[Obi-devel] Ontology Design patterns for settings in experimental assays

[Christian Bölling]

Hi all,

I'm looking for design patterns for representing detailed methodological
settings which might already have been developed or implemented by others
using OBI and/or other ontologies.

I'm having in mind representations of the following:
"The assay mixtures (0.5 ml) contained imidazole-HCl buffer (0.1M; pH 7.2),
2-mercaptoethanol (25 mM), L-glutamate (50 mM; pH 7.2), ATP (10mM), MgCl2(20
mM)."

And:
"The homogenate was centrifuged at 0°C for 30min at 16000g."

Christian



Dr. Christian Bölling
Computational Systems Biochemistry
Institute for Biochemistry
Charité Medical School

Mail: christian...@charite.de
Phone: +49 (0)30 450 528 449

Virchowweg 6
10117 Berlin
Germany




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[Philippe]

Hi Christian,

I believe there are only incomplete patterns so this is a timely post.
I will allow clarifying a number of issues about representing those things.
A number of discussions have taken place about instrument settings and
parameters but I feel that either the conclusions of these discussions
have not been properly documented or consensus could not be reached.

Starting with the mixture, things could look like this:

for mixture:

material entity=mixture has_part (some
mercaptoethanol(http://purl.obolibrary.org/obo/CHEBI_41218) and (scalar
measurement datum has_measurement_value 25 and
has_measurement_unit_label value mM
(http://purl.org/obo/owl/UO#UO/UO_0000300)))
has_part (some
L-glutamate(2-)(http://purl.obolibrary.org/obo/CHEBI_29988) and (scalar
measurement datum has_measurement_value 50 and
has_measurement_unit_label value
mM(http://purl.org/obo/owl/UO#UO/UO_0000300)))
has_part (some ATP(http://purl.obolibrary.org/obo/CHEBI_15422) and
(scalar measurement datum has_measurement_value 10 and
has_measurement_unit_label value
mM(http://purl.org/obo/owl/UO#UO/UO_0000300)))
has_part (some magnesium
dichloride(http://purl.obolibrary.org/obo/CHEBI_6636) and (scalar
measurement datum has_measurement_value 20 and
has_measurement_unit_label value
mM(http://purl.org/obo/owl/UO#UO/UO_0000300)))


(pH and ('is quality measured as' some ('ph measurement datum'
and ('has measurement value' value 7.2)) and is_about some material
entity=mixture)

>From the textual description you send, I have assume the pH is about the
final mixture (not the stock solutions).

*for the centrifugation conditions:
------------------------------------
homogenate is_specified_input of some (process=centrifugation
and
(time measurement datum has_value 30 and has_time_unit some min) and
is_duration_of some centrifugation)
and some 'exposure of material to environment'

Note 1: we are currently missing an inverse relation for 'is_duration_of'
something like a process *lasts_for* some (time measurement datum)

Note 2: we run into the unresolved issue of parameter settings and
associated datum.

concretizes/realizes some setting specifications (temperature
specification and acceleration specification)

We had a number of discussions about this but the current IAO.OBI
structure does not reflect the outcome of those discussions.

It would interesting to hear from you and folks from REO about their views.

Best wishes

Philippe