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docWorkflow2.0.owl
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<?xml version="1.0"?>
<!DOCTYPE rdf:RDF [
<!ENTITY terms "http://purl.org/dc/terms/" >
<!ENTITY vann "http://purl.org/vocab/vann/" >
<!ENTITY SO "http://purl.org/obo/owl/SO#" >
<!ENTITY p-plan "http://purl.org/net/p-plan#" >
<!ENTITY bfo "http://www.ifomis.org/bfo/1.1#" >
<!ENTITY owl "http://www.w3.org/2002/07/owl#" >
<!ENTITY obo "http://purl.obolibrary.org/obo/" >
<!ENTITY swrl "http://www.w3.org/2003/11/swrl#" >
<!ENTITY swrlb "http://www.w3.org/2003/11/swrlb#" >
<!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
<!ENTITY sp "http://purl.org/net/SMARTprotocol#" >
<!ENTITY owl2xml "http://www.w3.org/2006/12/owl2-xml#" >
<!ENTITY snap "http://www.ifomis.org/bfo/1.1/snap#" >
<!ENTITY span "http://www.ifomis.org/bfo/1.1/span#" >
<!ENTITY npo "http://purl.bioontology.org/ontology/npo#" >
<!ENTITY ro "http://www.obofoundry.org/ro/ro.owl#" >
<!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
<!ENTITY iao "http://purl.obolibrary.org/obo/iao.owl#" >
<!ENTITY MSH "http://purl.bioontology.org/ontology/MSH/" >
<!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
<!ENTITY protege "http://protege.stanford.edu/plugins/owl/protege#" >
<!ENTITY xsp "http://www.owl-ontologies.com/2005/08/07/xsp.owl#" >
<!ENTITY Thesaurus "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#" >
<!ENTITY Ontology1184060740 "http://www.owl-ontologies.com/Ontology1184060740.owl#" >
<!ENTITY MGEDOntology "http://mged.sourceforge.net/ontologies/MGEDOntology.owl#" >
<!ENTITY miProtocol "http://www.semanticweb.org/ontologies/2013/3/miProtocol.owl#" >
<!ENTITY p1 "http://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl#" >
<!ENTITY p2 "http://www.semanticweb.org/ontologies/2013/3/Ontology1365706525737.owl#" >
]>
<rdf:RDF xmlns="http://purl.org/net/SMARTprotocol#"
xml:base="http://purl.org/net/SMARTprotocol"
xmlns:p-plan="http://purl.org/net/p-plan#"
xmlns:ro="http://www.obofoundry.org/ro/ro.owl#"
xmlns:p2="http://www.semanticweb.org/ontologies/2013/3/Ontology1365706525737.owl#"
xmlns:iao="&obo;iao.owl#"
xmlns:p1="&obo;iao/dev/ontology-metadata.owl#"
xmlns:snap="http://www.ifomis.org/bfo/1.1/snap#"
xmlns:terms="http://purl.org/dc/terms/"
xmlns:vann="http://purl.org/vocab/vann/"
xmlns:bfo="http://www.ifomis.org/bfo/1.1#"
xmlns:npo="http://purl.bioontology.org/ontology/npo#"
xmlns:Thesaurus="http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:MSH="http://purl.bioontology.org/ontology/MSH/"
xmlns:swrl="http://www.w3.org/2003/11/swrl#"
xmlns:owl2xml="http://www.w3.org/2006/12/owl2-xml#"
xmlns:miProtocol="http://www.semanticweb.org/ontologies/2013/3/miProtocol.owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
xmlns:sp="http://purl.org/net/SMARTprotocol#"
xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#"
xmlns:Ontology1184060740="http://www.owl-ontologies.com/Ontology1184060740.owl#"
xmlns:SO="http://purl.org/obo/owl/SO#"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:MGEDOntology="http://mged.sourceforge.net/ontologies/MGEDOntology.owl#"
xmlns:span="http://www.ifomis.org/bfo/1.1/span#">
<owl:Ontology rdf:about="http://purl.org/net/SMARTprotocol#">
<rdfs:label xml:lang="en">SMART Protocols Ontology: Document Module</rdfs:label>
<terms:created rdf:datatype="&xsd;date">2013-07-01</terms:created>
<terms:contributor rdf:datatype="&xsd;anyURI">http://delicias.dia.fi.upm.es/members/DGarijo/#me</terms:contributor>
<terms:creator rdf:datatype="&xsd;anyURI">http://oxgiraldo.wordpress.com/</terms:creator>
<terms:contributor rdf:datatype="&xsd;anyURI">http://www.alexandergarcia.name/</terms:contributor>
<terms:contributor rdf:datatype="&xsd;anyURI">http://www.dia.fi.upm.es/index.php?page=oscar-corcho/</terms:contributor>
<terms:license>http://creativecommons.org/licenses/by-nc-sa/2.0/</terms:license>
<terms:title xml:lang="en">SMART Protocols Ontology: Document Module</terms:title>
<rdfs:comment xml:lang="en">SMART Protocols Ontology: Document Module is an ontology designed to represent metadata used to report a laboratory protocol.</rdfs:comment>
<terms:description xml:lang="en">SMART Protocols Ontology: Document Module is an ontology designed to represent metadata used to report a laboratory protocol.</terms:description>
<vann:preferredNamespacePrefix>sp</vann:preferredNamespacePrefix>
<owl:versionInfo xml:lang="en">2.0</owl:versionInfo>
<vann:preferredNamespaceUri>http://purl.org/net/SMARTprotocol#</vann:preferredNamespaceUri>
</owl:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/IAO_0000112 -->
<owl:AnnotationProperty rdf:about="&obo;IAO_0000112">
<rdfs:label rdf:datatype="&xsd;string">example of usage</rdfs:label>
<obo:IAO_0000115 rdf:datatype="&xsd;string">A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not</obo:IAO_0000115>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
