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Added metadata for the ontology itself, including description, authors, CC0 waiver, and links to repository, mailing list, and MIAPA home page.
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‎ontology/miapa.owl‎

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<!DOCTYPE rdf:RDF [
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<!ENTITY dsw "http://purl.org/dsw/" >
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<!ENTITY dcterms "http://purl.org/dc/terms/" >
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<!ENTITY edam "http://edamontology.org/" >
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<!ENTITY swo "http://www.ebi.ac.uk/swo/" >
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<!ENTITY dcterms "http://purl.org/dc/terms/" >
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<!ENTITY prov "http://www.w3.org/ns/prov#" >
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<!ENTITY swo2 "http://www.ebi.ac.uk/efo/swo/" >
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<!ENTITY owl "http://www.w3.org/2002/07/owl#" >
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<!ENTITY obo "http://purl.obolibrary.org/obo/" >
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<!ENTITY dc "http://purl.org/dc/elements/1.1/" >
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<!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
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<!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
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<!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
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<rdf:RDF xmlns="&obo;miapa.owl#"
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xml:base="&obo;miapa.owl"
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xmlns:obo="http://purl.obolibrary.org/obo/"
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xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
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xmlns:dc="http://purl.org/dc/elements/1.1/"
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xmlns:prov="http://www.w3.org/ns/prov#"
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xmlns:swo2="http://www.ebi.ac.uk/efo/swo/"
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xmlns:swo="http://www.ebi.ac.uk/swo/"
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xmlns:dsw="http://purl.org/dsw/"
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xmlns:owl="http://www.w3.org/2002/07/owl#"
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xmlns:dcterms="http://purl.org/dc/terms/"
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xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
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xmlns:obo="http://purl.obolibrary.org/obo/"
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xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
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xmlns:owl="http://www.w3.org/2002/07/owl#"
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xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
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xmlns:dcterms="http://purl.org/dc/terms/">
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xmlns:edam="http://edamontology.org/">
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<owl:Ontology rdf:about="&obo;miapa.owl">
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<dc:creator>Phylotastic Tree Annotation Team</dc:creator>
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<dc:rights>http://creativecommons.org/publicdomain/zero/1.0/</dc:rights>
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<dc:title>Minimum Information for A Phylogenetic Analysis (MIAPA) Ontology</dc:title>
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<dc:description>The MIAPA ontology is intended to be an application ontology for the purpose of semantic annotation of phylogenetic data according to the requirements and recommendations of the Minimum Information for A Phylogenetic Analysis (MIAPA) metadata reporting standard. The ontology leverages (imports) primarily from the CDAO (Comparative Data Analysis Ontology), PROV (W3C Provenance Ontology), and SWO (Software Ontology, which includes the EDAM ontologies) ontologies. It adds some assertions of its own, as well as some classes and individuals that may eventually get pushed down into one of the respective source ontologies.
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This ontology is maintained at http://github.com/miapa/miapa, and requests for changes or additions should be filed at the issue tracker there. The discussion list is at miapa-discuss@googlegroups.com. Further resources about MIAPA can be found at the project&apos;s main page at http://evoio.org/wiki/MIAPA.</dc:description>
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<dc:creator>Hilmar Lapp</dc:creator>
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<owl:imports rdf:resource="&obo;cdao.owl"/>
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<owl:versionIRI rdf:resource="&obo;miapa/2013-02-01/miapa.owl"/>
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<owl:imports rdf:resource="http://www.w3.org/ns/prov#"/>
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<!-- http://edamontology.org/operation_0004 -->
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<owl:Class rdf:about="http://edamontology.org/operation_0004">
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<owl:Class rdf:about="&edam;operation_0004">
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<rdfs:label>Operation</rdfs:label>
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<rdfs:subClassOf rdf:resource="&prov;Activity"/>
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<rdfs:comment>For the purposes of MIAPA annotation and cross-ontology interoperability, instances of edam:Operation are instances of a prov:Activity. They need to be further classified as to whether they are maipa:&apos;Manual procedure&apos; or miapa:&apos;Software procedure&apos; instances.</rdfs:comment>
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<!-- http://edamontology.org/operation_0323 -->
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<owl:Class rdf:about="http://edamontology.org/operation_0323">
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<owl:Class rdf:about="&edam;operation_0323">
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<rdfs:label>Phylogenetic tree construction</rdfs:label>
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<rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
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<rdfs:subClassOf rdf:resource="&edam;operation_0004"/>
