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Removed SILVA (#9), added parsimony algorithm (#7), created a class f…
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…or a set of trees (and networks) (#10), and added operation for pruning and grafting (#11).
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@hlapp
hlapp committed Feb 1, 2013
1 parent 5759cec commit 9b68e44
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101 changes: 92 additions & 9 deletions ontology/miapa.owl
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<!-- http://edamontology.org/operation_0539 -->

<owl:Class rdf:about="http://edamontology.org/operation_0539">
<rdfs:label>Phylogenetic tree construction (method centric)</rdfs:label>
<rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0323"/>
</owl:Class>



<!-- http://edamontology.org/operation_2928 -->

<owl:Class rdf:about="http://edamontology.org/operation_2928">
Expand Down Expand Up @@ -518,15 +527,6 @@ Alternatively, we could model this as dc:isPartOf some prov:Plan.</rdfs:comment>



<!-- http://purl.obolibrary.org/obo/MIAPA_0000023 -->

<owl:Class rdf:about="&obo;MIAPA_0000023">
<rdfs:label xml:lang="en">SILVA</rdfs:label>
<rdfs:subClassOf rdf:resource="&obo;IAO_0000010"/>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MIAPA_0000024 -->

<owl:Class rdf:about="&obo;MIAPA_0000024">
Expand Down Expand Up @@ -599,6 +599,89 @@ Alternatively, we could model this as dc:isPartOf some prov:Plan.</rdfs:comment>



<!-- http://purl.obolibrary.org/obo/MIAPA_0000037 -->

<owl:Class rdf:about="&obo;MIAPA_0000037">
<rdfs:label xml:lang="en">Parsimony method</rdfs:label>
<rdfs:subClassOf rdf:resource="&obo;IAO_0000064"/>
<obo:IAO_0000115>A method for finding the minimum transitions to account for a character given a phylogenetic tree, and by extension, a character-based phylogeny inference method in which the inferred phylogenetic tree (the &quot;maximum parsimony tree&quot;) is the phylogenetic tree that minimizes evolutionary transitions over all characters.</obo:IAO_0000115>
<obo:IAO_0000119>Prosdocimi, Francisco, Brandon Chisham, Enrico Pontelli, J.D. Thompson, and Arlin Stoltzfus. 2009. “Initial Implementation of a Comparative Data Analysis Ontology.” Evolutionary Bioinformatics Online (5): 47–66. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747124/</obo:IAO_0000119>
<obo:IAO_0000119>https://www.nescent.org/wg_evoinfo/Concept_Glossary#Parsimony_Method</obo:IAO_0000119>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MIAPA_0000038 -->

<owl:Class rdf:about="&obo;MIAPA_0000038">
<rdfs:label xml:lang="en">Phylogenetic tree construction (pruning and grafting)</rdfs:label>
<rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0539"/>
<obo:IAO_0000115>Phylogenetic tree construction that prunes and grafts a collection of one or more source trees to create the resulting tree.</obo:IAO_0000115>
<obo:IAO_0000117>Hilmar Lapp</obo:IAO_0000117>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MIAPA_0000039 -->

<owl:Class rdf:about="&obo;MIAPA_0000039">
<rdfs:label xml:lang="en">SetOfNetworks</rdfs:label>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="&prov;Collection"/>
<owl:Restriction>
<owl:onProperty rdf:resource="&prov;hadMember"/>
<owl:allValuesFrom rdf:resource="&obo;CDAO_0000006"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="&obo;CDAO_0000118"/>
<owl:Restriction>
<owl:onProperty rdf:resource="&obo;CDAO_0000198"/>
<owl:allValuesFrom rdf:resource="&obo;CDAO_0000006"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MIAPA_0000040 -->

<owl:Class rdf:about="&obo;MIAPA_0000040">
<rdfs:label xml:lang="en">SetOfTrees</rdfs:label>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="&obo;MIAPA_0000039"/>
<owl:Restriction>
<owl:onProperty rdf:resource="&obo;CDAO_0000198"/>
<owl:allValuesFrom rdf:resource="&obo;CDAO_0000110"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="&prov;Collection"/>
<owl:Restriction>
<owl:onProperty rdf:resource="&prov;hadMember"/>
<owl:allValuesFrom rdf:resource="&obo;CDAO_0000110"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
</owl:Class>



