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tmn-simple.owl
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tmn-simple.owl
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<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/tmn/tmn-simple.owl#"
xml:base="http://purl.obolibrary.org/obo/tmn/tmn-simple.owl"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns:obo="http://purl.obolibrary.org/obo/"
xmlns:owl="http://www.w3.org/2002/07/owl#"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:xml="http://www.w3.org/XML/1998/namespace"
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:terms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/tmn/tmn-simple.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/tmn/releases/2022-12-01/tmn-simple.owl"/>
<dc:description>This is an ontology that captures techniques and methods in neuroscience to support work at AIBS and BICCN. The techniques and methods ontology is designed to help scientists communicate about their experiments and results by defining a set of terms for techniques, methods, modalities, assays, devices, tools, and the like.</dc:description>
<dc:title>Techniques and Methods for Neuroscience Ontology</dc:title>
<terms:license rdf:resource="https://creativecommons.org/licenses/by/4.0/"/>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-12-01</owl:versionInfo>
</owl:Ontology>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Annotation properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/IAO_0000111 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000111">
<obo:IAO_0000111 xml:lang="en">editor preferred term</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">editor preferred term</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000112 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000112"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000114 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000114"/>
<!-- http://purl.obolibrary.org/obo/IAO_0000115 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
<obo:IAO_0000111 xml:lang="en">definition</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">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>
<obo:IAO_0000116 xml:lang="en">2012-04-05:
Barry Smith
The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.
Can you fix to something like:
A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.
Alan Ruttenberg
Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria.
On the specifics of the proposed definition:
We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition.
Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable.
We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. </obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label>definition</rdfs:label>
<rdfs:label xml:lang="en">definition</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000116 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000116">
<obo:IAO_0000111 xml:lang="en">editor note</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obofoundry.org/obo/obi></obo:IAO_0000119>
<oboInOwl:hasDbXref>IAO:0000116</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
<oboInOwl:id>editor_note</oboInOwl:id>
<oboInOwl:is_metadata_tag rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_metadata_tag>
<oboInOwl:shorthand>editor_note</oboInOwl:shorthand>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label>editor note</rdfs:label>
<rdfs:label xml:lang="en">editor note</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000117 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000117">
<obo:IAO_0000111 xml:lang="en">term editor</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">term editor</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000118 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000118">
<obo:IAO_0000111 xml:lang="en">alternative label</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like.</obo:IAO_0000115>
<obo:IAO_0000117>OBO Operations committee</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
<rdfs:comment>Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related).</rdfs:comment>
<rdfs:label xml:lang="en">alternative label</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000119 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000119">
<obo:IAO_0000111 xml:lang="en">definition source</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">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>
<obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w</obo:IAO_0000119>
<obo:IAO_0000119 xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">definition source</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000232 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000232">
<obo:IAO_0000111 xml:lang="en">curator note</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">An administrative note of use for a curator but of no use for a user</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Alan Ruttenberg</obo:IAO_0000117>
<oboInOwl:hasDbXref>IAO:0000232</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
<oboInOwl:id>curator_notes</oboInOwl:id>
<oboInOwl:is_metadata_tag rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_metadata_tag>
<oboInOwl:shorthand>curator_notes</oboInOwl:shorthand>
<rdfs:isDefinedBy rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
<rdfs:label xml:lang="en">curator note</rdfs:label>
<rdfs:label>curator notes</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/IAO_0000412 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000412"/>
<!-- http://purl.obolibrary.org/obo/RO_0001900 -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/RO_0001900"/>
<!-- http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/valid_for_go_ontology -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/valid_for_go_ontology">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
</owl:AnnotationProperty>
<!-- http://purl.obolibrary.org/obo/valid_for_gocam -->
