add nCounter assay

NF.jsonld

@@ -2037,6 +2037,8 @@
       "@id" : "bts:Pythonscript"
     }, {
       "@id" : "bts:Rscript"
+    }, {
+      "@id" : "bts:RCC"
     }, {
       "@id" : "bts:RData"
     }, {
@@ -14385,6 +14387,17 @@
     },
     "sms:displayName" : "University of Dayton",
     "sms:required" : "sms:false"
+  }, {
+    "@id" : "bts:RCC",
+    "@type" : "rdfs:Class",
+    "rdfs:comment" : "TBD",
+    "rdfs:label" : "RCC",
+    "rdfs:subClassOf" : [ ],
+    "schema:isPartOf" : {
+      "@id" : "http://schema.biothings.io/"
+    },
+    "sms:displayName" : "RCC",
+    "sms:required" : "sms:false"
   }, {
     "@id" : "bts:notaproblem",
     "@type" : "rdfs:Class",

modules/Assay/Assay.yaml

@@ -383,6 +383,9 @@ enums:
       nanoparticle tracking analysis:
         description: Particle sizing technique based on Brownian motion and scattered light.
         meaning: http://purl.enanomapper.org/onto/ENM_0000065
+      NanoString nCounter Analysis System:
+        description: A proprietary molecular analysis system for single molecule detection with no amplification. It uses unique fluorescent barcodes for direct, digital detection and copy number quantitation of hundreds of different target molecules in a single run. It requires only nanoscale amounts of RNA and has a detection sensitivity down to 1 copy per cell.
+        meaning: http://purl.obolibrary.org/obo/NCIT_C198498
       n-back task:
         description: A task in which items (e.g., letters) are presented one at a time and participants must identify each item that repeats relative to the item that occurred "n" items before its onset.
         meaning: https://www.cognitiveatlas.org/task/id/tsk_4a57abb949bcd/

