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 data_source freezer knockout_plasmid microarray_plate_reader researcher transfection_machine data data_collection go_term peptide_count phenotype protein_group_number sam_result 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 nucleic_acid primer 3_prime_primer 3_prime_forward_primer 3_prime_reverse_primer 5_prime_primer 5_prime_forward_primer 5_prime_reverse_primer purity transfection_buffer host_organism lifecycle_stage amastigote leishmania_sp_amastigote trypanosoma_cruzi_amastigote epimastigote trypanosoma_brucei_epimastigote trypanosoma_cruzi_epimastigote promastigote metacyclic_promastigote procyclic_promastigote trypomastigote trypanosoma_brucei_trypomastigote trypanosoma_cruzi_trypomastigote blood_stream_form_trypomastigote metacyclic|trypomastigote trypanosoma_brucei_metacyclic_trypomastigote trypanosoma_cruzi_metacyclic_trypomastigote procyclic_trypomastigote organism organism_strain chromosome genome transfected_genome region gene intergenic_region 3_prime_intergenic_region 3_prime_intergenic_forward_region 3_prime_intergenic_reverse_region 5_prime_intergenic_region 5_prime_intergenic_forward_region 5_prime_intergenic_reverse_region gene_function spatial_parameter freezer_location kinetoplast_position temporal_parameter DateTimeDescription dateCompleted dateOfLastModification dateStarted 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 hybridization 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

Alignment of PEO and OBI

List of the terms submitted to NCBO:

Mapping

PEO	Term	OBI	Term	Relation	Link
http://knoesis.wright.edu/provenir/provenir.owl#agent	agent	http://purl.obolibrary.org/obo/OBI_0000086	reagent role	http://www.w3.org/2004/02/skos/core#closeMatch	--
http://knoesis.wright.edu/ParasiteExperiment.owl#standard_deviation	standard_deviation	http://purl.obolibrary.org/obo/OBI_0200121	standard deviation calculation	standard deviation calculation	--
http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#Microarray_Analysis	Microarray_Analysis	http://purl.obolibrary.org/obo/OBI_0400147	microarray	http://www.w3.org/2004/02/skos/core#closeMatch	--
http://knoesis.wright.edu/ParasiteExperiment.owl#proteome_analysis	proteome_analysis	http://purl.obolibrary.org/obo/OBI_0000615	protein expression profiling	http://www.w3.org/2004/02/skos/core#closeMatch	--
http://purl.org/obo/owl/sequence#region	region	http://purl.org/obo/owl/SO#SO_0000001	region	http://www.w3.org/2004/02/skos/core#exactMatch	--
http://knoesis.wright.edu/provenir/provenir.owl#process	process	http://www.ifomis.org/bfo/1.1/span#ProcessualEntity	ProcessualEntity		--
http://purl.org/obo/owl/sequence#plasmid	plasmid	http://purl.obolibrary.org/obo/OBI_0000430	plasmid		--
http://knoesis.wright.edu/ParasiteExperiment.owl#drug	drug	http://purl.obolibrary.org/obo/OBI_0000040	drug role		--
http://knoesis.wright.edu/ParasiteExperiment.owl#nucleic_acid	ucleic_acid	http://purl.org/obo/owl/CHEBI#CHEBI_33696	nucleic acid		--
http://knoesis.wright.edu/ParasiteExperiment.owl#culture_medium	culture_medium	http://purl.obolibrary.org/obo/OBI_0000079	culture medium role		--
http://knoesis.wright.edu/ParasiteExperiment.owl#transfection	transfection	http://purl.obolibrary.org/obo/OBI_0600060	DNA transfection		--
http://paige.ctegd.uga.edu/ParasiteLifecycle.owl#organism	organism	http://purl.obolibrary.org/obo/OBI_0100026	organism		--
http://knoesis.wright.edu/ParasiteExperiment.owl#polymerase_chain_reaction	polymerase_chain_reaction	http://purl.obolibrary.org/obo/OBI_0000415	polymerase chain reaction		--
http://paige.ctegd.uga.edu/ParasiteLifecycle.owl#lifecycle_stage	lifecycle_stage	hhttp://purl.org/obo/owl/UBERON#UBERON_0000105	life cycle stage		--
http://knoesis.wright.edu/ParasiteExperiment.owl#researcher	researcher	http://purl.obolibrary.org/obo/OBI_0000116	worker role	http://www.w3.org/2004/02/skos/core#exactMatch	http://bioportal.bioontology.org/visualize/44899/?conceptid=obi%3AOBI_0000116#mappings
http://knoesis.wright.edu/ParasiteExperiment.owl#signal_intensity	signal_intensity	http://purl.obolibrary.org/obo/OBI_0000010			--
http://knoesis.wright.edu/ParasiteExperiment.owl#temperature_condition	temperature_condition	http://purl.org/obo/owl/PATO#PATO_0000146			--
http://knoesis.wright.edu/ParasiteExperiment.owl#purity	purity	http://purl.org/obo/owl/PATO#PATO_0001339			--
http://knoesis.wright.edu/ParasiteExperiment.owl#sample	sample	http://purl.obolibrary.org/obo/OBI_0100051			--
http://knoesis.wright.edu/ParasiteExperiment.owl#microarray_plate_reader	microarray_plate_reader	http://purl.obolibrary.org/obo/OBI_0400104	array scanner	http://www.w3.org/2004/02/skos/core#exactMatch	http://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Amicroarray_plate_reader&jump_to_nav=true#mappings
					--