<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/valid_for_gocam">
<rdfs:subPropertyOf rdf:resource="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/elements/1.1/description -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/description">
<oboInOwl:hasDbXref>http://purl.org/dc/elements/1.1/description</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
<oboInOwl:id>dc-description</oboInOwl:id>
<oboInOwl:is_metadata_tag rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_metadata_tag>
<oboInOwl:shorthand>dc-description</oboInOwl:shorthand>
<rdfs:label>description</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/elements/1.1/title -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/title">
<oboInOwl:hasDbXref>http://purl.org/dc/elements/1.1/title</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
<oboInOwl:id>dc-title</oboInOwl:id>
<oboInOwl:is_metadata_tag rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_metadata_tag>
<oboInOwl:shorthand>dc-title</oboInOwl:shorthand>
<rdfs:label>title</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/terms/license -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/license">
<oboInOwl:hasDbXref>http://purl.org/dc/terms/license</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
<oboInOwl:id>dcterms-license</oboInOwl:id>
<oboInOwl:is_metadata_tag rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</oboInOwl:is_metadata_tag>
<oboInOwl:shorthand>dcterms-license</oboInOwl:shorthand>
<rdfs:label>license</rdfs:label>
</owl:AnnotationProperty>
<!-- http://purl.org/dc/terms/source -->
<owl:AnnotationProperty rdf:about="http://purl.org/dc/terms/source"/>
<!-- http://www.geneontology.org/formats/oboInOwl#SubsetProperty -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#SubsetProperty"/>
<!-- http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty"/>
<!-- http://www.geneontology.org/formats/oboInOwl#created_by -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#created_by"/>
<!-- http://www.geneontology.org/formats/oboInOwl#creation_date -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#creation_date"/>
<!-- http://www.geneontology.org/formats/oboInOwl#hasAlternativeId -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasAlternativeId">
<rdfs:label>has_alternative_id</rdfs:label>
</owl:AnnotationProperty>
<!-- http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym">
<rdfs:label>has_broad_synonym</rdfs:label>
</owl:AnnotationProperty>
<!-- http://www.geneontology.org/formats/oboInOwl#hasDbXref -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasDbXref"/>
<!-- http://www.geneontology.org/formats/oboInOwl#hasExactSynonym -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasExactSynonym">
<rdfs:label>has_exact_synonym</rdfs:label>
</owl:AnnotationProperty>
<!-- http://www.geneontology.org/formats/oboInOwl#hasOBONamespace -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasOBONamespace"/>
<!-- http://www.geneontology.org/formats/oboInOwl#id -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#id"/>
<!-- http://www.geneontology.org/formats/oboInOwl#inSubset -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#inSubset"/>
<!-- http://www.geneontology.org/formats/oboInOwl#is_metadata_tag -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#is_metadata_tag"/>
<!-- http://www.geneontology.org/formats/oboInOwl#shorthand -->
<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#shorthand"/>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Object Properties
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/BFO_0000051 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/BFO_0000051">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
<obo:IAO_0000111 xml:lang="en">has part</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">my body has part my brain (continuant parthood, two material entities)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this year has part this day (occurrent parthood)</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">a core relation that holds between a whole and its part</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)
A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">has_part</obo:IAO_0000118>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<oboInOwl:hasDbXref>BFO:0000051</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace>external</oboInOwl:hasOBONamespace>
<oboInOwl:hasOBONamespace>quality</oboInOwl:hasOBONamespace>
<oboInOwl:hasOBONamespace>uberon</oboInOwl:hasOBONamespace>
<oboInOwl:id>has_part</oboInOwl:id>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_annotation_extension"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_go_ontology"/>
<oboInOwl:inSubset rdf:resource="http://purl.obolibrary.org/obo/valid_for_gocam"/>
<oboInOwl:shorthand>has_part</oboInOwl:shorthand>
<rdfs:label>has part</rdfs:label>
<rdfs:label xml:lang="en">has part</rdfs:label>
<rdfs:label>has_part</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/OBI_0000299 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/OBI_0000299">
<obo:IAO_0000111>has_specified_output</obo:IAO_0000111>
<obo:IAO_0000111 xml:lang="en">has_specified_output</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
<obo:IAO_0000115 xml:lang="en">The inverse property of is_specified_output_of</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117>PERSON: Bjoern Peters</obo:IAO_0000117>
<obo:IAO_0000117>PERSON: Larry Hunter</obo:IAO_0000117>
<obo:IAO_0000117>PERSON: Melanie Courtot</obo:IAO_0000117>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">has_specified_output</rdfs:label>
</owl:ObjectProperty>
<!-- http://purl.obolibrary.org/obo/RO_0000053 -->
<owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/RO_0000053">
<rdf:type rdf:resource="http://www.w3.org/2002/07/owl#InverseFunctionalProperty"/>
<obo:IAO_0000111 xml:lang="en">bearer of</obo:IAO_0000111>
<obo:IAO_0000112 xml:lang="en">this apple is bearer of this red color</obo:IAO_0000112>
