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]>
nf-osi · Mar 17, 2023 · 0323165 · 0323165
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diff --git a/NF.csv b/NF.csv
diff --git a/NF.jsonld b/NF.jsonld
diff --git a/ext_classes.csv b/ext_classes.csv
@@ -1,4 +1,5 @@
 Attribute,.ID,.Type,.Root,.SubOf
+Physiology_Assay,Physiology_Assay,Class,Assay,
 Experimental_Assay,Assay,Class,Assay,
 DNA_Assay,DNA_Assay,Class,Assay,Assay
 RNA_Assay,RNA_Assay,Class,Assay,Assay
@@ -10,8 +11,9 @@ Epigenetics_Assay,Epigenetics_Assay,Class,Assay,Assay
 Imaging_Assay,Imaging_Assay,Class,Assay,Assay
 Volume_Measurement_Assay,Volume_Measurement_Assay,Class,Assay,Assay
 Drug_Screen,Drug_Screen,Class,Assay,Assay
-Electrophysiology_Assay,Electrophysiology_Assay,Class,Assay,Assay
+Electrophysiology_Assay,Electrophysiology_Assay,Class,Assay,Physiology_Assay
 MRI_Assay,MRI_Assay,Class,Assay,Imaging_Assay
+Viral_Assay,MRI_Assay,Class,Assay,Assay
 Assay_Template,Assay_Template,Class,Template,Manifest_Template
 Non_Assay_Template,Non_Assay_Template,Class,Template,Template
 Manifest_Template,Manifest_Template,Class,Template,Template

