tmn-basic.obo

format-version: 1.2
data-version: tmn/releases/2022-12-01/tmn-basic.owl
ontology: tmn/tmn-basic
property_value: 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." xsd:string
property_value: dc-title "Techniques and Methods for Neuroscience Ontology" xsd:string
property_value: dcterms-license https://creativecommons.org/licenses/by/4.0/
property_value: owl:versionInfo "2022-12-01" xsd:string

[Term]
id: TMN:0000000
name: droplet-based single-cell RNA sequencing assay
def: "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." []
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "Dropseq" xsd:string
property_value: IAO:0000119 https://doi.org/10.1016/j.cell.2015.05.002 xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-03T20:04:39Z

[Term]
id: TMN:0000001
name: fluorescence in situ hybridization assay
def: "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." []
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "FISH" xsd:string
property_value: IAO:0000119 http://en.wikipedia.org/wiki/Fluorescence_in_situ_hybridization xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-03T21:04:00Z

[Term]
id: TMN:0000002
name: fluorescence micro-optical sectioning tomography assay
def: "An imaging assay that uses micro-optical sectioning tomography technology combined with fluorescence molecular labeling of neuronal projections." []
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "fMOST" xsd:string
property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6701528/ xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-03T21:32:43Z

[Term]
id: TMN:0000003
name: multiplexed error-robust fluorescence in situ hybridization assay
def: "An imaging assay that measures the copy number and spatial distribution of hundreds to thousands of RNA species in single cells." []
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "MERFISH" xsd:string
property_value: IAO:0000119 "DOI: 10.1126/science.aaa6090" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-03T23:18:34Z

[Term]
id: TMN:0000004
name: neuron morphology assay
def: "A 3D structure determination assay that determines the morphology of a neuron." []
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "3D structure determination assay of neuron" xsd:string
property_value: IAO:0000119 "PERSON: Patrick Ray" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-04T00:06:14Z

[Term]
id: TMN:0000005
name: mosaicism with repeat frameshift genetic sparse labeling assay
def: "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)." []
is_a: TMN:0000004 ! neuron morphology assay
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000119 https://biccn.org/teams/u01-yang xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-04T00:10:17Z

[Term]
id: TMN:0000006
name: serial two-photon tomography
def: "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." []
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "STPT" xsd:string
property_value: IAO:0000119 http://doi.org/10.1038/nmeth.1854 xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-04T00:30:35Z

[Term]
id: TMN:0000007
name: mouselight
def: "A serial two photon tomography assay that produces images of mouse brains with sufficient detail to represent axons of individual neurons." []
is_a: TMN:0000006 ! serial two-photon tomography
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000119 http://www.janelia.org/project-team/mouselight/research xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-04T00:34:49Z

[Term]
id: TMN:0000008
name: multi-electrode extracellular electrophysiology assay
def: "An electrophysiology assay that employs many electrodes to record extracellular field potentials." []
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000119 http://en.wikipedia.org/wiki/Microelectrode_array xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-10T23:56:39Z

[Term]
id: TMN:0000009
name: neuron morphology reconstruction assay
def: "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)." []
is_a: TMN:0000004 ! neuron morphology assay
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000119 http://doi.org/10.1101/675280 xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-11T00:15:55Z

[Term]
id: TMN:0000010
name: patch clamp single-cell RNA sequencing assay
def: "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." []
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "patch clamp sequencing assay" xsd:string
property_value: IAO:0000118 "patch-seq" xsd:string
property_value: IAO:0000119 http://doi.org/10.1038/nprot.2017.120 xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-11T00:26:12Z

[Term]
id: TMN:0000011
name: retrograde tracing assay
def: "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." []
synonym: "retrograde labeling" EXACT []
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "retrograde tracing" xsd:string
property_value: IAO:0000119 "PERSON: Patrick Ray" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-11T00:39:16Z

[Term]
id: TMN:0000012
name: retrograde transsynaptic tracing assay
def: "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." []
is_a: TMN:0000011 ! retrograde tracing assay
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000119 http://en.wikipedia.org/wiki/Retrograde_tracing xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-11T00:51:53Z

[Term]
id: TMN:0000013
name: sequential fluorescence in situ hybridization assay
def: "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." []
is_a: TMN:0000001 ! fluorescence in situ hybridization assay
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "seqFISH" xsd:string
property_value: IAO:0000119 http://www.seqfish.com/technology xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-11T01:00:00Z