<obo:IAO_0000112 xml:lang="en">this vase is bearer of this fragility</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">Inverse of characteristic_of</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.</obo:IAO_0000116>
<obo:IAO_0000118 xml:lang="en">bearer_of</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">is bearer of</obo:IAO_0000118>
<obo:RO_0001900 rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
<oboInOwl:hasDbXref>RO:0000053</oboInOwl:hasDbXref>
<oboInOwl:hasOBONamespace>external</oboInOwl:hasOBONamespace>
<oboInOwl:id>bearer_of</oboInOwl:id>
<oboInOwl:shorthand>bearer_of</oboInOwl:shorthand>
<rdfs:label>bearer of</rdfs:label>
<rdfs:label xml:lang="en">has characteristic</rdfs:label>
</owl:ObjectProperty>
<!--
///////////////////////////////////////////////////////////////////////////////////////
//
// Classes
//
///////////////////////////////////////////////////////////////////////////////////////
-->
<!-- http://purl.obolibrary.org/obo/TMN_0000000 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000000">
<obo:IAO_0000115 xml:lang="en">A sequencing assay that analyzes mRNA transcripts from droplets of individual cells. The droplets are compartmentalized via a microfluidic device. After the cells are compartmentalized, cells in droplets are lysed and the released mRNA hybridizes to the oligo(dT) tract of the primer beads. Then the droplets are pooled and broken to release the beads which are then isolated and reverse-transcribed with template switching. The resulting cDNA strands are PCR-amplified and the sequencing adapters are added. The barcoded mRNA samples are then sequenced.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">Dropseq</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">https://doi.org/10.1016/j.cell.2015.05.002</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-03T20:04:39Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">droplet-based single-cell RNA sequencing assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000001 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000001">
<obo:IAO_0000115 xml:lang="en">A sequencing assay that uses fluorescent probes that bind to parts of a nucleic acid sequence that have a high degree of sequence complementarity. Fluorescence microscopy can be used to find out where the fluorescent probes are bound on the chromosomes.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118 xml:lang="en">FISH</obo:IAO_0000118>
<obo:IAO_0000119 xml:lang="en">http://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-03T21:04:00Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">fluorescence in situ hybridization assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000002 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000002">
<obo:IAO_0000115>An imaging assay that uses micro-optical sectioning tomography technology combined with fluorescence molecular labeling of neuronal projections.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118>fMOST</obo:IAO_0000118>
<obo:IAO_0000119>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6701528/</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-03T21:32:43Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">fluorescence micro-optical sectioning tomography assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000003 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000003">
<obo:IAO_0000115>An imaging assay that measures the copy number and spatial distribution of hundreds to thousands of RNA species in single cells.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118>MERFISH</obo:IAO_0000118>
<obo:IAO_0000119>DOI: 10.1126/science.aaa6090</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-03T23:18:34Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">multiplexed error-robust fluorescence in situ hybridization assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000004 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000004">
<obo:IAO_0000115>A 3D structure determination assay that determines the morphology of a neuron.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118>3D structure determination assay of neuron</obo:IAO_0000118>
<obo:IAO_0000119>PERSON: Patrick Ray</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-04T00:06:14Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">neuron morphology assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000005 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000005">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/TMN_0000004"/>
<obo:IAO_0000115>A neuron morphology assay that enables sparse and stochastic labeling of genetically-defined neurons. MORF-labeled neurons are digitally reconstructed using a program (G-Cut).</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000119>https://biccn.org/teams/u01-yang</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-04T00:10:17Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">mosaicism with repeat frameshift genetic sparse labeling assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000006 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000006">
<obo:IAO_0000115>A fluorescence microscopy that generates high-throughput flourescence imaging of mouse brains by integrating two-photon microscopy and tissue sectioning. Serial two-photon tomography generates high-resolution datasets.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118>STPT</obo:IAO_0000118>
<obo:IAO_0000119>http://doi.org/10.1038/nmeth.1854</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-04T00:30:35Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">serial two-photon tomography</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000007 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000007">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/TMN_0000006"/>