<owl:AnnotationProperty rdf:about="&obo;IAO_0000115">
<rdfs:label rdf:datatype="&xsd;string">definition</rdfs:label>
<obo:IAO_0000115 rdf:datatype="&xsd;string">The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.</obo:IAO_0000115>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000118 -->
<owl:AnnotationProperty rdf:about="&obo;IAO_0000118">
<rdfs:label rdf:datatype="&xsd;string">alternative term</rdfs:label>
<obo:IAO_0000115 rdf:datatype="&xsd;string">An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)</obo:IAO_0000115>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000119 -->
<owl:AnnotationProperty rdf:about="&obo;IAO_0000119">
<rdfs:label rdf:datatype="&xsd;string">definition source</rdfs:label>
<obo:IAO_0000115 rdf:datatype="&xsd;string">formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007</obo:IAO_0000115>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000412 -->
<owl:AnnotationProperty rdf:about="&obo;IAO_0000412">
<rdfs:label rdf:datatype="&xsd;string">imported from</rdfs:label>
<obo:IAO_0000115 rdf:datatype="&xsd;string">For external terms/classes, the ontology from which the term was imported</obo:IAO_0000115>
</owl:AnnotationProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/BFO_0000061 -->
<owl:ObjectProperty rdf:about="&obo;BFO_0000061">
<rdf:type rdf:resource="&owl;TransitiveProperty"/>
<rdfs:label xml:lang="en">precedes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000062 -->
<owl:ObjectProperty rdf:about="&obo;BFO_0000062">
<rdf:type rdf:resource="&owl;TransitiveProperty"/>
<rdfs:label xml:lang="en">is preceded by</rdfs:label>
<obo:IAO_0000412 rdf:datatype="&xsd;string">OBI</obo:IAO_0000412>
<obo:IAO_0000118 rdf:datatype="&xsd;string">preceded by</obo:IAO_0000118>
<owl:inverseOf rdf:resource="&obo;BFO_0000061"/>
<rdfs:range>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="&Thesaurus;C25294"/>
<rdf:Description rdf:about="&p-plan;Step"/>
</owl:unionOf>
</owl:Class>
</rdfs:range>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="&Thesaurus;C25294"/>
<rdf:Description rdf:about="&p-plan;Step"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
</owl:ObjectProperty>
<!-- http://purl.org/net/SMARTprotocol#hasProtocol -->
<owl:ObjectProperty rdf:about="&sp;hasProtocol">
<rdfs:label xml:lang="en">has protocol</rdfs:label>
<obo:IAO_0000115 xml:lang="en">hasProtocol is a relation that binds a laboratory procedure to a laboratory protocol.</obo:IAO_0000115>
<rdfs:domain rdf:resource="&Thesaurus;C25294"/>
</owl:ObjectProperty>
<!-- http://purl.org/net/p-plan#hasInputVar -->
<owl:ObjectProperty rdf:about="&p-plan;hasInputVar">
<rdfs:label xml:lang="en">p-plan:hasInputVar</rdfs:label>
<obo:IAO_0000412 rdf:datatype="&xsd;string">The P-PLAN Ontology</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">p-plan:hasInputVar binds a p-plan:Step to the p-plan:Variable that takes as input for the planned execution.</obo:IAO_0000115>
<rdfs:domain rdf:resource="&p-plan;Step"/>
<rdfs:range rdf:resource="&p-plan;Variable"/>
</owl:ObjectProperty>
<!-- http://purl.org/net/p-plan#hasOutputVar -->
<owl:ObjectProperty rdf:about="&p-plan;hasOutputVar">
<rdfs:label xml:lang="en">p-plan:hasOutputVar</rdfs:label>
<obo:IAO_0000412 rdf:datatype="&xsd;string">The P-PLAN Ontology</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">p-plan:hasOutputVar binds a p-plan:Step to the p-plan:Variable that takes as Output for the planned execution.</obo:IAO_0000115>
<rdfs:domain rdf:resource="&p-plan;Step"/>
<rdfs:range rdf:resource="&p-plan;Variable"/>
</owl:ObjectProperty>
<!-- http://purl.org/net/p-plan#isStepOfPlan -->
<owl:ObjectProperty rdf:about="&p-plan;isStepOfPlan">
<rdfs:label xml:lang="en">p-plan:isStepOfPlan</rdfs:label>
<obo:IAO_0000412 rdf:datatype="&xsd;string">The P-PLAN Ontology</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">p-plan:isStepOfPlan links a p-plan:Step to the p-plan:Plan which it corresponds to.</obo:IAO_0000115>
<rdfs:range rdf:resource="&p-plan;Plan"/>
<rdfs:domain rdf:resource="&p-plan;Step"/>
</owl:ObjectProperty>
<!-- http://www.obofoundry.org/ro/ro.owl#has_part -->
<owl:ObjectProperty rdf:about="&ro;has_part">
<rdf:type rdf:resource="&owl;TransitiveProperty"/>
<rdfs:label xml:lang="en">has part</rdfs:label>
<obo:IAO_0000412 rdf:datatype="&xsd;string">OBO Relation Ontology</obo:IAO_0000412>
<owl:inverseOf rdf:resource="&ro;part_of"/>
</owl:ObjectProperty>
<!-- http://www.obofoundry.org/ro/ro.owl#part_of -->
<owl:ObjectProperty rdf:about="&ro;part_of">
<rdf:type rdf:resource="&owl;TransitiveProperty"/>
<rdfs:label xml:lang="en">part of</rdfs:label>
<obo:IAO_0000412 rdf:datatype="&xsd;string">OBO Relation Ontology</obo:IAO_0000412>
<obo:IAO_0000115 rdf:datatype="&xsd;string">Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell.</obo:IAO_0000115>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000061 -->
