Difference between revisions of "Parasite Experiment ontology"

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Line 14: Line 14:
 
{{#tree:id=OwlTree|openlevels=1|root=Owl:Thing|
 
{{#tree:id=OwlTree|openlevels=1|root=Owl:Thing|
 
*agent
 
*agent
 +
**[[Data_Source|data_source]]
 
**[[Freezer|freezer]]
 
**[[Freezer|freezer]]
 
**[[Knockout_Plasmid|knockout_plasmid]]
 
**[[Knockout_Plasmid|knockout_plasmid]]
−
**[[Researcher|researcher]]
 
 
**[[Microarray_Plate_Reader|microarray_plate_reader]]
 
**[[Microarray_Plate_Reader|microarray_plate_reader]]
 +
**[[Researcher|researcher]]
 
**[[Transfection_Machine|transfection_machine]]
 
**[[Transfection_Machine|transfection_machine]]
 
*data
 
*data
 
**data_collection
 
**data_collection
 +
***[[GO_Term|go_term]]
 
***[[Peptide_count|peptide_count]]
 
***[[Peptide_count|peptide_count]]
 
***[[Phenotype|phenotype]]
 
***[[Phenotype|phenotype]]
 
***[[Protein_group_number|protein_group_number]]
 
***[[Protein_group_number|protein_group_number]]
−
***[[sample]]
+
***[[SAM_result|sam_result]]
 +
***[[Sample|sample]]
 
****[[Tcruzi_Lifecyclestage_Subsample|Tcruzi_lifecyclestage_subsample]]
 
****[[Tcruzi_Lifecyclestage_Subsample|Tcruzi_lifecyclestage_subsample]]
 
****[[Tcruzi_Sample|Tcruzi_sample]]
 
****[[Tcruzi_Sample|Tcruzi_sample]]
Line 49: Line 52:
 
****[[Culture_Parameter|culture_parameter]]
 
****[[Culture_Parameter|culture_parameter]]
 
*****[[Temperature_Condition|temperature_condition]]
 
*****[[Temperature_Condition|temperature_condition]]
−
****[[drug]]
+
****[[Drug|drug]]
 
****[[Drug_Attribute|drug_attribute]]
 
****[[Drug_Attribute|drug_attribute]]
 
*****[[Drug_Concentration|drug_concentration]]
 
*****[[Drug_Concentration|drug_concentration]]
−
****[[Laboratory_Experiment_Parameter|laboratory_experiment_parameter]]
 
−
*****[[Allele_Designation|allele_designation]]
 
−
*****[[Experiment_Notes|experiment_notes]]
 
−
******[[Experiment_Justification|experiment_justification]]
 
−
******[[Researcher_Note|researcher_note]]
 
−
******[[Technician_Note|technician_note]]
 
−
*****[[Microarray_ANOVA_Cluster|microarray_ANOVA_cluster]]
 
−
*****[[Priority|priority]]
 
−
*****[[Status|status]]
 
−
******[[Plasmid_Construction_Step|plasmid_construction_step]]
 
 
****[[Nucleic_Acid|nucleic_acid]]
 
****[[Nucleic_Acid|nucleic_acid]]
 +
****[[Primer|primer]]
 +
*****[[3_Prime_Primer|3_prime_primer]]
 +
******[[3_Prime_Forward_Primer|3_prime_forward_primer]]
 +
******[[3_Prime_Reverse_Primer|3_prime_reverse_primer]]
 +
*****[[5_Prime_Primer|5_prime_primer]]
 +
******[[5_Prime_Forward_Primer|5_prime_forward_primer]]
 +
******[[5_Prime_Reverse_Primer|5_prime_reverse_primer]]
 