<obo:IAO_0000115>A serial two photon tomography assay that produces images of mouse brains with sufficient detail to represent axons of individual neurons.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000119>http://www.janelia.org/project-team/mouselight/research</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-04T00:34:49Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">mouselight</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000008 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000008">
<obo:IAO_0000115>An electrophysiology assay that employs many electrodes to record extracellular field potentials.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000119>http://en.wikipedia.org/wiki/Microelectrode_array</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-10T23:56:39Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">multi-electrode extracellular electrophysiology assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000009 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000009">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/TMN_0000004"/>
<obo:IAO_0000115>A neuron morphology assay where the morphology or structure of a neuron is represented through through another medium. Often, this assay is a combination of different assays (sparse labeling, fluorescent labeling, fMOST).</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000119>http://doi.org/10.1101/675280</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-11T00:15:55Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">neuron morphology reconstruction assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000010 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000010">
<obo:IAO_0000115>A single-cell RNA sequencing assay wherein a patch clamp recording is taken from a neuron and then scRNA sequencing is performed on the cell soma.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118>patch clamp sequencing assay</obo:IAO_0000118>
<obo:IAO_0000118>patch-seq</obo:IAO_0000118>
<obo:IAO_0000119>http://doi.org/10.1038/nprot.2017.120</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-11T00:26:12Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">patch clamp single-cell RNA sequencing assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000011 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000011">
<obo:IAO_0000115>An assay wherein a substance is taken up by an axon terminal and transported toward the soma to mark (or trace) some part of a cell.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118>retrograde tracing</obo:IAO_0000118>
<obo:IAO_0000119>PERSON: Patrick Ray</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-11T00:39:16Z</oboInOwl:creation_date>
<oboInOwl:hasExactSynonym xml:lang="en">retrograde labeling</oboInOwl:hasExactSynonym>
<rdfs:label xml:lang="en">retrograde tracing assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000012 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000012">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/TMN_0000011"/>
<obo:IAO_0000115>A retrograde tracing assay that traces the neural connections from a synapse to a soma allowing the mapping of connections between neurons in a structure and a target in the brain.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000119>http://en.wikipedia.org/wiki/Retrograde_tracing</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-11T00:51:53Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">retrograde transsynaptic tracing assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000013 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000013">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/TMN_0000001"/>
<obo:IAO_0000115>A fluorescence in situ hybridization assay where transcripts are labeled with fluorescent probes in sequential rounds of hybridization to read out the temporal barcode for each transcript. The temporal barcodes can then be decoded to uniquely identify the RNA transcripts present in the sample. RNA can be identified directly in a variety of samples from extracted RNA to tissues.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118>seqFISH</obo:IAO_0000118>
<obo:IAO_0000119>http://www.seqfish.com/technology</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-11T01:00:00Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">sequential fluorescence in situ hybridization assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000014 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000014">
<obo:IAO_0000115>A single cell sequencing assay wherein the target cells are lysed, and the RNA is hybridized to an oligo(dT)-containing primer. The first strand of the cDNA is synthesized with the addition of a few untemplated C nucleotides. This poly(C) overhang is added exclusively to full-length transcripts. An oligonucleotide primer is hybridized to the poly(C) overhang and used to synthesize the second strand. Full-length cDNAs are PCR-amplified to obtain nanogram amounts of DNA. The PCR products are purified for sequencing.</obo:IAO_0000115>
<obo:IAO_0000116>Definition needs curation.</obo:IAO_0000116>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118>SMART seq</obo:IAO_0000118>
<obo:IAO_0000118>SMARTseq</obo:IAO_0000118>
<obo:IAO_0000119>http://www.enseqlopedia.com/wiki-entry/rna-sequencing-methods/low-level-rna-detection/smart-seq/</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-11T01:10:58Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">switching mechanism at the 5' end of RNA template sequencing assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000015 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000015">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/TMN_0000024"/>
<obo:IAO_0000115>A switching mechanism at the 5' end of RNA template sequencing assay that is the fourth version of such an assay.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118>SMARTseq v4</obo:IAO_0000118>
<obo:IAO_0000119>PERSON: Patrick Ray</obo:IAO_0000119>