[Term]
id: TMN:0000014
name: switching mechanism at the 5' end of RNA template sequencing assay
def: "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." []
property_value: editor_note "Definition needs curation." xsd:string
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "SMART seq" xsd:string
property_value: IAO:0000118 "SMARTseq" xsd:string
property_value: IAO:0000119 http://www.enseqlopedia.com/wiki-entry/rna-sequencing-methods/low-level-rna-detection/smart-seq/ xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-11T01:10:58Z

[Term]
id: TMN:0000015
name: switching mechanism at the 5' end of RNA template sequencing assay v4
def: "A switching mechanism at the 5' end of RNA template sequencing assay that is the fourth version of such an assay." []
is_a: TMN:0000024 ! switching mechanism at the 5' end of RNA template sequencing assay 2
property_value: curator_notes "This is the commercial version of SMARTseq2 that has as an instrument the Takara kit." xsd:string
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "SMARTseq v4" xsd:string
property_value: IAO:0000119 "PERSON: Patrick Ray" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-11T01:21:33Z

[Term]
id: TMN:0000016
name: tracing the relationship between input and output study design
def: "A study design in which complementary viruses are to be injected into brain regions to monosynaptically label inputs to a specific projection neuron population." []
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "TRIO tracing" xsd:string
property_value: IAO:0000119 http://cic.ini.usc.edu/protocols/trio-tracing xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-11T01:43:24Z

[Term]
id: TMN:0000017
name: light sheet fluorescence microscopy assay
def: "A fluorescence microscopy assay that uses a laser light-sheet to illuminate a region of a sample that has been treated to excite fluorescently." []
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "light sheet microscopy" xsd:string
property_value: IAO:0000119 http://en.wikipedia.org/wiki/Light_sheet_fluorescence_microscopy xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-11T01:59:49Z

[Term]
id: TMN:0000018
name: cre-dependent anterograde tracing assay
def: "A anterograde tracing assay that uses a Cre recombinase-dependent as a tracer." []
is_a: TMN:0000019 ! anterograde tracing assay
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000119 http://doi.org/10.1016/j.neuron.2011.12.002 xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-15T18:11:42Z

[Term]
id: TMN:0000019
name: anterograde tracing assay
def: "An assay wherein axon projections are traced from their source (cell body or soma) to their point of termination (synapse)." []
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000119 https://en.wikipedia.org/wiki/Anterograde_tracing xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-15T18:13:29Z

[Term]
id: TMN:0000020
name: optical coherence tomography assay
def: "An imaging assay that has as an output label-free, cross-sectional imaging of biological tissue microstructure using tissue backscattering properties." []
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "OCT" xsd:string
property_value: IAO:0000119 "doi: 10.1155/2017/3409327" xsd:string
property_value: IAO:0000119 "PMID: 29214158" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-15T18:44:49Z

[Term]
id: TMN:0000021
name: volumetric imaging with synchronized on-the-fly oblique-scan and readout assay
def: "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." []
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "VISoR" xsd:string
property_value: IAO:0000118 "VISoR assay" xsd:string
property_value: IAO:0000119 "doi: 10.1093/nsr/nwz053" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-15T19:01:49Z

[Term]
id: TMN:0000022
name: single-nucleus chromatin accessibility and mRNA expression sequencing assay
def: "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." []
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "SNARE-seq" xsd:string
property_value: IAO:0000118 "SNARE-seq assay" xsd:string
property_value: IAO:0000119 https://doi.org/10.1038/s12276-020-0420-2 xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-15T19:09:43Z

[Term]
id: TMN:0000023
name: composite in situ imaging
def: "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." []
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "CISI" xsd:string
property_value: IAO:0000119 "DOI: 10.1101/743039" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-02-15T19:20:54Z

[Term]
id: TMN:0000024
name: switching mechanism at the 5' end of RNA template sequencing assay 2
def: "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." []
is_a: TMN:0000014 ! switching mechanism at the 5' end of RNA template sequencing assay
property_value: curator_notes "See also: https://scicrunch.org/scicrunch/interlex/view/ilx_0739685" xsd:string
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "SMARTseq2" xsd:string
property_value: IAO:0000119 https://doi.org/10.1038/nprot.2014.006 xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-04-22T19:49:20Z