<owl:ObjectProperty rdf:about="&obo;BFO_0000061">
<rdf:type rdf:resource="&owl;TransitiveProperty"/>
<rdfs:label xml:lang="en">precedes</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/BFO_0000062 -->
<owl:ObjectProperty rdf:about="&obo;BFO_0000062">
<rdf:type rdf:resource="&owl;TransitiveProperty"/>
<rdfs:label xml:lang="en">is preceded by</rdfs:label>
<obo:IAO_0000412 rdf:datatype="&xsd;string">OBI</obo:IAO_0000412>
<obo:IAO_0000118 rdf:datatype="&xsd;string">preceded by</obo:IAO_0000118>
<owl:inverseOf rdf:resource="&obo;BFO_0000061"/>
<rdfs:range>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="&Thesaurus;C25294"/>
<rdf:Description rdf:about="&p-plan;Step"/>
</owl:unionOf>
</owl:Class>
</rdfs:range>
<rdfs:domain>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="&Thesaurus;C25294"/>
<rdf:Description rdf:about="&p-plan;Step"/>
</owl:unionOf>
</owl:Class>
</rdfs:domain>
</owl:ObjectProperty>
<!-- http://purl.org/net/SMARTprotocol#hasProtocol -->
<owl:ObjectProperty rdf:about="&sp;hasProtocol">
<rdfs:label xml:lang="en">has protocol</rdfs:label>
<obo:IAO_0000115 xml:lang="en">hasProtocol is a relation that binds a laboratory procedure to a laboratory protocol.</obo:IAO_0000115>
<rdfs:domain rdf:resource="&Thesaurus;C25294"/>
</owl:ObjectProperty>
<!-- http://purl.org/net/p-plan#hasInputVar -->
<owl:ObjectProperty rdf:about="&p-plan;hasInputVar">
<rdfs:label xml:lang="en">p-plan:hasInputVar</rdfs:label>
<obo:IAO_0000412 rdf:datatype="&xsd;string">The P-PLAN Ontology</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">p-plan:hasInputVar binds a p-plan:Step to the p-plan:Variable that takes as input for the planned execution.</obo:IAO_0000115>
<rdfs:domain rdf:resource="&p-plan;Step"/>
<rdfs:range rdf:resource="&p-plan;Variable"/>
</owl:ObjectProperty>
<!-- http://purl.org/net/p-plan#hasOutputVar -->
<owl:ObjectProperty rdf:about="&p-plan;hasOutputVar">
<rdfs:label xml:lang="en">p-plan:hasOutputVar</rdfs:label>
<obo:IAO_0000412 rdf:datatype="&xsd;string">The P-PLAN Ontology</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">p-plan:hasOutputVar binds a p-plan:Step to the p-plan:Variable that takes as Output for the planned execution.</obo:IAO_0000115>
<rdfs:domain rdf:resource="&p-plan;Step"/>
<rdfs:range rdf:resource="&p-plan;Variable"/>
</owl:ObjectProperty>
<!-- http://purl.org/net/p-plan#isStepOfPlan -->
<owl:ObjectProperty rdf:about="&p-plan;isStepOfPlan">
<rdfs:label xml:lang="en">p-plan:isStepOfPlan</rdfs:label>
<obo:IAO_0000412 rdf:datatype="&xsd;string">The P-PLAN Ontology</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">p-plan:isStepOfPlan links a p-plan:Step to the p-plan:Plan which it corresponds to.</obo:IAO_0000115>
<rdfs:range rdf:resource="&p-plan;Plan"/>
<rdfs:domain rdf:resource="&p-plan;Step"/>
</owl:ObjectProperty>
<!-- http://www.obofoundry.org/ro/ro.owl#has_part -->
<owl:ObjectProperty rdf:about="&ro;has_part">
<rdf:type rdf:resource="&owl;TransitiveProperty"/>
<rdfs:label xml:lang="en">has part</rdfs:label>
<obo:IAO_0000412 rdf:datatype="&xsd;string">OBO Relation Ontology</obo:IAO_0000412>
<owl:inverseOf rdf:resource="&ro;part_of"/>
</owl:ObjectProperty>
<!-- http://www.obofoundry.org/ro/ro.owl#part_of -->
<owl:ObjectProperty rdf:about="&ro;part_of">
<rdf:type rdf:resource="&owl;TransitiveProperty"/>
<rdfs:label xml:lang="en">part of</rdfs:label>
<obo:IAO_0000412 rdf:datatype="&xsd;string">OBO Relation Ontology</obo:IAO_0000412>
<obo:IAO_0000115 rdf:datatype="&xsd;string">Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell.</obo:IAO_0000115>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000304 -->
<owl:ObjectProperty rdf:about="&obo;OBI_0000304">
<rdfs:label>is manufactured by</rdfs:label>
<obo:IAO_0000412 rdf:datatype="&xsd;string">OBI</obo:IAO_0000412>
<obo:IAO_0000118 rdf:datatype="&xsd;string">has_manufacturer</obo:IAO_0000118>
<obo:IAO_0000115 xml:lang="en">c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the &quot;Manufacturer Role&quot;, and those people/and or machines were members or of directed by the organization to do this.</obo:IAO_0000115>
<obo:IAO_0000112 xml:lang="en">http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)</obo:IAO_0000112>
<rdfs:range rdf:resource="&sp;Manufacturer"/>
<rdfs:domain rdf:resource="&snap;MaterialEntity"/>
</owl:ObjectProperty>
<!-- http://purl.org/net/SMARTprotocol#hasAlertMessage -->
<owl:ObjectProperty rdf:about="&sp;hasAlertMessage">
<rdfs:label xml:lang="en">has alert message</rdfs:label>
<obo:IAO_0000112 rdf:datatype="&xsd;string">"DNA Extraction Protocol" hasAlertMessage "Critical Step"</obo:IAO_0000112>
<obo:IAO_0000115 rdf:datatype="&xsd;string">hasAlertMessage is a relation that binds a chemical substance or protocol to an alert message such as caution, critical step, timing, etc.</obo:IAO_0000115>
