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

[Matt]

On 4/3/07, Nicolas Le Novere <[EMAIL PROTECTED]> wrote:
> > You will always need to pull apart the 'URI' (table2 MIRIAM document)
> > to retrieve the datatype and identifier.
>
> Well, yes you have to recognise what belongs to the data-type and what
> belong to the identifier. But you do that all the time in RDF anyway. And
> beside, we do it for you and can return one or more URLs.

In what part of RDF is this done?

>
> > I guess I'm not sure why it isn't easier to keep the meaning of
> > datatype and identifier seperate within the language context you are
> > using - which is basically RDF. So that instead you would have
> > something like:
> >
> > $X $QUALIFIER $DATATYPEINSTANCE
> >
> > $DATATYPEINSTANCE isA $DATATYPE
> > $DATATYPEINSTANCE hasIdentifier $IDENTIFIER
> > $DATATYPEINSTANCE hasPhysicalUrl $URL
>
> Something like:
>
> species calmodulin is calmodulin_in_uniprot
> calmodulin_in_uniprot isA UniProt_entry
> calmodulin_in_uniprot hasIdentifier P62158
> calmodulin_in_uniprot hasPhysicalUrl http://www.ebi.uniprot.org/entry/P62158
>
> - One cannot recognize "UniProt_entry" if it is a free string? This is why
> there are MIRIAM data-types
>
> - The physical URL being not stable, one cannot store actual URLs in the
> models themselves.

Nope. I should be clearer about what would be published globally and
what should be in a particular model.

Published globally:

calmodulin_in_uniprot isA UniProt_entry
calmodulin_in_uniprot hasIdentifier P62158
calmodulin_in_uniprot hasPhysicalUrl http://www.ebi.uniprot.org/entry/P62158

UniProt_entry subClassOf DatabaseRecord  (that's quite generic)
hasUniprotEntry subPropertyOf hasDatabaseRecord
hasDatabaseRecord subPropertyOf isDescribedBy

In the model:

x hasUniProtEntry calmodulin_in_uniprot


Now one can filter all annotations in a model for database links only,
or uniprot links only etc. It all just works when using RDF Schema.


>
> So we are down to:
>
> species calmodulin is calmodulin_in_uniprot
> calmodulin_in_uniprot isA http://www.uniprot.org/
> calmodulin_in_uniprot hasIdentifier P62158
>
> How is-it different (in term of information content and of computing steps
> necessary to parse) from:
>
> species calmodulin is http://www.uniprot.org/#P62158
>

For the reason's I give above.

> >> We do not need to relate them to specify that they all deal with
> >> publications. It is already done by the bqmodel:isDescribedBy
> >
> > No, isDescribedBy has no semantic meaning - there is nothing to say
> > that it explicitly defines a publication in a journal article or a
> > vocabulary term.
>
> Of course not, because we do not want to restrict the type of data used to
> describe the component. This is what I said just above. What do-you mean
> by
> "isDescribedBy has no semantic meaning".
>
> isDescribedBy exactly means the "is described by". How is that not a meaning?

In the RDF world you have not attributed any meaning. It could be used
for anything.


>
> What comes after the "by" can be a journal article, a webpage, a song, a
> poem, a control vocabulary term, or a telepathic transmission.

Right, and so if it can be followed by anything then it has no meaning
 there is nothing to distinguish it from any property that someone
may make up.

>
> > So there is no way to determine if some set of URIs are controlled
> > vocab terms and some set are journal articles and some set are
> > experimental result sets?
>
> No. It is up to the user to decide what to do with what. See my ChEBI
> example before. For some people ChEBI is a controlled vocabulary, for some
> it is a database of chemical compound. For me, CAS is a database of
> chemical compound, for CellML, it is a bibliographic resource.

But when a person uses it, they will have a context. It may be one or
more of those from your list, but it is still useful for them to
restrict the intention of the property to something close to what they
mean. I don't particularly want to guess whether someone is intending
the DataType to mean 'chemical compound' as opposed to 'bibliographic
resource'. For all I know the record that I may be able to locate
based on this URI might have value in both domains and I would want to
know what they were intending. Of course you'd hope the record was RDF
anyway and you were able to point to the record attribute by a full
URI.

>
>
> --
> 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:[EMAIL PROTECTED]
>
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>
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Re: [cellml-discussion] new scholarpedia article on model sharing in computational neuroscience

[Tommy Yu]

Tom Morse wrote:
> Dear CellML'ers,
> 
> I wanted to solicit your feedback on an invited article I wrote for 
> Scholarpedia late last week on model sharing in computational neuroscience:
> 
> http://www.scholarpedia.org/article/Model_Sharing_in_Computational_Neuroscience
> 

The uri to the CellML site is 'http://www.cellml.org/', as 'cellml.org'
(without the 'www') does not point to anywhere.