[Term]
id: TMN:0000025
name: sci-RNA-seq3
def: "A RNA sequencing assay that involves three levels of indexing." [] {http://purl.obolibrary.org/obo/IAO_0000119="https://www.protocols.io/view/sci-rna-seq3-9yih7ue"}
property_value: IAO:0000118 "3-level sci-RNA-seq" xsd:string
property_value: IAO:0000118 "3-level single-cell combinatorial indexing RNA sequencing assay" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-09-02T02:12:07Z

[Term]
id: TMN:0000026
name: sci-ATAC-seq3
def: "An ATAC-seq assay that involves single-cell combinatorial indexing at three levels." [] {http://purl.obolibrary.org/obo/IAO_0000119="https://www.protocols.io/view/sci-atac-seq3-be8mjhu6"}
property_value: IAO:0000118 "3-level sci-ATAC-seq" xsd:string
property_value: IAO:0000118 "3-level single-cell combinatorial indexing ATAC sequencing assay" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-09-02T02:16:18Z

[Term]
id: TMN:0000027
name: 10x chromium ATAC-seq
def: "An ATAC-seq assay that involves use of the 10x sequencing technology assay for transposase-accessible chromatin using sequencing (ATAC-seq)." [] {http://purl.obolibrary.org/obo/IAO_0000119="PERSON: Patrick Ray"}
property_value: IAO:0000118 "10x chromium ATAC sequencing assay" xsd:string
property_value: IAO:0000118 "10x chromium ATAC-seq assay" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-09-02T02:18:54Z

[Term]
id: TMN:0000028
name: slide-seq assay
def: "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." []
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "slide-seq" xsd:string
property_value: IAO:0000118 "slide-sequencing assay" xsd:string
property_value: IAO:0000119 "doi: 10.1126/science.aaw1219" xsd:string
property_value: IAO:0000119 "PERSON: Patrick Ray" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-10-04T22:03:50Z

[Term]
id: TMN:0000029
name: SHARE-seq assay
def: "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." []
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "SHARE-seq" xsd:string
property_value: IAO:0000118 "SHARE-sequencing" xsd:string
property_value: IAO:0000119 https://doi.org/10.1016/j.cell.2020.09.056 xsd:string
property_value: IAO:0000119 "PERSON: Patrick Ray" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-10-04T22:09:37Z

[Term]
id: TMN:0000030
name: single cell multiome ATAC + gene expression assay
def: "An ATAC-seq assay that provides information about both transcriptome and epigenome from a single cell." []
property_value: IAO:0000117 "PERSON: Patrick Ray" xsd:string
property_value: IAO:0000118 "single cell multiome ATAC + gene expression" xsd:string
property_value: IAO:0000119 https://www.10xgenomics.com/blog/introducing-chromium-single-cell-multiome-atac-gene-expression xsd:string
property_value: IAO:0000119 https://www.10xgenomics.com/products/single-cell-multiome-atac-plus-gene-expression xsd:string
property_value: IAO:0000119 "PERSON: Patrick Ray" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2021-10-04T22:12:23Z

[Term]
id: TMN:0000031
name: double in vitro transcription with absoluted counts sequencing assay
def: "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." [] {http://purl.obolibrary.org/obo/IAO_0000119="http://doi.org/10.3791/58690"}
property_value: IAO:0000118 "DIVA-seq" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2022-04-05T20:19:26Z

[Term]
id: TMN:0000032
name: oblique light sheet tomography assay
def: "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." [] {http://purl.obolibrary.org/obo/IAO_0000119="http://doi.org/10.1101/132423", http://purl.obolibrary.org/obo/IAO_0000119="http://doi.org/10.17504/protocols.io.smwec7e"}
is_a: TMN:0000017 ! light sheet fluorescence microscopy assay
property_value: IAO:0000118 "OLST" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2022-04-05T20:22:10Z

[Term]
id: TMN:0000033
name: cyclic single-molecule fluorescence in situ hybridization assay
def: "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." [] {http://purl.obolibrary.org/obo/IAO_0000119="http://doi.org/10.1038/s41592-018-0175-z", http://purl.obolibrary.org/obo/IAO_0000119="http://doi.org/10.17504/protocols.io.psednbe"}
is_a: TMN:0000001 ! fluorescence in situ hybridization assay
property_value: IAO:0000118 "osmFISH" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2022-04-05T20:26:01Z