modules/Data/FileFormat.yaml

@@ -9,49 +9,52 @@ enums:
         meaning: http://purl.obolibrary.org/obo/NCIT_C49059
       MATLAB data:
         description: A MATLAB formatted data file with expected extension “.mat”.
-        meaning: Sage Bionetworks
+        source: Sage Bionetworks
       MATLAB script:
         description: A MATLAB script file with expected extension “.m”. Note that files with a “.mat” extension contains MATLAB formatted data.
-        meaning: Sage Bionetworks
+        source: Sage Bionetworks
       NWB:
         description: Neurodata Without Borders (NWB) is a data standard for neurophysiology data, designed to store data including from intracellular and extracellular electrophysiology experiments, data from optical physiology experiments, and tracking and stimulus data.
-        meaning: https://www.nwb.org/
+        source: https://www.nwb.org/
       PAR:
         description: This is yet another MRI image format generated by Philips scanners. It is an ASCII header (PAR) plus a binary blob (REC).
-        meaning: https://nipy.org/nibabel/reference/nibabel.parrec.html
+        source: https://nipy.org/nibabel/reference/nibabel.parrec.html
       Python script:
         description: Python script with expected extension “.py”.
-        meaning: Sage Bionetworks
+        source: Sage Bionetworks
       R script:
         description: R script with expected extension “.R”.
-        meaning: Sage Bionetworks
+        source: Sage Bionetworks
+      RCC: 
+        description: Reporter Code Count-A data file (.csv) output by the Nanostring nCounter Digital Analyzer, which contains gene sample information, probe information and probe counts.
+        meaning: http://edamontology.org/format_3580
       RData:
         description: The RData format (usually with extension .rdata or .rda) is a format designed for use with R, a system for statistical computation and related graphics, for storing a complete R workspace or selected 'objects' from a workspace in a form that can be loaded back by R.
-        meaning: https://www.loc.gov/preservation/digital/formats/fdd/fdd000470.shtml
+        source: https://www.loc.gov/preservation/digital/formats/fdd/fdd000470.shtml
       REC:
         description: This is yet another MRI image format generated by Philips scanners. It is an ASCII header (PAR) plus a binary blob (REC).
-        meaning: https://nipy.org/nibabel/reference/nibabel.parrec.html
+        source: https://nipy.org/nibabel/reference/nibabel.parrec.html
       SDAT:
         description: Phillips MRS Data File
-        meaning: https://github.com/chenkonturek/MRS_MRI_libs
+        source: https://github.com/chenkonturek/MRS_MRI_libs
       SPAR:
         description: Phillips MRS Header File
-        meaning: https://github.com/chenkonturek/MRS_MRI_libs
+        source: https://github.com/chenkonturek/MRS_MRI_libs
       Sentrix descriptor file:
         description: A BeadScan specific file needed to perform scan setting checks for different array formats and assay type.
-        meaning: https://support.illumina.com/content/dam/illumina-support/documents/myillumina/dd0aff11-2664-481b-a8ce-26831a907cae/beadscan_3.0_software_addendum.pdf
+        source: https://support.illumina.com/content/dam/illumina-support/documents/myillumina/dd0aff11-2664-481b-a8ce-26831a907cae/beadscan_3.0_software_addendum.pdf
       ab1:
         description: TAB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence.
         meaning: http://edamontology.org/format_3000
       abf:
         description: The Axon Binary File format (ABF) was created for the storage of binary experimental data.
-        meaning: https://mdc.custhelp.com/euf/assets/content/ABFHelp.pdf
+        source: https://mdc.custhelp.com/euf/assets/content/ABFHelp.pdf
       ai:
         description: Adobe Illustrator format
         meaning: http://www.ebi.ac.uk/swo/data/SWO_3000023
       avi:
         description: AVI files can contain both audio and video data in a file container that allows synchronous audio-with-video playback.
-        meaning: https://en.wikipedia.org/wiki/Audio_Video_Interleave
+        source: https://en.wikipedia.org/wiki/Audio_Video_Interleave
       bai:
         description: BAM indexing format
         meaning: http://edamontology.org/format_3327
@@ -60,7 +63,7 @@ enums:
         meaning: http://edamontology.org/format_2572
       bash script:
         description: Bash Shell Script
-        meaning: https://en.wikipedia.org/wiki/Shell_script
+        source: https://en.wikipedia.org/wiki/Shell_script
       bcf:
         description: BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation)
         meaning: http://edamontology.org/format_3016
@@ -69,13 +72,13 @@ enums:
         meaning: http://edamontology.org/format_3003
       bed broadPeak:
         description: This format is used to provide called regions of signal enrichment based on pooled, normalized (interpreted) data. It is a BED 6+3 format.
-        meaning: http://genome.ucsc.edu/FAQ/FAQformat.html#format13
+        source: http://genome.ucsc.edu/FAQ/FAQformat.html#format13
       bed gappedPeak:
         description: This format is used to provide called regions of signal enrichment based on pooled, normalized (interpreted) data where the regions may be spliced or incorporate gaps in the genomic sequence. It is a BED12+3 format.
-        meaning: http://genome.ucsc.edu/FAQ/FAQformat.html#format14
+        source: http://genome.ucsc.edu/FAQ/FAQformat.html#format14
       bed narrowPeak:
         description: This format is used to provide called peaks of signal enrichment based on pooled, normalized (interpreted) data. It is a BED6+4 format.
-        meaning: http://genome.ucsc.edu/FAQ/FAQformat.html#format12
+        source: http://genome.ucsc.edu/FAQ/FAQformat.html#format12
       bedgraph:
         description: Holds a tab-delimited chromosome /start /end / datavalue dataset. The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data
         meaning: http://edamontology.org/format_3583
@@ -90,7 +93,7 @@ enums:
         meaning: http://edamontology.org/format_3592
       bpm:
         description: A beaded pool manifest. Describe the SNP or probe content on a BeadChip or in an assay pool.
-        meaning: https://support.illumina.com/datafiles.html
+        source: https://support.illumina.com/datafiles.html
       cel:
         description: Format of Affymetrix data file of information about (raw) expression levels of the individual probes
         meaning: http://edamontology.org/format_1638
@@ -122,7 +125,7 @@ enums:
         source: https://github.com/alyssafrazee/ballgown#ballgown-readable-expression-output
       czi:
         description: microscopy imaging file format that saves multidimensional images such as time lapse, Z-stacks, multiposition experiments and virtual slides, combined with relevant meta information
-        meaning: https://www.zeiss.com/microscopy/int/products/microscope-software/zen/czi.html
+        source: https://www.zeiss.com/microscopy/int/products/microscope-software/zen/czi.html
       dat:
         description: Format of Affymetrix data file of raw image data.
         meaning: http://edamontology.org/format_1637
@@ -131,7 +134,6 @@ enums:
       docker image:
         description: >
           A Docker image is a file, comprised of multiple layers, that is used to execute code in a Docker container.  An image is essentially built from the instructions for a complete and executable version of an application, which relies on the host OS kernel
-
         meaning: http://edamontology.org/format_3973
       dup:
         description: output of the Picard MarkDuplicates tool.
@@ -152,7 +154,7 @@ enums:
         meaning: http://purl.obolibrary.org/obo/OBI_0000327
       fig:
         description: Line drawing saved in the Xfig format; stored as a vector image that may include lines, shapes, arcs, splines, arrows, and text objects; may also include images, colors, and patterns.
-        meaning: https://fileinfo.com/extension/fig
+        source: https://fileinfo.com/extension/fig
       flagstat:
         description: Output of samtools flagstat tool
       gct:
@@ -206,13 +208,13 @@ enums:
         meaning: http://edamontology.org/format_3464
       locs:
         description: Illumina iScan bead location file.
-        meaning: https://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/iscan/iscan-system-guide-11313539-01.pdf
+        source: https://support.illumina.com/content/dam/illumina-support/documents/documentation/system_documentation/iscan/iscan-system-guide-11313539-01.pdf
       maf:
         description: Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth
         meaning: http://edamontology.org/format_3008
       md:
         description: Markdown (MD) is a lightweight markup language with plain text formatting syntax
-        meaning: https://en.wikipedia.org/wiki/Markdown
+        source: https://en.wikipedia.org/wiki/Markdown
       mov:
         description: A video file format with the .mov extension
         meaning: Sage Bionetworks
@@ -224,13 +226,13 @@ enums:
         meaning: http://edamontology.org/format_3702
       mtx:
         description: Matrix Market Exchange Format
-        meaning: https://math.nist.gov/MatrixMarket/formats.html#MMformat
+        source: https://math.nist.gov/MatrixMarket/formats.html#MMformat
       mzML:
         description: mzML format for raw spectrometer output data, standardised by HUPO PSI MSS.
         meaning: http://edamontology.org/format_3244
       nii:
         description: NIfTI-1 can store image data from any modality such as PET, MRI, CT, EEG that produces regularly sampled 1-5D rasters.
-        meaning: https://nifti.nimh.nih.gov/nifti-1/documentation/faq
+        source: https://nifti.nimh.nih.gov/nifti-1/documentation/faq
       ome-tiff:
         description: OME-TIFF is a preferred open image format
         meaning: http://edamontology.org/format_3727
@@ -239,15 +241,15 @@ enums:
         meaning: http://edamontology.org/format_3508
       plink:
         description: Any Plink file format (MAP/PED/BED/BIM/FAM)
-        meaning: https://www.cog-genomics.org/plink2/formats
+        source: https://www.cog-genomics.org/plink2/formats
       png:
         description: PNG is a file format for image compression
         meaning: http://edamontology.org/format_3603
       powerpoint:
         description: Microsoft Powerpoint slide format
       pzfx:
         description: A PZFX file is a Prism project created by GraphPad Prism, a scientific application used to analyze and graph data. It contains project data including graphs and layouts, notes, and tables.
-        meaning: https://fileinfo.com/extension/pzfx
+        source: https://fileinfo.com/extension/pzfx
       psydat:
         description: TrialHandler or StairHandler object that has been saved to disk with the python cPickle module, ideal for batch analysis and plotting with Python.
         source: https://www.psychopy.org/general/dataOutputs.html

