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Merge pull request #83 from anngvu/feature-granular-viability-assays
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Updates for issues #81 #82 #83
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@allaway
allaway authored Nov 3, 2021
2 parents 71c2bf6 + 4ad6bad commit 570d792
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12 changes: 9 additions & 3 deletions NF.csv
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Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,10 @@ westernBlot,A multistep process in which a mixture of proteins is separated by g
wholeGenomeSeq,Laboratory technique to sequence the complete DNA sequence of an organism's genome at a single time,,,FALSE,http://edamontology.org/topic_3673,assay,,,
polymeraseChainReaction,"A rapid technique for in vitro amplification of specific DNA or RNA sequences, allowing small quantities of short sequences to be analyzed without cloning",,,FALSE,http://purl.obolibrary.org/obo/MMO_0000459,assay,,,
cellViabilityAssay,This assay type measures the cellular state of living or dying by measuring an indicator of life or death,,,FALSE,http://www.bioassayontology.org/bao#BAO_0003009,assay,,,
2D Incucyte,,,,FALSE,,assay,,,
2D CellTiter-Glo,,,,FALSE,https://www.promega.com/products/cell-health-assays/cell-viability-and-cytotoxicity-assays/celltiter_glo-2_0-assay/?catNum=G9241,assay,,,
3D microtissue viability,,,,FALSE,https://www.ncbi.nlm.nih.gov/books/NBK343426/,assay,,,
in vivo PDX viability,Assay to assess viability using PDX model.,,,FALSE,,assay,,,
atomicForceMicroscopy,Microscopy which uses a sharp spike (known as a 'tip') mounted on the end of a cantilever to scan the surface of the specimen,,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000113,assay,,,
brightfieldMicroscopy,Microscopy where the specimen is illuminated with light transmitted from a source on the opposite side of the specimen from the objective,,,FALSE,http://purl.obolibrary.org/obo/CHMO_0000104,assay,,,
tractionForceMicroscopy,An experimental method for determining the tractions on the surface of a biological cell by obtaining measurements of the surrounding displacement field within an in vitro extracellular matrix (ECM),,,FALSE,https://en.wikipedia.org/wiki/Traction_force_microscopy,assay,,,
Expand Down Expand Up @@ -175,7 +179,7 @@ singleMolecule,An experiment in which a single molecule was used in an assay,,,F
smallMoleculeLibraryScreen,"High throughput sample analysis of small molecules for purpose such as drug discovery, or biochemical, genetic or pharmacological tests.",,,FALSE,http://purl.obolibrary.org/obo/ERO_0001726,drugScreenType,,,
combinationLibraryScreen,High throughput sample analysis of collections of compounds that provide a variety of chemically diverse structures that can be used to identify structure types that have affinity with pharmacological targets.,,,FALSE,http://purl.obolibrary.org/obo/ERO_0001686,drugScreenType,,,
combinationScreen,,,,FALSE,,drugScreenType,,,
assay,The technology used to generate the data in this file,"elevated plus maze test, open field test, rotarod performance test, mRNAcounts, high content screen, Immunocytochemistry, immunofluorescence, autoradiography, electrochemiluminescence, Real Time PCR, in vivo tumor growth, scale, Blood Chemistry Measurement, in vivo bioluminescence, immunohistochemistry, NOMe-Seq, FIA-MSMS, UPLC-MSMS, HPLC-MSMS, liquid chromatography-electrochemical detection, rnaSeq, mirnaSeq, LC-MSMS, LC-MS, lncrnaSeq, Whole Exome Sequencing, Sanger sequencing, ChIPSeq, rnaArray, snpArray, methylationArray, mirnaArray, bisulfiteSeq, ATACSeq, HI-C, errBisulfiteSeq, ISOSeq, westernBlot, wholeGenomeSeq, polymeraseChainReaction, cellViabilityAssay, atomicForceMicroscopy, brightfieldMicroscopy, tractionForceMicroscopy, nextGenerationTargetedSequencing, jumpingLibrary, MIB/MS, scCGIseq, MudPIT, questionnaire, DNA optical mapping, oxBS-Seq, Ribo-Seq, Positron Emission Tomography, RPPA, ELISA, LTP, LFP, whole-cell patch clamp, sandwich ELISA, Laser Speckle Imaging, Genotyping, TMT quantitation, label free mass spectrometry, cell count, reporter gene assay, Single Cell RNA Sequencing, Conventional MRI, Functional MRI, Magnetic Resonance Spectroscopy",,TRUE,,experimentalData,,,