[Term]
id: TMN:0000034
name: single-nucleus chromatin accessibility and mRNA expression sequencing assay version 2
def: "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.\n\nThis is the second version of SNARE-seq." []
is_a: TMN:0000022 ! single-nucleus chromatin accessibility and mRNA expression sequencing assay
property_value: IAO:0000118 "SNARE-seq2" xsd:string
property_value: IAO:0000118 "SNARE-seq2 assay" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2022-04-05T20:36:54Z

[Term]
id: TMN:0000035
name: single-nucleus chromatin accessibility and mRNA expression sequencing assay version 2 with assay for transposase-accessible chromatin using sequencing assay
def: "A SNARE-seq v2 assay that utilizes ATAC-seq as a part." []
is_a: TMN:0000034 ! single-nucleus chromatin accessibility and mRNA expression sequencing assay version 2
property_value: IAO:0000118 "SNARE-seq2 (ATAC-seq)" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2022-04-05T20:43:10Z

[Term]
id: TMN:0000036
name: single-nucleus chromatin accessibility and mRNA expression sequencing assay version 2 with RNA sequencing assay
def: "A SNARE-seq v2 assay that utilizes RNA-seq as a part." []
is_a: TMN:0000034 ! single-nucleus chromatin accessibility and mRNA expression sequencing assay version 2
property_value: IAO:0000118 "SNARE-seq2 (RNA-seq)" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2022-04-05T20:44:55Z

[Term]
id: TMN:0000037
name: nanopore DNA sequencing assay
def: "A DNA sequencing assay that provides direct, real-time analysis of long DNA or RNA fragments by monitoring changes to an electrical current as nucleic acids are passed through a protein nanopore. The resulting signal is decoded to provide the specific DNA or RNA sequence." [] {http://purl.obolibrary.org/obo/IAO_0000119="https://nanoporetech.com/applications/dna-nanopore-sequencing"}
created_by: patrick-lloyd-ray
creation_date: 2022-05-05T17:35:14Z

[Term]
id: TMN:0000038
name: single cell isoform RNA sequencing assay
def: "An isoform sequencing assay that begins with bulk tissue and identifies single-cell types and their full-length RNA isoforms without fluorescence-activated cell sorting." [] {http://purl.obolibrary.org/obo/IAO_0000119="PMID:30320766", http://purl.obolibrary.org/obo/IAO_0000119="https://doi.org/10.1038/nbt.4259"}
property_value: IAO:0000118 "ScISOr-seq" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2022-05-05T17:59:23Z

[Term]
id: TMN:0000039
name: single-nucleus methyl-3C sequencing assay
def: "A single-cell RNA sequencing assay that jointly profiles chromatin conformation and DNA methylation information from the same cell." [] {http://purl.obolibrary.org/obo/IAO_0000119="https://doi.org/10.1038/s41592-019-0547-z"}
property_value: IAO:0000118 "sn-m3C-seq" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2022-05-05T19:17:37Z

[Term]
id: TMN:0000040
name: single-nucleus methyl-C sequencing assay version 2
def: "A library preparation method for single-nucleus methylome library preparation that provides significant improvements in read mapping, amount of artifactual reads, throughput, library complexity, and coverage uniformity over snmC-seq." [] {http://purl.obolibrary.org/obo/IAO_0000119="http://doi.org/10.1038/s41467-018-06355-2"}
property_value: IAO:0000118 "snmC-seq2" xsd:string
created_by: patrick-lloyd-ray
creation_date: 2022-05-05T20:16:03Z

[Term]
id: TMN:0000041
name: mC-seq3
is_a: TMN:0000040 ! single-nucleus methyl-C sequencing assay version 2
created_by: patrick-lloyd-ray
creation_date: 2022-05-05T21:09:57Z

[Term]
id: TMN:0000042
name: single-cell combinatorial indexing with WGBS methylation analysis version 2
def: "The second version of the single-cell combinatorial indexing with WGBS methylation analysis." []
created_by: patrick-lloyd-ray
creation_date: 2022-05-05T21:34:40Z

[Term]
id: TMN:0000043
name: multiplex immunoassay
def: "An immunoassay that uses magnetic beads to measure multiple analytes in a single assay." []
is_a: TMN:0000044 ! immunoassay
created_by: patrick-lloyd-ray
creation_date: 2022-05-05T22:19:17Z

