format-version: 1.2 data-version: 1.1.2 date: 03:16:2021 10:38 saved-by: Malcolm Fisher auto-generated-by: OBO-Edit 2.3.2 subsetdef: Antibody_methods "Antibody methods" subsetdef: assay "Experimental Assay" subsetdef: Article_content_types "Article content types" subsetdef: Copyright_access "Copyright access types" subsetdef: Corpus "Corpus Assesment" subsetdef: ChIP_type "ChIP_type" subsetdef: GEO_assay_types "GEO_assay_types" subsetdef: GEO_manipulation_types "GEO_manipulation_types" subsetdef: manipulation "Experimental Manipulation" subsetdef: morpholino_type "morpholino types" subsetdef: PHENO_assay_types "PHENO_assay_types" subsetdef: XED_copyright_pmc_subset "XED copyright pmc subset" subsetdef: XED_Orthology_prediction_finding "XED Orthology prediction finding" subsetdef: XED_Orthology_prediction_method "XED Orthology prediction method" subsetdef: Temperature_degC "Temperature in degrees Celsius" synonymtypedef: ABBREVIATION "Abbreviation" synonymtypedef: PLURAL "Plural" default-namespace: xenbase_experimental_data [Term] id: XBED:0000000 name: Curatable Data subset: Article_content_types xref: ECO:0000000 creation_date: 2010-12-19T09:23:26Z [Term] id: XBED:0000001 name: Gene Expression Assay subset: Article_content_types xref: ECO:0000008 is_a: XBED:0000000 ! Curatable Data created_by: Jeff creation_date: 2010-12-19T09:24:42Z [Term] id: XBED:0000002 name: Phenotype subset: assay subset: Article_content_types xref: ECO:0000059 is_a: XBED:0000000 ! Curatable Data created_by: Jeff creation_date: 2010-12-19T09:25:55Z [Term] id: XBED:0000003 name: in situ hybridization subset: Article_content_types subset: assay subset: PHENO_assay_types synonym: "ISH" EXACT ABBREVIATION [] synonym: "whole mount in situ hybridization" EXACT [] synonym: "WMISH" EXACT [] xref: ECO:0000289 xref: MMO:0000658 is_a: XBED:0000001 ! Gene Expression Assay created_by: Jeff creation_date: 2010-12-19T09:26:48Z [Term] id: XBED:0000004 name: immunohistochemistry subset: Article_content_types subset: Antibody_methods subset: assay subset: PHENO_assay_types synonym: "IF" RELATED [] synonym: "IHC" EXACT ABBREVIATION [] synonym: "immunofluorescence" RELATED [] xref: ECO:0001189 xref: MMO:0000498 is_a: XBED:0000001 ! Gene Expression Assay is_a: XBED:0000055 ! Protein Localization is_a: XBED:0000194 ! histochemistry created_by: Jeff creation_date: 2010-12-19T09:27:20Z [Term] id: XBED:0000005 name: microarray subset: Article_content_types subset: assay subset: GEO_assay_types synonym: "Affymetrix" RELATED [] xref: ECO:0000058 is_a: XBED:0000001 ! Gene Expression Assay created_by: Jeff creation_date: 2010-12-19T09:29:32Z [Term] id: XBED:0000006 name: Experimental Manipulation synonym: "Experimental Treatment" EXACT [] synonym: "Treatment" EXACT [] xref: ECO:0000059 is_a: XBED:0000000 ! Curatable Data created_by: lab creation_date: 2011-10-14T01:52:50Z [Term] id: XBED:0000007 name: gain of function synonym: "GOF" EXACT [] synonym: "overexpression" RELATED [] subset: Article_content_types xref: ECO:0000042 is_a: XBED:0000002 ! Phenotype created_by: Jeff creation_date: 2010-12-19T09:31:05Z [Term] id: XBED:0000008 name: loss of function synonym: "knockdown" RELATED [] synonym: "knockout" RELATED [] synonym: "LOF" EXACT [] subset: Article_content_types xref: ECO:0000016 is_a: XBED:0000002 ! Phenotype created_by: Jeff creation_date: 2010-12-19T09:31:57Z [Term] id: XBED:0000009 name: morpholino oligo synonym: "MO" EXACT [] synonym: "morphant" RELATED [] subset: Article_content_types xref: ECO:0000292 is_a: XBED:0000018 ! Reagent created_by: Jeff creation_date: 2010-12-19T09:34:47Z [Term] id: XBED:0000010 name: mRNA injection subset: Article_content_types subset: GEO_manipulation_types subset: manipulation xref: ECO:0000017 is_a: XBED:0000086 ! Genetic material injection created_by: Jeff creation_date: 2010-12-19T09:36:08Z [Term] id: XBED:0000011 name: western blot subset: Article_content_types subset: Antibody_methods subset: assay subset: PHENO_assay_types xref: ECO:0000279 xref: MMO:0000669 is_a: XBED:0000001 ! Gene Expression Assay created_by: Jeff creation_date: 2010-12-21T05:07:03Z [Term] id: XBED:0000012 name: RT-PCR subset: Article_content_types subset: assay subset: PHENO_assay_types synonym: "reverse transcriptase PCR" EXACT [] xref: ECO:0001808 xref: MMO:0000461 is_a: XBED:0000001 ! Gene Expression Assay created_by: Jeff creation_date: 2010-12-21T05:08:29Z [Term] id: XBED:0000013 name: northern blot subset: Article_content_types subset: assay subset: PHENO_assay_types xref: ECO:0005653 is_a: XBED:0000001 ! Gene Expression Assay created_by: Jeff creation_date: 2010-12-21T05:09:23Z [Term] id: XBED:0000014 name: RNA interference subset: Article_content_types subset: manipulation synonym: "cosuppression" EXACT [] synonym: "posttranscriptional silencing" EXACT [] synonym: "quelling" EXACT [] synonym: "RNAi" EXACT [] xref: ECO:0000019 is_a: XBED:0000008 ! loss of function created_by: Jeff creation_date: 2010-12-21T05:12:35Z [Term] id: XBED:0000015 name: microRNA subset: Article_content_types subset: GEO_manipulation_types subset: manipulation xref: ECO:0000019 is_a: XBED:0000086 ! Genetic material injection created_by: Jeff creation_date: 2010-12-21T05:13:37Z [Term] id: XBED:0000016 name: siRNA subset: Article_content_types subset: GEO_manipulation_types subset: manipulation xref: ECO:0000019 is_a: XBED:0000022 ! microinjection is_a: XBED:0000014 ! RNA interference created_by: Jeff creation_date: 2010-12-21T05:14:10Z [Term] id: XBED:0000017 name: loss of function mutation synonym: "LOF mutation" EXACT [] subset: Article_content_types xref: ECO:0000016 is_a: XBED:0000008 ! loss of function created_by: Jeff creation_date: 2010-12-21T05:14:45Z [Term] id: XBED:0000018 name: Reagent xref: ECO:0000241 is_a: XBED:0000000 ! Curatable Data created_by: lab creation_date: 2011-10-14T01:53:13Z [Term] id: XBED:0000019 name: electroporation/transfection subset: Article_content_types subset: GEO_manipulation_types subset: manipulation synonym: "electroporation" EXACT [] synonym: "lipofection" EXACT [] synonym: "transfection" EXACT [] is_a: XBED:0000006 ! Experimental Manipulation