Parasite Experiment ontology - Revision history

Priti at 14:13, 17 March 2011

2011-03-17T14:13:30Z

Mpanahiazar at 20:39, 14 March 2011

2011-03-14T20:39:06Z

Mpanahiazar at 20:37, 14 March 2011

2011-03-14T20:37:52Z

Mpanahiazar at 20:37, 14 March 2011

2011-03-14T20:37:00Z

Mpanahiazar at 20:32, 14 March 2011

2011-03-14T20:32:23Z

Mpanahiazar at 20:28, 14 March 2011

2011-03-14T20:28:48Z

Mpanahiazar at 20:15, 14 March 2011

2011-03-14T20:15:54Z

Mpanahiazar at 20:04, 14 March 2011

2011-03-14T20:04:21Z

Mpanahiazar at 20:02, 14 March 2011

2011-03-14T20:02:58Z

Mpanahiazar at 20:01, 14 March 2011

2011-03-14T20:01:52Z

@@ Line 146: / Line 146: @@
    |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.
 }}
-==Mapping between PEO and OBI submitted to NCBO:==
+==Mappings between PEO and OBI submitted to NCBO BioPortal:==
 {| border="1" cellpadding="5"

@@ Line 194: / Line 194: @@
 |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
 |}

@@ Line 144: / Line 144: @@
    |title= Alignment of PEO and OBI
    |title_background=#b0e2ff
-   |content='''mapping between PEO and OBI submitted to NCBO: 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.'''
+   |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.
 }}
   <br>
-==Mapping==
+==Mapping between PEO and OBI submitted to NCBO:==
 {| border="1" cellpadding="5"

@@ Line 144: / Line 144: @@
    |title= Alignment of PEO and OBI
    |title_background=#b0e2ff
-   |content='''mapping between PEO and OBI submitted to NCBO:'''
+   |content='''mapping between PEO and OBI submitted to NCBO: 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.'''
 }}
   <br>

@@ Line 155: / Line 155: @@
 |-  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="center"
+|-  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"
-|- align="center"
 | 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"
-|- align="center"
 |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"
-|- align="center"
 | 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"
-|- align="center"
 |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"
-|- align="center"
 |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"
-−
-|- align="center"
 |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"
-−
-|- align="center"
 |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"
-−
-|- align="center"
 |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"
-−
-|- align="center"
 | 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"
-−
-|- align="center"
 |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"
-|- align="center"
 |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"
-|- align="center"
 | 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"
-|- align="center"
 | 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"
-|- align="center"
 | 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"
-|- align="center"
 | 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"
-|- align="center"
 | 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"
-|- align="center"
 | 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"
-|- align="center"
 |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
 |- align="center"
 |  ||  ||  ||  || ||--
 |}

@@ Line 157: / Line 157: @@
 |-  align="center"
-| http://knoesis.wright.edu/ParasiteExperiment.owl#standard_deviation || standard_deviation || http://purl.obolibrary.org/obo/OBI_0200121 || standard deviation calculation || 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
+| 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="center"