TcruziExperiri ontology

The ontology comprehensively models the processes, instruments, parameters, and sample details that will be used to annotate experimental results with “provenance” metadata (derivation history of results). For example, given a drug selected sample (a sample that has been grown under selective drug pressure. source: Parasite Experiment ontology), details about the drug, drug concentration, the duration for the drug selection process, and the transfected sample used as input to the drug selection process are modeled in the ontology. This extensive provenance metadata modeled in this ontology will enable publication of results in journals, conferences with details of the method used to arrive at the result. Parasite Experiment ontology currently has 71 classes and 15 properties with a DL expressivity of ALCHF(D) and incorporates concepts defined in Parasite Life Cycle ontology to maximize re-use of existing ontological resources.

List of ontology classes

Snapshot of Parasite Experiment ontology in Protege toolkit

table width=65%

   tr valign=top
       td

A

ul li Accession Number/li /li /ul

C

                               ul
                                       liCell Cloning/li
                                       liCloned Sample/li
                               /ul

D

                               ul
                                       liDrug/li
                                       liDrug Concentration/li
                                       liDrug Resistant Plasmid/li
                                       liDrug Selected Sample/li
                                       liDrug Selection/li
                               /ul

G

                               ul
                                        liGene Knockout Protocol/li
                               /ul

H

                               ul
                                        liHost organism/li
                                        liHybridisation/li
                               /ul

K

                               ul
                                        liKnockout Construct Plasmid/li
                                        liKnockout Plasmid/li
                               /ul

L

                               ul
                                        liLabelling/li
                                        liLifecycle stage/li
                               /ul

M

                               ul
                                        liMedium/li
                                        liMicroarray Analysis/li
                                        liMicroarray Plate Reader/li
                               /ul

N

                               ul
                                        liNucleic Acid/li
                               /ul

O

                               ul
                                        liOrganism/li
                               /ul
       

P

                               ul
                                       liPhenotype/li
                                        liPlasmid/li
                                        liPlasmid Construction/li
                                        liPolymerase Chain Reaction/li
                                        liPrehybridisation/li
                                        liPurity/li
                               /ul

S

                               ul
                                        liSample/li
                                        liSequence Extraction/li
                                        liSignal Intensity/li
                                        liStrains/li
                               /ul

       /td       

       td

T

                               ul
                                        liTcruzi Sample/li
                                        liTranscriptome Protocol/li
                                        liTransfected Sample/li
                                        liTransfection/li
                                        liTransfection Buffer/li
                                        liTransfection Machine/li
                               /ul

       /td

   /tr

/table br/br/br/br/br/

Collaborating Institutions

• Kno.e.sis Research Center, Wright State University
• Tarleton Research Group, University of Georgia

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We invite new members to collaborate with us in extending this ontology.

Feedback/Comments

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