIRIAM
are separate entities. I am just using SBML as an example).

Finally, when was CellML metadata made public, how was the community
consulted, and how its feedback was incorporated in the specification? (I
am not even talking about BQS. As I said this is NOT a community standard.
It is a data-model developed by one person for a very specific project).

>> > I think more I am misunderstanding the range of use isDescribedBy is
>> ok for.
>>
>> isDescribedBy is a relationships.
>
> are you meaning is-a relation? as in Type?

Yes,

<model id="EPSP_Edelstein" metaid="_000001">
[...]
<rdf:Description rdf:about="#_000001">
<bqmodel:isDescribedBy>
<rdf:Bag>
<rdf:li rdf:resource="http://www.pubmed.gov/#8983160"/>
</rdf:Bag>
</bqmodel:isDescribedBy>

means:

the model contained in the SBML model "EPSP_Edelstein" is described in the
metadata "8983160" of the data-type "http://www.pubmed.gov/";

> I don't see this at all. isVersionOf and hasVersion is about
> "versions" as in successors where both subject and object of the
> relation are talking about the same thing in the same format but
> differ somewhat in the content - e.g. a newer SBML file. Here is a
> paste of what dublin core say:

We are not using Dublic Qualifiers exactly for that reason. Andrew Finney
pointed out the difference of semantics, and that's why it was decided to
develop biomodels qualifiers. The definition of biomodels qualifiers is
described at:

http://www.ebi.ac.uk/compneur-srv/miriam-main/mdb?section=qualifiers

and

http://biomodels.net/index.php?s=Qualifiers

> Why wouldn't the dublincore references and isReferencedBy be a useful
> substitute for isDescribedBy when you are referring to a publication?
>>From the dublin core spec:
>
> "The isReferencedBy and References refinements enable the expression
> of relationships that aid the user but are not necessary tied to the
> life cycle or necessary for the intended use of the resource. This
> relationship might be used to link an article critical of a resource
> to that resource, a satire of a speech to the original speech, etc."
>
> Surely that provides some semantic value?

:-)

This is what we used until the end of 2006 in fact! But then we decided to
stop confusing people with DC qualifiers for some metadata and not for the
others. Besides, isReferencedBy really link a document to another
document. Here we want to describe the relationship between a document and
a model. Finally, we will use isDescribedBy also to link parameters and
the literature that described the measure of this parameter


--
Nicolas LE NOVERE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223494521, Fax: +44(0)1223494468, Mob: +44(0)7833147074
http://www.ebi.ac.uk/~lenov, AIM:nlenovere, MSN:nlenovere at hotmail.com



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