[Mged-mage] DerivedBioAssayType ontology entry

[White, J. A. <JW...@ti...>]

Hello Everyone,

The ontology working group has been collecting terms and definitions for use
in generating MAGE-ML, as well as in submissions to ArrayExpress.  One item
for which we don't have enough information is 'DerivedBioAssayType'.  The
MAGE documentation lists the following definition for DBAT:

'The type association indicates the derivation type, for instance collapsed
spot replicate, ratio, averaged intensity, bioassay replicates, etc.'

A DerivedBioAssay is the result of some form of Transformation of
BioAssayData, including but not limited to averaging, normalization and
clustering.  The DerivedBioAssayType association to OntologyEntry is
supposed to describe the DerivedBioAssay.  

Below is a list of suggested terms for DerivedBioAssayType.  The terms in it
describe the data items, not the methods used to obtain them. Compiling the
list was not straightforward because there is overlap with QuantitationType
and NormalizationDescriptionType.  At this time, we plan to use terms from
this list, but leave the list open for new suggestions, since this is a
rapidly changing area of research.  We would like to sollicit from the
members of the Ontologies, MAGE and DataProccessing working groups approval
or disapproval of each term listed below--a simple yes or no will suffice.
(If you believe the definitions listed are completely unacceptable, please
suggest a brief alternative.)  Since the first four terms are listed in the
MAGE documentation, they must be used; however the others are fair game, so
please fire away!

We would like to have responses by Aug 1st in order to tally the lists for
our next ontology working group meeting in August.  

Thanks for any help you all can provide.  

Cheers,

Joe

DerivedBioAssayType
(term: proposed definition)

required terms

collapsed_spot_replicate: results of data reduction involving computation of
a representative value, e.g. by averaging, for a group of replicated
Features from an array.  

ratio: results of data reduction involving computation of the ratio of
intensities from a 2-channel spotted-cDNA hybridization.

averaged_intensity: results of data reduction involving computation of the
average intensity from identical Features, Reporters or CompositeSequences
in different hybridizations.

bioassay_replicate_reduction: results of data reduction involving
computation of a representative value, e.g. by averaging, for a group of
replicated Features from multiple BioAssays.

additional terms

log_ratio: results of data reduction involving computation of the ratio of
intensities from a 2-channel spotted-cDNA hybridization, followed by log
transformation.

clustered_data: results of an analysis method that groups data based on some
measure of similarity, e.g. Pearson correlation coeficient, Euclidean
distance.  (Although clustered data can be reported in HigherLevelAnalysis,
they are DerivedBioAssayData nonetheless.)  

dye_swap_replicate_reduction: results of data reduction involving
computation of a representative value, e.g. by averaging, for identical
Features from 2 BioAssays employing dye-swapped LabeledExtracts.  (Note:
dye_swap_replicate_reduction is not merely a set of bioassay_replicates;
bioassay_replicates and dye_swap_replicates are processed in different but
significant ways.)  

normalized_intensities: intensities from one or both channels resulting from
normalization of MeasuredBioAssayData. 
 
normalized_ratios: ratios resulting from normalization of
MeasuredBioAssayData.  

mean_and_standard_deviation: the mean and standard deviation values
resulting from computationally combining 2 or more sets of BioAssayData.  

mean_and_variance: the mean and variance values resulting from
computationally combining 2  or more sets of BioAssayData.  

mean_and_coeficient_of_variation: the mean and coeficient of variation
values resulting from computationally combining 2 or more sets of
BioAssayData.  

mean_and_p_values: the mean and associated p-values resulting from
computationally combining 2 or more sets of BioAssayData.  

mean_and_confidence_indicators: the mean and associated calculated
confidence resulting from computationally combining 2 or more sets of
BioAssayData.  The confidence indicators include, but are not limited to:
confidence interval, standard deviation, coeficient of variation, and
p-value.  

filtered_data: A data reduction method that involves removal of Features
from the data set based on some criteria, e.g. low-intensity threshhold.  

average_difference: the method used by Affymetrix to obtain mean signal
intensity from a group  of related Features.  This involves calculation of
the overall sum of perfect match minus  mismatch pairs divided by the number
of pairs.