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<rdfs:subClassOf rdf:resource="&obo;CDAO_0000014"/>
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</owl:Class>
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<!-- http://edamontology.org/operation_0539 -->
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<owl:Class rdf:about="http://edamontology.org/operation_0539">
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<owl:Class rdf:about="&edam;operation_0539">
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<rdfs:label>Phylogenetic tree construction (method centric)</rdfs:label>
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<rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0323"/>
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<rdfs:subClassOf rdf:resource="&edam;operation_0323"/>
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</owl:Class>
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<!-- http://edamontology.org/operation_2928 -->
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<owl:Class rdf:about="http://edamontology.org/operation_2928">
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<owl:Class rdf:about="&edam;operation_2928">
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<rdfs:label>Alignment construction</rdfs:label>
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<rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0004"/>
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<rdfs:subClassOf rdf:resource="&edam;operation_0004"/>
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<rdfs:subClassOf rdf:resource="&obo;CDAO_0000032"/>
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</owl:Class>
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<obo:IAO_0000115>A procedure that generates the tree.</obo:IAO_0000115>
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<rdfs:comment>For provenance annotation in MIAPA, the activity that generated the tree should be asserted as an instance of cdao:TreeProcedure.</rdfs:comment>
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</rdf:Description>
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<owl:Axiom>
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<obo:IAO_0000116>See https://github.com/miapa/miapa/issues/5</obo:IAO_0000116>
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<owl:annotatedSource rdf:resource="&obo;CDAO_0000014"/>
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<owl:annotatedProperty rdf:resource="&rdfs;subClassOf"/>
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<owl:annotatedTarget rdf:resource="&prov;Activity"/>
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</owl:Axiom>
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<obo:IAO_0000115>A procedure that generates the alignment.</obo:IAO_0000115>
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<rdfs:comment>For provenance annotation in MIAPA, the activity that generated the alignment should be asserted as an instance of cdao:AlignmentProcedure.</rdfs:comment>
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</rdf:Description>
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<owl:Axiom>
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<obo:IAO_0000116>https://github.com/miapa/miapa/issues/5</obo:IAO_0000116>
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<owl:annotatedSource rdf:resource="&obo;CDAO_0000032"/>
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<owl:annotatedProperty rdf:resource="&rdfs;subClassOf"/>
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<owl:annotatedTarget rdf:resource="&prov;Activity"/>
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</owl:Axiom>
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<rdf:Description rdf:about="&obo;CDAO_0000046">
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<owl:equivalentClass rdf:resource="&obo;CDAO_0000063"/>
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</rdf:Description>
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<owl:Axiom>
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<obo:IAO_0000116>To be proposed to and fixed in CDAO. That would then make the has_type some EdgeLengthType restriction obsolete.</obo:IAO_0000116>
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<owl:annotatedSource rdf:resource="&obo;CDAO_0000046"/>
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<owl:annotatedTarget rdf:resource="&obo;CDAO_0000063"/>
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<owl:annotatedProperty rdf:resource="&owl;equivalentClass"/>
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</owl:Axiom>
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<!-- http://purl.obolibrary.org/obo/CDAO_0000063 -->
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<rdf:Description rdf:about="&obo;CDAO_0000063"/>
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<owl:Axiom>
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<obo:IAO_0000116>To be proposed to and fixed in CDAO. That would then make the has_type some EdgeLengthType restriction obsolete.</obo:IAO_0000116>
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<owl:annotatedSource rdf:resource="&obo;CDAO_0000046"/>
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<owl:annotatedTarget rdf:resource="&obo;CDAO_0000063"/>
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<owl:annotatedProperty rdf:resource="&owl;equivalentClass"/>
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</owl:Axiom>
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<owl:Class rdf:about="&obo;MIAPA_0000015">
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<rdfs:label xml:lang="en">Maximum likelihood method</rdfs:label>
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<rdfs:subClassOf rdf:resource="&swo2;SWO_0000592"/>
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<obo:IAO_0000116>Should be pushed down to SWO.</obo:IAO_0000116>
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</owl:Class>
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<owl:Class rdf:about="&obo;MIAPA_0000016">
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<rdfs:label xml:lang="en">RAxML</rdfs:label>
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<rdfs:subClassOf rdf:resource="&obo;IAO_0000010"/>
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<obo:IAO_0000116>Should be pushed down to SWO.</obo:IAO_0000116>
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</owl:Class>
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<owl:Class rdf:about="&obo;MIAPA_0000020">
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<rdfs:label xml:lang="en">MAFFT</rdfs:label>
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<rdfs:subClassOf rdf:resource="&obo;IAO_0000010"/>