<rdfs:range rdf:resource="&Ontology1184060740;Class_121"/>
</owl:ObjectProperty>
<!-- http://purl.org/net/SMARTprotocol#hasAuthor -->
<owl:ObjectProperty rdf:about="&sp;hasAuthor">
<rdfs:label xml:lang="en">has author</rdfs:label>
<obo:IAO_0000112 rdf:datatype="&xsd;string">"Laboratory protocol" hasAuthor "John Smith"</obo:IAO_0000112>
<obo:IAO_0000115 rdf:datatype="&xsd;string">hasAuthor is a relation that binds a document such as laboratory protocol to an author of protocol.</obo:IAO_0000115>
</owl:ObjectProperty>
<!-- http://purl.org/net/SMARTprotocol#hasCatalogNumber -->
<owl:ObjectProperty rdf:about="&sp;hasCatalogNumber">
<rdfs:label xml:lang="en">has catalog number</rdfs:label>
<obo:IAO_0000112 rdf:datatype="&xsd;string">"Nalgene Cryogenic Tube" hasCatalogNumber "5000-0012"</obo:IAO_0000112>
<obo:IAO_0000115 rdf:datatype="&xsd;string">hasCatalogNumber binds a thing to a numeral or string of numerals that is used for identification.</obo:IAO_0000115>
<rdfs:range rdf:resource="&sp;CatalogNumber"/>
<rdfs:domain rdf:resource="&snap;MaterialEntity"/>
</owl:ObjectProperty>
<!-- http://purl.org/net/SMARTprotocol#hasName -->
<owl:ObjectProperty rdf:about="&sp;hasName">
<rdfs:label xml:lang="en">has name</rdfs:label>
<obo:IAO_0000112 rdf:datatype="&xsd;string">"Buffer" hasName "1X Queen’s lysis buffer (1L)"</obo:IAO_0000112>
<obo:IAO_0000115 rdf:datatype="&xsd;string">hasName binds to a person, animal, place or thing to a word or set of words by which someone or something is known, addressed, or referred to.</obo:IAO_0000115>
<rdfs:range rdf:resource="&Thesaurus;C42614"/>
<rdfs:domain rdf:resource="&snap;MaterialEntity"/>
</owl:ObjectProperty>
<!-- http://purl.org/net/SMARTprotocol#hasSequence -->
<owl:ObjectProperty rdf:about="&sp;hasSequence">
<rdfs:label xml:lang="en">has sequence</rdfs:label>
<obo:IAO_0000112 rdf:datatype="&xsd;string">The primer CII-fw hasSequence 5′-GAATGATGTACCACCTTTG-3′</obo:IAO_0000112>
<obo:IAO_0000115 rdf:datatype="&xsd;string">hasSequence binds a oligonucleotide or nucleic acid to a sequence.</obo:IAO_0000115>
<rdfs:domain rdf:resource="&sp;Primer"/>
<rdfs:range rdf:resource="&sp;PrimerSequence"/>
</owl:ObjectProperty>
<!-- http://purl.org/net/SMARTprotocol#hasTitle -->
<owl:ObjectProperty rdf:about="&sp;hasTitle">
<rdfs:label xml:lang="en">has title</rdfs:label>
<obo:IAO_0000112 rdf:datatype="&xsd;string">"Laboratory protocol" hasTitle "An Optimized Chloroplast DNA Extraction Protocol for Grasses (Poaceae) Proves Suitable for Whole Plastid Genome Sequencing and SNP Detection"</obo:IAO_0000112>
<obo:IAO_0000115 rdf:datatype="&xsd;string">hasTitle is a relation that binds a document such as laboratory protocol to a title of protocol.</obo:IAO_0000115>
<rdfs:range rdf:resource="&sp;TitleOfProtocol"/>
</owl:ObjectProperty>
<!-- http://purl.org/net/SMARTprotocol#hasVersion -->
<owl:ObjectProperty rdf:about="&sp;hasVersion">
<rdfs:label xml:lang="en">has version</rdfs:label>
<obo:IAO_0000112 rdf:datatype="&xsd;string">"LightCycler 480 Software" hasVersion "Version 1.5"</obo:IAO_0000112>
<obo:IAO_0000115 rdf:datatype="&xsd;string">hasVersion binds a document, software, or other type of information content entity to a version (one of a sequence of copies of a program, document or software).</obo:IAO_0000115>
<rdfs:range rdf:resource="&Thesaurus;C25714"/>
<rdfs:domain rdf:resource="&obo;IAO_0000030"/>
</owl:ObjectProperty>
<!-- http://www.obofoundry.org/ro/ro.owl#has_part -->
<owl:ObjectProperty rdf:about="&ro;has_part">
<rdf:type rdf:resource="&owl;TransitiveProperty"/>
<rdfs:label xml:lang="en">has part</rdfs:label>
<obo:IAO_0000412 rdf:datatype="&xsd;string">OBI</obo:IAO_0000412>
<owl:inverseOf rdf:resource="&ro;part_of"/>
</owl:ObjectProperty>
<!-- http://www.obofoundry.org/ro/ro.owl#part_of -->
<owl:ObjectProperty rdf:about="&ro;part_of">
<rdf:type rdf:resource="&owl;TransitiveProperty"/>
<rdfs:label xml:lang="en">part of</rdfs:label>
<obo:IAO_0000412 rdf:datatype="&xsd;string">OBO Relation Ontology</obo:IAO_0000412>
<obo:IAO_0000115 rdf:datatype="&xsd;string">Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell.</obo:IAO_0000115>
</owl:ObjectProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Cultivar -->
<owl:Class rdf:about="&MGEDOntology;Cultivar">
<rdfs:label xml:lang="en">cultivar</rdfs:label>
<rdfs:subClassOf rdf:resource="&MGEDOntology;StrainOrLine"/>
<obo:IAO_0000412 rdf:datatype="&xsd;string">Microarray and Gene Expression Data Ontology (MGEDO)</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">a plant variety obtained in agriculture in horticulture.</obo:IAO_0000115>
</owl:Class>
<!-- http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Ecotype -->
<owl:Class rdf:about="&MGEDOntology;Ecotype">
<rdfs:label xml:lang="en">ecotype</rdfs:label>
<rdfs:subClassOf rdf:resource="&MGEDOntology;StrainOrLine"/>
