Merge pull request #223 from nf-osi/patch/NFOSI-360

Patch/NFOSI-360

NF.csv

@@ -98,6 +98,8 @@ Dynamic Light Scattering,"Dynamic Light Scattering (DLS), also known as photocor
 Static Light Scattering,"Static Light Scattering is a method for determining structure by measuring the total or time-averaged scattering intensity of scattered visible light as a function of angle.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000180,assay,,,,Static_Light_Scattering,Class,Assay,Assay,Light_Scattering_Assay,,,
 Light Scattering Assay,"A method for determining structure by measuring the change in direction or energy of scattered visible light. Light is scattered by the electrons surrounding the atomic nuclei in the sample.",,Assay,FALSE,http://purl.obolibrary.org/obo/CHMO_0000166,assay,,,,Light_Scattering_Assay,Class,Assay,Assay,Spectroscopy,,,
 flow cytometry,"A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution",,,FALSE,http://purl.obolibrary.org/obo/OBI_0000916,assay,,,,Flow_Cytometry_Assay,Class,Assay,Assay,Assay,,,
+Pattern electroretinogram,"Pattern electroretinogram (PERG) is an electrophysiologic ophthalmologic test that provides non-invasive objective, quantitative measurement of central retinal function. PERG is the retinal response to a pattern-reversing, black-and-white checkerboard or stripped stimulus. The PERG assesses both macular and retinal ganglion cell electrical activity and can help differentiate between diseases of macular versus optic nerve dysfunction.",,,FALSE,https://www.ncbi.nlm.nih.gov/books/NBK560641,assay,,,,Pattern_Electroretinogram,Class,Assay,Assay,Assay,,,
+Optokinetic reflex assay,"The optokinetic reflex (OKR), which serves to stabilize a moving image on the retina, is a behavioral response that has many favorable attributes as a test of CNS function. The OKR requires no training, assesses the function of diverse CNS circuits, can be induced repeatedly with minimal fatigue or adaptation, and produces an electronic record that is readily and objectively quantifiable.",,,FALSE,https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0002055,assay,,,,Optokinetic_Reflex_Assay,Class,Assay,Assay,Assay,,,
 channel,Fluorescent color labeling for an array,"Cy5, Cy3","",TRUE,"",array,,"","",Channel,"",Assay,Assay_Parameter,"","","",""
 photograph,An image recorded by a camera.,"","",FALSE,http://purl.obolibrary.org/obo/NCIT_C86035,assay,,"","",Photograph,"",Assay,Assay_Parameter,"","","",""
 MRISequence,The scanning sequence/modality that is used for a conventional MRI scan.,"T1-weighted,T2-weighted,PD-weighted,Short Tau Inversion Recovery","",FALSE,Sage Bionetworks,experimentalData,,"","",MRI_Sequence,Class,Assay,Assay_Parameter,"","","",""
@@ -206,7 +208,7 @@ Cherry Imaging FACE Platform,"(From vendor) A micro-ultrasound imaging system fo
 LifeViz Micro System,"(From vendor) Portable 3D imaging system for skin microstructure analysis.",,,FALSE,https://www.quantificare.com/3d-photography-systems_old/lifeviz-micro/,platform,,,,LifeViz_Micro_System,Class,Assay,Platform,Platform,,,
 LifeViz Infinity System,"(From vendor) All-in-one 3D imaging system for face, body and breast.",,,FALSE,https://www.quantificare.com/3d-photography-systems_old/lifeviz-infinity/,platform,,,,LifeViz_Infinity_System,Class,Assay,Platform,Platform,,,
 drugScreenType,String describing general class of drug screen,"singleMolecule, smallMoleculeLibraryScreen, combinationLibraryScreen, combinationScreen",,FALSE,,compoundScreen,,,,drugScreenType,Property,Assay,annotationProperty,,,,
-assay,The technology used to generate the data in this file,"elevated plus maze test, open field test, rotarod performance test, mRNAcounts, high content screen, Immunocytochemistry, immunofluorescence, autoradiography, electrochemiluminescence, Real Time PCR, in vivo tumor growth, scale, Blood Chemistry Measurement, in vivo bioluminescence, immunohistochemistry, NOMe-Seq, FIA-MSMS, UPLC-MSMS, HPLC-MSMS, liquid chromatography-electrochemical detection, rnaSeq, mirnaSeq, LC-MSMS, LC-MS, lncrnaSeq, Whole Exome Sequencing, Sanger sequencing, ChIPSeq, rnaArray, snpArray, methylationArray, mirnaArray, bisulfiteSeq, ATACSeq, HI-C, errBisulfiteSeq, ISOSeq, westernBlot, wholeGenomeSeq, polymeraseChainReaction, cellViabilityAssay, atomicForceMicroscopy, brightfieldMicroscopy, tractionForceMicroscopy, nextGenerationTargetedSequencing, jumpingLibrary, MIB/MS, scCGIseq, MudPIT, questionnaire, DNA optical mapping, oxBS-Seq, Ribo-Seq, Positron Emission Tomography, RPPA, ELISA, LTP, LFP, whole-cell