OBI

Hi Tina,

Attached are the additional terms that may fit in as Data Transformation 
terms that we missed from MO.

Trish

Hi.
Bjoern has posted the schedule of talks for the first day (Monday) of  
the upcoming OBI workshop. We need a volunteer to give the 5 minute  
presentation on our behalf? Any takers from those attending the  
workshop?
I think there may even be slides from an earlier workshop to use as a  
starting point.

Thanks.
Chris

Chris Stoeckert, Ph.D.
Research Professor, Dept. of Genetics
1415 Blockley Hall, Center for Bioinformatics
423 Guardian Dr., University of Pennsylvania
Philadelphia, PA 19104
Ph: 215-573-4409 FAX: 215-573-3111
http://www.cbil.upenn.edu

Attached are a set of terms that were being discussed by members of the 
Transcriptomics group before bringing forward to the larger OBI group. 
They are being proposed as "factor" terms.

The internal discussion of this work was in progress and therefore the 
information in the file is pretty rough WRT to getting these into shape 
for inclusion into OBI.


If you or Susanna have any questions or requests for updates to any 
of the term lists sent in these last 3 emails, please let us know.

Trish

Attached are the terms previously proposed to the fugo-devel list as 
"objective" terms, those that describe the reason for performing the 
investigation. These are being proposed as needed by at least the 
Transcriptomics community for future mapping of MGED Ontology terms to OBI 
terms.

Trish

Hi Philippe,

In reviewing the email list and files, I have come across 2 lists 
that were sent in emails to the fugo-devel list and a 2 Word documents. 
The Word documents contain information that was not finalized before the 
developers switched topics from Study to Hardware, I believe, and 
therefore these were probably not sent to the fugo-devel list. These will 
be attached in a separate mail.

The list below contains terms proposed as "factor" terms, i.e. variables 
under study in the experiment. These are being proposed as needed for at 
least the Transcriptomics community for future mapping of MGED Ontology 
terms to OBI.

Trish



=-=-=-=-=

term: array_design
class
parent:  continuant > dependent_enduring_entity >
realizable_enduring_entity > design
def: The arrangement of Features on a solid support, ie an Array. (Note:
not the best def, but I'm short of time, so...)

term: array_platform
class
parent: continuant > independent_enduring_entity > object >
platform > microarray_platform > array
def: The technology used to manufacture an Array, eg. Affymetrix,
2-color cDNA, Imagene.

term: data_transformation
class
parent: continuant > dependent_enduring_entity >
realizable_enduring_entity > cardinal_part_of_design > protocol
def: A method or algorithm used to alter each member of a set of data.

term: classifier_assessment
class
parent: continuant > dependent_enduring_entity >
realizable_enduring_entity > cardinal_part_of_design > protocol
def: A method or algorithm used to compare the results of analysis using
one of two classifiers with
the outcome in a group of patients.


term: spiked_in_control
class
parent: continuant > dependent_enduring_entity >
realizable_enduring_entity > control
def: An exogenous material dded at a defined stage or stages in sample
preparation, labelling and/or
hybridisation e.g., a sequence of nucleic acids, amino acids or
metabolites, used for a number
of purposes including quality control, calibration or normalisation.



term: operator -> split to person (synonym of study_organism) and organization
(synonym of study_population?, see another option below)
location in hierarchy
parent: enduring_entity > independent_enduring_entity > object > study_object
OR study_organization, def: A group of individuals structured for a
specific purpose.


term: nucleic_acid_protocol
location in hierarchy: enduring_entity > dependent_enduring_entity > realizable
_enduring_entity > cardinal_part_of_design > protocol
def: A protocol which is used to extract DNA or RNA from a biomaterial.


term: amplification_protocol
location in hierarchy: enduring_entity > dependent_enduring_entity > realizable
_enduring_entity > cardinal_part_of_design > protocol
def: A protocol which is used to increase the amount of a whole or a
defined subpopulation of a material.

term: linear_amplification_protocol
location in hierarchy: enduring_entity > dependent_enduring_entity > realizable
_enduring_entity > cardinal_part_of_design > protocol > amplification_protocol
def:  A protocol which is used to increase the amount of RNA, e.g. the use of
the T7 promoter to amplify RNA.
Synonym: Eberwine procedure

term: hybridization_protocol
location in hierarchy: enduring_entity > dependent_enduring_entity > realizable
_enduring_entity > cardinal_part_of_design > protocol
def: A protocol which is used for annealing complementary strands of nucleic
acid.
Note: indicate temperature, time and buffer.


term: labelling_protocol
location in hierarchy: enduring_entity > dependent_enduring_entity > realizable
_enduring_entity > cardinal_part_of_design > protocol
def: A protocol which is used to attachment different traceable compounds to a
population of biomaterials or materials, usually a flourescent dye to a nucleic
acid or protein.

term: image_quantitation_protocol
location in hierarchy: enduring_entity > dependent_enduring_entity > realizable
_enduring_entity > cardinal_part_of_design > protocol
def: A protocol which is used to obtain values from an image.

=-=-=-=



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