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Patch/assays (#267)
* Reorg and start new mappings * Tidy assay labels per #236 * Add new assay per #260 * Add assays per #258 and #259 * Add new assay terms for #261 #262 #263, allow generic mass spec term * Update portal assay cleanup mappings * Add assay referenced in #264 * Add behavioral assays per #265 * Update assay valid values * Update mapping title and description * Update superdataset registered schema * Lint YAML file * Clean description in mapping file * Update mapping README and mapping file name-version * Close issue #266 * Build jsonld * Apply batch of de-acronym suggestions Co-authored-by: Robert Allaway <[email protected]> * Build jsonld * Apply suggestions from code review Co-authored-by: Robert Allaway <[email protected]> * Fix missing quotes and correct internal class IDS * Tweak label to be more consistent and update descriptions * De-acronym LFP * De-acronym LTP * Update assay valid values * Make mapping consistent with one correction * Update registered schema again * Build jsonld --------- Co-authored-by: nf-osi[bot] <[email protected]> Co-authored-by: Robert Allaway <[email protected]>
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‎NF.csv‎

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‎NF.jsonld‎

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‎ext_classes.csv‎

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Attribute,.ID,.Type,.Root,.SubOf
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Physiology_Assay,Physiology_Assay,Class,Assay,
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Experimental_Assay,Assay,Class,Assay,
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DNA_Assay,DNA_Assay,Class,Assay,Assay
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RNA_Assay,RNA_Assay,Class,Assay,Assay
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Imaging_Assay,Imaging_Assay,Class,Assay,Assay
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Volume_Measurement_Assay,Volume_Measurement_Assay,Class,Assay,Assay
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Drug_Screen,Drug_Screen,Class,Assay,Assay
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Electrophysiology_Assay,Electrophysiology_Assay,Class,Assay,Assay
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Electrophysiology_Assay,Electrophysiology_Assay,Class,Assay,Physiology_Assay
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MRI_Assay,MRI_Assay,Class,Assay,Imaging_Assay
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Viral_Assay,MRI_Assay,Class,Assay,Assay
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Assay_Template,Assay_Template,Class,Template,Manifest_Template
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Non_Assay_Template,Non_Assay_Template,Class,Template,Template
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Manifest_Template,Manifest_Template,Class,Template,Template