****[[Purity|purity]]
 
****[[Purity|purity]]
 
****[[Transfection_Buffer|transfection_buffer]]
 
****[[Transfection_Buffer|transfection_buffer]]
−
****[[Gene_Function|Gene_Function]]
+
****[[Host_Organism|host_organism]]
−
****[[Host_organism|host_organism]]
+
****[[Lifecycle_Stage|lifecycle_stage]]
−
****[[Lifecycle_stage|lifecycle_stage]]
+
*****[[Amastigote|amastigote]]
 +
******[[Leishmania_SP_Amastigote|leishmania_sp_amastigote]]
 +
******[[Trypanosoma_Cruzi_Amastigote|trypanosoma_cruzi_amastigote]]
 +
*****[[Epimastigote|epimastigote]]
 +
******[[Trypanosoma_Brucei_Epimastigote|trypanosoma_brucei_epimastigote]]
 +
******[[Trypanosoma_Cruzi_Epimastigote|trypanosoma_cruzi_epimastigote]]
 +
*****[[Promastigote|promastigote]]
 +
******[[Metacyclic_Promastigote|metacyclic_promastigote]]
 +
******[[Procyclic_Promastigote|procyclic_promastigote]]
 +
*****[[Trypomastigote|trypomastigote]]
 +
******[[Trypanosoma_Brucei_Trypomastigote|trypanosoma_brucei_trypomastigote]]
 +
******[[Trypanosoma_Cruzi_Trypomastigote|trypanosoma_cruzi_trypomastigote]]
 +
******[[Blood_Stream_Form_Trypomastigote|blood_stream_form_trypomastigote]]
 +
******[[Metacyclic_Trypomastigote|metacyclic|trypomastigote]]
 +
*******[[Trypanosoma_brucei_Metacyclic_Trypomastigote|trypanosoma_brucei_metacyclic_trypomastigote]]
 +
*******[[Trypanosoma_Cruzi_Metacyclic_Trypomastigote|trypanosoma_cruzi_metacyclic_trypomastigote]]
 +
******[[Procyclic_Trypomastigote|procyclic_trypomastigote]]
 
****[[organism]]
 
****[[organism]]
 
****[[Organism_Strain|organism_strain]]
 
****[[Organism_Strain|organism_strain]]
Line 73: Line 89:
 
****[[Genome|genome]]
 
****[[Genome|genome]]
 
*****[[Transfected_Genome|transfected_genome]]
 
*****[[Transfected_Genome|transfected_genome]]
−
*****[[Region|region]]
+
****[[Region|region]]
−
******[[Flanking_Region|flanking_region]]
+
*****[[Gene|gene]]
−
******[[Gene|gene]]
+
*****[[Intergenic_Region|intergenic_region]]
−
******[[Intergenic_Region|intergenic_region]]
+
******[[3_Prime_Intergenic_Region|3_prime_intergenic_region]]
 +
*******[[3_Prime_Intergenic_Forward_Region|3_prime_intergenic_forward_region]]
 +
*******[[3_Prime_Intergenic_Reverse_Region|3_prime_intergenic_reverse_region]]
 +
******[[5_Prime_Intergenic_Region|5_prime_intergenic_region]]
 +
*******[[5_Prime_Intergenic_Forward_Region|5_prime_intergenic_forward_region]]
 +
*******[[5_Prime_Intergenic_Reverse_Region|5_prime_intergenic_reverse_region]]
 +
****[[Gene_Function|gene_function]]
 
***spatial_parameter
 
***spatial_parameter
 
****[[Freezer_Location|freezer_location]]
 
****[[Freezer_Location|freezer_location]]
Line 82: Line 104:
 
***temporal_parameter
 
***temporal_parameter
 
****[[Date_Time_Description|DateTimeDescription]]
 
****[[Date_Time_Description|DateTimeDescription]]
 +
*****[[DateCompleted|dateCompleted]]
 +
*****[[DateOfLastModification|dateOfLastModification]]
 +
*****[[DateStarted|dateStarted]]
 
