gully apc burns, jessica a turner

Bottom-up curation of terminology for experimental

variables: the Ontology of Experimental Variables and

Values (OoEVV)

Gully APC Burns, Jessica A Turner

Science is Cyclic

Cycles of Scientific Investigation (‘CoSI’ model)☐ ☐☐☐ ☐☐☐☐☐

Focus on Experimental Variables

This statistically-significant effect is the experimental basis for the findings of this study.

‘CDNF protects nigral dopaminergic neurons in-vivo’

from Lindholm, P. et al. (2007), Nature, 448(7149): p. 73-7

Cycles of Scientific Investigation (‘CoSI’ model)☐ ☐☐☐ ☐☐☐☐☐

Capturing Experimental Variables in Context

Knowledge Engineering from Experimental Design (KEfED)☐☐ ☐ ☐☐☐☐☐

http://www.bioscholar.org/

Knowledge Engineering from

Experimental Design (‘KEfED’)

Khan et al. (2007), J. Neurosci. 27:7344-60 [expt 2]

Knowledge Engineering from Experimental Design (KEfED)☐☐ ☐ ☐☐☐☐☐

OoEVV Basic Design

VariableQuality Scale

‘Handedness’

Simple-handedness-category [‘left’, ‘right’, ‘ambidextrous’]

Edinburgh-handedness-score [ -100 … +100 ]

Quality being measured

(conceptual, no encoding)

1 * * 1

Variable measuring the

quality

Mathematical encoding of the variable

Ontology of Variables and Values (OoEVV)☐☐ ☐☐ ☐☐☐☐

OoEVV Implementation

☐☐ ☐☐ ☐☐☐☐Ontology of Variables and Values (OoEVV)

Measurement Scales

☐☐ ☐☐ ☐☐☐☐Ontology of Variables and Values (OoEVV)

Software Development

☐☐ ☐☐ ☐☐☐☐Ontology of Variables and Values (OoEVV)

OoEVV Software

http://www.isi.edu/projects/ooevv/ooevv_software

☐☐ ☐☐ ☐☐☐☐Ontology of Variables and Values (OoEVV)

OoEVV Viewer

☐☐ ☐☐ ☐☐☐☐Ontology of Variables and Values (OoEVV)

Acknowledgements

BMKEG@ISIMarcelo TallisDrashti DaveEd Hovy

Biomedical Informatics Research Network (BIRN)Joe AmesJose Luis AmbiteNaveen Ashish

FundingFBIRN: RR021992 BIRN: RR025736CogPO: MH084812BioScholar: GM083871

Thank you for listening!