created_by: Jeff creation_date: 2010-12-21T05:16:13Z [Term] id: XBED:0000020 name: environmental treatment xref: ECO:0000241 subset: GEO_manipulation_types subset: manipulation is_a: XBED:0000006 ! Experimental Manipulation created_by: lab creation_date: 2011-10-14T02:20:06Z [Term] id: XBED:0000021 name: microdissection subset: manipulation synonym: "microsurgery" EXACT [] synonym: "surgery" EXACT [] xref: ECO:0000240 is_a: XBED:0000006 ! Experimental Manipulation created_by: lab creation_date: 2011-10-14T02:20:27Z [Term] id: XBED:0000022 name: microinjection is_a: XBED:0000006 ! Experimental Manipulation created_by: lab creation_date: 2011-10-14T02:20:43Z [Term] id: XBED:0000023 name: cell culture manipulation synonym: "tissue culture cells (from Xenopus)" EXACT [] xref: ECO:0000182 is_a: XBED:0000006 ! Experimental Manipulation created_by: lab creation_date: 2011-10-14T02:21:02Z [Term] id: XBED:0000024 name: transgenesis subset: GEO_manipulation_types subset: manipulation synonym: "transgenic" RELATED [] synonym: "transgenic line" RELATED [] synonym: "transgenics" EXACT [] xref: ECO:0001131 is_a: XBED:0000006 ! Experimental Manipulation created_by: lab creation_date: 2011-10-14T02:21:49Z [Term] id: XBED:0000025 name: chemical subset: GEO_manipulation_types subset: manipulation synonym: "chemical mutagenesis" RELATED [] synonym: "chemical treatment" EXACT [] xref: ECO:0000241 is_a: XBED:0000020 ! environmental treatment created_by: lab creation_date: 2011-10-14T02:22:23Z [Term] id: XBED:0000026 name: heat shock subset: GEO_manipulation_types subset: manipulation xref: ECO:0000241 is_a: XBED:0000020 ! environmental treatment created_by: lab creation_date: 2011-10-14T02:22:41Z [Term] id: XBED:0000027 name: peptide/protein subset: GEO_manipulation_types subset: manipulation synonym: "growth factor treatment" EXACT [] xref: ECO:0000241 is_a: XBED:0000020 ! environmental treatment created_by: lab creation_date: 2011-10-14T02:22:52Z [Term] id: XBED:0000028 name: UV light subset: GEO_manipulation_types subset: manipulation synonym: "ultraviolet light" EXACT [] synonym: "ultraviolet radiation" EXACT [] synonym: "UV irradiation" EXACT [] xref: ECO:0000241 is_a: XBED:0000104 ! radiation created_by: lab creation_date: 2011-10-14T02:23:10Z [Term] id: XBED:0000029 name: electrophysiology subset: assay subset: PHENO_assay_types xref: ECO:0006006 is_a: XBED:0000025 ! chemical created_by: lab creation_date: 2011-10-14T02:55:04Z [Term] id: XBED:0000030 name: toxicology xref: ECO:0000241 is_a: XBED:0000025 ! chemical created_by: lab creation_date: 2011-10-14T02:55:27Z [Term] id: XBED:0000031 name: tissue ablation subset: GEO_manipulation_types subset: manipulation synonym: "cell ablation" RELATED [] synonym: "partial tissue removal" EXACT [] synonym: "tissue removal" RELATED [] xref: ECO:0000242 is_a: XBED:0000021 ! microdissection created_by: lab creation_date: 2011-10-14T02:55:58Z [Term] id: XBED:0000032 name: explant subset: GEO_manipulation_types subset: manipulation synonym: "explant culture" EXACT [] synonym: "explantation" EXACT [] xref: ECO:0000242 is_a: XBED:0000021 ! microdissection created_by: lab creation_date: 2011-10-14T02:56:15Z [Term] id: XBED:0000033 name: transplant subset: GEO_manipulation_types subset: manipulation synonym: "transplantation" EXACT [] xref: ECO:0000243 is_a: XBED:0000021 ! microdissection created_by: lab creation_date: 2011-10-14T02:56:32Z [Term] id: XBED:0000034 name: DNA injection subset: GEO_manipulation_types subset: manipulation xref: ECO:0000017 ! ectopic expression evidence is_a: XBED:0000086 ! Genetic material injection created_by: lab creation_date: 2011-10-14T02:57:13Z [Term] id: XBED:0000035 name: lineage tracer subset: GEO_manipulation_types subset: manipulation synonym: "fate mapping" RELATED [] is_a: XBED:0000022 ! microinjection created_by: lab creation_date: 2011-10-14T02:57:27Z [Term] id: XBED:0000036 name: morpholino injection subset: GEO_manipulation_types subset: manipulation xref: ECO:0000292 is_a: XBED:0000089 ! antisense oligonucleotide injection created_by: lab creation_date: 2011-10-14T02:57:43Z [Term] id: XBED:0000037 name: protein injection subset: GEO_manipulation_types subset: manipulation is_a: XBED:0000022 ! microinjection created_by: lab creation_date: 2011-10-14T02:58:02Z [Term] id: XBED:0000038 name: stable line synonym: "stable transgenic" RELATED [] synonym: "stable transgenic line" RELATED [] xref: ECO:0001131 is_a: XBED:0000024 ! transgenesis created_by: lab creation_date: 2011-10-14T02:58:46Z [Term] id: XBED:0000039 name: transient synonym: "transient transgenesis" RELATED [] synonym: "transient transgenic" EXACT [] xref: ECO:0001131 is_a: XBED:0000024 ! transgenesis created_by: lab creation_date: 2011-10-14T02:58:57Z [Term] id: XBED:0000040 name: real time PCR subset: assay synonym: "real time RT-PCR" EXACT [] xref: ECO:0000108 is_a: XBED:0000001 ! Gene Expression Assay created_by: lab creation_date: 2011-10-14T02:59:15Z [Term] id: XBED:0000041 name: antibody is_a: XBED:0000018 ! Reagent created_by: lab creation_date: 2011-10-14T02:59:44Z [Term] id: XBED:0000042 name: clone is_a: XBED:0000018 ! Reagent created_by: lab creation_date: 2011-10-14T02:59:55Z [Term] id: XBED:0000043 name: transgene synonym: "transgenic construct" RELATED [] xref: ECO:0001131 is_a: XBED:0000018 ! Reagent created_by: lab creation_date: 2011-10-14T03:00:16Z [Term] id: XBED:0000044 name: ELISA subset: Antibody_methods subset: assay subset: PHENO_assay_types synonym: "enzyme linked immunosorbent assay" EXACT [] xref: ECO:0005581 is_a: XBED:0000046 ! Other Detection Assay created_by: lab creation_date: 2011-10-17T09:08:22Z [Term] id: XBED:0000045 name: flow cytometry subset: Antibody_methods subset: assay subset: PHENO_assay_types synonym: "FACS" NARROW [] synonym: "FC" EXACT [] xref: ECO:0005580 is_a: XBED:0000046 ! Other Detection Assay created_by: lab creation_date: 2011-10-17T09:08:37Z [Term] id: XBED:0000046 name: Other Detection Assay subset: Antibody_methods subset: assay subset: PHENO_assay_types xref: ECO:0000314 is_a: XBED:0000000 ! Curatable Data created_by: lab creation_date: 