*process
 
*process
 
**[[Gene_Knockout_Process|gene_knockout_process]]
 
**[[Gene_Knockout_Process|gene_knockout_process]]
Line 113: Line 138:
 
     </tr>
 
     </tr>
 
</table>
 
</table>
 +
 
<!--start section 2 -->
 
<!--start section 2 -->
 +
 +
{{block
 +
  |title= Alignment of PEO and OBI
 +
  |title_background=#b0e2ff
 +
  |content= 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:==
 +
 +
{| border="1" cellpadding="5"
 +
|- bgcolor=lightgrey
 +
! #No !!PEO !! Term!! OBI !! Term !! Relation !! Link
 +
|-  align="left"
 +
| 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
 +
|-  align="left"
 +
| 2||http://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
 +
|-  align="left"
 +
| 3||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://bioportal.bioontology.org/visualize/42093/?conceptid=Thesaurus%3AMicroarray_Analysis&jump_to_nav=true#mappings
 +
|- align="left"
 +
|4||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://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Aproteome_analysis#mappings
 +
|- align="left"
 +
| 5||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://bioportal.bioontology.org/visualize/42093/?conceptid=sequence%3Aregion&jump_to_nav=true#mappings
 +
|- align="left"
 +
|6||http://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
 +
|- align="left"
 +
|7||http://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
 +
|- align="left"
 +
|8||http://knoesis.wright.edu/ParasiteExperiment.owl#drug  ||drug  || http://purl.obolibrary.org/obo/OBI_0000040 || drug role || http://www.w3.org/2004/02/skos/core#exactMatch||http://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Adrug&jump_to_nav=true#mappings
 +
|- align="left"
 +
|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#exactMatch||http://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Anucleic_acid&jump_to_nav=true#mappings
 +
|- align="left"
 +
|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#exactMatch||http://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Aculture_medium&jump_to_nav=true#mappings
 +
|- align="left"
 +
| 11||http://knoesis.wright.edu/ParasiteExperiment.owl#transfection ||  transfection|| http://purl.obolibrary.org/obo/OBI_0600060 || DNA transfection || http://www.w3.org/2004/02/skos/core#exactMatch||http://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Atransfection&jump_to_nav=true#mappings
 +
|- align="left"
 +
|12||http://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
 +
|- align="left"
 +
|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
 +
|- align="left"
 +
| 14||http://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#exactMatch||http://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteLifecycle%3Alifecycle_stage&jump_to_nav=true#mappings
 +
|- align="left"
 +
| 15||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
 +
|- align="left"
 +
| 16|| http://knoesis.wright.edu/ParasiteExperiment.owl#signal_intensity||signal_intensity  || http://purl.obolibrary.org/obo/OBI_0000010 || fluorescent reporter intensity || http://www.w3.org/2004/02/skos/core#exactMatch||http://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Asignal_intensity&jump_to_nav=true#mappings
 +
|- align="left"
 +
| 17||http://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#exactMatch||http://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Atemperature_condition&jump_to_nav=true#mappings
 +
|- align="left"
 +
| 18||http://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#exactMatch||http://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Apurity&jump_to_nav=true#mappings
 +
|- align="left"
 +
| 19||http://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#exactMatch||http://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Asample&jump_to_nav=true#mappings
 +
|- align="left"
 +
|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
 +
|}
 +
 +
 +
 +
<!--end section 2 -->
 +
 +
<!--start section 3 -->
  
 
{{block
 
{{block
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     <tr valign="top">
 
     <tr valign="top">
 
         <td>
 
         <td>
 +
<ul>
 +
<li>[[3 Prime Forward Primer]]</li>
 +
<li>[[3 Prime Intergenic Forward Region]]</li>
 +
<li>[[3 Prime Intergenic Region]]</li>
 +
<li>[[3 Prime Intergenic Reverse Region]]</li>
 +
<li>[[3 Prime Primer]]</li>
 +
<li>[[3 Prime Reverse Primer]]</li>
 +
<li>[[5 Prime Forward Primer]]</li>
 +
<li>[[5 Prime Intergenic Forward Region]]</li>
 +
<li>[[5 Prime Intergenic Region]]</li>
 +
<li>[[5 Prime Intergenic Reverse Region]]</li>
 +
<li>[[5 Prime Primer]]</li>
 +
<li>[[5 Prime Reverse Primer]]</li>
 +
</ul>
 
;A
 
;A
 
<ul>
 
<ul>
−
<li> [[Accession Number]]</li>
+
<li> [[Accession Number]]</li>
−
<li> [[Allele Designation]]</li>
+
 
<li> [[Amastigote]]</li>
 
<li> [[Amastigote]]</li>
 
</ul>
 
</ul>
 +
 +
;B
 +
<ul>
 +
<li>[[Blood Stream Form Trypomastigote]]</li>
 +
</ul>
  
 
;C
 
;C
 
                                 <ul>
 
                                 <ul>
−
                                        <li>[[Cell Cloning]]</li>
+
<li>[[Cell Cloning]]</li>
 
<li>[[Chromosome]]</li>
 
<li>[[Chromosome]]</li>
−
                                        <li>[[Cloned Sample]]</li>
+
<li>[[Cloned Sample]]</li>
−
                                        <li>[[Cloned Sample Designate]]</li>
+
<li>[[Cloned Sample Designate]]</li>
 