<obo:IAO_0000412 rdf:datatype="&xsd;string">Microarray and Gene Expression Data Ontology (MGEDO)</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">a biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler</obo:IAO_0000115>
</owl:Class>
<!-- http://mged.sourceforge.net/ontologies/MGEDOntology.owl#StrainOrLine -->
<owl:Class rdf:about="&MGEDOntology;StrainOrLine">
<rdfs:label xml:lang="en">strain or line</rdfs:label>
<rdfs:subClassOf rdf:resource="&obo;OBI_0100026"/>
<obo:IAO_0000412 rdf:datatype="&xsd;string">Microarray and Gene Expression Data Ontology (MGEDO)</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">A strain or line is an animal or plant offspring that has a single ancestral breeding pair or parent as a result of brother x sister or parent x offspring matings. This class is extended to include F1 offspring and established breeding lines. For microbes, these are isolates derived from nature or in the laboratory.</obo:IAO_0000115>
</owl:Class>
<!-- http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C12801 -->
<owl:Class rdf:about="&Thesaurus;C12801">
<rdfs:label xml:lang="en">tissue</rdfs:label>
<rdfs:subClassOf rdf:resource="&obo;OBI_0000671"/>
<rdfs:subClassOf rdf:resource="&p-plan;Variable"/>
<obo:IAO_0000119 rdf:datatype="&xsd;string">CDISC</obo:IAO_0000119>
<obo:IAO_0000412 rdf:datatype="&xsd;string">NCI thesaurus</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">An anatomical structure consisting of similarly specialized cells and intercellular matrix, aggregated according to genetically determined spatial relationships, performing a specific function.</obo:IAO_0000115>
</owl:Class>
<!-- http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25294 -->
<owl:Class rdf:about="&Thesaurus;C25294">
<rdfs:label xml:lang="en">laboratory procedure</rdfs:label>
<rdfs:subClassOf rdf:resource="&span;Occurrent"/>
<obo:IAO_0000412 rdf:datatype="&xsd;string">NCI thesaurus</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">Any procedure that involves testing or manipulating a sample of blood, urine, or other body substance in a laboratory setting.</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">Test
LBTEST
Laboratory Test
Tests
Lab Test
Lab Tests</obo:IAO_0000118>
</owl:Class>
<!-- http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C70830 -->
<owl:Class rdf:about="&Thesaurus;C70830">
<rdfs:label xml:lang="en">solution</rdfs:label>
<rdfs:subClassOf rdf:resource="&snap;MaterialEntity"/>
<owl:disjointWith rdf:resource="&obo;CHEBI_33695"/>
<owl:disjointWith rdf:resource="&obo;OBI_0000747"/>
<owl:disjointWith rdf:resource="&obo;OBI_0100026"/>
<obo:IAO_0000412 rdf:datatype="&xsd;string">NCI thesaurus</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">A homogeneous mixture of two or more substances; frequently (but not necessarily) a liquid solution.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.bioontology.org/ontology/npo#NPO_1504 -->
<owl:Class rdf:about="&npo;NPO_1504">
<rdfs:label xml:lang="en">liquid state</rdfs:label>
<rdfs:subClassOf rdf:resource="&npo;NPO_888"/>
<owl:disjointWith rdf:resource="&npo;NPO_1509"/>
<obo:IAO_0000412 rdf:datatype="&xsd;string">NanoParticle Ontology</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">Physical state which is characteristic of a liquid.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.bioontology.org/ontology/npo#NPO_1509 -->
<owl:Class rdf:about="&npo;NPO_1509">
<rdfs:label xml:lang="en">gel state</rdfs:label>
<rdfs:subClassOf rdf:resource="&npo;NPO_888"/>
<obo:IAO_0000412 rdf:datatype="&xsd;string">NanoParticle Ontology</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">Physical state which is characteristic of a gel.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.bioontology.org/ontology/npo#NPO_888 -->
<owl:Class rdf:about="&npo;NPO_888">
<rdfs:label xml:lang="en">physical state</rdfs:label>
<rdfs:subClassOf rdf:resource="&snap;Quality"/>
<obo:IAO_0000412 rdf:datatype="&xsd;string">NanoParticle Ontology</obo:IAO_0000412>
<obo:IAO_0000118 rdf:datatype="&xsd;string">state of matter</obo:IAO_0000118>
<obo:IAO_0000115 xml:lang="en">A quality, which is the physical condition of a material entity, based on its chemical composition and structure.100428NPODennis Thomas</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_16991 -->
<owl:Class rdf:about="&obo;CHEBI_16991">
<rdfs:label xml:lang="en">deoxyribonucleic acid</rdfs:label>
<rdfs:subClassOf rdf:resource="&obo;CHEBI_33696"/>
<owl:disjointWith rdf:resource="&obo;CHEBI_33697"/>
<obo:IAO_0000412 rdf:datatype="&xsd;string">ChEBI</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_33695 -->
<owl:Class rdf:about="&obo;CHEBI_33695">
<rdfs:label xml:lang="en">information biomacromolecule</rdfs:label>
<rdfs:subClassOf rdf:resource="&snap;MaterialEntity"/>
<owl:disjointWith rdf:resource="&obo;CHEBI_33893"/>
<owl:disjointWith rdf:resource="&obo;CHEBI_35225"/>