<obo:IAO_0000232>This is the commercial version of SMARTseq2 that has as an instrument the Takara kit.</obo:IAO_0000232>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-11T01:21:33Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">switching mechanism at the 5' end of RNA template sequencing assay v4</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000016 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000016">
<obo:IAO_0000115>A study design in which complementary viruses are to be injected into brain regions to monosynaptically label inputs to a specific projection neuron population.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118>TRIO tracing</obo:IAO_0000118>
<obo:IAO_0000119>http://cic.ini.usc.edu/protocols/trio-tracing</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-11T01:43:24Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">tracing the relationship between input and output study design</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000017 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000017">
<obo:IAO_0000115>A fluorescence microscopy assay that uses a laser light-sheet to illuminate a region of a sample that has been treated to excite fluorescently.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118>light sheet microscopy</obo:IAO_0000118>
<obo:IAO_0000119>http://en.wikipedia.org/wiki/Light_sheet_fluorescence_microscopy</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-11T01:59:49Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">light sheet fluorescence microscopy assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000018 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000018">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/TMN_0000019"/>
<obo:IAO_0000115>A anterograde tracing assay that uses a Cre recombinase-dependent as a tracer.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000119>http://doi.org/10.1016/j.neuron.2011.12.002</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-15T18:11:42Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">cre-dependent anterograde tracing assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000019 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000019">
<obo:IAO_0000115>An assay wherein axon projections are traced from their source (cell body or soma) to their point of termination (synapse).</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000119>https://en.wikipedia.org/wiki/Anterograde_tracing</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-15T18:13:29Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">anterograde tracing assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000020 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000020">
<obo:IAO_0000115>An imaging assay that has as an output label-free, cross-sectional imaging of biological tissue microstructure using tissue backscattering properties.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118>OCT</obo:IAO_0000118>
<obo:IAO_0000119>PMID: 29214158</obo:IAO_0000119>
<obo:IAO_0000119>doi: 10.1155/2017/3409327</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-15T18:44:49Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">optical coherence tomography assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000021 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000021">
<obo:IAO_0000115>A light sheet microscopy assay that combines synchronized scanning illumination and oblique imaging over cleared, thick tissue sections in smooth motion that produces a 3D image of a brain.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118>VISoR</obo:IAO_0000118>
<obo:IAO_0000118>VISoR assay</obo:IAO_0000118>
<obo:IAO_0000119>doi: 10.1093/nsr/nwz053</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-15T19:01:49Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">volumetric imaging with synchronized on-the-fly oblique-scan and readout assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000022 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000022">
<obo:IAO_0000115>A single-cell RNA sequencing assay that involves the isolation of single nuclei and open chromatin tagmentation in the isolated nuclei using a transposase. The tagmented nuclei are then encapsulated in a droplet including both an oligo-dT-containing barcoded bead and a splint oligonucleotide, which links the tagmented gDNA fragments to the bead, enabling the bead to capture both mRNAs and open chromatin fragments. After mRNAs and gDNA fragments are released from the bead by heating, RT and PCR amplification are performed to generate a library of cDNA and open chromatin gDNA fragments.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118>SNARE-seq</obo:IAO_0000118>
<obo:IAO_0000118>SNARE-seq assay</obo:IAO_0000118>
<obo:IAO_0000119>https://doi.org/10.1038/s12276-020-0420-2</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-15T19:09:43Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">single-nucleus chromatin accessibility and mRNA expression sequencing assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000023 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000023">
<obo:IAO_0000115>A fluorescence microscopy assay wherein fluorescence in situ hybridization is leveraged with multiplexed analysis that uses each channel to measure the composite (sum) abundances of multiple genes in each channel and decompresses and determines individual gene level.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118>CISI</obo:IAO_0000118>
<obo:IAO_0000119>DOI: 10.1101/743039</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-02-15T19:20:54Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">composite in situ imaging</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000024 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000024">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/TMN_0000014"/>