<li>[[Culture Medium]]</li>
 
<li>[[Culture Medium]]</li>
 
<li>[[Culture Parameter]]</li>
 
<li>[[Culture Parameter]]</li>
Line 141: Line 245:
 
;D
 
;D
 
                                 <ul>
 
                                 <ul>
 +
<li>[[Data Source]]</li>
 +
<li>[[Date Completed]]</li>
 +
<li>[[Date of Last Modification]]</li>
 +
<li>[[Date Started]]</li>
 
<li>[[Date Time Description]]</li>                                         
 
<li>[[Date Time Description]]</li>                                         
 
<li>[[Drug]]</li>
 
<li>[[Drug]]</li>
 
<li>[[Drug Attribute]]</li>
 
<li>[[Drug Attribute]]</li>
−
                                        <li>[[Drug Concentration]]</li>
+
<li>[[Drug Concentration]]</li>
−
                                        <li>[[Drug Resistant Plasmid]]</li>
+
<li>[[Drug Resistant Plasmid]]</li>
−
                                        <li>[[Drug Selected Sample]]</li>
+
<li>[[Drug Selected Sample]]</li>
−
                                        <li>[[Drug Selection]]</li>
+
<li>[[Drug Selection]]</li>
 
                                 </ul>
 
                                 </ul>
 
;E
 
;E
 
                                 <ul>
 
                                 <ul>
 
<li>[[Epimastigote]]</li>                                         
 
<li>[[Epimastigote]]</li>                                         
−
<li>[[Experiment Notes]]</li>
 
−
<li>[[Experiment Justification]]</li>
 
 
                                          
 
                                          
 
                                 </ul>
 
                                 </ul>
 
;F
 
;F
 
                                 <ul>
 
                                 <ul>
−
<li>[[Flanking Region]]</li>
 
 
<li>[[Freezer]]</li>                                       
 
<li>[[Freezer]]</li>                                       
 
<li>[[Freezer Location]]</li>
 
<li>[[Freezer Location]]</li>
Line 168: Line 273:
 
                                 <ul>
 
                                 <ul>
 
<li>[[Gene]]</li>
 
<li>[[Gene]]</li>
−
<li>[[Gene Function]]</li>                                      
+
<li>[[Gene Function]]</li>        
−
<li>[[Gene Knockout Protocol]]</li>
+
<li>[[Gene Knockout Process]]</li>                              
 
<li>[[Genome]]</li>
 
<li>[[Genome]]</li>
 +
<li>[[GO Term]]</li>
 
                                 </ul>
 
                                 </ul>
 
;H
 
;H
 
                                 <ul>
 
                                 <ul>
−
                                        <li>[[Host organism]]</li>
+
<li>[[Host organism]]</li>
−
                                        <li>[[Hybridisation]]</li>
+
<li>[[Hybridisation]]</li>
 
                                 </ul>
 
                                 </ul>
 
;I
 
;I
 
                                 <ul>
 
                                 <ul>
−
                                        <li>[[Intergenic Region]]</li>
+
<li>[[Intergenic Region]]</li>
 
                                          
 
                                          
 
                                 </ul>
 
                                 </ul>
Line 187: Line 293:
 
<li>[[Kinetoplast Position]]</li>                                         
 
<li>[[Kinetoplast Position]]</li>                                         
 
<li>[[Knockout Construct Plasmid]]</li>
 
<li>[[Knockout Construct Plasmid]]</li>
−
                                        <li>[[Knockout Plasmid]]</li>
+
<li>[[Knockout Plasmid]]</li>
 
<li>[[Knockout Plasmid Construction]]</li>
 
<li>[[Knockout Plasmid Construction]]</li>
 
<li>[[Knockout Project Protocol]]</li>
 
<li>[[Knockout Project Protocol]]</li>
Line 195: Line 301:
 
;L
 
;L
 
                                 <ul>
 
                                 <ul>
−
                                        <li>[[Labelling]]</li>
+
<li>[[Labelling]]</li>
 
<li>[[Laboratory Experiment Parameter]]</li>
 
<li>[[Laboratory Experiment Parameter]]</li>
−
                                        <li>[[Lifecycle stage]]</li>
+
<li>[[Leishmania SP Amastigote]]</li>
−
<li>[[Log base2 Ratio]]</li>                                </ul>
+
<li>[[Lifecycle stage]]</li>
 +
<li>[[Log base2 Ratio]]</li>                                 
 +
                                </ul>
 
