[Fuge-devel] Datatype ontology

[Nigel Hardy]

Do any groups have recommended or required ontologies for
Measurement/_datatype/@Ontology_ref ?

Nigel

[Allyson Lister]

There is the Unit Ontology (don't know much about it though):

http://www.obofoundry.org/cgi-bin/detail.cgi?id=unit

does that help? :)

2009/9/4 Nigel Hardy <n...@aber.ac.uk>

Do any groups have recommended or required ontologies for  Measurement/_datatype/@Ontology_ref ?

Nigel

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[Nigel Hardy]

Allyson,

I had assumed to use that for Measurement/_unit/@Ontology_ref but I
can't see anything there for "real", "positive integer" etc. and that's
how I expected to use _datatype (in the absence of the type of
constraint I am trying to achieve in XML).

Nigel

Allyson Lister wrote:
> There is the Unit Ontology (don't know much about it though):
>
> http://www.obofoundry.org/cgi-bin/detail.cgi?id=unit
>
> does that help? :)
>

> 2009/9/4 Nigel Hardy <n...@aber.ac.uk <mailto:n...@aber.ac.uk>>

>
> Do any groups have recommended or required ontologies for
> Measurement/_datatype/@Ontology_ref ?
>
> Nigel
>
>
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>
>
>
> --
> Allyson Lister
> http://themindwobbles.wordpress.com
>
> CISBAN, http://www.cisban.ac.uk
> Newcastle University

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[Jones, Andy]

Hi Nigel,

I'm not sure there is a dedicated ontology of datatypes. In other standards that are primarily XML-based, we have just encoded XSD datatypes within the CV, to indicate that these are the legal datatypes to use:

For example an entry in PSI-MS OBO format looks like this:

[Term]
id: MS:1001437
name: ProteinExtractor:SequestUniqueScore
xref: value-type:xsd\:double "The allowed value-type for this CV term."
is_a: MS:1001302 ! search engine specific input parameter

I'm not sure this really helps though if you want generic datatypes in an ontology, perhaps this is something to contact OBI about?
Cheers
Andy

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[Miller, Michael D (Rosetta)]

hi nigel,

another possibility to mix in are the corba definitions:

(from http://www.omg.org/docs/formal/08-01-04.pdf, section 5.2.4)

* 16-bit, 32-bit, and 64-bit signed and unsigned 2's complement
integers.
* Single-precision (32-bit), double-precision (64-bit), and
double-extended (a mantissa of at least 64 bits, a sign bit and an
exponent of at least 15 bits) IEEE floating point numbers.
* Fixed-point decimal numbers of up to 31 significant digits.
* Characters, as defined in ISO Latin-1 (8859.1) and other single- or
multi-byte character sets.
* A boolean type taking the values TRUE and FALSE.
* An 8-bit opaque detectable, guaranteed to not undergo any conversion
during transfer between systems.
* Enumerated types consisting of ordered sequences of identifiers.
* A string type, which consists of a variable-length array of
characters; the length of the string is a non-negative integer, and is
available at run-time. The length may have a maximum bound defined.
* A wide character string type, which consists of a variable-length
array of (fixed width) wide characters; the length of
the wide string is a non-negative integer, and is available at run-time.
The length may have a maximum bound defined.
* A container type "any," which can represent any possible basic or
constructed type.
* Wide characters that may represent characters from any wide character
set.
* Wide character strings, which consist of a length, available at
runtime, and a variable-length array of (fixed width)
wide characters.

cheers,
michael

Michael Miller
Lead Software Developer
Rosetta Biosoftware Business Unit
www.rosettabio.com

[Melanie Courtot]

(I tried to reply a few days ago, but somehow the post never made it
to the list - apologies if you get multiple copies)

The Information Artifact Ontology (IAO, http://code.google.com/p/information-artifact-ontology/)
, originally a spin-off of OBI, may be relevant. Datatypes are on the
list of issues to address, at http://code.google.com/p/information-artifact-ontology/issues/list
. Suggestions and help to include them are welcome :)

Cheers,
Melanie