<!-- http://purl.org/dc/terms/Location -->

<owl:Class rdf:about="&dcterms;Location"/>
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101 changes: 92 additions & 9 deletions ontology/miapa_no-imports.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -293,6 +293,15 @@



<!-- http://edamontology.org/operation_0539 -->

<owl:Class rdf:about="http://edamontology.org/operation_0539">
<rdfs:label>Phylogenetic tree construction (method centric)</rdfs:label>
<rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0323"/>
</owl:Class>



<!-- http://edamontology.org/operation_2928 -->

<owl:Class rdf:about="http://edamontology.org/operation_2928">
Expand Down Expand Up @@ -516,15 +525,6 @@ Alternatively, we could model this as dc:isPartOf some prov:Plan.</rdfs:comment>



<!-- http://purl.obolibrary.org/obo/MIAPA_0000023 -->

<owl:Class rdf:about="&obo;MIAPA_0000023">
<rdfs:label xml:lang="en">SILVA</rdfs:label>
<rdfs:subClassOf rdf:resource="&obo;IAO_0000010"/>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MIAPA_0000024 -->

<owl:Class rdf:about="&obo;MIAPA_0000024">
Expand Down Expand Up @@ -597,6 +597,89 @@ Alternatively, we could model this as dc:isPartOf some prov:Plan.</rdfs:comment>



<!-- http://purl.obolibrary.org/obo/MIAPA_0000037 -->

<owl:Class rdf:about="&obo;MIAPA_0000037">
<rdfs:label xml:lang="en">Parsimony method</rdfs:label>
<rdfs:subClassOf rdf:resource="&obo;IAO_0000064"/>
<obo:IAO_0000115>A method for finding the minimum transitions to account for a character given a phylogenetic tree, and by extension, a character-based phylogeny inference method in which the inferred phylogenetic tree (the &quot;maximum parsimony tree&quot;) is the phylogenetic tree that minimizes evolutionary transitions over all characters.</obo:IAO_0000115>
<obo:IAO_0000119>Prosdocimi, Francisco, Brandon Chisham, Enrico Pontelli, J.D. Thompson, and Arlin Stoltzfus. 2009. “Initial Implementation of a Comparative Data Analysis Ontology.” Evolutionary Bioinformatics Online (5): 47–66. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747124/</obo:IAO_0000119>
<obo:IAO_0000119>https://www.nescent.org/wg_evoinfo/Concept_Glossary#Parsimony_Method</obo:IAO_0000119>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MIAPA_0000038 -->

<owl:Class rdf:about="&obo;MIAPA_0000038">
<rdfs:label xml:lang="en">Phylogenetic tree construction (pruning and grafting)</rdfs:label>
<rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0539"/>
<obo:IAO_0000115>Phylogenetic tree construction that prunes and grafts a collection of one or more source trees to create the resulting tree.</obo:IAO_0000115>
<obo:IAO_0000117>Hilmar Lapp</obo:IAO_0000117>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MIAPA_0000039 -->

<owl:Class rdf:about="&obo;MIAPA_0000039">
<rdfs:label xml:lang="en">SetOfNetworks</rdfs:label>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="&prov;Collection"/>
<owl:Restriction>
<owl:onProperty rdf:resource="&prov;hadMember"/>
<owl:allValuesFrom rdf:resource="&obo;CDAO_0000006"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="&obo;CDAO_0000118"/>
<owl:Restriction>
<owl:onProperty rdf:resource="&obo;CDAO_0000198"/>
<owl:allValuesFrom rdf:resource="&obo;CDAO_0000006"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MIAPA_0000040 -->

<owl:Class rdf:about="&obo;MIAPA_0000040">
<rdfs:label xml:lang="en">SetOfTrees</rdfs:label>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="&obo;MIAPA_0000039"/>
<owl:Restriction>
<owl:onProperty rdf:resource="&obo;CDAO_0000198"/>
<owl:allValuesFrom rdf:resource="&obo;CDAO_0000110"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
<rdf:Description rdf:about="&prov;Collection"/>
<owl:Restriction>
<owl:onProperty rdf:resource="&prov;hadMember"/>
<owl:allValuesFrom rdf:resource="&obo;CDAO_0000110"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</rdfs:subClassOf>
</owl:Class>



<!-- http://purl.org/dc/terms/Location -->

<owl:Class rdf:about="&dcterms;Location"/>
Expand Down

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