</td>
 
</td>
 
<td>
 
<td>
 
;M
 
;M
 
                                 <ul>
 
                                 <ul>
−
                                        <li>[[Medium]]</li>
+
<li>[[Metacyclic_Promastigote]]</li>
−
                                        <li>[[Microarray Analysis]]</li>
+
<li>[[Metacyclic_Trypomastigote]]</li>
−
<li>[[Microarray ANOVA Cluster]]</li>
+
<li>[[Microarray Analysis]]</li>
 
<li>[[Microarray Oligonucleotide]]</li>
 
<li>[[Microarray Oligonucleotide]]</li>
−
                                        <li>[[Microarray Plate Reader]]</li>
+
<li>[[Microarray Plate Reader]]</li>
 
                                 </ul>
 
                                 </ul>
  
 
;N
 
;N
 
                                 <ul>
 
                                 <ul>
−
                                        <li>[[Nucleic Acid]]</li>
+
<li>[[Nucleic Acid]]</li>
 
                                 </ul>
 
                                 </ul>
  
Line 224: Line 332:
 
;P
 
;P
 
                                 <ul>
 
                                 <ul>
−
                                        <li>[[Peptide count]]</li>  
+
<li>[[Peptide count]]</li>  
−
                                        <li>[[Phenotype]]</li>     
+
<li>[[Phenotype]]</li>     
−
                                        <li>[[Plasmid]]</li>
+
<li>[[Plasmid]]</li>
−
                                        <li>[[Plasmid Construction]]</li>
+
<li>[[Plasmid Construction]]</li>
−
<li>[[Plasmid Construction Step]]</li>
+
<li>[[Polymerase Chain Reaction]]</li>
−
                                        <li>[[Polymerase Chain Reaction]]</li>
+
<li>[[Prehybridisation]]</li>
−
                                        <li>[[Prehybridisation]]</li>
+
<li>[[Primer]]</li>
−
<li>[[Priority]]</li>
+
<li>[[Priority]]</li>
−
<li>[[Probability]]</li>
+
<li>[[Probability]]</li>
 +
<li>[[Procyclic Promastigote]]</li>
 +
<li>[[Procyclic Trypomastigote]]</li>
 
<li>[[Promastigote]]</li>  
 
<li>[[Promastigote]]</li>  
 
<li>[[Protein group number]]</li>
 
<li>[[Protein group number]]</li>
Line 246: Line 356:
 
                                 <ul>
 
                                 <ul>
 
<li>[[Region]]</li>                                         
 
<li>[[Region]]</li>                                         
−
<li>[[Researcher]]</li>
+
<li>[[Researcher]]</li>                                         
−
<li>[[Researcher Note]]</li>                                         
+
 
                                 </ul>
 
                                 </ul>
 
;S
 
;S
 
                                 <ul>
 
                                 <ul>
−
                                        <li>[[Sample]]</li>
+
<li>[[SAM Result]]</li>
 +
<li>[[Sample]]</li>
 
<li>[[Sample Characterization]]</li>
 
<li>[[Sample Characterization]]</li>
 
<li>[[Scanning]]</li>
 
<li>[[Scanning]]</li>
 
<li>[[Sequence Coverage]]</li>
 
<li>[[Sequence Coverage]]</li>
−
                                        <li>[[Sequence Extraction]]</li>
+
<li>[[Sequence Extraction]]</li>
−
                                        <li>[[Signal Intensity]]</li>
+
<li>[[Signal Intensity]]</li>
 
<li>[[Spectral Count]]</li>
 
<li>[[Spectral Count]]</li>
 
<li>[[Stage Purity Determination]]</li>
 
<li>[[Stage Purity Determination]]</li>
Line 262: Line 372:
 
<li>[[Statistical Measure]]</li>
 
<li>[[Statistical Measure]]</li>
 
<li>[[Status]]</li>
 
<li>[[Status]]</li>
−
                                        <li>[[Strains]]</li>
 
 
<li>[[Strain Creation Process]]</li>
 
<li>[[Strain Creation Process]]</li>
 
<li>[[Strain Creation Protocol]]</li>
 
<li>[[Strain Creation Protocol]]</li>
Line 270: Line 379:
 
