add FISH

NF.jsonld

@@ -4491,6 +4491,8 @@
       "@id" : "bts:FIA-MSMS"
     }, {
       "@id" : "bts:FLIPRhigh-throughputcellularscreening"
+    }, {
+      "@id" : "bts:FluorescenceInSituHybridization"
     }, {
       "@id" : "bts:Focusgroup"
     }, {
@@ -4828,6 +4830,8 @@
       "@id" : "bts:FIA-MSMS"
     }, {
       "@id" : "bts:FLIPRhigh-throughputcellularscreening"
+    }, {
+      "@id" : "bts:FluorescenceInSituHybridization"
     }, {
       "@id" : "bts:Focusgroup"
     }, {
@@ -12607,6 +12611,17 @@
     },
     "sms:displayName" : "University of Missouri, Saint Louis",
     "sms:required" : "sms:false"
+  }, {
+    "@id" : "bts:FluorescenceInSituHybridization",
+    "@type" : "rdfs:Class",
+    "rdfs:comment" : "TBD",
+    "rdfs:label" : "FluorescenceInSituHybridization",
+    "rdfs:subClassOf" : [ ],
+    "schema:isPartOf" : {
+      "@id" : "http://schema.biothings.io/"
+    },
+    "sms:displayName" : "Fluorescence In Situ Hybridization",
+    "sms:required" : "sms:false"
   }, {
     "@id" : "bts:noveltyresponsebehaviorassay",
     "@type" : "rdfs:Class",

modules/Assay/Assay.yaml

@@ -83,11 +83,16 @@ enums:
           An imaging-based system that allows measurement and analysis of peaks of human-derived induced pluripotent stem cells (hiPSCs), 
           differentiated into cardiomyocytes and neurons,  up to 100 times per second and quickly cherry pick events such as Early-After-Depolarization-like events (EAD-like events), fibrillation, and irregular beating.
         source: https://www.moleculardevices.com/products/flipr-penta-high-throughput-cellular-screening-system
+      Fluorescence In Situ Hybridization:
+        description: > 
+          A physical mapping approach that uses fluorescent tags to detect hybridization of probes within metaphase chromosomes or less condensed somatic interphase chromatin. 
+          This technique can be used for identification of chromosomal abnormalities and for gene mapping.
+        meaning: http://purl.obolibrary.org/obo/NCIT_C17563
       Focus group:
         description: > 
           A small, usually diverse group of people whose response to something is studied to determine the response that can be expected from a larger population. 
           It is used especially in market research and political analysis.
-        source: http://purl.obolibrary.org/obo/NCIT_C154589
+        meaning: http://purl.obolibrary.org/obo/NCIT_C154589
       FTIR spectroscopy:
         description: > 
           Fourier transform infrared (FTIR) spectroscopy is a technique used to obtain an infrared spectrum of absorption or emission of a solid, liquid or gas. 

modules/Data/FileFormat.yaml

@@ -164,9 +164,12 @@ enums:
         meaning: http://purl.obolibrary.org/obo/NCIT_C80220
       hdf5:
         description: >
-          HDF5 is the new version, according to the HDF group, a completely different technology (https://support.hdfgroup.org/products/hdf4/ compared to HDF.  An HDF5 file appears to the user as a directed graph. The nodes of this graph are the higher-level HDF5 objects that are exposed by the HDF5 APIs:  Groups, Datasets, Named datatypes. Currently supported by the Python MDTraj package. HDF5 is a data model, library, and file format for storing and managing data, based on Hierarchical Data Format (HDF).
-
+          HDF5 is the new version, according to the HDF group, a completely different technology (https://support.hdfgroup.org/products/hdf4/ compared to HDF.  
+          An HDF5 file appears to the user as a directed graph. The nodes of this graph are the higher-level HDF5 objects that are exposed by the HDF5 APIs:  Groups, Datasets, Named datatypes. 
+          Currently supported by the Python MDTraj package. HDF5 is a data model, library, and file format for storing and managing data, based on Hierarchical Data Format (HDF).
         meaning: http://edamontology.org/format_3590
+        notes:
+          - This file format encompasses/includes the h5ad anndata format commonly used for scRNAseq data sharing. 
       hdr:
         description: MRI Header file, as in the NIFTI-1 Analyze 7.5 format
         meaning: https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h

tests/validate/ScRNASeqTemplate_1.csv

@@ -2,4 +2,4 @@ Component,Filename,fileFormat,resourceType,dataType,dataSubtype,assay,individual
 ScRNASeqTemplate,a,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,A,Homo sapiens,,,,,,,,,A1,A1-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,oligodendrocyte,No,,enzymatic,,,,10x,,,,,,
 ScRNASeqTemplate,b,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,B,Homo sapiens,,,,,,,,,B2,B2-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,oligodendrocyte,No,,enzymatic,,,,10x,,,,,,
 ScRNASeqTemplate,c,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,C,Homo sapiens,,,,,,,,,C3,C3-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,schwann,No,,enzymatic,,,,10x,,,,,,
-ScRNASeqTemplate,d,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,D,Homo sapiens,,,,,,,,,D4,D4-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,schwann,No,,enzymatic,,,,10x,,,,,,
+ScRNASeqTemplate,d,fastq,experimentalData,geneExpression,raw,single-cell RNA-seq,D,Homo sapiens,,,,,,,,,D4,D4-1,Low-Grade Glioma NOS,Illumina NextSeq 1000,single cell,Viably frozen,schwann,No,,enzymatic,,,,10x,,,,,,