-
Notifications
You must be signed in to change notification settings - Fork 2
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* 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]>
- Loading branch information
1 parent
f16da5e
commit 0323165
Showing
9 changed files
with
970 additions
and
445 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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) | ||
|
||
|
File renamed without changes.
Oops, something went wrong.