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clkgho.obo
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format-version: 1.2
data-version: releases/2024-10-18
idspace: dce http://purl.org/dc/elements/1.1/
idspace: dcterms http://purl.org/dc/terms/
idspace: efo http://www.ebi.ac.uk/efo/
idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl#
ontology: clkgho
property_value: dcterms:description "None" xsd:string
property_value: dcterms:license https://creativecommons.org/licenses/unspecified
property_value: dcterms:title "CL KG Helper Ontology" xsd:string
property_value: owl:versionInfo "2024-10-18" xsd:string
[Term]
id: CLKGHO:0000000
name: root node
[Term]
id: efo:EFO_0001457
name: RNA assay
def: "An assay with input RNA" []
is_a: efo:EFO_0002772 ! assay by molecule
is_a: OBI:0000070
property_value: efo:ArrayExpress_label "RNA assay" xsd:string
property_value: IAO:0000117 "James Malone" xsd:string
[Term]
id: efo:EFO_0002697
name: assay by high throughput sequencer
def: "An assay which uses high throughput sequencing technology to determine the sequence of nucleic acids" []
synonym: "high throughput sequencing assay" EXACT []
is_a: efo:EFO_0003740 ! assay by sequencer
property_value: IAO:0000112 "Solexa sequencing of coding RNA" xsd:string
property_value: IAO:0000117 "Helen Parkinson" xsd:string
[Term]
id: efo:EFO_0002772
name: assay by molecule
property_value: efo:ArrayExpress_label "Assay by molecule" xsd:string
[Term]
id: efo:EFO_0002773
name: assay by instrument
is_a: OBI:0000070
property_value: efo:ArrayExpress_label "Assay by technology" xsd:string
[Term]
id: efo:EFO_0003740
name: assay by sequencer
def: "An assay that exploits a sequencer as the instrument to find results." []
synonym: "sequencing assay" EXACT []
is_a: efo:EFO_0002773 ! assay by instrument
property_value: efo:ArrayExpress_label "Sequencing assay" xsd:string
property_value: IAO:0000117 "James Malone" xsd:string
[Term]
id: efo:EFO_0008931
name: Smart-seq2
def: "Switch mechanism at the 5’ end of RNA templates (Smart). According to the authors, Smart-seq2 transcriptome libraries have improved detection, coverage, bias and accuracy compared to Smart-seq libraries, and are generated with off-the-shelf reagents at lower cost." []
xref: PMID:24056875
is_a: efo:EFO_0001457 ! RNA assay
is_a: efo:EFO_0010184 ! Smart-like
property_value: IAO:0000117 "Dani Welter" xsd:string
[Term]
id: efo:EFO_0008994
name: spatial transcriptomics
def: "assay that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections" []
xref: PMID:27365449
is_a: efo:EFO_0001457 ! RNA assay
property_value: IAO:0000117 "Dani Welter" xsd:string
[Term]
id: efo:EFO_0008995
name: 10x technology
def: "10x is a \"synthetic long-read\" technology and works by capturing a barcoded oligo-coated gel-bead and 0.3x genome copies into a single emulsion droplet, processing the equivalent of 1 million pipetting steps. Successive versions of the 10x chemistry use different barcode locations to improve the sequencing yield and quality of 10x experiments." []
synonym: "10X" BROAD []
synonym: "10x" BROAD []
synonym: "10x Genomics" EXACT []
synonym: "10X sequencing" RELATED []
synonym: "10x sequencing" RELATED []
synonym: "10x single cell library construction" EXACT []
is_a: efo:EFO_0010183 ! single cell library construction
property_value: IAO:0000117 "Dani Welter" xsd:string
[Term]
id: efo:EFO_0009899
name: 10x 3' v2
def: "10X 3' v2 is the second version of the 10x sequencing technology that sequences from the 3' end of nucleic acid molecules. In the 3' assay, the polyd(T) sequence is part of the gel bead oligo (which also contains the 10x Barcode, UMI, and partial Illumina Read 1 sequence), with the template switch oligo (TSO) supplied in the RT Primer." []
synonym: "10X 3' v2" EXACT []
synonym: "10X 3' v2 sequencing" RELATED []
synonym: "10x 3' v2 sequencing" RELATED []
synonym: "10X v2" RELATED []
synonym: "10x v2" RELATED []
synonym: "10X v2 sequencing" RELATED []
synonym: "10x v2 sequencing" RELATED []
synonym: "10x_v2" RELATED []
synonym: "10XV2" RELATED []
is_a: efo:EFO_0030003 ! 10x 3' transcription profiling
property_value: IAO:0000117 "Dani Welter" xsd:string
[Term]
id: efo:EFO_0009900
name: 10x 5' v2
def: "10X 5' v2 is the second version of the 10x sequencing technology that sequences from the 5' end of nucleic acid molecules. In the 5' assay, the polyd(T) is supplied in the RT Primer, and the template switch oligo (TSO) is part of the gel bead oligo." []
synonym: "10X 5' v2" EXACT []
synonym: "10X 5' v2 sequencing" RELATED []
synonym: "10x 5' v2 sequencing" RELATED []
is_a: efo:EFO_0030004 ! 10x 5' transcription profiling
property_value: IAO:0000117 "Dani Welter" xsd:string
[Term]
id: efo:EFO_0009922
name: 10x 3' v3
def: "10X 3' v3 is the third version of the 10x sequencing technology that sequences from the 3' end of nucleic acid molecules." []