<obo:IAO_0000115>A switching mechanism at the 5' end of RNA template sequencing assay that allows the generation of full-length cDNA and sequencing libraries by using standard reagents.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118>SMARTseq2</obo:IAO_0000118>
<obo:IAO_0000119>https://doi.org/10.1038/nprot.2014.006</obo:IAO_0000119>
<obo:IAO_0000232>See also: https://scicrunch.org/scicrunch/interlex/view/ilx_0739685</obo:IAO_0000232>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-04-22T19:49:20Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">switching mechanism at the 5' end of RNA template sequencing assay 2</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000025 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000025">
<obo:IAO_0000115 xml:lang="en">A RNA sequencing assay that involves three levels of indexing.</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">3-level sci-RNA-seq</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">3-level single-cell combinatorial indexing RNA sequencing assay</obo:IAO_0000118>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-09-02T02:12:07Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">sci-RNA-seq3</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/TMN_0000025"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget xml:lang="en">A RNA sequencing assay that involves three levels of indexing.</owl:annotatedTarget>
<obo:IAO_0000119>https://www.protocols.io/view/sci-rna-seq3-9yih7ue</obo:IAO_0000119>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/TMN_0000026 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000026">
<obo:IAO_0000115 xml:lang="en">An ATAC-seq assay that involves single-cell combinatorial indexing at three levels.</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">3-level sci-ATAC-seq</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">3-level single-cell combinatorial indexing ATAC sequencing assay</obo:IAO_0000118>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-09-02T02:16:18Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">sci-ATAC-seq3</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/TMN_0000026"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget xml:lang="en">An ATAC-seq assay that involves single-cell combinatorial indexing at three levels.</owl:annotatedTarget>
<obo:IAO_0000119>https://www.protocols.io/view/sci-atac-seq3-be8mjhu6</obo:IAO_0000119>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/TMN_0000027 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000027">
<obo:IAO_0000115 xml:lang="en">An ATAC-seq assay that involves use of the 10x sequencing technology assay for transposase-accessible chromatin using sequencing (ATAC-seq).</obo:IAO_0000115>
<obo:IAO_0000118 xml:lang="en">10x chromium ATAC sequencing assay</obo:IAO_0000118>
<obo:IAO_0000118 xml:lang="en">10x chromium ATAC-seq assay</obo:IAO_0000118>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-09-02T02:18:54Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">10x chromium ATAC-seq</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/TMN_0000027"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget xml:lang="en">An ATAC-seq assay that involves use of the 10x sequencing technology assay for transposase-accessible chromatin using sequencing (ATAC-seq).</owl:annotatedTarget>
<obo:IAO_0000119>PERSON: Patrick Ray</obo:IAO_0000119>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/TMN_0000028 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000028">
<obo:IAO_0000115>A RNA-seq assay for transferring RNA from tissue sections onto a surface covered in DNA-barcoded beads with known positions, allowing the locations of the RNA to be inferred by sequencing.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118>slide-seq</obo:IAO_0000118>
<obo:IAO_0000118>slide-sequencing assay</obo:IAO_0000118>
<obo:IAO_0000119>PERSON: Patrick Ray</obo:IAO_0000119>
<obo:IAO_0000119>doi: 10.1126/science.aaw1219</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-10-04T22:03:50Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">slide-seq assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000029 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000029">
<obo:IAO_0000115>A RNA-seq assay that uses high-throughput ATAC and RNA expression with sequencing to measure chromatin accessibility and gene expression in the same single cell.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118>SHARE-seq</obo:IAO_0000118>
<obo:IAO_0000118>SHARE-sequencing</obo:IAO_0000118>
<obo:IAO_0000119>PERSON: Patrick Ray</obo:IAO_0000119>
<obo:IAO_0000119>https://doi.org/10.1016/j.cell.2020.09.056</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-10-04T22:09:37Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">SHARE-seq assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000030 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000030">
<obo:IAO_0000115>An ATAC-seq assay that provides information about both transcriptome and epigenome from a single cell.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Patrick Ray</obo:IAO_0000117>
<obo:IAO_0000118>single cell multiome ATAC + gene expression</obo:IAO_0000118>
<obo:IAO_0000119>PERSON: Patrick Ray</obo:IAO_0000119>
<obo:IAO_0000119>https://www.10xgenomics.com/blog/introducing-chromium-single-cell-multiome-atac-gene-expression</obo:IAO_0000119>
<obo:IAO_0000119>https://www.10xgenomics.com/products/single-cell-multiome-atac-plus-gene-expression</obo:IAO_0000119>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2021-10-04T22:12:23Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">single cell multiome ATAC + gene expression assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000031 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000031">