assay,The technology used to generate the data in this file,"elevated plus maze test, open field test, rotarod performance test, mRNAcounts, high content screen, Immunocytochemistry, immunofluorescence, autoradiography, electrochemiluminescence, Real Time PCR, in vivo tumor growth, scale, Blood Chemistry Measurement, in vivo bioluminescence, immunohistochemistry, NOMe-Seq, FIA-MSMS, UPLC-MSMS, HPLC-MSMS, liquid chromatography-electrochemical detection, rnaSeq, mirnaSeq, LC-MSMS, LC-MS, lncrnaSeq, Whole Exome Sequencing, Sanger sequencing, ChIPSeq, rnaArray, snpArray, methylationArray, mirnaArray, bisulfiteSeq, ATACSeq, HI-C, errBisulfiteSeq, ISOSeq, westernBlot, wholeGenomeSeq, polymeraseChainReaction, cellViabilityAssay, atomicForceMicroscopy, brightfieldMicroscopy, tractionForceMicroscopy, nextGenerationTargetedSequencing, jumpingLibrary, MIB/MS, scCGIseq, MudPIT, questionnaire, DNA optical mapping, oxBS-Seq, Ribo-Seq, Positron Emission Tomography, RPPA, ELISA, LTP, LFP, whole-cell patch clamp, sandwich ELISA, Laser Speckle Imaging, Genotyping, TMT quantitation, label free mass spectrometry, cell count, reporter gene assay, Single Cell RNA Sequencing, Conventional MRI, Functional MRI, Magnetic Resonance Spectroscopy, 2D Incucyte, 2D CellTiter-Glo, 3D microtissue viability, in vivo PDX viability",,TRUE,,experimentalData,,,
dataSubtype,"Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","normalized, dataMatrix, raw, processed, metadata, representative",,TRUE,,experimentalData,,,
metadataType,"For files of dataSubtype: metadata, a description of the type of metadata in the file.","individual, biospecimen, assay, data dictionary, manifest, protocol",,FALSE,,experimentalData,,,
bodyPart,"Sample location referring to a named area of the body, inclusive of gross anatomical structures and organ parts. ","head, neck, scalp, leg, pelvis, mesentery, axilla, acetabulum, forearm, muscle, finger, thoracic spine, groin, back, iliac spine, spine, shoulder, scapula, lymph node, kidney, skin, mammary gland, nerves, brain, blood, breast, colon, lung, liver, prostate, pancreas, ovary, spleen, bone marrow, Bursa Of Fabricius, nose",,FALSE,,experimentalData,,,
Expand Down Expand Up @@ -409,10 +413,12 @@ Unknown,unknown,,,FALSE,Sage Bionetworks,nf2Genotype,,,
runType,Is the sequencing run single or paired end?,"singleEnd, pairedEnd",,FALSE,Sage Bionetworks,ngs,,,
readPair,The read of origin,"1, 2",,FALSE,,ngs,,,
isStranded,Whether or not the library is stranded. (Note: TRUE = Yes; FALSE = No),"TRUE, FALSE",,FALSE,,ngs,,,
readPairOrientation,The relative orientation of the reads in a paired-end protocol,"inward, outward, matching",,FALSE,,ngs,,,
fr-firststrand,,,,FALSE,,,,,
readPairOrientation,The relative orientation of the reads in a paired-end protocol,"inward, outward, matching, fr-firststrand",,FALSE,,ngs,,,
readStrandOrigin,The strand from which the read originates in a strand-specific protocol,"forward, reverse",,FALSE,,ngs,,,
libraryPrep,The general strategy by which the library was prepared,"rRNAdepletion, polyAselection, lncRNAenrichment, miRNAenrichment",,FALSE,,ngs,,,
libraryPreparationMethod,Method by which library was prepared,"10x, CEL-seq, Drop-Seq, Smart-seq2, TruSeq, Smart-seq4, Omni-ATAC, NEBNext mRNA Library Prep Reagent Set for Illumina, IDT xGen Exome Research Panel",,FALSE,,ngs,,,