[Term]
id: TMN:0000044
name: immunoassay
def: "An assay that enables the presence or the concentration of a substance in a material to be measured by exploiting the specific binding between an analyte and the corresponding detection antibody." []
created_by: http://orcid.org/0000-0002-5260-9315
creation_date: 2022-06-07T16:53:51Z

[Term]
id: TMN:0000045
name: calcium imaging assay
def: "An imaging assay that is designed to show the calcium (Ca2+) levels of a tissue or medium." [] {http://purl.org/dc/terms/source="ERO:0000634", http://purl.obolibrary.org/obo/IAO_0000119="http://en.wikipedia.org/wiki/Calcium_imaging"}
synonym: "Ca imaging" EXACT []
synonym: "Ca imaging assay" EXACT []
synonym: "Ca2+ imaging" EXACT []
synonym: "Ca2+ imaging assay" EXACT []
created_by: http://orcid.org/0000-0002-5260-9315
creation_date: 2022-06-07T16:56:02Z

[Term]
id: TMN:0000046
name: cellular assay
def: "An assay that generates data about the presence, quantity, structure, function, behavior, or activity of cells, or a process that occurs at a cellular level of anatomical granularity (includes subcellular structures and organelles)." []
synonym: "cell analysis" BROAD []
created_by: http://orcid.org/0000-0002-5260-9315
creation_date: 2022-06-07T16:59:58Z

[Term]
id: TMN:0000049
name: human brain optimized light sheet microscopy assay
def: "A light sheet fluorescence microscopy assay that employs high-speed scanning single-objective light sheet imaging with spectral multiplexing and cell-type encoding. Human brain samples are processed using a clearing and immunostaining approach called HuB.Clear which can generate optically clear, 5 mm thick, whole-mount brain slabs. High-field magnetic resonance imaging (MRI) data acquired on the intact, fixed brain prior to sectioning will provide a vital cross-reference for comparison while also facilitating registration of data to a common coordinate frameworks. HOLiS data will be analyzed to extract cell locations and cell type identities, generating databases that can be compared to standard neuroanatomical atlases, while also permitting careful examination of brain-wide patterns and inter-subject differences." [] {http://purl.obolibrary.org/obo/IAO_0000119="https://www.humanbrainmapping.org/files/2022/Annual%20Meeting%20Symposia/1511_Imaging_and_analysis_of_3D%5B1%5D.pdf"}
is_a: TMN:0000017 ! light sheet fluorescence microscopy assay
property_value: IAO:0000118 "HOLiS" xsd:string
created_by: http://orcid.org/0000-0002-5260-9315
creation_date: 2022-07-11T22:11:00Z

[Term]
id: TMN:0000050
name: osmFISH
def: "A non-barcoded and unamplified cyclic smFISH method (osmFISH) in which the number of targets scales linearly. In osmFISH, each RNA molecule is visualized as a diffraction limited spot after the binding of 20 nt long fluorescently labelled DNA probes. Multiple transcripts are targeted at each round of hybridization, separated by fluorescent color. After image acquisition, the detection probes are removed by formamide melting in preparation for the next round of hybridization." [] {http://purl.obolibrary.org/obo/IAO_0000119="https://doi.org/10.1038/s41592-018-0175-z"}
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." []
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"}
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." []
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"}
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

[Typedef]
id: curator_notes
name: curator note
name: curator notes
namespace: uberon
def: "An administrative note of use for a curator but of no use for a user" []
xref: IAO:0000232
property_value: IAO:0000111 "curator note" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "PERSON:Alan Ruttenberg" xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl
is_metadata_tag: true

[Typedef]
id: dc-description
name: description
namespace: uberon
xref: http://purl.org/dc/elements/1.1/description
is_metadata_tag: true

[Typedef]
id: dc-title
name: title
namespace: uberon
xref: http://purl.org/dc/elements/1.1/title
is_metadata_tag: true

[Typedef]
id: dcterms-license
name: license
namespace: uberon
xref: http://purl.org/dc/terms/license
is_metadata_tag: true

[Typedef]
id: editor_note
name: editor note
namespace: uberon
def: "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." []
xref: IAO:0000116
property_value: IAO:0000111 "editor note" xsd:string
property_value: IAO:0000114 IAO:0000122
property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string
property_value: IAO:0000119 GROUP:OBI:<http://purl.obofoundry.org/obo/obi> xsd:string
property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl
is_metadata_tag: true