‎mappings/NFDataPortal/assay_v75.yaml‎

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title: Mapping of NF data portal assay concept labels to assay labels in NF data model v6.4
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description: This translates NF data portal assay labels in use around March 2023 (Portal - Files table version 75) to new preferred labels in NF data model v6.4. (Only assay labels being translated are included.)
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source_scope: https://www.synapse.org/#!Synapse:syn16858331.75/tables/
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target_scope: hhttps://github.com/nf-osi/nf-metadata-dictionary/releases/tag/v6.4
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mapping:
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- source: Whole Exome Sequencing
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target:
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label: whole exome sequencing
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- source: rnaSeq
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target:
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label: RNA-seq
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- source: wholeGenomeSeq
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target:
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label: whole genome sequencing
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- source: Conventional MRI
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target:
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label: conventional MRI
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- source: cellViabilityAssay
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target:
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label: cell viability assay
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- source: westernBlot
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target:
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label: western blot
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- source: brightfieldMicroscopy
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target:
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label: brightfield microscopy
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- source: High Frequency Ultrasound
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target:
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label: high frequency ultrasound
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- source: methylationArray
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target:
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label: methylation array
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- source: nextGenerationTargetedSequencing
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target:
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label: next generation targeted sequencing
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- source: confocalMicroscopy
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target:
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label: confocal microscopy
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- source: 3D Imaging
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target:
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label: 3D imaging
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- source: Positron Emission Tomography
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target:
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label: positron emission tomography
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- source: Immunocytochemistry
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target:
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label: immunocytochemistry
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- source: bisulfiteSeq
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target:
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label: bisulfite sequencing
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- source: snpArray
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target:
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label: SNP array
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- source: single-cell RNAseq
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target:
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label: single-cell RNA-seq
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- source: Single Cell RNA Sequencing
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target:
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label: single-cell RNA-seq
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- source: rnaArray
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target:
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label: RNA array
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- source: Blood Chemistry Measurement
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target:
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label: blood chemistry measurement
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- source: Mass spectrometry
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target:
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label: mass spectrometry
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- source: ATACSeq
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target:
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label: ATAC-seq
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- source: Real Time PCR
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target:
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label: real-time PCR
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- source: jumpingLibrary
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target:
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label: jumping library
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- source: ChIPSeq
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target:
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label: ChIP-seq
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- source: T cell receptor sequencing
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target:
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label: T cell receptor repertoire sequencing
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- source: Microscopy
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target:
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label: microscopy
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- source: SDH enzymatic activity
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target:
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label: sorbitol dehydrogenase activity level assay
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- source: exomeSeq-private
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target:
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label: whole exome sequencing
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- source: polymeraseChainReaction
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target:
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label: polymerase chain reaction
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- source: Focus forming assay
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target:
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label: focus forming assay
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- source: FACS
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target:
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label: flow cytometry
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- source: Flow Cytometry
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target:
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label: flow cytometry
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- source: Immunoassay
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target:
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label: immunoassay
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- source: Cell proliferation
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target:
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label: cell proliferation assay
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- source: Phase-Contrast Microscopy
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target:
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label: phase-contrast microscopy
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- source: atomicForceMicroscopy
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target:
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label: atomic force microscopy
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- source: Cell viability assay
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target:
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label: cell viability assay
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- source: cell counts
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target:
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label: cell count
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- source: drugScreen
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target:
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label: drug screen
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- source: Gel chromatography
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target:
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label: gel filtration chromatography
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- source: novelty response behavior, in vivo bioluminescence
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target:
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label: novelty response behavior assay
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- source: TRAP1 and Hsp90 ATPase activities
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target:
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label: ATPase activity assay
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- source: TRAP1 ATPase activity
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target:
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label: ATPase activity assay
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- source: ATP hydrolisi rate
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target:
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label: ATPase activity assay
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- source: ATP hydrolisis rate
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target:
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label: ATPase activity assay
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- source: contextual conditioning behavior, in vivo bioluminescence
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target:
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label: contextual conditioning behavior assay
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- source: Magnetic Resonance Spectroscopy
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target:
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label: magnetic resonance spectroscopy
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- source: Mass identification
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target:
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label: mass spectrometry
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- source: Measurement of ROS levels
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target:
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label: reactive oxygen species assay
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- source: OCR
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target:
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label: oxygen consumption assay
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- source: Oxigen compustion rate
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target:
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label: oxygen consumption assay
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- source: Oxigen comsuption rate
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target:
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label: oxygen consumption assay
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- source: scale,elevated T maze apparatus method,von Frey,FitBark
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target:
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label: elevated plus maze test
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- source: SDS page
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target:
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label: SDS-PAGE
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- source: wholeGenomeSeq,MudPIT
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target:
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label: whole genome sequencing
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- source: Zeno Electronic Walkway
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target:
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label: gait measurement
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- source: UPLC-MSMS
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target:
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label: ultra high-performance liquid chromatography/tandem mass spectrometry
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- source: HPLC-MSMS
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target:
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label: high-performance liquid chromatography/tandem mass spectrometry
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- source: LC-MSMS
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target:
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label: liquid chromatography/tandem mass spectrometry
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- source: LC-MS
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target:
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label: liquid chromatography/mass spectrometry

‎mappings/README.md‎

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## Mappings
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This directory stores mapping specifications from the NF data model to other data model/dictionaries as needed in a specific YAML/JSON format.
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These mappings are very much in development so both format and content may change.
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This directory stores mapping specifications for the NF data model in a specific YAML/JSON format:
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1. Translation of NF concepts to *other* data models/dictionaries.
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2. Translation of messy or legacy NF Data Portal annotations to versioned, standardized NF data model concepts.
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These mappings help document what was done when metadata are translated or updated in harmonization or migration efforts.
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The mappings themselves are in development so both format and content may change.
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Currently, the map spec is inspired by and vaguely resembles a [concept map](https://build.fhir.org/conceptmap-example.json.html),
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though [SSOM](https://github.com/mapping-commons/sssom) was also considered.
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Mappings may not map from NF to other models in full scope; that is, often we don't map every single data element, only what is needed and applicable given the two models.
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Mappings may not map from NF to other models in full scope; that is, often we don't map every single data element, only what is needed and applicable at the time.
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Additional future mappings that might be useful are:
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(To other data models)
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- NF to [CSBC](https://www.synapse.org/#!Synapse:syn26433610/tables/)
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- NF to [HTAN](https://github.com/ncihtan/data-models)
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- NF to [synapseAnnotations](https://github.com/Sage-Bionetworks/synapseAnnotations/) (NF terms originally derived from here, but there has been some drift/divergence)
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‎mappings/cBioPortal.yaml‎ renamed to ‎mappings/cBioPortal/cBioPortal.yaml‎

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