[Obi-devel] MeDIP-SEQ assay

[Alan Ruttenberg]

Changing primary structure of macromolecule to GDC made the following
unsatisfiable, but I think exposes a true error.
The definition:

has_specified_output some
('measurement datum'
and ('is about' some
('primary structure of DNA macromolecule'
and 'DNA residue methylation')))

has the conjunction ('primary structure of DNA macromolecule' and
'DNA residue methylation')

Which should be empty - these were distinct qualities - just no
disjoint asserted. I'm changing it to.

has_specified_output some
('measurement datum'
and ('is about' some 'primary structure of DNA macromolecule')
and ('is about' some 'DNA residue methylation'))

However comments on what it should be are welcome.

-Alan

------------------------------------------------------------------------------
This SF.net email is sponsored by Sprint
What will you do first with EVO, the first 4G phone?
Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first
_______________________________________________
Obi-devel mailing list
Obi-...@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/obi-devel

[Chris Stoeckert]

Alan,
The output of MeDIP-Seq is sequence data on DNA fragments containing methylated residues so how about:

has_specified_output some ('sequence data'
'is about' some primary structure of DNA macromolecule' (inheres_in some 'deoxyribonucleic acids (has_quality DNA residue methylation'))

<if this is the way to go theres a separate discussion point on domain of inheres_in>
Chris

[Philippe Rocca-Serra]

Hi Chris, Alan,

'DNA residue methylation' sounds like a process to me, appending it with
'status' is probably more inline with a quality.

Alternately, we could possibly play with the notion of "methylated
nucleobase residue" located_in 'deoxyribonucleic acids'.

We could also be more specific about the type of output data by
specifying the position of the methylated nucleobase residue.

Cheers

Philippe

--
/-----------------------------------------------\
Philippe Rocca-Serra (PhD)
EMBL-EBI
NET-Project Technical Coordinator
Tel: +44 (0)1223 492553
Fax: +44 (0)1223 494
URL:
http://www.ebi.ac.uk/net-project/
http://isatab.sourceforge.net/index.html
\-----------------------------------------------/