<owl:disjointWith rdf:resource="&obo;OBI_0100026"/>
<owl:disjointWith rdf:resource="&sp;Primer"/>
<obo:IAO_0000412 rdf:datatype="&xsd;string">ChEBI</obo:IAO_0000412>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_33696 -->
<owl:Class rdf:about="&obo;CHEBI_33696">
<rdfs:label xml:lang="en">nucleic acid</rdfs:label>
<rdfs:subClassOf rdf:resource="&obo;CHEBI_33695"/>
<owl:disjointWith rdf:resource="&obo;CHEBI_36080"/>
<obo:IAO_0000412 rdf:datatype="&xsd;string">ChEBI</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_33697 -->
<owl:Class rdf:about="&obo;CHEBI_33697">
<rdfs:label xml:lang="en">ribonucleic acid</rdfs:label>
<rdfs:subClassOf rdf:resource="&obo;CHEBI_33696"/>
<obo:IAO_0000412 rdf:datatype="&xsd;string">ChEBI</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_33893 -->
<owl:Class rdf:about="&obo;CHEBI_33893">
<rdfs:label xml:lang="en">reagent</rdfs:label>
<rdfs:subClassOf rdf:resource="&snap;MaterialEntity"/>
<owl:disjointWith rdf:resource="&obo;OBI_0000747"/>
<owl:disjointWith rdf:resource="&obo;OBI_0100026"/>
<obo:IAO_0000412 rdf:datatype="&xsd;string">ChEBI</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">A substance used in a chemical reaction to detect, measure, examine, or produce other substances.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_35225 -->
<owl:Class rdf:about="&obo;CHEBI_35225">
<rdfs:label xml:lang="en">buffer</rdfs:label>
<rdfs:subClassOf rdf:resource="&snap;MaterialEntity"/>
<owl:disjointWith rdf:resource="&obo;OBI_0000747"/>
<owl:disjointWith rdf:resource="&obo;OBI_0100026"/>
<owl:disjointWith rdf:resource="&sp;Primer"/>
<obo:IAO_0000115 rdf:datatype="&xsd;string">Any substance or mixture of substances that, in solution (typically aqueous), resists change in pH upon addition of small amounts of acid or base.</obo:IAO_0000115>
<obo:IAO_0000412 rdf:datatype="&xsd;string">ChEBI</obo:IAO_0000412>
<obo:IAO_0000118 rdf:datatype="&xsd;string">buffer compound
buffer compounds</obo:IAO_0000118>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/CHEBI_36080 -->
<owl:Class rdf:about="&obo;CHEBI_36080">
<rdfs:label xml:lang="en">protein</rdfs:label>
<rdfs:subClassOf rdf:resource="&obo;CHEBI_33695"/>
<obo:IAO_0000412 rdf:datatype="&xsd;string">ChEBI</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000030 -->
<owl:Class rdf:about="&obo;IAO_0000030">
<rdfs:label xml:lang="en">information content entity</rdfs:label>
<rdfs:subClassOf rdf:resource="&snap;GenericallyDependentContinuant"/>
<obo:IAO_0000112 rdf:datatype="&xsd;string">Examples of information content entites include journal articles, data, graphical layouts, and graphs.</obo:IAO_0000112>
<obo:IAO_0000412 rdf:datatype="&xsd;string">OBI</obo:IAO_0000412>
<obo:IAO_0000119 rdf:datatype="&xsd;string">OBI_0000142</obo:IAO_0000119>
<obo:IAO_0000115 rdf:datatype="&xsd;string">an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000100 -->
<owl:Class rdf:about="&obo;IAO_0000100">
<rdfs:label xml:lang="en">data set</rdfs:label>
<rdfs:subClassOf rdf:resource="&obo;IAO_0000030"/>
<obo:IAO_0000115 rdf:datatype="&xsd;string">A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets.</obo:IAO_0000115>
<obo:IAO_0000112 rdf:datatype="&xsd;string">Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves).</obo:IAO_0000112>
<obo:IAO_0000412 rdf:datatype="&xsd;string">OBI</obo:IAO_0000412>
<obo:IAO_0000119 rdf:datatype="&xsd;string">group:OBI
OBI_0000042</obo:IAO_0000119>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/IAO_0000300 -->
<owl:Class rdf:about="&obo;IAO_0000300">
<rdfs:label xml:lang="en">textual entity</rdfs:label>
<rdfs:subClassOf rdf:resource="&obo;IAO_0000030"/>
<obo:IAO_0000412 rdf:datatype="&xsd;string">OBI</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc.</obo:IAO_0000115>
<obo:IAO_0000112 xml:lang="en">Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities</obo:IAO_0000112>
<obo:IAO_0000118 xml:lang="en">text</obo:IAO_0000118>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000671 -->
<owl:Class rdf:about="&obo;OBI_0000671">
<rdfs:label xml:lang="en">sample from organism</rdfs:label>
<rdfs:subClassOf rdf:resource="&obo;OBI_0000747"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="&ro;part_of"/>
<owl:someValuesFrom rdf:resource="&obo;OBI_0100026"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000412 rdf:datatype="&xsd;string">OBI</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">a material obtained from an organism in order to be a representative of the whole</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000747 -->
<owl:Class rdf:about="&obo;OBI_0000747">
<rdfs:label xml:lang="en">material sample</rdfs:label>
<rdfs:subClassOf rdf:resource="&snap;MaterialEntity"/>
<owl:disjointWith rdf:resource="&sp;Primer"/>
<obo:IAO_0000412 rdf:datatype="&xsd;string">OBI</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">A material entity that has the material sample role</obo:IAO_0000115>
