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Merge pull request #109 from BICCN/DT-4278
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DT-4278
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patrick-lloyd-ray authored Dec 1, 2022
2 parents 392edc2 + c3bb16c commit 90cf0bd
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42 changes: 40 additions & 2 deletions TMN-base.obo
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format-version: 1.2
data-version: tmn/releases/2022-07-11/tmn-base.owl
data-version: tmn/releases/2022-12-01/tmn-base.owl
ontology: tmn/tmn-base
property_value: http://purl.org/dc/elements/1.1/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." xsd:string
property_value: http://purl.org/dc/elements/1.1/title "Techniques and Methods for Neuroscience Ontology" xsd:string
property_value: http://purl.org/dc/elements/1.1/type IAO:8000001
property_value: http://purl.org/dc/terms/license https://creativecommons.org/licenses/by/4.0/
property_value: owl:versionInfo "2022-07-11" xsd:string
property_value: owl:versionInfo "2022-12-01" xsd:string

[Term]
id: APOLLO_SV:00000796
Expand Down Expand Up @@ -612,6 +612,44 @@ is_a: OBI:0003094
created_by: http://orcid.org/0000-0002-5260-9315
creation_date: 2022-07-11T22:15:28Z

[Term]
id: TMN:0000051
name: temp-O sequencing assay
def: "A RNA sequencing assay based on BioSpyder Technologies' Templated Oligo Detection Assay that targets RNAs with detector olives and removes excess probes and enzymatic inhibitors before the first enzymatic step. Correctly hybridized detector olives are ligated, then amplified through primer landing sites that are share among all probes." []
is_a: OBI:0001271
property_value: IAO:0000118 "temp-O seq" xsd:string
property_value: IAO:0000118 "templated Oligo sequencing assay" xsd:string
created_by: http://orcid.org/0000-0002-5260-9315
creation_date: 2022-11-29T21:05:47Z

[Term]
id: TMN:0000052
name: x-ray holographic nano-tomography assay
def: "A 3D structure determination assay that employs X-ray holographic nano-tomography to determine the three-dimensional structure of an entity." [] {http://purl.obolibrary.org/obo/IAO_0000119="https://doi.org/10.1038/s41593-020-0704-9"}
is_a: OBI:0600045
property_value: IAO:0000118 "x-ray holographic nano-tomography" xsd:string
property_value: IAO:0000118 "XHN" xsd:string
created_by: http://orcid.org/0000-0002-5260-9315
creation_date: 2022-11-29T21:08:51Z

[Term]
id: TMN:0000053
name: Pacific Bioscience long-read sequencing assay
def: "A DNA sequencing assay wherein a single DNA polymerase enzyme is affixed at the bottom of a zero-mode waveguide (ZMW) with a single molecule of DNA as a template. The Pacific Biotechnologies version is a single-molecule real-time (SMRT) sequencing assay. The ZMW is a structure that creates an illuminated observation volume that is small enough to observe only a single nucleotide of DNA being incorporated by DNA polymerase. Each of the four DNA bases is attached to one of four different fluorescent dyes. When a nucleotide is incorporated by the DNA polymerase, the fluorescent tag is cleaved off and diffuses out of the observation area of the ZMW where its fluorescence is no longer observable. A detector detects the fluorescent signal of the nucleotide incorporation, and the base call is made according to the corresponding fluorescence of the dye." []
is_a: OBI:0000626
property_value: IAO:0000118 "Pac-Bio long-read sequencing assay" xsd:string
created_by: http://orcid.org/0000-0002-5260-9315
creation_date: 2022-11-29T21:12:31Z

[Term]
id: TMN:0000054
name: enhancer virus labelling assay
def: "An imaging assay wherein chromatin accessibility data is collected from cells and enhancers specific to cell types are identified, cloned into recombinant adeno-associated viruses (AAVs) and delivered to the brain, which drive trans gene expression in specific cell types. Then, an image of the marked cell class is generated through fluorescence microscopy." [] {http://purl.obolibrary.org/obo/IAO_0000119="https://doi.org/10.1016/j.neuron.2021.03.011"}
is_a: CHMO:0000087 ! fluorescence microscopy
property_value: IAO:0000118 "enhancer virus labelling" xsd:string
created_by: http://orcid.org/0000-0002-5260-9315
creation_date: 2022-11-29T21:14:49Z