2011-10-17T09:21:01Z [Term] id: XBED:0000047 name: ChIP subset: Antibody_methods subset: assay synonym: "chromatin immunoprecipitation" RELATED [] synonym: "chromatin IP" EXACT [] xref: ECO:0007706 is_a: XBED:0000054 ! immunoprecipitation created_by: lab creation_date: 2011-10-17T09:21:36Z [Term] id: XBED:0000048 name: EMSA subset: Antibody_methods subset: assay subset: PHENO_assay_types synonym: "electromobility shift assay" RELATED [] xref: ECO:0001807 is_a: XBED:0000046 ! Other Detection Assay created_by: lab creation_date: 2011-10-17T09:23:26Z [Term] id: XBED:0000049 name: No Curatable Data synonym: "NCD" EXACT [] created_by: lab creation_date: 2011-10-17T10:05:49Z [Term] id: XBED:0000050 name: gain of function mutation synonym: "GOF mutation" EXACT [] xref: ECO:0000042 is_a: XBED:0000007 ! gain of function created_by: lab creation_date: 2011-10-17T10:11:26Z [Term] id: XBED:0000051 name: overexpression subset: manipulation xref: ECO:0000120 is_a: XBED:0000007 ! gain of function created_by: lab creation_date: 2011-10-17T10:11:46Z [Term] id: XBED:0000052 name: tissue regeneration synonym: "limb regeneration" RELATED [] synonym: "regenerating tissue" EXACT [] xref: ECO:0000242 is_a: XBED:0000002 ! Phenotype created_by: lab creation_date: 2011-10-17T10:12:13Z [Term] id: XBED:0000053 name: southern blot subset: assay xref: ECO:0000078 is_a: XBED:0000046 ! Other Detection Assay created_by: lab creation_date: 2011-10-18T12:34:23Z [Term] id: XBED:0000054 name: immunoprecipitation subset: assay synonym: "IP" EXACT [] xref: ECO:0005644 is_a: XBED:0000046 ! Other Detection Assay created_by: lab creation_date: 2011-10-27T02:20:28Z [Term] id: XBED:0000055 name: Protein Localization subset: assay xref: ECO:0000045 is_a: XBED:0000000 ! Curatable Data created_by: lab creation_date: 2011-10-27T02:23:12Z [Term] id: XBED:0000056 name: cell extract manipulation subset: assay synonym: "cell extract" EXACT [] xref: ECO:0000183 is_a: XBED:0000006 ! Experimental Manipulation created_by: lab creation_date: 2011-10-27T02:27:52Z [Term] id: XBED:0000057 name: fluorescent protein tag subset: assay xref: ECO:0000045 is_a: XBED:0000055 ! Protein Localization created_by: lab creation_date: 2011-10-28T09:14:03Z [Term] id: XBED:0000058 name: amputation/regeneration subset: GEO_manipulation_types subset: manipulation synonym: "amputation" EXACT [] synonym: "regeneration" EXACT [] xref: ECO:0000242 is_a: XBED:0000031 ! tissue ablation created_by: lab creation_date: 2012-04-30T01:03:27Z [Term] id: XBED:0000059 name: RNA-Seq subset: assay subset: GEO_assay_types subset: PHENO_assay_types xref: ECO:0000295 ! RNA-sequencing evidence is_a: XBED:0000001 ! Gene Expression Assay created_by: lab creation_date: 2012-10-24T01:46:56Z [Term] id: XBED:0000060 name: ChIP-Seq subset: Antibody_methods subset: assay subset: GEO_assay_types subset: PHENO_assay_types synonym: "Chromatin immunoprecipitation sequencing" EXACT [] xref: ECO:0000229 ! chromatin immunoprecipitation-seq evidence is_a: XBED:0000047 ! ChIP created_by: lab creation_date: 2012-10-24T01:47:21Z [Term] id: XBED:0000061 name: cell fractionation subset: assay xref: ECO:0000004 is_a: XBED:0000055 ! Protein Localization created_by: lab creation_date: 2012-10-24T01:48:29Z [Term] id: XBED:0000062 name: cell death detection assay subset: assay subset: PHENO_assay_types synonym: "TUNEL assay" RELATED [] xref: ECO:0001264 is_a: XBED:0000046 ! Other Detection Assay created_by: lab creation_date: 2012-10-24T02:06:06Z [Term] id: XBED:0000063 name: cell proliferation assay subset: assay subset: PHENO_assay_types synonym: "BrDU incorporation" RELATED [] synonym: "thymidine uptake" RELATED [] synonym: "tritiated thymidine assay" RELATED [] xref: ECO:0001807 is_a: XBED:0000046 ! Other Detection Assay created_by: lab creation_date: 2012-10-24T02:21:25Z [Term] id: XBED:0000064 name: cell viability assay is_a: XBED:0000046 ! Other Detection Assay created_by: lab creation_date: 2012-10-24T03:00:05Z [Term] id: XBED:0000065 name: morphology subset: assay subset: PHENO_assay_types synonym: "microscopy" RELATED [] xref: ECO:0007634 is_a: XBED:0000046 ! Other Detection Assay created_by: lab creation_date: 2012-10-25T10:24:16Z [Term] id: XBED:0000066 name: whole-mount microscopy subset: assay subset: PHENO_assay_types synonym: "light microscopy" RELATED [] xref: ECO:0001232 is_a: XBED:0000065 ! morphology created_by: lab creation_date: 2012-10-25T10:24:38Z [Term] id: XBED:0000067 name: scanning electron microscopy subset: assay subset: PHENO_assay_types synonym: "SEM" RELATED [] xref: ECO:0001232 is_a: XBED:0000065 ! morphology created_by: lab creation_date: 2012-10-25T10:25:08Z [Term] id: XBED:0000068 name: transmission electron microscopy subset: assay subset: PHENO_assay_types synonym: "TEM" RELATED [] xref: ECO:0001232 is_a: XBED:0000065 ! morphology created_by: lab creation_date: 2012-10-25T10:25:40Z [Term] id: XBED:0000069 name: histology subset: assay subset: PHENO_assay_types xref: ECO:0001187 is_a: XBED:0000065 ! morphology created_by: lab creation_date: 2012-10-25T10:50:32Z [Term] id: XBED:0000070 name: stained tissue microscopy subset: assay subset: PHENO_assay_types xref: ECO:0001232 is_a: XBED:0000065 ! morphology created_by: lab creation_date: 2012-10-25T10:53:37Z [Term] id: XBED:0000071 name: 3D imaging subset: assay subset: PHENO_assay_types synonym: "3 dimensional reconstruction" RELATED [] synonym: "three-dimensional imaging" RELATED [] xref: ECO:0001232 is_a: XBED:0000065 ! morphology created_by: lab creation_date: 2012-10-26T11:53:56Z [Term] id: XBED:0000072 name: MBD-Seq subset: assay subset: GEO_assay_types synonym: "methyl binding domain sequencing" EXACT [] xref: EFO:0003750 is_a: XBED:0000046 ! Other Detection Assay created_by: Joshua Fortriede creation_date: 2017-08-31T07:09:56Z [Term] id: XBED:0000073 name: Bisulfite-Seq subset: assay subset: GEO_assay_types xref: EFO:0003753 is_a: XBED:0000046 ! Other Detection Assay created_by: Joshua Fortriede creation_date: 2017-08-31T07:09:56Z [Term] id: XBED:0000074 name: MNase-Seq subset: assay subset: GEO_assay_types synonym: "Micrococcal nuclease sequencing" EXACT [] xref: EFO:0003751 xref: ECO:0000219 ! nucleotide sequencing assay evidence is_a: XBED:0000046 ! Other Detection Assay created_by: Joshua Fortriede creation_date: 2017-08-31T07:09:56Z [Term] id: XBED:0000075 name: ncRNA-Seq def: "Non-coding RNA sequencing." [] subset: assay subset: GEO_assay_types synonym: "RNA-Seq of non coding RNA" RELATED [] xref: EFO:0003737 xref: ECO:0000219 ! nucleotide sequencing assay evidence is_a: XBED:0000059 ! RNA-Seq created_by: Joshua Fortriede creation_date: 2017-08-31T07:09:56Z [Term] id: XBED:0000076 name: RIP-Seq def: "RNA immunoprecipitation experiment assayed by sequencing." [] subset: assay subset: GEO_assay_types synonym: "RNA immunoprecipitation sequencing" EXACT [] xref: EFO:0005310 xref: ECO:0000219 ! nucleotide sequencing assay evidence is_a: XBED:0000054 ! immunoprecipitation created_by: Joshua Fortriede creation_date: 2017-08-31T07:09:56Z [Term] id: XBED:0000077 name: miRNA-Seq def: "MicroRNA sequencing." [] subset: assay subset: GEO_assay_types synonym: "micro-RNA sequencing" EXACT [] xref: EFO: is_a: XBED:0000059 ! RNA-Seq created_by: Joshua Fortriede creation_date: 2017-08-31T07:09:56Z [Term] id: XBED:0000078 name: ChIP-chip def: "A chromatin immunoprecipitation experiment assayed by microarray." [] subset: Antibody_methods subset: assay subset: GEO_assay_types synonym: "ChIP on chip" EXACT [] xref: EFO:0000748 is_a: XBED:0000047 ! ChIP created_by: Malcolm Fisher creation_date: 2017-09-20T10:15:22Z [Term] id: XBED:0000079 name: RIP-chip def: "RNA immunoprecipitation experiment assayed by microarray." [] subset: Antibody_methods subset: assay subset: GEO_assay_types synonym: "RNA immunoprecipitation chip" EXACT [] xref: EFO:0005517 xref: ECO:0000219 ! nucleotide sequencing assay evidence is_a: XBED:0000054 ! immunoprecipitation created_by: Malcolm Fisher creation_date: 2017-09-20T10:45:53Z [Term] id: XBED:0000080 name: ATAC-Seq def: "Assay for transposase-accessible chromatin using sequencing (ATAC-Seq), is a method based on direct in vitro transposition of sequencing adaptors into native chromatin, and is a rapid and sensitive method for integrative epigenomic analysis. ATAC-Seq captures open chromatin sites using a simple two-step protocol." [] subset: assay subset: GEO_assay_types synonym: "Assay for transposase-accessible chromatin sequencing" EXACT [] xref: EFO:0007045 xref: ECO:0000219 ! nucleotide sequencing assay evidence is_a: XBED:0000046 ! Other Detection Assay created_by: Malcolm Fisher creation_date: 2017-09-20T10:55:56Z [Term] id: XBED:0000081 name: Bio-CAP-Seq subset: assay subset: GEO_assay_types synonym: "BioCap-seq" EXACT [] synonym: "biotinylated CxxC affinity purification sequencing" EXACT [] is_a: XBED:0000046 ! Other Detection Assay created_by: Malcolm Fisher creation_date: 2017-09-20T15:55:43Z [Term] id: XBED:0000082 name: MeDIP-seq def: "An assay in which DNA is the input molecule derived from an antibody based selection process using antibodies targeting methylated DNA, which is then sequenced using high throughput sequencing technology." [] subset: assay subset: GEO_assay_types synonym: "mDIP-seq" EXACT [] synonym: "methylated DNA immunoprecipitation sequencing" EXACT [] xref: EFO:0003749 is_a: XBED:0000054 ! immunoprecipitation created_by: Malcolm Fisher creation_date: 2017-09-20T16:03:49Z [Term] id: XBED:0000083 name: Hi-C def: "Hi-C is a method for analysing 3-dimensional organisation and interaction of chromatin, belonging to the class of techniques collectively called \"Chromosome Conformation Capture\", in which chromatin is crosslinked, then digested, and re-ligated in such a way that only DNA fragments that are covalently linked together form ligation products. Together with 5C, Hi-C does not limit to the study to a specific locus in the genome, and can be used to study chromatin interaction across the genome. To achieve high-throughput, a biotin-labeled nucleotide is incorporated at the ligation junction, enabling selective purification of chimeric DNA ligation junctions followed by deep sequencing. Mapping the sequenced reads back to genome will reveal the origin of the fragments involved in the ligation events." [] subset: assay subset: GEO_assay_types synonym: "Tethered Chromosome Conformation Capture" RELATED [] xref: EFO:0007693 is_a: XBED:0000046 ! Other Detection Assay created_by: Malcolm Fisher creation_date: 2017-09-20T16:26:01Z [Term] id: XBED:0000084 name: Intracytoplasmic sperm injection def: "Intracytoplasmic sperm injection." [XAO:0003147] subset: GEO_manipulation_types subset: manipulation synonym: "DISCO" EXACT [] synonym: "ICSI" EXACT [] xref: ERO:0000641 "Injection of a single sperm into a single celled embryo or an egg for the purpose of in vitro fertilization." is_a: XBED:0000086 ! Genetic material injection created_by: Malcolm Fisher creation_date: 2017-09-22T09:09:49Z [Term] id: XBED:0000085 name: SCNT def: "Somatic cell nuclear transfer." [] subset: GEO_manipulation_types subset: manipulation synonym: "Somatic cell nuclear transfer." EXACT [] is_a: XBED:0000086 ! Genetic material injection created_by: Malcolm Fisher creation_date: 2017-09-22T10:08:18Z [Term] id: XBED:0000086 name: Genetic material injection is_a: XBED:0000022 ! microinjection created_by: Malcolm Fisher creation_date: 2017-09-22T10:23:25Z [Term] id: XBED:0000087 name: Intracytoplasmic spermatid injection subset: GEO_manipulation_types subset: manipulation is_a: XBED:0000086 ! Genetic material injection created_by: Malcolm Fisher creation_date: 2017-09-22T10:33:22Z [Term] id: XBED:0000088 name: WTTS-Seq def: "Whole Transcriptome Termini Site Sequencing." [] subset: assay subset: GEO_assay_types synonym: "Whole Transcriptome Termini Site Sequencing" EXACT [] is_a: XBED:0000059 ! RNA-Seq xref: ECO:0000295 ! RNA-sequencing evidence created_by: Malcolm Fisher creation_date: 2017-10-03T15:56:57Z [Term] id: XBED:0000089 name: antisense oligonucleotide injection synonym: "ASO" EXACT [] is_a: XBED:0000022 ! microinjection xref: ECO:0000018 ! anti-sense experiment evidence created_by: Malcolm Fisher creation_date: 2017-10-06T09:30:10Z [Term] id: XBED:0000090 