<li>[[Target Region Plasmid]]</li>                                         
 
<li>[[Target Region Plasmid]]</li>                                         
 
<li>[[Tcruzi Lifecyclestage Subsample]]</li>
 
<li>[[Tcruzi Lifecyclestage Subsample]]</li>
−
                                        <li>[[Tcruzi Sample]]</li>
+
<li>[[Tcruzi Sample]]</li>
−
<li>[[Technician Note]]</li>
+
 
<li>[[Temperature Condition]]</li>
 
<li>[[Temperature Condition]]</li>
 
<li>[[Transcriptome Process]]</li>                                         
 
<li>[[Transcriptome Process]]</li>                                         
−
<li>[[Transcriptome Protocol]]</li>
 
 
<li>[[Transfected Genome]]</li>                                         
 
<li>[[Transfected Genome]]</li>                                         
 
<li>[[Transfected Sample]]</li>
 
<li>[[Transfected Sample]]</li>
−
                                        <li>[[Transfection]]</li>
+
<li>[[Transfection]]</li>
−
                                        <li>[[Transfection Buffer]]</li>
+
<li>[[Transfection Buffer]]</li>
−
                                        <li>[[Transfection Machine]]</li>
+
<li>[[Transfection Machine]]</li>
 +
<li>[[Trypanosoma Brucei Epimastigote]]</li>
 +
<li>[[Trypanosoma Brucei Metacyclic Trypomastigote]]</li>
 +
<li>[[Trypanosoma Brucei Trypomastigote]]</li>
 +
<li>[[Trypanosoma Cruzi Amastigote]]</li>
 +
<li>[[Trypanosoma_Cruzi_Epimastigote]]</li>
 +
<li>[[Trypanosoma Cruzi Metacyclic Trypomastigote]]</li>
 +
<li>[[Trypanosoma Cruzi Trypomastigote]]</li>
 
<li>[[Trypomastigote]]</li>
 
<li>[[Trypomastigote]]</li>
 
                                 </ul>
 
                                 </ul>
Line 289: Line 403:
 
</table>  
 
</table>  
 
}}
 
}}
−
<!--end section 2 -->
+
<!--end section 3 -->
−
<!--start section 3 -->
+
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{{block
 
{{block
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   |content=Please add feedback/comments in [http://wiki.knoesis.org/index.php?title=Talk:TcruziExperiri_ontology&action=edit Discussion Section] on the top of this wiki page.
 
   |content=Please add feedback/comments in [http://wiki.knoesis.org/index.php?title=Talk:TcruziExperiri_ontology&action=edit Discussion Section] on the top of this wiki page.
 
}}
 
}}
−
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+
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Latest revision as of 14:13, 17 March 2011


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
2 http://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
3 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://bioportal.bioontology.org/visualize/42093/?conceptid=Thesaurus%3AMicroarray_Analysis&jump_to_nav=true#mappings
4 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://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Aproteome_analysis#mappings
5 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://bioportal.bioontology.org/visualize/42093/?conceptid=sequence%3Aregion&jump_to_nav=true#mappings
6 http://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
7 http://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
8 http://knoesis.wright.edu/ParasiteExperiment.owl#drug drug http://purl.obolibrary.org/obo/OBI_0000040 drug role http://www.w3.org/2004/02/skos/core#exactMatch http://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#exactMatch http://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#exactMatch http://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Aculture_medium&jump_to_nav=true#mappings
11 http://knoesis.wright.edu/ParasiteExperiment.owl#transfection transfection http://purl.obolibrary.org/obo/OBI_0600060 DNA transfection http://www.w3.org/2004/02/skos/core#exactMatch http://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Atransfection&jump_to_nav=true#mappings
12 http://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
14 http://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#exactMatch http://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteLifecycle%3Alifecycle_stage&jump_to_nav=true#mappings
15 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
16 http://knoesis.wright.edu/ParasiteExperiment.owl#signal_intensity signal_intensity http://purl.obolibrary.org/obo/OBI_0000010 fluorescent reporter intensity http://www.w3.org/2004/02/skos/core#exactMatch http://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Asignal_intensity&jump_to_nav=true#mappings
17 http://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#exactMatch http://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Atemperature_condition&jump_to_nav=true#mappings
18 http://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#exactMatch http://bioportal.bioontology.org/visualize/42093/?conceptid=ParasiteExperiment%3Apurity&jump_to_nav=true#mappings
19 http://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#exactMatch http://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
Feedback/Comments

Please add feedback/comments in Discussion Section on the top of this wiki page.

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