<obo:IAO_0000112 xml:lang="en">blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.</obo:IAO_0000112>
<obo:IAO_0000118 xml:lang="en">sample population</obo:IAO_0000118>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000809 -->
<owl:Class rdf:about="&obo;OBI_0000809">
<rdfs:label xml:lang="en">amplified DNA</rdfs:label>
<rdfs:subClassOf rdf:resource="&sp;ProcessedDNA"/>
<rdfs:subClassOf rdf:resource="&p-plan;Variable"/>
<obo:IAO_0000119 rdf:datatype="&xsd;string">Alan Ruttenberg</obo:IAO_0000119>
<obo:IAO_0000112 xml:lang="en">Amplied DNA created by PCR</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">DNA that has been produced in an enzymatic amplification process</obo:IAO_0000115>
<obo:IAO_0000412 xml:lang="en">OBI</obo:IAO_0000412>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0000880 -->
<owl:Class rdf:about="&obo;OBI_0000880">
<rdfs:label xml:lang="en">RNA extract</rdfs:label>
<rdfs:subClassOf rdf:resource="&sp;ProcessedRNA"/>
<rdfs:subClassOf rdf:resource="&p-plan;Variable"/>
<obo:IAO_0000119 xml:lang="en">Group: UPenn Group</obo:IAO_0000119>
<obo:IAO_0000412 xml:lang="en">OBI</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0001051 -->
<owl:Class rdf:about="&obo;OBI_0001051">
<rdfs:label xml:lang="en">DNA extract</rdfs:label>
<rdfs:subClassOf rdf:resource="&sp;ProcessedDNA"/>
<rdfs:subClassOf rdf:resource="&p-plan;Variable"/>
<obo:IAO_0000119 xml:lang="en">Group: UPenn group</obo:IAO_0000119>
<obo:IAO_0000412 xml:lang="en">OBI</obo:IAO_0000412>
<obo:IAO_0000115 xml:lang="en">The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/OBI_0100026 -->
<owl:Class rdf:about="&obo;OBI_0100026">
<rdfs:label xml:lang="en">organism</rdfs:label>
<rdfs:subClassOf rdf:resource="&snap;MaterialEntity"/>
<owl:disjointWith rdf:resource="&sp;Primer"/>
<obo:IAO_0000412 rdf:datatype="&xsd;string">OBI</obo:IAO_0000412>
<obo:IAO_0000119 rdf:datatype="&xsd;string">http://en.wikipedia.org/wiki/Organism</obo:IAO_0000119>
<obo:IAO_0000115 xml:lang="en">A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.</obo:IAO_0000115>
<obo:IAO_0000112 xml:lang="en">fungus, animal, virus, plant</obo:IAO_0000112>
</owl:Class>
<!-- http://purl.org/net/SMARTprotocol#AgaroseGelElectrophoresisProtocol -->
<owl:Class rdf:about="&sp;AgaroseGelElectrophoresisProtocol">
<rdfs:label xml:lang="en">agarose gel electrophoresis protocol</rdfs:label>
<rdfs:subClassOf rdf:resource="&sp;ElectrophoresisProtocol"/>
<obo:IAO_0000115 xml:lang="en">Agarose Gel Electrophoresis Protocol is a subclass of laboratory protocol. Agarose Gel Electrophoresis Protocol is a step by step description of a procedure used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.org/net/SMARTprotocol#AgaroseInGelState -->
<owl:Class rdf:about="&sp;AgaroseInGelState">
<rdfs:label xml:lang="en">agarose in gel state</rdfs:label>
<rdfs:subClassOf rdf:resource="&npo;NPO_1509"/>
<rdfs:subClassOf rdf:resource="&p-plan;Variable"/>
<obo:IAO_0000119 rdf:datatype="&xsd;string">Adapted from OBI</obo:IAO_0000119>
<obo:IAO_0000115 xml:lang="en">AgaroseInGelState Is a gel resulting from the polymerization of agarose after heating agarose suspended in some buffer solution.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.org/net/SMARTprotocol#AgaroseInLiquidState -->
<owl:Class rdf:about="&sp;AgaroseInLiquidState">
<rdfs:label xml:lang="en">agarose in liquid state</rdfs:label>
<rdfs:subClassOf rdf:resource="&npo;NPO_1504"/>
<rdfs:subClassOf rdf:resource="&p-plan;Variable"/>
<obo:IAO_0000115 xml:lang="en">The agarose will be in a liquid state acording to its gelling temperature and concentration.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.org/net/SMARTprotocol#AnalyzedDataSet -->
<owl:Class rdf:about="&sp;AnalyzedDataSet">
<rdfs:label xml:lang="en">analyzed data set</rdfs:label>
<rdfs:subClassOf rdf:resource="&obo;IAO_0000100"/>
<rdfs:subClassOf rdf:resource="&p-plan;Variable"/>
<owl:disjointWith rdf:resource="&sp;RawDataSet"/>
<obo:IAO_0000119 rdf:datatype="&xsd;string">Adapted from: www.unit5.org/villhauer/Glossary/Glossary.htm</obo:IAO_0000119>
<obo:IAO_0000115 xml:lang="en">Is the result of data analysis process. This data can be organized into charts, graphs and tables to better visualize the information.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.org/net/SMARTprotocol#AnalyzingSampleData -->
<owl:Class rdf:about="&sp;AnalyzingSampleData">
<rdfs:label xml:lang="en">analyzing sample data</rdfs:label>
<rdfs:subClassOf rdf:resource="&sp;BasicStepOfElectrophoresis"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="&p-plan;hasInputVar"/>
<owl:someValuesFrom rdf:resource="&sp;RawDataSet"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="&p-plan;hasOutputVar"/>
<owl:someValuesFrom rdf:resource="&sp;AnalyzedDataSet"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="&obo;BFO_0000062"/>