synonym: "10X 3' v3" EXACT []
synonym: "10x 3' v3 sequencing" RELATED []
synonym: "10X v3" RELATED []
synonym: "10x v3" RELATED []
synonym: "10X v3 sequencing" RELATED []
synonym: "10x v3 sequencing" RELATED []
synonym: "10XV3" RELATED []
is_a: efo:EFO_0030003 ! 10x 3' transcription profiling
property_value: IAO:0000117 "Dani Welter" xsd:string
[Term]
id: efo:EFO_0010183
name: single cell library construction
def: "A library preparation process that starts from a single cell." []
synonym: "single cell library preparation" EXACT []
synonym: "single-cell library construction" EXACT []
synonym: "single-cell library preparation" EXACT []
property_value: dce:creator "Olamidipupo Ajigboye" xsd:string
[Term]
id: efo:EFO_0010184
name: Smart-like
def: "Library construction method using the SMART (Switching Mechanism at the 5' end of the RNA Template) or SMARTer technology, producing full-length cDNA libraries." []
is_a: efo:EFO_0010183 ! single cell library construction
property_value: dce:creator "Olamidipupo Ajigboye" xsd:string
[Term]
id: efo:EFO_0010961
name: Visium Spatial Gene Expression
def: "A spatial transcriptomics method developed by 10x Genomics that measures either the whole transcriptome or a defined set of transcripts in intact tissue sections and maps where gene activity is occurring." [http://orcid.org/0000-0001-7505-5418, https://pages.10xgenomics.com/rs/446-PBO-704/images/10x_LIT059_ProductSheet_VisiumSpatialGeneExpression_Letter_digital.pdf]
subset: efo:added_for_HCA
synonym: "10X Visium" EXACT []
synonym: "Visium" EXACT []
is_a: efo:EFO_0008995 ! 10x technology
is_a: efo:EFO_0030005 ! spatial transcriptomics by high-throughput sequencing
property_value: dce:creator "paola" xsd:string
[Term]
id: efo:EFO_0011025
name: 10x 5' v1
def: "10x 5' v1 is the first version of the 10X sequencing technology that sequences from the 5' end of nucleic acid molecules. Differs from 3' v1 in the captured end from the polyadenylated transcript." []
subset: efo:added_for_HCA
synonym: "10X 5' v1" EXACT []
synonym: "10x 5' v1" EXACT []
synonym: "10x 5' v1 sequencing" RELATED []
synonym: "10X 5' v3" RELATED []
synonym: "10x 5' v3" RELATED []
synonym: "10x 5' v3 sequencing" RELATED []
synonym: "10x v1 5' sequencing" RELATED []
is_a: efo:EFO_0030004 ! 10x 5' transcription profiling
property_value: dce:creator "paola" xsd:string
[Term]
id: efo:EFO_0030003
name: 10x 3' transcription profiling
def: "10x 3' transcription profiling is the 10x-based single-cell technology that sequences mRNA molecules from their 3' end." [https://orcid.org/0000-0002-8674-0039]
is_a: efo:EFO_0030080 ! 10x transcription profiling
property_value: dce:creator "paola" xsd:string
[Term]
id: efo:EFO_0030004
name: 10x 5' transcription profiling
def: "10x 5' transcription profiling is the 10x-based single-cell technology that sequences mRNA molecules from their 5' end." [https://orcid.org/0000-0002-8674-0039]
is_a: efo:EFO_0030080 ! 10x transcription profiling
property_value: dce:creator "paola" xsd:string
[Term]
id: efo:EFO_0030005
name: spatial transcriptomics by high-throughput sequencing
def: "A spatial transcriptomics assay that measures spatially defined transcription by high-throughput sequencing." [https://orcid.org/0000-0002-8674-0039]
is_a: efo:EFO_0002697 ! assay by high throughput sequencer
is_a: efo:EFO_0008994 ! spatial transcriptomics
property_value: dce:creator "paola" xsd:string
[Term]
id: efo:EFO_0030062
name: Slide-seqV2
def: "More sensitive version of the Slide-seq method for transferring RNA from tissue sections onto a surface covered in DNA-barcoded beads with known positions, which differs from Slide-seq in the use of a monobase encoding scheme with sequencing by ligation using sequential interrogation by offset primer, and improved parameters for split-pool synthesis of barcoded beads." [http://orcid.org/0000-0001-8134-3037, https://www.biorxiv.org/content/10.1101/2020.03.12.989806v1]
is_a: efo:EFO_0010183 ! single cell library construction
is_a: efo:EFO_0030005 ! spatial transcriptomics by high-throughput sequencing
property_value: dce:creator "paola" xsd:string
property_value: dce:date "2021-12-16T08:53:05Z" xsd:dateTime
[Term]
id: efo:EFO_0030080
name: 10x transcription profiling
def: "The 10x-based single-cell technology that sequences mRNA molecules." [http://orcid.org/0000-0002-3564-4813]
comment: This term should only be used when a single-cell RNA-seq dataset is known to be generated using 10x, but the specific protocol (5' vs. 3') isn't specified. Whenever that information is available, please use EFO:0030003 '10x 3' transcription profiling' or EFO:0030004 '10x 5' transcription profiling'.
is_a: efo:EFO_0008995 ! 10x technology
property_value: dce:creator "paola" xsd:string
property_value: seeAlso "https://github.com/EBISPOT/efo/issues/1558" xsd:string