diff --git a/mappings/NFDataPortal/assay_v75.yaml b/mappings/NFDataPortal/assay_v75.yaml
@@ -0,0 +1,188 @@
+title: Mapping of NF data portal assay concept labels to assay labels in NF data model v6.4
+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.) 
+source_scope: https://www.synapse.org/#!Synapse:syn16858331.75/tables/
+target_scope: hhttps://github.com/nf-osi/nf-metadata-dictionary/releases/tag/v6.4
+mapping:
+  - source: Whole Exome Sequencing
+    target:
+      label: whole exome sequencing
+  - source: rnaSeq
+    target:
+      label: RNA-seq   
+  - source: wholeGenomeSeq
+    target:
+      label: whole genome sequencing
+  - source: Conventional MRI
+    target:
+      label: conventional MRI
+  - source: cellViabilityAssay
+    target:
+      label: cell viability assay
+  - source: westernBlot
+    target:
+      label: western blot
+  - source: brightfieldMicroscopy
+    target:
+      label: brightfield microscopy
+  - source: High Frequency Ultrasound
+    target:
+      label: high frequency ultrasound
+  - source: methylationArray
+    target:
+      label: methylation array
+  - source: nextGenerationTargetedSequencing
+    target:
+      label: next generation targeted sequencing
+  - source: confocalMicroscopy
+    target:
+      label: confocal microscopy
+  - source: 3D Imaging
+    target:
+      label: 3D imaging
+  - source: Positron Emission Tomography
+    target:
+      label: positron emission tomography
+  - source: Immunocytochemistry
+    target:
+      label: immunocytochemistry
+  - source: bisulfiteSeq
+    target:
+      label: bisulfite sequencing
+  - source: snpArray
+    target:
+      label: SNP array
+  - source: single-cell RNAseq
+    target:
+      label: single-cell RNA-seq
+  - source: Single Cell RNA Sequencing
+    target:
+      label: single-cell RNA-seq
+  - source: rnaArray
+    target:
+      label: RNA array
+  - source: Blood Chemistry Measurement
+    target:
+      label: blood chemistry measurement
+  - source: Mass spectrometry
+    target:
+      label: mass spectrometry
+  - source: ATACSeq
+    target:
+      label: ATAC-seq
+  - source: Real Time PCR
+    target:
+      label: real-time PCR
+  - source: jumpingLibrary
+    target:
+      label: jumping library
+  - source: ChIPSeq
+    target:
+      label: ChIP-seq
+  - source: T cell receptor sequencing
+    target:
+      label: T cell receptor repertoire sequencing
+  - source: Microscopy
+    target:
+      label: microscopy
+  - source: SDH enzymatic activity
+    target:
+      label: sorbitol dehydrogenase activity level assay
+  - source: exomeSeq-private
+    target:
+      label: whole exome sequencing
+  - source: polymeraseChainReaction
+    target:
+      label: polymerase chain reaction
+  - source: Focus forming assay
+    target:
+      label: focus forming assay
+  - source: FACS
+    target:
+      label: flow cytometry
+  - source: Flow Cytometry
+    target:
+      label: flow cytometry
+  - source: Immunoassay
+    target:
+      label: immunoassay
+  - source: Cell proliferation
+    target:
+      label: cell proliferation assay
+  - source: Phase-Contrast Microscopy
+    target:
+      label: phase-contrast microscopy
+  - source: atomicForceMicroscopy
+    target:
+      label: atomic force microscopy
+  - source: Cell viability assay
+    target:
+      label: cell viability assay
+  - source: cell counts
+    target:
+      label: cell count
+  - source: drugScreen
+    target:
+      label: drug screen
+  - source: Gel chromatography
+    target:
+      label: gel filtration chromatography
+  - source: novelty response behavior, in vivo bioluminescence
+    target:
+      label: novelty response behavior assay
+  - source: TRAP1 and Hsp90 ATPase activities
+    target:
+      label: ATPase activity assay
+  - source: TRAP1 ATPase activity
+    target:
+      label: ATPase activity assay
+  - source: ATP hydrolisi rate
+    target:
+      label: ATPase activity assay
+   - source: ATP hydrolisis rate
+    target:
+      label: ATPase activity assay
+  - source: contextual conditioning behavior, in vivo bioluminescence
+    target:
+      label: contextual conditioning behavior assay
+  - source: Magnetic Resonance Spectroscopy
+    target:
+      label: magnetic resonance spectroscopy
+  - source: Mass identification
+    target:
+      label: mass spectrometry
+  - source: Measurement of ROS levels
+    target:
+      label: reactive oxygen species assay
+  - source: OCR
+    target:
+      label: oxygen consumption assay
+  - source: Oxigen compustion rate
+    target:
+      label: oxygen consumption assay
+  - source: Oxigen comsuption rate
+    target:
+      label: oxygen consumption assay
+  - source: scale,elevated T maze apparatus method,von Frey,FitBark
+    target:
+      label: elevated plus maze test
+  - source: SDS page
+    target:
+      label: SDS-PAGE
+  - source: wholeGenomeSeq,MudPIT
+    target:
+      label: whole genome sequencing
+  - source: Zeno Electronic Walkway 
+    target:
+      label: gait measurement
+- source: UPLC-MSMS
+   target: 
+     label: ultra high-performance liquid chromatography/tandem mass spectrometry
+- source: HPLC-MSMS
+   target: 
+     label: high-performance liquid chromatography/tandem mass spectrometry
+- source: LC-MSMS
+   target: 
+     label: liquid chromatography/tandem mass spectrometry
+- source: LC-MS
+   target: 
+     label: liquid chromatography/mass spectrometry
diff --git a/mappings/README.md b/mappings/README.md
@@ -1,15 +1,19 @@
 ## Mappings 
 
-This directory stores mapping specifications from the NF data model to other data model/dictionaries as needed in a specific YAML/JSON format. 
-These mappings are very much in development so both format and content may change.
+This directory stores mapping specifications for the NF data model in a specific YAML/JSON format:
+1. Translation of NF concepts to *other* data models/dictionaries. 
+2. Translation of messy or legacy NF Data Portal annotations to versioned, standardized NF data model concepts.
+
+These mappings help document what was done when metadata are translated or updated in harmonization or migration efforts. 
+The mappings themselves are in development so both format and content may change.
 Currently, the map spec is inspired by and vaguely resembles a [concept map](https://build.fhir.org/conceptmap-example.json.html), 
 though [SSOM](https://github.com/mapping-commons/sssom) was also considered. 
 
-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.
+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.
 Additional future mappings that might be useful are:
 
+(To other data models)
 - NF to [CSBC](https://www.synapse.org/#!Synapse:syn26433610/tables/)
 - NF to [HTAN](https://github.com/ncihtan/data-models)
 - NF to [synapseAnnotations](https://github.com/Sage-Bionetworks/synapseAnnotations/) (NF terms originally derived from here, but there has been some drift/divergence)
 
-
diff --git a/mappings/cBioPortal.yaml → mappings/cBioPortal/cBioPortal.yaml b/mappings/cBioPortal.yaml → mappings/cBioPortal/cBioPortal.yaml