<owl:someValuesFrom rdf:resource="&sp;LoadingAndRunningTheGel"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="&p-plan;isStepOfPlan"/>
<owl:someValuesFrom rdf:resource="&sp;ElectrophoresisProtocol"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">Analyzing sample data is the third basic step in a electrophoresis procedure. This step include the data collection and analysis of sample data.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.org/net/SMARTprotocol#BasicStepOfDNAExtraction -->
<owl:Class rdf:about="&sp;BasicStepOfDNAExtraction">
<rdfs:label xml:lang="en">basic step of DNA extraction</rdfs:label>
<rdfs:subClassOf rdf:resource="&p-plan;Step"/>
<owl:disjointWith rdf:resource="&sp;BasicStepOfElectrophoresis"/>
<owl:disjointWith rdf:resource="&sp;BasicStepOfPCR"/>
<obo:IAO_0000115 xml:lang="en">Basic steps of DNA extraction are the steps commonly used in any DNA extraction protocol.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.org/net/SMARTprotocol#BasicStepOfElectrophoresis -->
<owl:Class rdf:about="&sp;BasicStepOfElectrophoresis">
<rdfs:label xml:lang="en">basic step of electrophoresis</rdfs:label>
<rdfs:subClassOf rdf:resource="&p-plan;Step"/>
<owl:disjointWith rdf:resource="&sp;BasicStepOfPCR"/>
<obo:IAO_0000115 rdf:datatype="&xsd;string">Basic steps of electrophoresis are the steps commonly used in any electrophoresis protocol.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.org/net/SMARTprotocol#BasicStepOfPCR -->
<owl:Class rdf:about="&sp;BasicStepOfPCR">
<rdfs:label xml:lang="en">basic step of PCR</rdfs:label>
<rdfs:subClassOf rdf:resource="&p-plan;Step"/>
<obo:IAO_0000115 rdf:datatype="&xsd;string">Basic steps of PCR are the steps commonly used in any PCR protocol.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.org/net/SMARTprotocol#CastingTheGel -->
<owl:Class rdf:about="&sp;CastingTheGel">
<rdfs:label xml:lang="en">casting the gel</rdfs:label>
<rdfs:subClassOf rdf:resource="&sp;BasicStepOfElectrophoresis"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="&p-plan;hasOutputVar"/>
<owl:someValuesFrom rdf:resource="&sp;AgaroseInGelState"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="&p-plan;isStepOfPlan"/>
<owl:someValuesFrom rdf:resource="&sp;AgaroseGelElectrophoresisProtocol"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="&p-plan;hasInputVar"/>
<owl:someValuesFrom rdf:resource="&sp;AgaroseInLiquidState"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">This is the first basic step in a electrophoresis procedure. This step include:1) the preparation of the gel matrix, 2) its solidification and 3) place it into electrophoresis apparatus.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.org/net/SMARTprotocol#CellDisruption -->
<owl:Class rdf:about="&sp;CellDisruption">
<rdfs:label xml:lang="en">cell disruption</rdfs:label>
<rdfs:subClassOf rdf:resource="&sp;BasicStepOfDNAExtraction"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="&p-plan;hasInputVar"/>
<owl:someValuesFrom rdf:resource="&sp;PlantTissue"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="&p-plan;isStepOfPlan"/>
<owl:someValuesFrom rdf:resource="&sp;DNAExtractionProtocol"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="&p-plan;hasOutputVar"/>
<owl:someValuesFrom rdf:resource="&sp;PowderedTissue"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">Breaking the cells open, is the first basic step in a DNA extraction. This is commonly achieved by chemical and physical methods-blending, grinding or sonicating the sample.</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">Cell lysis</obo:IAO_0000118>
</owl:Class>
<!-- http://purl.org/net/SMARTprotocol#ChoosingPCRReactionCondition -->
<owl:Class rdf:about="&sp;ChoosingPCRReactionCondition">
<rdfs:label xml:lang="en">choosing PCR reaction condition</rdfs:label>
<rdfs:subClassOf rdf:resource="&sp;BasicStepOfPCR"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="&p-plan;hasOutputVar"/>
<owl:someValuesFrom rdf:resource="&sp;PCRProgram"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="&p-plan;isStepOfPlan"/>
<owl:someValuesFrom rdf:resource="&sp;PolimeraseChainReactionProtocol"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="&obo;BFO_0000062"/>
<owl:someValuesFrom rdf:resource="&sp;SettingUpThePCRReaction"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">Choosing the Reaction Conditions is the third basic step in a PCR reaction. The reaction conditions of a PCR amplification are composed of the total number of cycles to be run and the temperature and duration of each step in those cycles. The decision as to how many cycles to run is based upon the amount of DNA target material. In general, 25 to 35 cycles is the standard for a PCR reaction.</obo:IAO_0000115>
</owl:Class>
<!-- http://purl.org/net/SMARTprotocol#ChoosingTargetSubstrateAndPCRPrimer -->