modules/Template/Data.yaml

@@ -194,8 +194,27 @@ classes:
         assay:
         - single-cell RNA-seq
         dataType:
-        - SequenceReads
-
+        - eneExpression
+
+    #Saving this for later/more time to think through
+    #GeoMXSpatialTranscriptomicsTemplate:
+    #is_a: GeneticsAssayTemplate
+    #description: Files contain raw data output from the NanoString GeoMx DSP Pipeline. These can include RCC or DCC Files.
+    #source: https://raw.githubusercontent.com/ncihtan/data-models/main/HTAN.model.csv
+    #slots:
+    #- libraryPrep
+    #- libraryPreparationMethod
+    #annotations:
+    #  requiresComponent: ''
+    #  required: false
+    #  match:
+    #    assay:
+    #    - spatial transcriptomics
+    #    dataType:
+    #    - SequenceReads
+    #close_mappings:
+    #- htan:NanoStringGeoMxDSPSpatialTranscriptomicsLevel1
+
   PdxGenomicsAssayTemplate:
     is_a: GenomicsAssayTemplate
     description: Raw genomics data from patient-derived xenograft (PDX) experiment, with additional PDX-relevant metadata.
@@ -287,8 +306,7 @@ classes:
         - miRNA array
         - RNA array
         - SNP array
-        dataType:
-        - geneExpression
+        - nCounter
 
   MethylationArrayTemplate:
     is_a: GenomicsArrayTemplate