<obo:IAO_0000115>A single-cell RNA sequencing assay wherein sparse fluorescently labeled single neurons are collected manually from freshly dissociated mouse brain tissue. Then single-labeled neurons with high purity are integrated with an in vitro transcription-based amplification protocol that preserves endogenous transcript ratios. Subsequently a double linear amplification method that uses unique molecule identifiers (UMIs) is used to generate individual mRNA counts. Two rounds of amplification follow.</obo:IAO_0000115>
<obo:IAO_0000118>DIVA-seq</obo:IAO_0000118>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-04-05T20:19:26Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">double in vitro transcription with absoluted counts sequencing assay</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/TMN_0000031"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>A single-cell RNA sequencing assay wherein sparse fluorescently labeled single neurons are collected manually from freshly dissociated mouse brain tissue. Then single-labeled neurons with high purity are integrated with an in vitro transcription-based amplification protocol that preserves endogenous transcript ratios. Subsequently a double linear amplification method that uses unique molecule identifiers (UMIs) is used to generate individual mRNA counts. Two rounds of amplification follow.</owl:annotatedTarget>
<obo:IAO_0000119>http://doi.org/10.3791/58690</obo:IAO_0000119>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/TMN_0000032 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000032">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/TMN_0000017"/>
<obo:IAO_0000115>A light sheet tomography assay wherein the sample is imaged from the top using oblique light sheet fluorescence microscopy illumination and detection strategy and the imaged top portion of the tissue is removed by vibratome sectioning.</obo:IAO_0000115>
<obo:IAO_0000118>OLST</obo:IAO_0000118>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-04-05T20:22:10Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">oblique light sheet tomography assay</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/TMN_0000032"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>A light sheet tomography assay wherein the sample is imaged from the top using oblique light sheet fluorescence microscopy illumination and detection strategy and the imaged top portion of the tissue is removed by vibratome sectioning.</owl:annotatedTarget>
<obo:IAO_0000119>http://doi.org/10.1101/132423</obo:IAO_0000119>
<obo:IAO_0000119>http://doi.org/10.17504/protocols.io.smwec7e</obo:IAO_0000119>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/TMN_0000033 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000033">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/TMN_0000001"/>
<obo:IAO_0000115>A cyclic single molecule fluorescent in situ hybridization assay used to quantify the expression level of specific transcripts in tissue sections by direct labeling of individual RNA molecules.</obo:IAO_0000115>
<obo:IAO_0000118>osmFISH</obo:IAO_0000118>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-04-05T20:26:01Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">cyclic single-molecule fluorescence in situ hybridization assay</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/TMN_0000033"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>A cyclic single molecule fluorescent in situ hybridization assay used to quantify the expression level of specific transcripts in tissue sections by direct labeling of individual RNA molecules.</owl:annotatedTarget>
<obo:IAO_0000119>http://doi.org/10.1038/s41592-018-0175-z</obo:IAO_0000119>
<obo:IAO_0000119>http://doi.org/10.17504/protocols.io.psednbe</obo:IAO_0000119>
</owl:Axiom>
<!-- http://purl.obolibrary.org/obo/TMN_0000034 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000034">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/TMN_0000022"/>
<obo:IAO_0000115>A single-cell RNA sequencing assay that involves the isolation of single nuclei and open chromatin tagmentation in the isolated nuclei using a transposase. The tagmented nuclei are then encapsulated in a droplet including both an oligo-dT-containing barcoded bead and a splint oligonucleotide, which links the tagmented gDNA fragments to the bead, enabling the bead to capture both mRNAs and open chromatin fragments. After mRNAs and gDNA fragments are released from the bead by heating, RT and PCR amplification are performed to generate a library of cDNA and open chromatin gDNA fragments.
This is the second version of SNARE-seq.</obo:IAO_0000115>
<obo:IAO_0000118>SNARE-seq2</obo:IAO_0000118>
<obo:IAO_0000118>SNARE-seq2 assay</obo:IAO_0000118>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-04-05T20:36:54Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">single-nucleus chromatin accessibility and mRNA expression sequencing assay version 2</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000035 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000035">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/TMN_0000034"/>
<obo:IAO_0000115>A SNARE-seq v2 assay that utilizes ATAC-seq as a part.</obo:IAO_0000115>
<obo:IAO_0000118>SNARE-seq2 (ATAC-seq)</obo:IAO_0000118>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-04-05T20:43:10Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">single-nucleus chromatin accessibility and mRNA expression sequencing assay version 2 with assay for transposase-accessible chromatin using sequencing assay</rdfs:label>
</owl:Class>
<!-- http://purl.obolibrary.org/obo/TMN_0000036 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000036">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/TMN_0000034"/>
<obo:IAO_0000115>A SNARE-seq v2 assay that utilizes RNA-seq as a part.</obo:IAO_0000115>
<obo:IAO_0000118>SNARE-seq2 (RNA-seq)</obo:IAO_0000118>
<oboInOwl:created_by>patrick-lloyd-ray</oboInOwl:created_by>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-04-05T20:44:55Z</oboInOwl:creation_date>
<rdfs:label xml:lang="en">single-nucleus chromatin accessibility and mRNA expression sequencing assay version 2 with RNA sequencing assay</rdfs:label>
</owl:Class>