First post: File/Column ontology

[lindenb]

Hi all,
I'm new on this list, so first, let me introduce myself: I'm Pierre
Lindenbaum, I work as a Bioinformatician at the "Center for the Study
of Human Polymorphisms" (France).

I've been recently asked to organize a set of files related to some
statistical studies about "Genetic Linkage". Of course :-) , most of
the files are stored with a different format so my first idea was to
create some annotations to describe the files (e.g. File -> Plain
Text File -> Structured
File -> Column Delimited File -> PedigreeFile) and the columns( e.g.
Any-Type -> Biological Entity-> Genetic
Marker -> SNP -> RS-Id ).

I started to create two ontologies today (please , note that these are
just a draft) to set down my ideas

http://code.google.com/p/fileontology/source/browse/trunk/files/ont/columns.rdf
http://code.google.com/p/fileontology/source/browse/trunk/files/ont/files.rdf

Using those ontologies, I expect to create a robot to find , for
example, all the structured files containing a given SNP.

Today on FriendFeed (http://friendfeed.com/e/
a301b4b2-86dd-0c03-371f-11b040686715/Writing-a-type-of-file-ontology-
to-describe-the/ ) Frank Gibson suggested me to join this list
because I may find some existing tool/specs/ontologies here.

I've not a clear view of all the information contained in
http://code.google.com/p/information-artifact-ontology/
Is it redundant with my needs ? Or could I help this project by
creating a new ontology ?

Many thanks for your help and suggestions (if any !) :-)

Pierre Lindenbaum PhD.
http://plindenbaum.blogspot.com

[Melanie Courtot]

Hi Pierre,

I think the part regarding the file format is something we should
address: we currently have data format specification (IAO_0000098),
and this class has been instantiated in OBI with things like what I
think you are looking for, i.e. XML, RDF....

Regarding describing the structure of the file itself, I had the same
discussion with Richard Scheuermann (cc) 2 weeks ago, who expressed
the same needs that yours, i.e. being able to describe the internal
structure of his files. As far as I know we haven't discussed that
yet. As a starting point, I would think about something like "column
has_label X and is_about entity Y"

Does that sound like something that would fit your needs?

Cheers,
Melanie

On Dec 16, 8:38 am, lindenb <plindenbaum.c...@googlemail.com> wrote:
> Hi all,
> I'm new on this list, so first, let me introduce myself: I'm Pierre
> Lindenbaum, I work as a Bioinformatician at the "Center for the Study
> of Human Polymorphisms" (France).
>
> I've been recently asked to organize a set of files related to some
> statistical studies about "Genetic Linkage". Of course :-)  , most of
> the files are stored with a different  format so my first idea was to
> create some annotations to describe the files  (e.g. File -> Plain
> Text File -> Structured
> File -> Column Delimited File -> PedigreeFile) and the columns( e.g.
> Any-Type -> Biological Entity-> Genetic
> Marker -> SNP -> RS-Id ).
>
> I started to create two ontologies today (please , note that these are
> just a draft) to set down my ideas
>

>  http://code.google.com/p/fileontology/source/browse/trunk/files/ont/c...
>  http://code.google.com/p/fileontology/source/browse/trunk/files/ont/f...

>
> Using those ontologies, I expect to create a robot to find , for
> example, all the structured files containing a given SNP.
>
> Today on FriendFeed (http://friendfeed.com/e/
> a301b4b2-86dd-0c03-371f-11b040686715/Writing-a-type-of-file-ontology-
> to-describe-the/  ) Frank Gibson suggested me to join this list
> because I may find some existing tool/specs/ontologies here.
>

> I've not a clear view of all the information contained inhttp://code.google.com/p/information-artifact-ontology/

[lindenb]

Melanie,
thank you for your answer.
I need to have a deeper look at the current content of the
'Information Artifact Ontology'.
I will most probably write back (next year...) with some questions
and/or suggestions.

Cheers

Pierre