List of ontology classes

3 Prime Forward Primer 3 Prime Intergenic Forward Region 3 Prime Intergenic Region 3 Prime Intergenic Reverse Region 3 Prime Primer 3 Prime Reverse Primer 5 Prime Forward Primer 5 Prime Intergenic Forward Region 5 Prime Intergenic Region 5 Prime Intergenic Reverse Region 5 Prime Primer 5 Prime Reverse Primer A Accession Number Amastigote B Blood Stream Form Trypomastigote C Cell Cloning Chromosome Cloned Sample Cloned Sample Designate Culture Medium Culture Parameter D Data Source Date Completed Date of Last Modification Date Started Date Time Description Drug Drug Attribute Drug Concentration Drug Resistant Plasmid Drug Selected Sample Drug Selection E Epimastigote F Freezer Freezer Location G Gene Gene Function Gene Knockout Process Genome GO Term H Host organism Hybridisation I Intergenic Region K Kinetoplast Position Knockout Construct Plasmid Knockout Plasmid Knockout Plasmid Construction Knockout Project Protocol Knockout Region Construct Protocol L Labelling Laboratory Experiment Parameter Leishmania SP Amastigote Lifecycle stage Log base2 Ratio M Metacyclic_Promastigote Metacyclic_Trypomastigote Microarray Analysis Microarray Oligonucleotide Microarray Plate Reader N Nucleic Acid O Oligo to Gene Assignment Organism Organism Strain P Peptide count Phenotype Plasmid Plasmid Construction Polymerase Chain Reaction Prehybridisation Primer Priority Probability Procyclic Promastigote Procyclic Trypomastigote Promastigote Protein group number Proteome Analysis Purity R Region Researcher S SAM Result Sample Sample Characterization Scanning Sequence Coverage Sequence Extraction Signal Intensity Spectral Count Stage Purity Determination Standard Deviation Statistical Measure Status Strain Creation Process Strain Creation Protocol T Target Region Plasmid Tcruzi Lifecyclestage Subsample Tcruzi Sample Temperature Condition Transcriptome Process Transfected Genome Transfected Sample Transfection Transfection Buffer Transfection Machine Trypanosoma Brucei Epimastigote Trypanosoma Brucei Metacyclic Trypomastigote Trypanosoma Brucei Trypomastigote Trypanosoma Cruzi Amastigote Trypanosoma_Cruzi_Epimastigote Trypanosoma Cruzi Metacyclic Trypomastigote Trypanosoma Cruzi Trypomastigote Trypomastigote

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