name: DMED injection def: "DMED injection." [] subset: GEO_manipulation_types subset: manipulation synonym: "N,N-dimethylethylenediamine (DMED) phosphoramidate-modified antisense oligonucleotide injection." EXACT [] is_a: XBED:0000089 ! antisense oligonucleotide injection xref: ECO:0000018 ! anti-sense experiment evidence created_by: Malcolm Fisher creation_date: 2017-10-06T09:32:30Z [Term] id: XBED:0000091 name: LNA injection subset: GEO_manipulation_types subset: manipulation synonym: "Locked Nucleic Acid antisense oligonucleotide injection." EXACT [] is_a: XBED:0000089 ! antisense oligonucleotide injection xref: ECO:0000018 ! anti-sense experiment evidence created_by: Malcolm Fisher creation_date: 2017-10-06T09:41:12Z [Term] id: XBED:0000092 name: Phosphorothioate injection def: "Phosphorothioate injection." [] subset: GEO_manipulation_types subset: manipulation synonym: "maternal depletion" RELATED [] is_a: XBED:0000089 ! antisense oligonucleotide injection xref: ECO:0000018 ! anti-sense experiment evidence created_by: Malcolm Fisher creation_date: 2017-10-06T09:42:48Z [Term] id: XBED:0000093 name: CRISPR def: "A method of gene targetting transgenesis, both transisent and heritable, using the bacterial CRISPR system with specificity from guide RNA sequences." [] subset: GEO_manipulation_types subset: manipulation synonym: "clustered regularly interspaced short palindromic repeats-associated system." EXACT [] synonym: "CRISPR/Cas9" RELATED [] is_a: XBED:0000022 ! microinjection is_a: XBED:0000038 ! stable line is_a: XBED:0000039 ! transient xref: ECO:0005027 ! genetic transformation evidence created_by: Malcolm Fisher creation_date: 2017-10-06T16:06:45Z [Term] id: XBED:0000094 name: CLIP-Seq def: "CLIP is an antibody-based technique used to study RNA-protein interactions related to RNA immunoprecipitation (RIP), but differs from RIP in the use of UV radiation to cross-link RNA binding proteins to the RNA that they are bound to." [] subset: assay subset: GEO_assay_types synonym: "HITS-CLIP" RELATED [] synonym: "iCLIP" RELATED [] synonym: "PAR-CLIP" RELATED [] synonym: "UV Cross-Linking and Immunoprecipitation " EXACT [] is_a: XBED:0000054 ! immunoprecipitation created_by: Malcolm Fisher creation_date: 2017-10-11T15:34:53Z [Term] id: XBED:0000095 name: Epigenetic def: "A chromatin immunoprecipitation assay targeting epigenetic modifications." [] subset: ChIP_type synonym: "Epigenetic ChIP" EXACT [] is_a: XBED:0000047 ! ChIP created_by: Malcolm Fisher creation_date: 2018-04-04T15:14:38Z [Term] id: XBED:0000096 name: Transcription Factor def: "A chromatin immunoprecipitation assay targeting transcription factors." [] subset: ChIP_type synonym: "TF ChIP" EXACT [] synonym: "Transcription Factor ChIP" EXACT [] is_a: XBED:0000047 ! ChIP created_by: Malcolm Fisher creation_date: 2018-04-04T15:17:53Z [Term] id: XBED:0000097 name: Other def: "Immunoprecipitation assay on otherwise unclassified targets." [] subset: ChIP_type synonym: "Other ChIP" NARROW [] is_a: XBED:0000054 ! immunoprecipitation created_by: Malcolm Fisher creation_date: 2018-04-04T15:20:39Z [Term] id: XBED:0000098 name: antisense DNA injection def: "DNA based antisense oligonucleotide." [] subset: GEO_manipulation_types subset: manipulation is_a: XBED:0000089 ! antisense oligonucleotide injection created_by: Malcolm Fisher creation_date: 2018-04-18T15:09:08Z [Term] id: XBED:0000099 name: control morpholino def: "A morpholino which is intended as an experimental control." [] subset: morpholino_type synonym: "cMO" EXACT [] synonym: "CMO" EXACT [] synonym: "control MO" EXACT [] synonym: "mismatch control" NARROW [] synonym: "random control morpholino" NARROW [] is_a: XBED:0000009 ! morpholino oligo created_by: Malcolm Fisher creation_date: 2018-08-30T14:19:59Z [Term] id: XBED:0000100 name: splice blocking morpholino def: "A morpholino targeting a splice site within an mRNA." [] subset: morpholino_type synonym: "splice blocking MO" EXACT [] is_a: XBED:0000009 ! morpholino oligo created_by: Malcolm Fisher creation_date: 2018-08-30T14:28:40Z [Term] id: XBED:0000101 name: translation blocking morpholino def: "A morpholino targeting the translational start site of an mRNA, blocking translation and protein production." [] subset: morpholino_type synonym: "ATG morpholino" NARROW [] synonym: "translation blocking MO" EXACT [] is_a: XBED:0000009 ! morpholino oligo created_by: Malcolm Fisher creation_date: 2018-08-30T14:31:01Z [Term] id: XBED:0000102 name: uncategorized morpholino def: "A morpholino that has not been characterized." [] subset: morpholino_type synonym: "uncategorized MO" EXACT [] is_a: XBED:0000009 ! morpholino oligo created_by: Malcolm Fisher creation_date: 2018-12-19T15:16:01Z [Term] id: XBED:0000103 name: photo morpholino def: "A morpholino that contains a photosensitive cleavage site." [] subset: morpholino_type synonym: "photo MO" EXACT [] synonym: "Photo-cleavable Morpholino" EXACT [] synonym: "Photo-Morpholino" EXACT [] synonym: "pMO" EXACT [] is_a: XBED:0000009 ! morpholino oligo created_by: Malcolm Fisher creation_date: 2019-01-23T11:05:01Z [Term] id: XBED:0000104 name: radiation def: "The emission of energy as electromagnetic waves or as moving subatomic particles, especially high-energy particles which cause ionization." [] synonym: "ionising radiation" EXACT [] is_a: XBED:0000020 ! environmental treatment created_by: Malcolm Fisher creation_date: 2019-01-23T11:05:01Z [Term] id: XBED:0000105 name: x-rays def: "X-radiation, a form of electromagnetic radiation." [] subset: GEO_manipulation_types subset: manipulation synonym: "gamma radiation" RELATED [] synonym: "X-radiation" EXACT [] synonym: "X-ray" EXACT [] is_a: XBED:0000104 ! radiation created_by: Malcolm Fisher creation_date: 2019-01-23T11:05:01Z [Term] id: XBED:0000106 name: TALEN def: "A method of gene targetting transgenesis, both transisent and heritable, using modified Fokl endonuclease domain recognition domains coupled to bacterial TAL effector system domains for specificity." [] subset: GEO_manipulation_types subset: manipulation synonym: "transcription activator-like effector nucleases" EXACT [] is_a: XBED:0000022 ! microinjection is_a: XBED:0000038 ! stable line is_a: XBED:0000039 ! transient xref: ECO:0005027 ! genetic transformation evidence created_by: Malcolm Fisher creation_date: 2019-02-26T09:59:45Z [Term] id: XBED:0000107 name: Gene Ontology (GO) Annotation def: "Data about protein function suitable for GO curation." [] subset: Article_content_types is_a: XBED:0000000 ! Curatable Data created_by: Malcolm Fisher creation_date: 2019-11-08T15:24:24Z [Term] id: XBED:0000108 name: Human Disease Annotation def: "Data relevant to human diseases are contained within the article." [] subset: Article_content_types is_a: XBED:0000000 ! Curatable Data created_by: Malcolm Fisher creation_date: 2019-11-08T15:26:12Z [Term] id: XBED:0000109 name: Article Permissions def: "Data relevant to the copyright classification of an article for curation." [] subset: Article_content_types is_a: XBED:0000000 ! Curatable Data created_by: Malcolm Fisher creation_date: 2019-12-02T16:50:12Z [Term] id: XBED:0000110 name: Open Access def: "Open Access copyright permissions classification for an article." [] subset: Copyright_access is_a: XBED:0000109 ! Article Permissions created_by: Malcolm Fisher creation_date: 2019-12-02T16:50:12Z [Term] id: XBED:0000111 name: No Access def: "No Access copyright permissions classification for an article." [] subset: Copyright_access is_a: XBED:0000109 ! Article Permissions created_by: Malcolm Fisher creation_date: 2019-12-02T16:50:12Z [Term] id: XBED:0000112 name: Full Access: Request Permission def: "Full Access: Request Permission copyright classification for an article." [] subset: Copyright_access is_a: XBED:0000109 ! Article Permissions created_by: Malcolm Fisher creation_date: 2019-12-02T16:50:12Z [Term] id: XBED:0000113 name: Full Access: Permission Requested def: "Full Access: Permission Requested copyright classification for an article." [] subset: Copyright_access is_a: XBED:0000109 ! Article Permissions created_by: Malcolm Fisher creation_date: 2019-12-02T16:50:12Z [Term] id: XBED:0000114 name: Full Access: Permission Granted def: "Full Access: Permission Granted copyright classification for an article." [] subset: Copyright_access is_a: XBED:0000109 ! Article Permissions created_by: Malcolm Fisher creation_date: 2019-12-02T16:50:12Z [Term] id: XBED:0000115 name: Full Access: Permission Denied def: "Full Access: Permission Denied copyright classification for an article." [] subset: Copyright_access is_a: XBED:0000109 ! Article Permissions created_by: Malcolm Fisher creation_date: 2019-12-02T16:50:12Z [Term] id: XBED:0000116 name: Curatable Temporal Development Data subset: Temperature_degC xref: ECO:0000000 created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000117 name: Development Environment Temperature subset: Temperature_degC is_a: XBED:0000116 ! Curatable Temporal Development Data created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000118 name: unknown degC subset: Temperature_degC synonym: "na degC" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000119 name: Four degC subset: Temperature_degC synonym: "4 degC" EXACT ABBREVIATION [] synonym: "39.2 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000120 name: Five degC subset: Temperature_degC synonym: "5 degC" EXACT ABBREVIATION [] synonym: "41 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000121 name: Six degC subset: Temperature_degC synonym: "6 degC" EXACT ABBREVIATION [] synonym: "42.8 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000122 name: Seven degC subset: Temperature_degC synonym: "7 degC" EXACT ABBREVIATION [] synonym: "44.6 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000123 name: Eight degC subset: Temperature_degC synonym: "8 degC" EXACT ABBREVIATION [] synonym: "46.4 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000124 name: Nine degC subset: Temperature_degC synonym: "9 degC" EXACT ABBREVIATION [] synonym: "48.2 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000125 name: Ten degC subset: Temperature_degC synonym: "10 degC" EXACT ABBREVIATION [] synonym: "50 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000126 name: Eleven degC subset: Temperature_degC synonym: "11 degC" EXACT ABBREVIATION [] synonym: "51.8 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000127 name: Twelve degC subset: Temperature_degC synonym: "12 degC" EXACT ABBREVIATION [] synonym: "53.6 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000128 name: Thirteen degC subset: Temperature_degC synonym: "13 degC" EXACT ABBREVIATION [] synonym: "55.4 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000129 name: Fourteen degC subset: Temperature_degC synonym: "14 degC" EXACT ABBREVIATION [] synonym: "57.2 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000130 name: Fifteen degC subset: Temperature_degC synonym: "15 degC" EXACT ABBREVIATION [] synonym: "59 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000131 name: Sixteen degC subset: Temperature_degC synonym: "16 degC" EXACT ABBREVIATION [] synonym: "60.8 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000132 name: Seventeen degC subset: Temperature_degC synonym: "17 degC" EXACT ABBREVIATION [] synonym: "62.6 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000133 name: Eighteen degC subset: Temperature_degC synonym: "18 degC" EXACT ABBREVIATION [] synonym: "64.4 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000134 name: Nineteen degC subset: Temperature_degC synonym: "19 degC" EXACT ABBREVIATION [] synonym: "66.2 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000135 name: Twenty degC subset: Temperature_degC synonym: "20 degC" EXACT ABBREVIATION [] synonym: "68 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000136 name: TwentyOne degC subset: Temperature_degC synonym: "21 degC" EXACT ABBREVIATION [] synonym: "69.8 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000137 name: TwentyTwo degC subset: Temperature_degC synonym: "22 degC" EXACT ABBREVIATION [] synonym: "71.6 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000138 name: TwentyThree degC subset: Temperature_degC synonym: "23 degC" EXACT ABBREVIATION [] synonym: "73.4 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000139 name: TwentyFour degC subset: Temperature_degC synonym: "24 degC" EXACT ABBREVIATION [] synonym: "75.2 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000140 name: TwentyFive degC subset: Temperature_degC synonym: "25 degC" EXACT ABBREVIATION [] synonym: "77 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000141 name: TwentySix degC subset: Temperature_degC synonym: "26 degC" EXACT ABBREVIATION [] synonym: "78.8 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000142 name: TwentySeven degC subset: Temperature_degC synonym: "27 degC" EXACT ABBREVIATION [] synonym: "80.6 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000143 name: TwentyEight degC subset: Temperature_degC synonym: "28 degC" EXACT ABBREVIATION [] synonym: "82.4 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000144 name: TwentyNine degC subset: Temperature_degC synonym: "29 degC" EXACT ABBREVIATION [] synonym: "84.2 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000145 name: Thirty degC subset: Temperature_degC synonym: "30 degC" EXACT ABBREVIATION [] synonym: "86 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000146 name: ThirtyOne degC subset: Temperature_degC synonym: "31 degC" EXACT ABBREVIATION [] synonym: "87.8 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000147 name: ThirtyTwo degC subset: Temperature_degC synonym: "32 degC" EXACT ABBREVIATION [] synonym: "89.6 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000148 name: ThirtyThree degC subset: Temperature_degC synonym: "33 degC" EXACT ABBREVIATION [] synonym: "91.4 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000149 name: ThirtyFour degC subset: Temperature_degC synonym: "34 degC" EXACT ABBREVIATION [] synonym: "95 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000150 name: ThirtyFive degC subset: Temperature_degC synonym: "35 degC" EXACT ABBREVIATION [] synonym: "95 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000151 name: ThirtySix degC subset: Temperature_degC synonym: "36 degC" EXACT ABBREVIATION [] synonym: "96.8 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000152 name: ThirtySeven degC subset: Temperature_degC synonym: "37 degC" EXACT ABBREVIATION [] synonym: "98.6 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000153 name: ThirtyEight degC subset: Temperature_degC synonym: "38 degC" EXACT ABBREVIATION [] synonym: "100.4 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000154 name: ThirtyNine degC subset: Temperature_degC synonym: "39 degC" EXACT ABBREVIATION [] synonym: "102.2 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000155 name: Fourty degC subset: Temperature_degC synonym: "40 degC" EXACT ABBREVIATION [] synonym: "104 degF" EXACT ABBREVIATION [] is_a: XBED:0000117 ! Development Environment Temperature created_by: Malcolm Fisher creation_date: 2020-06-18T20:3:26Z [Term] id: XBED:0000156 name: DNase-Seq subset: assay subset: GEO_assay_types synonym: "DNA nuclease sequencing" EXACT [] synonym: "DNase I hypersensitive sites sequencing" EXACT [] synonym: "DNaseI-Seq" EXACT [] synonym: "DNase-hypersensitivity seq" EXACT [] xref: EFO:0003752 is_a: XBED:0000046 ! Other Detection Assay created_by: Malcolm Fisher creation_date: 2020-07-27T14:57:56Z [Term] id: XBED:0000157 name: predation subset: GEO_manipulation_types subset: manipulation synonym: "chronic predation" RELATED [] synonym: "acute predation" RELATED [] xref: ECOCORE:00000102 is_a: XBED:0000020 ! environmental treatment created_by: Malcolm Fisher creation_date: 2020-08-13T10:26:52Z [Term] id: XBED:0000158 name: Open Access: Any CC license subset: XED_copyright_pmc_subset is_a: XBED:0000110 ! Open Access created_by: Malcolm Fisher creation_date: 20202-10-08T10:53:23Z [Term] id: XBED:0000159 name: Open Access: CC BY (Attribution) def: "Creative Commons Attribution license" [CC BY] subset: XED_copyright_pmc_subset synonym: "CC BY" EXACT [] is_a: XBED:0000158 ! Open Access: Any CC license created_by: Malcolm Fisher creation_date: 2020-10-08T10:53:23Z [Term] id: XBED:0000160 name: Open Access: CC BY-ND (Attribution, no derivatives) def: "Creative Commons Attribution-NoDerivatives license" [CC BY-ND] subset: XED_copyright_pmc_subset synonym: "CC BY-ND" EXACT [] synonym: "CC BY ND" EXACT [] is_a: XBED:0000158 ! Open Access: Any CC license created_by: Malcolm Fisher creation_date: 2020-10-08T10:53:23Z [Term] id: XBED:0000161 name: Open Access: CC BY-NC (Attribution, noncommercial) def: "Creative Commons Attribution-NonCommercial license" [CC BY-NC] subset: XED_copyright_pmc_subset synonym: "CC BY-NC" EXACT [] synonym: "CC BY NC" EXACT [] is_a: XBED:0000158 ! Open Access: Any CC license created_by: Malcolm Fisher creation_date: 2020-10-08T10:53:23Z [Term] id: XBED:0000162 name: Open Access: CC BY-NC-ND (Attribution, noncommercial, no derivatives) def: "Creative Commons Attribution-NonCommercial-NoDerivatives license" [CC BY-NC-ND] subset: XED_copyright_pmc_subset synonym: "CC BY-NC-ND" EXACT [] synonym: "CC BY NC ND" EXACT [] is_a: XBED:0000158 ! Open Access: Any CC license created_by: Malcolm Fisher creation_date: 2020-10-08T10:53:23Z [Term] id: XBED:0000163 name: Open Access: CC BY-NC-SA (Attribution, noncommercial, share-alike) def: "Creative Commons Attribution-NonCommercial-ShareAlike license" [CC BY-NC-SA] subset: XED_copyright_pmc_subset synonym: "CC BY-NC-SA" EXACT [] synonym: "CC BY NC SA" EXACT [] is_a: XBED:0000158 ! Open Access: Any CC license created_by: Malcolm Fisher creation_date: 2020-10-08T10:53:23Z [Term] id: XBED:0000164 name: Open Access: CC BY-SA (Attribution, share-alike) def: "Creative Commons Attribution-ShareAlike license" [CC BY-SA] subset: XED_copyright_pmc_subset synonym: "CC BY-SA" EXACT [] synonym: "CC BY SA" EXACT [] is_a: XBED:0000158 ! Open Access: Any CC license created_by: Malcolm Fisher creation_date: 2020-10-08T10:53:23Z [Term] id: XBED:0000165 name: Open Access: CC0 (Public domain) def: "No Rights Reserved" [CC0] subset: XED_copyright_pmc_subset synonym: "CC0" EXACT [] is_a: XBED:0000158 ! Open Access: Any CC license created_by: Malcolm Fisher creation_date: 2020-10-08T10:53:23Z [Term] id: XBED:0000167 name: cDNA clone-based transcript expression assay def: "A method which assesses transcript expression by reverse transcription of purified mRNA into the corresponding complementary DNA (cDNA) before insertion into a vector, allowing synthesis of a large number of copies of the sequence for analysis." [Mosby:Mosbys_Medical_Dictionary--8th_Ed, Segen:Segens_Medical_Dictionary_2012] synonym: "cDNA" RELATED [] xref: MMO:0000645 xref: OBI:0600064 is_a: XBED:0000001 ! Gene Expression Assay created_by: Malcolm Fisher creation_date: 2021-02-08T22:55:23Z [Term] id: XBED:0000168 name: PAM def: "A sequence of 3-6 nucleotides, typically of the form NGG, immediately adjacent to a guide RNA target site. This site is required for cleavage to occur in the CRISPR gene editing system." [] synonym: "protospacer adjacent motif" EXACT [] is_a: XBED:0000000 ! Curatable Data created_by: Malcolm Fisher creation_date: 2021-03-16T10:38:51Z [Term] id: XBED:0000169 name: predictionMethodsMatched subset: XED_Orthology_prediction_finding is_a: XBED:0000174 ! Orthology status created_by: Malcolm Fisher creation_date: 2021-04-01T10:38:51Z [Term] id: XBED:0000170 name: predictionMethodsNotMatched subset: XED_Orthology_prediction_finding is_a: XBED:0000174 ! Orthology status created_by: Malcolm Fisher creation_date: 2021-04-01T10:38:51Z [Term] id: XBED:0000171 name: predictionMethodsNotCalled subset: XED_Orthology_prediction_finding is_a: XBED:0000174 ! Orthology status created_by: Malcolm Fisher creation_date: 2021-04-01T10:38:51Z [Term] id: XBED:0000172 name: Orthology Source is_a: XBED:0000000 ! Curatable Data created_by: Malcolm Fisher creation_date: 2021-04-01T10:38:51Z [Term] id: XBED:0000173 name: Ensembl Compara subset: XED_Orthology_prediction_method is_a: XBED:0000172 ! Orthology Source created_by: Malcolm Fisher creation_date: 2021-04-01T10:38:51Z [Term] id: XBED:0000174 name: Orthology status is_a: XBED:0000000 ! Curatable Data created_by: Malcolm Fisher creation_date: 2021-04-01T10:38:51Z [Term] id: XBED:0000175 name: HGNC subset: XED_Orthology_prediction_method is_a: XBED:0000172 ! Orthology Source created_by: Malcolm Fisher creation_date: 2021-04-01T10:38:51Z [Term] id: XBED:0000176 name: Hieranoid subset: XED_Orthology_prediction_method is_a: XBED:0000172 ! Orthology Source created_by: Malcolm Fisher creation_date: 2021-04-01T10:38:51Z [Term] id: XBED:0000177 name: InParanoid subset: XED_Orthology_prediction_method is_a: XBED:0000172 ! Orthology Source created_by: Malcolm Fisher creation_date: 2021-04-01T10:38:51Z [Term] id: XBED:0000178 name: OMA subset: XED_Orthology_prediction_method synonym: "Orthologous MAtrix" EXACT [] is_a: XBED:0000172 ! Orthology Source created_by: Malcolm Fisher creation_date: 2021-04-01T10:38:51Z [Term] id: XBED:0000179 name: OrthoFinder subset: XED_Orthology_prediction_method is_a: XBED:0000172 ! Orthology Source created_by: Malcolm Fisher creation_date: 2021-04-01T10:38:51Z [Term] id: XBED:0000180 name: OrthoInspector subset: XED_Orthology_prediction_method is_a: XBED:0000172 ! Orthology Source created_by: Malcolm Fisher creation_date: 2021-04-01T10:38:51Z [Term] id: XBED:0000181 name: PANTHER subset: XED_Orthology_prediction_method is_a: XBED:0000172 ! Orthology Source created_by: Malcolm Fisher creation_date: 2021-04-01T10:38:51Z [Term] id: XBED:0000182 name: PhylomeDB subset: XED_Orthology_prediction_method is_a: XBED:0000172 ! Orthology Source created_by: Malcolm Fisher creation_date: 2021-04-01T10:38:51Z [Term] id: XBED:0000184 name: Roundup subset: XED_Orthology_prediction_method is_a: XBED:0000172 ! Orthology Source created_by: Malcolm Fisher creation_date: 2021-04-01T10:38:51Z [Term] id: XBED:0000185 name: TreeFam subset: XED_Orthology_prediction_method is_a: XBED:0000172 ! Orthology Source created_by: Malcolm Fisher creation_date: 2021-04-01T10:38:51Z [Term] id: XBED:0000186 name: ZFIN subset: XED_Orthology_prediction_method is_a: XBED:0000172 ! Orthology Source created_by: Malcolm Fisher creation_date: 2021-04-01T10:38:51Z [Term] id: XBED:0000187 name: fastortho subset: XED_Orthology_prediction_method is_a: XBED:0000172 ! Orthology Source created_by: Malcolm Fisher creation_date: 2021-05-27T10:38:51Z [Term] id: XBED:0000188 name: proteinortho subset: XED_Orthology_prediction_method is_a: XBED:0000172 ! Orthology Source created_by: Malcolm Fisher creation_date: 2021-05-28T12:23:51Z [Term] id: XBED:0000189 name: swiftortho subset: XED_Orthology_prediction_method is_a: XBED:0000172 ! Orthology Source created_by: Malcolm Fisher creation_date: 2021-05-28T12:23:51Z [Term] id: XBED:0000191 name: genotype def: "A genotype is a variant genome, complete or incomplete." [] xref: SO:0001027 is_a: XBED:0000000 ! Curatable Data created_by: Malcolm Fisher creation_date: 2021-08-31T17:38:51Z [Term] id: XBED:0000192 name: mutant gene def: "A variation in the nucleic acid sequence of a specific gene." [] xref: UMLS:C0678941 is_a: XBED:0000191 ! genotype created_by: Malcolm Fisher creation_date: 2021-08-31T17:38:51Z [Term] id: XBED:0000193 name: vivo morpholino def: "A morpholino with a delivery moiety promoting uptake through the cell membrane." [] subset: morpholino_type synonym: "vivo MO" EXACT [] synonym: "vivo-morpholino" EXACT [] is_a: XBED:0000009 ! morpholino oligo created_by: Malcolm Fisher creation_date: 2021-11-19T19:55:51Z [Term] id: XBED:0000194 name: histochemistry subset: assay synonym: "HC" EXACT ABBREVIATION [] xref: ECO:0001050 xref: MMO:0000497 is_a: XBED:0000069 ! histology created_by: Malcolm Fisher creation_date: 2022-03-25T11:22:20Z [Term] id: XBED:0000195 name: in corpus assessment is_a: XBED:0000000 ! Curatable Data created_by: Malcolm Fisher creation_date: 2022-09-01T16:36:40Z [Term] id: XBED:0000196 name: in corpus subset: Corpus is_a: XBED:0000195 ! in corpus assessment created_by: Malcolm Fisher creation_date: 2022-09-01T16:36:40Z [Term] id: XBED:0000197 name: outside corpus subset: Corpus is_a: XBED:0000195 ! in corpus assessment created_by: Malcolm Fisher creation_date: 2022-09-01T16:36:40Z