patch clamp, sandwich ELISA, Laser Speckle Imaging, Genotyping, TMT quantitation, label free mass spectrometry, cell count, reporter gene assay, Single Cell RNA Sequencing, spatial transcriptomics, Conventional MRI, Functional MRI, Magnetic Resonance Spectroscopy, 2D Incucyte, 2D CellTiter-Glo, 3D microtissue viability, in vivo PDX viability, 2D AlamarBlue fluorescence, 2D AlamarBlue absorbance, rheometry, FTIR Spectroscopy, differential scanning calorimetry, Gel filtration chromatography, Massively Parallel Reporter Assay,Riccardi and Ablon scales,Spatial Frequency Domain Imaging,Optical Coherence Tomography,CUT&RUN,High Frequency Ultrasound, 3D Imaging,Dynamic Light Scattering,Static Light Scattering,flow cytometry",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one,
+assay,The technology used to generate the data in this file,"elevated plus maze test, open field test, rotarod performance test, mRNAcounts, high content screen, Immunocytochemistry, immunofluorescence, autoradiography, electrochemiluminescence, Real Time PCR, in vivo tumor growth, scale, Blood Chemistry Measurement, in vivo bioluminescence, immunohistochemistry, NOMe-Seq, FIA-MSMS, UPLC-MSMS, HPLC-MSMS, liquid chromatography-electrochemical detection, rnaSeq, mirnaSeq, LC-MSMS, LC-MS, lncrnaSeq, Whole Exome Sequencing, Sanger sequencing, ChIPSeq, rnaArray, snpArray, methylationArray, mirnaArray, bisulfiteSeq, ATACSeq, HI-C, errBisulfiteSeq, ISOSeq, westernBlot, wholeGenomeSeq, polymeraseChainReaction, cellViabilityAssay, atomicForceMicroscopy, brightfieldMicroscopy, tractionForceMicroscopy, nextGenerationTargetedSequencing, jumpingLibrary, MIB/MS, scCGIseq, MudPIT, questionnaire, DNA optical mapping, oxBS-Seq, Ribo-Seq, Positron Emission Tomography, RPPA, ELISA, LTP, LFP, whole-cell patch clamp, sandwich ELISA, Laser Speckle Imaging, Genotyping, TMT quantitation, label free mass spectrometry, cell count, reporter gene assay, Single Cell RNA Sequencing, spatial transcriptomics, Conventional MRI, Functional MRI, Magnetic Resonance Spectroscopy, 2D Incucyte, 2D CellTiter-Glo, 3D microtissue viability, in vivo PDX viability, 2D AlamarBlue fluorescence, 2D AlamarBlue absorbance, rheometry, FTIR Spectroscopy, differential scanning calorimetry, Gel filtration chromatography, Massively Parallel Reporter Assay,Riccardi and Ablon scales,Spatial Frequency Domain Imaging,Optical Coherence Tomography,CUT&RUN,High Frequency Ultrasound, 3D Imaging,Dynamic Light Scattering,Static Light Scattering,flow cytometry,Pattern electroretinogram,Optokinetic reflex assay",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one,
 platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","Illumina HiSeq 3000, Illumina HiSeq 2500, Illumina HiSeq 4000, Illumina NextSeq 500, Illumina HiSeq 2000, Illumina MiSeq, Zeiss LSM 980, Affymetrix Genome-Wide Human SNP 5.0 Array, Affymetrix Genome-Wide Human SNP 6.0 Array, PacBio RS II, Illumina Genome Analyzer IIx, Illumina HumanOmni1-Quadv1.0, Illumina 1M, Illumina h650, Illumina Omni2pt5M, Illumina Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen 300Karray, Agilent 44Karray, Illumina WholeGenome DASL, Illumina HumanHap300, Nanostring Counter, LTQ Orbitrap XL, Illumina HumanMethylation450, Illumina Infinium MethylationEPIC BeadChip, Affymetrix U133AB, Affymetrix Human Gene 1.0 ST Array, Affymetrix Human Genome U133 Plus 2.0 Array, Illumina HiSeq X, Bionano Irys, Infinium HumanOmniExpressExome, Illumina NextSeq 550, Illumina NextSeq 1000, Illumina NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, Nanostring GeoMx, LI-COR Odyssey CLx, Spectramax M Series, Olympus DP80, Orbitrap Fusion Lumos Tribrid, Illumina NovaSeq 6000, Chromium X,EnVision 2103 Multiplate Reader,Vectra H1 3D Imaging System,Vevo 3100 Imaging System,10x Visium Spatial Gene Expression,Cherry Imaging TRACE Platform,Cherry Imaging FACE Platform,LifeViz Micro System,LifeViz Infinity System",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,,platform,Property,Assay,annotationProperty,,Platform,,
 targetCaptureKitID,"A unique identifier for the kit used to construct a genomic library using target capture-based techniques, which should be composed of the vendor name, kit name and kit version.",,,TRUE,http://purl.obolibrary.org/obo/NCIT_C177583,experimentalData,,,,targetCaptureKitID,Property,Assay,annotationProperty,,,,"For WES processing, the target BED used could be provided based on the target capture kit."
 libraryID,,,,TRUE,,experimentalData,,,,libraryID,Property,Assay,annotationProperty,,,,

