Parasite Experiment 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.

Owl:Thing agent knockout_plasmid researcher sample_culture_agent cold_storage_agent freezer liquid_nitrogen_tank transfection_machine data data_collection phenotype sample Tcruzi_sample cloned_sample cloned_sample_designate drug_selected_sample transfected_sample signal_intensity plasmid drug_resistant_plasmid knockout_construct_plasmid target_region_plasmid parameter domain_parameter accession_number culture_medium culture_parameter temperature_condition drug drug_attribute drug_concentration laboratory_experiment_parameters allele_designation experiment_notes experiment_justification researcher_note technician_note priority status purity transfection_buffer host_organism lifecycle_stage organism organism_strain genome transfected_genome Gene_Function chromosome region flanking_region gene intergenic_region spatial_parameter cold_storage_location kinetoplast_position temporal_parameter DateTimeDescription process gene_knockout_process knockout_project_protocol knockout_region_construct_protocol sample_characterization sequence_extraction plasmid_construction knockout_plasmid_construction strain_creation_protocol cell_cloning drug_selection strain_creation_protocol transfection Owl:Thing agent data process

Snapshot of class hierarchy of the parasite experiment ontology using Protege toolkit. Detail of this ontology is available at NCBO BioPortal

List of ontology classes

A Accession Number Allele Designation Amastigote C Cell Cloning Chromosome Cloned Sample Cloned Sample Designate Culture Medium Culture Parameter D Drug Drug Attribute Drug Concentration Drug Resistant Plasmid Drug Selected Sample Drug Selection E Epimastigote Experiment Notes Experiment Justification F Flanking Region Freezer Location

G Gene Gene Function Gene Knockout Protocol Genome H Host organism Hybridisation I Intergenic Region Knockout Plasmid K Kinetoplast Position Knockout Construct Plasmid Knockout Plasmid Knockout Plasmid Construction L Labelling Laboratory Experiment Parameter Lifecycle stage Log base2 Ratio

M Medium Microarray Analysis Microarray ANOVA Cluster Microarray Oligonucleotide Microarray Plate Reader N Nucleic Acid O Oligo to Gene Assignment Organism Organism Strain P Peptide count Phenotype Plasmid Plasmid Construction Plasmid Construction Step Polymerase Chain Reaction Prehybridisation Priority Probability Promastigote Protein group number Proteome Analysis Purity

R Region Researcher Researcher Note S Sample Scanning Sequence Coverage Sequence Extraction Signal Intensity Spectral Count Stage Purity Determination Standard Deviation Statistical Measure Status Strains Strain Creation Process Strain Creation Protocol T Target Region Plasmid Tcruzi Lifecyclestage Subsample Tcruzi Sample Technician Note Temperature Condition Transcriptome Process Transcriptome Protocol Transfected Genome Transfected Sample Transfection Transfection Buffer Transfection Machine Trypomastigote

Collaborating Institutions

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

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

Feedback/Comments

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