libraryPreparationMethod,Method by which library was prepared,"10x, CEL-seq, Drop-Seq, Smart-seq2, TruSeq, Smart-seq4, Omni-ATAC, NEBNext mRNA Library Prep Reagent Set for Illumina, IDT xGen Exome Research Panel, TruSeq standard total RNA library kit",,FALSE,,ngs,,,
TruSeq standard total RNA library kit,,,,FALSE,https://www.illumina.com/products/by-type/sequencing-kits/library-prep-kits/truseq-stranded-total-rna.html,,,,
nucleicAcidSource,Source of the extracted nucleic acid used in the experiment,"bulk cell, single cell, bulk nuclei, single nucleus, mitochondria",,FALSE,Sage Bionetworks,ngs,,,
dissociationMethod,Procedure by which a biological specimen is dissociated into individual cells or a cell suspension,"10x_v2, FACS, Fluidigm C1, drop-seq, inDrop, mouth pipette, bulk, enzymatic, mechanical, none",,FALSE,https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0009088,ngs,,,
readLength,,,,FALSE,,ngs,,,
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120 changes: 120 additions & 0 deletions NF.jsonld
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Original file line number Diff line number Diff line change
Expand Up @@ -2745,6 +2745,74 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:2DIncucyte",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "2DIncucyte",
"rdfs:subClassOf": [
{
"@id": "bts:Assay"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "2D Incucyte",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:2DCellTiter-Glo",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "2DCellTiter-Glo",
"rdfs:subClassOf": [
{
"@id": "bts:Assay"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "2D CellTiter-Glo",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:3Dmicrotissueviability",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "3Dmicrotissueviability",
"rdfs:subClassOf": [
{
"@id": "bts:Assay"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "3D microtissue viability",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:InvivoPDXviability",
"@type": "rdfs:Class",
"rdfs:comment": "Assay to assess viability using PDX model.",
"rdfs:label": "InvivoPDXviability",
"rdfs:subClassOf": [
{
"@id": "bts:Assay"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "in vivo PDX viability",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:AtomicForceMicroscopy",
"@type": "rdfs:Class",
Expand Down Expand Up @@ -5509,6 +5577,18 @@
},
{
"@id": "bts:MagneticResonanceSpectroscopy"
},
{
"@id": "bts:2DIncucyte"
},
{
"@id": "bts:2DCellTiter-Glo"
},
{
"@id": "bts:3Dmicrotissueviability"
},
{
"@id": "bts:InvivoPDXviability"
}
],
"sms:displayName": "assay",
Expand Down Expand Up @@ -11090,6 +11170,23 @@
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:Fr-firststrand",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "Fr-firststrand",
"rdfs:subClassOf": [
{
"@id": "schema:Thing"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "fr-firststrand",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:ReadPairOrientation",
"@type": "rdfs:Class",
Expand All @@ -11112,6 +11209,9 @@
},
{
"@id": "bts:Matching"
},
{
"@id": "bts:Fr-firststrand"
}
],
"sms:displayName": "readPairOrientation",
Expand Down Expand Up @@ -11214,12 +11314,32 @@
},
{
"@id": "bts:IDTxGenExomeResearchPanel"
},
{
"@id": "bts:TruSeqstandardtotalRNAlibrarykit"
}
],
"sms:displayName": "libraryPreparationMethod",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:TruSeqstandardtotalRNAlibrarykit",
"@type": "rdfs:Class",
"rdfs:comment": "TBD",
"rdfs:label": "TruSeqstandardtotalRNAlibrarykit",
"rdfs:subClassOf": [
{
"@id": "schema:Thing"
}
],
"schema:isPartOf": {
"@id": "http://schema.biothings.io"
},
"sms:displayName": "TruSeq standard total RNA library kit",
"sms:required": "sms:false",
"sms:validationRules": []
},
{
"@id": "bts:NucleicAcidSource",
"@type": "rdfs:Class",
Expand Down

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