NF.jsonld

@@ -3685,6 +3685,40 @@
             "sms:required": "sms:false",
             "sms:validationRules": []
         },
+        {
+            "@id": "bts:Patternelectroretinogram",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "Pattern electroretinogram (PERG) is an electrophysiologic ophthalmologic test that provides non-invasive objective, quantitative measurement of central retinal function. PERG is the retinal response to a pattern-reversing, black-and-white checkerboard or stripped stimulus. The PERG assesses both macular and retinal ganglion cell electrical activity and can help differentiate between diseases of macular versus optic nerve dysfunction.",
+            "rdfs:label": "Patternelectroretinogram",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Assay"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Pattern electroretinogram",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
+        {
+            "@id": "bts:Optokineticreflexassay",
+            "@type": "rdfs:Class",
+            "rdfs:comment": "The optokinetic reflex (OKR), which serves to stabilize a moving image on the retina, is a behavioral response that has many favorable attributes as a test of CNS function. The OKR requires no training, assesses the function of diverse CNS circuits, can be induced repeatedly with minimal fatigue or adaptation, and produces an electronic record that is readily and objectively quantifiable.",
+            "rdfs:label": "Optokineticreflexassay",
+            "rdfs:subClassOf": [
+                {
+                    "@id": "bts:Assay"
+                }
+            ],
+            "schema:isPartOf": {
+                "@id": "http://schema.biothings.io"
+            },
+            "sms:displayName": "Optokinetic reflex assay",
+            "sms:required": "sms:false",
+            "sms:validationRules": []
+        },
         {
             "@id": "bts:Channel",
             "@type": "rdfs:Class",
@@ -5843,6 +5877,12 @@
                 },
                 {
                     "@id": "bts:Flowcytometry"
+                },
+                {
+                    "@id": "bts:Patternelectroretinogram"
+                },
+                {
+                    "@id": "bts:Optokineticreflexassay"
                 }
             ],
             "sms:displayName": "assay",