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<obo:IAO_0000116>Should be pushed down to SWO.</obo:IAO_0000116>
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</owl:Class>
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<owl:Class rdf:about="&obo;MIAPA_0000022">
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<rdfs:label xml:lang="en">SINA</rdfs:label>
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<rdfs:subClassOf rdf:resource="&obo;IAO_0000010"/>
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<obo:IAO_0000116>Should be pushed down to SWO.</obo:IAO_0000116>
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</owl:Class>
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<owl:Class rdf:about="&obo;MIAPA_0000024">
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<rdfs:label xml:lang="en">PRANK</rdfs:label>
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<rdfs:subClassOf rdf:resource="&obo;IAO_0000010"/>
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<obo:IAO_0000116>Should be pushed down to SWO.</obo:IAO_0000116>
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</owl:Class>
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<owl:Class rdf:about="&obo;MIAPA_0000025">
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<rdfs:label xml:lang="en">PAUP*</rdfs:label>
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<rdfs:subClassOf rdf:resource="&obo;IAO_0000010"/>
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<obo:IAO_0000116>Should be pushed down to SWO.</obo:IAO_0000116>
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</owl:Class>
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<owl:Class rdf:about="&obo;MIAPA_0000026">
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<rdfs:label xml:lang="en">TNT</rdfs:label>
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<rdfs:subClassOf rdf:resource="&obo;IAO_0000010"/>
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<obo:IAO_0000116>Should be pushed down to SWO.</obo:IAO_0000116>
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</owl:Class>
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<owl:Class rdf:about="&obo;MIAPA_0000027">
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<rdfs:label xml:lang="en">PhyML</rdfs:label>
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<rdfs:subClassOf rdf:resource="&obo;IAO_0000010"/>
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<obo:IAO_0000116>Should be pushed down to SWO.</obo:IAO_0000116>
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</owl:Class>
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<owl:Class rdf:about="&obo;MIAPA_0000028">
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<rdfs:label xml:lang="en">AMPHORA</rdfs:label>
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<rdfs:subClassOf rdf:resource="&obo;IAO_0000010"/>
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<obo:IAO_0000116>Should be pushed down to SWO.</obo:IAO_0000116>
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</owl:Class>
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<rdfs:label xml:lang="en">Parsimony method</rdfs:label>
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<rdfs:subClassOf rdf:resource="&obo;IAO_0000064"/>
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<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>
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<obo:IAO_0000116>Should be pushed down to SWO.</obo:IAO_0000116>
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<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>
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<obo:IAO_0000119>https://www.nescent.org/wg_evoinfo/Concept_Glossary#Parsimony_Method</obo:IAO_0000119>
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</owl:Class>
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<owl:Class rdf:about="&obo;MIAPA_0000038">
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<rdfs:label xml:lang="en">Phylogenetic tree construction (pruning and grafting)</rdfs:label>
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<rdfs:subClassOf rdf:resource="http://edamontology.org/operation_0539"/>
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<rdfs:subClassOf rdf:resource="&edam;operation_0539"/>
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<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>
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<obo:IAO_0000116>Should be pushed down to SWO.</obo:IAO_0000116>
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<obo:IAO_0000117>Hilmar Lapp</obo:IAO_0000117>
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</owl:Class>
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</owl:intersectionOf>
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</owl:Class>
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</rdfs:subClassOf>
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<obo:IAO_0000116>To be pushed down to CDAO. This would retain though in MIAPA the equivalence to &quot;prov:Collection and provhadMember only cdao:Network&quot;.</obo:IAO_0000116>
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</owl:Class>
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</owl:intersectionOf>
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</owl:Class>
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</rdfs:subClassOf>
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<obo:IAO_0000116>To be pushed down to CDAO. This would retain though in MIAPA the equivalence to &quot;prov:Collection and provhadMember only cdao:Network&quot;.</obo:IAO_0000116>
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</owl:Class>
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<owl:Class rdf:about="&obo;MIAPA_0000041">
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<rdfs:label xml:lang="en">MrBayes</rdfs:label>
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<rdfs:subClassOf rdf:resource="&obo;IAO_0000010"/>
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<obo:IAO_0000116>Should be pushed down to SWO.</obo:IAO_0000116>
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</owl:Class>
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<owl:Class rdf:about="&obo;MIAPA_0000044">
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<rdfs:label xml:lang="en">BEAST</rdfs:label>
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<rdfs:subClassOf rdf:resource="&obo;IAO_0000010"/>
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<obo:IAO_0000116>Should be pushed down to SWO.</obo:IAO_0000116>
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</owl:Class>
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