Kind Regards,
Tommy.

> Your suggestions for improvement and/or comments would be gratefully 
> received,
> 
> Best wishes,
> 
> Tom Morse
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Re: [cellml-discussion] new scholarpedia article on model sharing in computational neuroscience

[Andrew Miller]

Tom Morse wrote:
> Dear CellML'ers,
>
> I wanted to solicit your feedback on an invited article I wrote for 
> Scholarpedia late last week on model sharing in computational neuroscience:
>
> http://www.scholarpedia.org/article/Model_Sharing_in_Computational_Neuroscience
>   
The page you linked says the CellML stands for "Cell Markup Language". I 
note that some other external papers and websites have used this 
expansion. However, this is not very accurate, because CellML doesn't 
really 'mark up' cells, it only describes the mathematics.

You also say, below a list including CellML: "Each of the above sites 
started out with a particular domain of interest, for example ModelDB 
(Olfaction) and Visiome (Vision 
), and Biomodels and DOQCS 
(Cell Signaling Pathways), and have subsequently expanded to broader 
categories of neuroscience and biological mathematical models."

However, CellML didn't really start out modelling a particular domain. 
CellML has always been intended as a generic way to represent 
mathematical models (although, as the name implies, it was initially 
developed by groups with an interest in representing biological models, 
and its use in practice has been for biological mathematical models).

I would also suggest that you mention metadata specifications (in terms 
of annotating parts of the model, linking them to other databases, and 
other machine-readable data describing how a model relates to reality).

The need for sharing information needed to create and validate models is 
also a major area. In particular, it would be worth mentioning the 
information in box 3 in:/ "Nature Biotechnology/ *23*, 1509 - 1515 
(2005)  Minimum information requested in the annotation of biochemical 
models (MIRIAM); Le Novere et. al.", as many existing models would 
become more sharable were all the criteria met.

Best regards,
Andrew

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

[Nicolas Le Novere]

> You will always need to pull apart the 'URI' (table2 MIRIAM document)
> to retrieve the datatype and identifier.

Well, yes you have to recognise what belongs to the data-type and what
belong to the identifier. But you do that all the time in RDF anyway. And
beside, we do it for you and can return one or more URLs.

> I guess I'm not sure why it isn't easier to keep the meaning of
> datatype and identifier seperate within the language context you are
> using - which is basically RDF. So that instead you would have
> something like:
>
> $X $QUALIFIER $DATATYPEINSTANCE
>
> $DATATYPEINSTANCE isA $DATATYPE
> $DATATYPEINSTANCE hasIdentifier $IDENTIFIER
> $DATATYPEINSTANCE hasPhysicalUrl $URL

Something like:

species calmodulin is calmodulin_in_uniprot
calmodulin_in_uniprot isA UniProt_entry
calmodulin_in_uniprot hasIdentifier P62158
calmodulin_in_uniprot hasPhysicalUrl http://www.ebi.uniprot.org/entry/P62158

- One cannot recognize "UniProt_entry" if it is a free string? This is why
there are MIRIAM data-types

- The physical URL being not stable, one cannot store actual URLs in the
models themselves.

So we are down to:

species calmodulin is calmodulin_in_uniprot
calmodulin_in_uniprot isA http://www.uniprot.org/
calmodulin_in_uniprot hasIdentifier P62158

How is-it different (in term of information content and of computing steps
necessary to parse) from:

species calmodulin is http://www.uniprot.org/#P62158

>> We do not need to relate them to specify that they all deal with
>> publications. It is already done by the bqmodel:isDescribedBy
>
> No, isDescribedBy has no semantic meaning - there is nothing to say
> that it explicitly defines a publication in a journal article or a
> vocabulary term.

Of course not, because we do not want to restrict the type of data used to
describe the component. This is what I said just above. What do-you mean
by
"isDescribedBy has no semantic meaning".

isDescribedBy exactly means the "is described by". How is that not a meaning?

What comes after the "by" can be a journal article, a webpage, a song, a
poem, a control vocabulary term, or a telepathic transmission.

> So there is no way to determine if some set of URIs are controlled
> vocab terms and some set are journal articles and some set are
> experimental result sets?

No. It is up to the user to decide what to do with what. See my ChEBI
example before. For some people ChEBI is a controlled vocabulary, for some
it is a database of chemical compound. For me, CAS is a database of
chemical compound, for CellML, it is a bibliographic resource.


-- 
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:[EMAIL PROTECTED]

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

[Matt]

On 4/1/07, Nicolas Le Novere <[EMAIL PROTECTED]> wrote:
>
> >> > 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.
> >
> > Though you have to pull apart the URI correctly to discover the key.
>
> You mean to split urn:MyURI:12345 into urn:MyURI and 12345?
> (I voluntarily use URN form rather than URL to avoid confusion)
>
> Yes we may have to so that in some cases.