docs/templates/Clinical_Assay_Template.csv

@@ -6,6 +6,7 @@
 "dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","required","#Data",""
 "fileFormat","Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","required","#File_Format",""
 "resourceType","The type of resource being stored and annotated","required","#Resource",""
+"species","The name of a species (typically a taxonomic group) of organism.","required","#Species",""
 "age","A numeric value representing age of the individual. Use with ageUnit.","optional","",""
 "ageUnit","A time unit that can be used with a given age value, e.g. years.","optional","days, months, years",""
 "aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ","optional","",""
@@ -22,10 +23,9 @@
 "nf2Genotype","Genotype of NF2 gene in the biospecimen from which the data were derived, if known","optional","#Genotype",""
 "organ","A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.","optional","#Organ",""
 "parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
-"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","optional","#Platform",""
 "progressReportNumber","Indicates milestone the  data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1.  Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
 "sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex",""
-"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
 "specimenID","A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the","optional","","Typically annotated with a single ID, but many allowed for summary data."
 "specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","optional","#Specimen_State",""
 "timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""

docs/templates/Epigenetics_Assay_Template.csv

@@ -6,6 +6,7 @@
 "dataType","A type of experimental, clinical, or other data. This typically refers to a high-level data type that can be related to an assay type. For example, a file of dataType `genomicVariants` might have an assay value of `whole genome sequencing`.","required","#Data",""
 "fileFormat","Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software","required","#File_Format",""
 "resourceType","The type of resource being stored and annotated","required","#Resource",""
+"species","The name of a species (typically a taxonomic group) of organism.","required","#Species",""
 "age","A numeric value representing age of the individual. Use with ageUnit.","optional","",""
 "ageUnit","A time unit that can be used with a given age value, e.g. years.","optional","days, months, years",""
 "aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ","optional","",""
@@ -26,10 +27,9 @@
 "nucleicAcidSource","Source of the extracted nucleic acid used in the experiment","optional","#Nucleic_Acid_Source",""
 "organ","A unique macroscopic (gross) anatomic structure that performs specific functions. It is composed of various tissues. An organ is part of an anatomic system or a body region.","optional","#Organ",""
 "parentSpecimenID","A unique identifier (non-PII) that represents the parent specimen (sample) from which the data came from, e.g. the single parent tumor. The parentSpecimenIDcan be the same as specimenID when there is no subsectioning.","optional","",""
-"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","optional","#Platform",""
+"platform","A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data.","optional","#Platform",""
 "progressReportNumber","Indicates milestone the  data is associated with. Currently only required for projects funded by NTAP, GFF, and NFRI. For GFF studies, this is the ‘progress report’ timeline. Example: if submitting data for the 6-month milestone report for NTAP, progressReportNumber=1.  Also if submitting data associated with first milestone, progressReportNumber =1","optional","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",""
 "sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex",""
-"species","The name of a species (typically a taxonomic group) of organism.","optional","#Species",""
 "specimenID","A unique identifier (non-PII) that represents the subspecimen (subsample) from which the data came, e.g. an ID that distinguishes between different parts of the same parent tumor specimen. This can be the A A unique identifier (non-PII) that represents the","optional","","Typically annotated with a single ID, but many allowed for summary data."
 "specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","optional","#Specimen_State",""
 "timePointUnit","For timed experiments this represents the unit of time measured","optional","#Time_Unit",""