Parasite Experiment ontology

What is Parasite Experiment Ontology (PEO)?

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. PEO has 110 classes and 27 properties with a logic expressivity of ALCHQ(D) and incorporates concepts defined in Parasite Life Cycle ontology (PLO) to maximize reuse of existing ontological resources. The new version of PEO (ver 0.2) was released for listing and public use at NCBO’s BioPortal in December 2009.

{"openlevels":1,"minExpandLevel":2} Owl:Thing agent freezer knockout_plasmid researcher microarray_plate_reader transfection_machine data data_collection peptide_count phenotype protein_group_number sample Tcruzi_lifecyclestage_subsample Tcruzi_sample cloned_sample cloned_sample_designate drug_selected_sample sequence_coverage transfected_sample signal_intensity spectral_count statistical_measure log_base2_ratio standard_deviation Probability microarray_oligonucleotide 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_parameter allele_designation experiment_notes experiment_justification researcher_note technician_note microarray_ANOVA_cluster priority status plasmid_construction_step nucleic_acid purity transfection_buffer Gene_Function host_organism lifecycle_stage organism organism_strain chromosome genome transfected_genome region flanking_region gene intergenic_region spatial_parameter freezer_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 polymerase_chain_reaction proteome_analysis stage_purity_determination strain_creation_process cell_cloning drug_selection strain_creation_protocol Transfection transcriptome_process hybridisation labelling oligo_to_gene_assignment prehybridisation scanning Microarray_Analysis

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.

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