Isn't this what you have to do every time? E.g.:

x bqmodel:isDescribedBy http://www.pubmed.gov/#8983160

or the more general case:

one of:
$X $QUALIFIER [$DATATYPE-1#$IDENTIFIER-1,
   $DATATYPE-2#$IDENTIFIER-2,
   ... $DATATYPE-k#$IDENTIFIER-n
   ... $DATATYPE-K#$IDENTIFIER-N]

$X $QUALIFIER [urn:$DATATYPE-1':$IDENTIFIER-1,
   urn:$DATATYPE-2':$IDENTIFIER-2,
   ... urn:$DATATYPE-k':$IDENTIFIER-n
   ... urn:$DATATYPE-K':$IDENTIFIER-N]

where
$DATATYPE-k represents datatype k in URL form
and $DATATYPE-k' represents datatype k in URN form
and $IDENTIFIER-n can be any string allowed in URIs
and $X is a model constituent
and $QUALIFIER is the qualifier property of the annotation of constituent $X

You will always need to pull apart the 'URI' (table2 MIRIAM document)
to retrieve the datatype and identifier.

I guess I'm not sure why it isn't easier to keep the meaning of
datatype and identifier seperate within the language context you are
using - which is basically RDF. So that instead you would have
something like:

$X $QUALIFIER $DATATYPEINSTANCE

$DATATYPEINSTANCE isA $DATATYPE
$DATATYPEINSTANCE hasIdentifier $IDENTIFIER
$DATATYPEINSTANCE hasPhysicalUrl $URL

$QUALIFIER could be as general as isDescribedBy, or as specific as,
for example, isDescribedByPubMedRecord

$QUALIFIER would have domain and range constraints.

I see the end result been the same, but the latter method is easier to
extend and specialise. It also remains within the RDF standard which I
think the MIRIAM document should have focused on more rather than
inventing a very specific non-standard way of representing identifers
and datatypes.

>
> >> 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/";
> >
> > So you say somewhere in the dictionary that there is a set of things
> > that are Publications and this set is denoted by any URI that starts
> > with http://www.pubmed.gov/ ?
>
> No. "Publication" is a human notion. We are dealing we software here.
> http://www.pubmed.gov/ is sufficient to uniquely identify a type of data.
> What the software does with it is its own business.

Publication is a useful semantic term for a machine to resolve to.
Publication could have many may representations in machine form, it's
just important that the annotation language implies they are all to be
equivalent.

>
> > I presume there are other URI bases that
> > also mean publication? Something like:
> >
> > http://www.pubmed.gov/ isA Publication
> > http://not.in.pubmed/ isA Publication
>
> Yes. At the moment, we just have PubMed and DOI, we are adding arXiv.

So you do have a machine interpretation of Publication - yours is a lookup list.

>
> We do not need to relate them to specify that they all deal with
> publications. It is already done by the bqmodel:isDescribedBy

No, isDescribedBy has no semantic meaning - there is nothing to say
that it explicitly defines a publication in a journal article or a
vocabulary term.

>
> > How do you extend the mapping of URI where the URI points to a general
> > identification service that resolves across, for example, different
> > publication indexes/databases. Do you need to ask people to replace
> > this URI (which may actually be usable to return some more RDF) with a
> > new one that uses a seperate namespace for each publication
> > index/databases?
>
> I think there are maybe two misunderstandings here. The first one is
> between the MIRIAM notions of data-type and of resource. MIRIAM URIs
> describe data using data-type and identifiers. This data can be
> distributed through various resources. But we do not want to put
> information about those resources in the models. The life-span of
> resources is in general pretty short.

Yes, I think we agree on that.

>
> And that brings-me to the deeper misunderstanding, that is maybe the cause
> of all this discussion. The only purpose of MIRIAM annotation is to
> uniquely identify an annotation, in a perennial way. It is not to
> implement a semantic web infrastructure where you can go directly from the
> annotation to the resource pointed by the annotation.

While there are some semantic web languages that say the identifier
for a resource is also the location of the resource - I'm certainly
not implying that here. The exam

[cellml-discussion] new scholarpedia article on model sharing in computational neuroscience

[Tom Morse]

Dear CellML'ers,

I wanted to solicit your feedback on an invited article I wrote for 
Scholarpedia late last week on model sharing in computational neuroscience:

http://www.scholarpedia.org/article/Model_Sharing_in_Computational_Neuroscience

Your suggestions for improvement and/or comments would be gratefully 
received,

Best wishes,

Tom Morse
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