Parasite Experiment ontology

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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.

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

These two ontologies present an interesting but different scenario from the OAEI anatomy subtrack. The PEO is being collaboratively developed as part of an NIH funded project to develop and deploy an ontology-driven semantic problem-solving environment for parasite research. The PEO models experiment details and provenance information. It is an application-oriented and more specific domain ontology than OBI, which describes biomedical investigations. In contrast, the OAEI anatomy subtrack ontologies have many common entities since both ontologies describe the same domain (i.e. anatomy) for different species (mouse vs. human). Mapping more specific ontologies such as PEO to a more general ontology such as OBI is an important step towards helping establish a common point of reference that can serve to foster cooperation and interoperability among researchers. Given the explosion of metadata available on the web, our case study to align two related ontologies in the biomedical field has the potential to impact not just the biomedical field but also any research fields that take advantage of semantic web technologies.

Mappings between PEO and OBI submitted to NCBO BioPortal:

#No PEO Term OBI Term Relation Link
1 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://bioportal.bioontology.org/visualize/42093/?conceptid=agent&jump_to_nav=true#mappings
2http://knoesis.wright.edu/ParasiteExperiment.owl#standard_deviation standard_deviation http://purl.obolibrary.org/obo/OBI_0200121 standard deviation calculation http://www.w3.org/2004/02/skos/core#closeMatch http://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Astandard_deviation&jump_to_nav=true#mappings
3http://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://bioportal.bioontology.org/visualize/42093/?conceptid=Thesaurus%3AMicroarray_Analysis&jump_to_nav=true#mappings
4http://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://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Aproteome_analysis#mappings
5http://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://bioportal.bioontology.org/visualize/42093/?conceptid=sequence%3Aregion&jump_to_nav=true#mappings
6http://knoesis.wright.edu/provenir/provenir.owl#process process http://www.ifomis.org/bfo/1.1/span#ProcessualEntity ProcessualEntity http://www.w3.org/2004/02/skos/core#exactMatch http://bioportal.bioontology.org/visualize/42093/?conceptid=process&jump_to_nav=true#mappings
7http://purl.org/obo/owl/sequence#plasmid plasmid http://purl.obolibrary.org/obo/OBI_0000430 plasmid http://www.w3.org/2004/02/skos/core#exactMatch http://bioportal.bioontology.org/visualize/42093/?conceptid=sequence%3Aplasmid&jump_to_nav=true#mappings
8http://knoesis.wright.edu/ParasiteExperiment.owl#drug drug http://purl.obolibrary.org/obo/OBI_0000040 drug role http://www.w3.org/2004/02/skos/core#exactMatchhttp://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Adrug&jump_to_nav=true#mappings
9 http://knoesis.wright.edu/ParasiteExperiment.owl#nucleic_acid nucleic_acid http://purl.org/obo/owl/CHEBI#CHEBI_33696 nucleic acid http://www.w3.org/2004/02/skos/core#exactMatchhttp://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Anucleic_acid&jump_to_nav=true#mappings
10 http://knoesis.wright.edu/ParasiteExperiment.owl#culture_medium culture_medium http://purl.obolibrary.org/obo/OBI_0000079 culture medium role http://www.w3.org/2004/02/skos/core#exactMatchhttp://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Aculture_medium&jump_to_nav=true#mappings
11http://knoesis.wright.edu/ParasiteExperiment.owl#transfection transfection http://purl.obolibrary.org/obo/OBI_0600060 DNA transfection http://www.w3.org/2004/02/skos/core#exactMatchhttp://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Atransfection&jump_to_nav=true#mappings
12http://paige.ctegd.uga.edu/ParasiteLifecycle.owl#organism organism http://purl.obolibrary.org/obo/OBI_0100026 organism http://www.w3.org/2004/02/skos/core#exactMatch http://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteLifecycle%3Aorganism
13 http://knoesis.wright.edu/ParasiteExperiment.owl#polymerase_chain_reaction polymerase_chain_reaction http://purl.obolibrary.org/obo/OBI_0000415 polymerase chain reaction http://www.w3.org/2004/02/skos/core#exactMatch http://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Apolymerase_chain_reaction&jump_to_nav=true#mappings
14http://paige.ctegd.uga.edu/ParasiteLifecycle.owl#lifecycle_stage lifecycle_stage hhttp://purl.org/obo/owl/UBERON#UBERON_0000105 life cycle stage http://www.w3.org/2004/02/skos/core#exactMatchhttp://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteLifecycle%3Alifecycle_stage&jump_to_nav=true#mappings
15http://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
16 http://knoesis.wright.edu/ParasiteExperiment.owl#signal_intensitysignal_intensity http://purl.obolibrary.org/obo/OBI_0000010 fluorescent reporter intensity http://www.w3.org/2004/02/skos/core#exactMatchhttp://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Asignal_intensity&jump_to_nav=true#mappings
17http://knoesis.wright.edu/ParasiteExperiment.owl#temperature_condition temperature_condition http://purl.org/obo/owl/PATO#PATO_0000146 temperature http://www.w3.org/2004/02/skos/core#exactMatchhttp://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Atemperature_condition&jump_to_nav=true#mappings
18http://knoesis.wright.edu/ParasiteExperiment.owl#purity purity http://purl.org/obo/owl/PATO#PATO_0001339 biomaterial purity http://www.w3.org/2004/02/skos/core#exactMatchhttp://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Apurity&jump_to_nav=true#mappings
19http://knoesis.wright.edu/ParasiteExperiment.owl#sample sample http://purl.obolibrary.org/obo/OBI_0100051 specimen http://www.w3.org/2004/02/skos/core#exactMatchhttp://www.w3.org/2004/02/skos/core#exactMatchhttp://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Asample&jump_to_nav=true#mappings
20 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
A
B
C
D
E
F
G
H
I
K
L
M
N
O
P
R
S
T
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