[Term]
id: UBERON:0000000
is_a: BFO:0000003
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70 changes: 68 additions & 2 deletions TMN-base.owl
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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-base.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/tmn/releases/2022-07-11/tmn-base.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/tmn/releases/2022-12-01/tmn-base.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>
<dc:type rdf:resource="http://purl.obolibrary.org/obo/IAO_8000001"/>
<terms:license rdf:resource="https://creativecommons.org/licenses/by/4.0/"/>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-07-11</owl:versionInfo>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2022-12-01</owl:versionInfo>
</owl:Ontology>


Expand Down Expand Up @@ -1296,6 +1296,72 @@ This is the second version of SNARE-seq.</obo:IAO_0000115>



<!-- http://purl.obolibrary.org/obo/TMN_0000051 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000051">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0001271"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A RNA sequencing assay based on BioSpyder Technologies&apos; Templated Oligo Detection Assay that targets RNAs with detector olives and removes excess probes and enzymatic inhibitors before the first enzymatic step. Correctly hybridized detector olives are ligated, then amplified through primer landing sites that are share among all probes.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">temp-O seq</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">templated Oligo sequencing assay</obo:IAO_0000118>
<oboInOwl:created_by rdf:resource="http://orcid.org/0000-0002-5260-9315"/>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-11-29T21:05:47Z</oboInOwl:creation_date>
<rdfs:label>temp-O sequencing assay</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/TMN_0000052 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000052">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0600045"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A 3D structure determination assay that employs X-ray holographic nano-tomography to determine the three-dimensional structure of an entity.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">XHN</obo:IAO_0000118>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">x-ray holographic nano-tomography</obo:IAO_0000118>
<oboInOwl:created_by rdf:resource="http://orcid.org/0000-0002-5260-9315"/>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-11-29T21:08:51Z</oboInOwl:creation_date>
<rdfs:label>x-ray holographic nano-tomography assay</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/TMN_0000052"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A 3D structure determination assay that employs X-ray holographic nano-tomography to determine the three-dimensional structure of an entity.</owl:annotatedTarget>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://doi.org/10.1038/s41593-020-0704-9</obo:IAO_0000119>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/TMN_0000053 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000053">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000626"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A DNA sequencing assay wherein a single DNA polymerase enzyme is affixed at the bottom of a zero-mode waveguide (ZMW) with a single molecule of DNA as a template. The Pacific Biotechnologies version is a single-molecule real-time (SMRT) sequencing assay. The ZMW is a structure that creates an illuminated observation volume that is small enough to observe only a single nucleotide of DNA being incorporated by DNA polymerase. Each of the four DNA bases is attached to one of four different fluorescent dyes. When a nucleotide is incorporated by the DNA polymerase, the fluorescent tag is cleaved off and diffuses out of the observation area of the ZMW where its fluorescence is no longer observable. A detector detects the fluorescent signal of the nucleotide incorporation, and the base call is made according to the corresponding fluorescence of the dye.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Pac-Bio long-read sequencing assay</obo:IAO_0000118>
<oboInOwl:created_by rdf:resource="http://orcid.org/0000-0002-5260-9315"/>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-11-29T21:12:31Z</oboInOwl:creation_date>
<rdfs:label>Pacific Bioscience long-read sequencing assay</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/TMN_0000054 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/TMN_0000054">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/CHMO_0000087"/>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An imaging assay wherein chromatin accessibility data is collected from cells and enhancers specific to cell types are identified, cloned into recombinant adeno-associated viruses (AAVs) and delivered to the brain, which drive trans gene expression in specific cell types. Then, an image of the marked cell class is generated through fluorescence microscopy.</obo:IAO_0000115>
<obo:IAO_0000118 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">enhancer virus labelling</obo:IAO_0000118>
<oboInOwl:created_by rdf:resource="http://orcid.org/0000-0002-5260-9315"/>
<oboInOwl:creation_date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2022-11-29T21:14:49Z</oboInOwl:creation_date>
<rdfs:label>enhancer virus labelling assay</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/TMN_0000054"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An imaging assay wherein chromatin accessibility data is collected from cells and enhancers specific to cell types are identified, cloned into recombinant adeno-associated viruses (AAVs) and delivered to the brain, which drive trans gene expression in specific cell types. Then, an image of the marked cell class is generated through fluorescence microscopy.</owl:annotatedTarget>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">https://doi.org/10.1016/j.neuron.2021.03.011</obo:IAO_0000119>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/UBERON_0000000 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/UBERON_0000000">
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