From 13398e68cd0ec657d152a60ccf873c473316f19f Mon Sep 17 00:00:00 2001 From: anngvu <32753274+anngvu@users.noreply.github.com> Date: Tue, 31 May 2022 03:36:49 -0700 Subject: [PATCH] Terms for ticket NFOSI-191 (#153) * Add tom file format * Add Riccardi and Ablon scales to assay * Add changes * Regenerate docs Co-authored-by: nf-osi[bot] --- NF.csv | 6 +- NF.jsonld | 40 ++++++ docs/index.html | 128 +++++++++--------- docs/templates/Behavioral_Assay_Template.csv | 1 + docs/templates/Biospecimen_Template.csv | 1 + .../Biospecimen_Template_Normalized.csv | 5 +- docs/templates/Clinical_Assay_Template.csv | 1 + .../Clinical_Assay_Template_Extended.csv | 1 + docs/templates/Epigenetics_Assay_Template.csv | 1 + docs/templates/Genomics_Assay_Template.csv | 1 + .../Genomics_Assay_Template_Extended.csv | 1 + .../Genomics_Assay_Template_Normalized.csv | 1 + docs/templates/Imaging_Assay_Template.csv | 1 + .../Imaging_Assay_Template_Extended.csv | 1 + docs/templates/Individual_Template.csv | 1 + docs/templates/MRI_Assay_Template.csv | 1 + .../templates/PDX_Genomics_Assay_Template.csv | 1 + .../templates/Patient_Timepoints_Template.csv | 1 + .../Pharmacokinetics_Assay_Template.csv | 1 + .../Plate_Based_Reporter_Assay_Template.csv | 1 + docs/templates/Proteomics_Assay_Template.csv | 1 + docs/templates/Protocol_Template.csv | 1 + docs/templates/Source_Code_Template.csv | 1 + docs/templates/Update_Milestone_Report.csv | 1 + modules/Assay/Assay.csv | 1 + modules/Assay/annotationProperty.csv | 2 +- modules/Data/File_Format.csv | 1 + modules/Data/annotationProperty.csv | 2 +- 28 files changed, 135 insertions(+), 70 deletions(-) diff --git a/NF.csv b/NF.csv index 05fe0d7a..b60d0d71 100644 --- a/NF.csv +++ b/NF.csv @@ -87,6 +87,7 @@ compoundScreen,,,,FALSE,,assay,,,,Compound_Screen,Class,Assay,Assay,Drug_Screen, array,,,,FALSE,,assay,,,,Array,Class,Assay,Assay,Assay,,, Single Cell RNA Sequencing,A procedure that can determine the nucleotide sequence for all of the RNA transcripts in an amplified nucleotide sample that was derived from a single cell.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C171152,assay,,,,ScRNA_Seq,Class,Assay,Assay,RNA-Seq,,, Massively Parallel Reporter Assay,An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences.,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002675,assay,,,,Massively_Parallel_Reporter_Assay,Class,Assay,Assay,Reporter_Gene_Assay,,, +Riccardi and Ablon scales,"The Riccardi and Ablon scales score severity and visibility of disease, respectively, and are commonly used as a combined assessment for NF1 patients in clinical settings. See https://doi.org/10.1001/archderm.137.11.1421 for example usage.",,,FALSE,https://doi.org/10.1001/archderm.137.11.1421,assay,,,,Riccardi_Ablon_Scales,Class,Assay,Assay,Clinical_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,"","","","" @@ -187,7 +188,7 @@ NanostringGeoMx,NanostringGeoMx,,,FALSE,,platform,,,,Nanostring_GeoMx,Class,Assa Chromium X,"(From 10x Genomics) Single-cell platform that can analyze hundreds to hundreds of thousands of cells in single run for e.g. gene expression, chromatin accessibility, cell surface proteins, immune clonotype, antigen specificity, CRISPR perturbation screens).",,,FALSE,https://www.10xgenomics.com/chromium-x,platform,,,,Chromium_X,Class,Assay,Platform,Platform,,, EnVision 2103 Multiplate Reader,EnVision 2103 Multiplate Reader,,,FALSE,,platform,,,,EnVision_2103,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, 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",,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, 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",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one, platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","HiSeq3000, HiSeq2500, HiSeq4000, NextSeq500, HiSeq2000, MiSeq, Zeiss LSM 980, Affy5.0, Affy6.0, PacBioRSII, GAIIx, Illumina_HumanOmni1-Quadv1.0, Illumina_1M, Illumina_h650, Illumina_Omni2pt5M, Illumina_Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen300Karray, Agilent44Karray, IlluminaWholeGenomeDASL, IlluminaHumanHap300, NanostringnCounter, LTQOrbitrapXL, IlluminaHumanMethylation450, Illumina Infinium MethylationEPIC BeadChip, AffymetrixU133AB, Affymetrix Human Gene 1.0 ST Array, AffymetrixU133Plus2, HiSeqX, Bionano Irys, Infinium HumanOmniExpressExome, NextSeq 550, NextSeq 1000, NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, NanostringGeoMx, LI-COR Odyssey CLx, Spectramax M Series, Olympus DP80, Orbitrap Fusion Lumos Tribrid, Illumina NovaSeq 6000, Chromium X,EnVision 2103 Multiplate Reader",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,,platform,Property,Assay,annotationProperty,,Platform,, libraryID,,,,TRUE,,experimentalData,,,,libraryID,Property,Assay,annotationProperty,,,, assayTarget,The HUGO gene symbol that represents the target analyte assayed.,,,FALSE,Sage Bionetworks,experimentalData,,,,assayTarget,Property,Assay,annotationProperty,,,, @@ -629,6 +630,7 @@ REC,This is yet another MRI image format generated by Philips scanners. It is an hdr,"MRI Header file, as in the NIFTI-1 Analyze 7.5 format","","",FALSE,https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h,fileFormat,,"","",hdr,Class,Data,File_Format,"","","","" img,"MRI Data file, as in the NIFTI-1 Analyze 7.5 format","","",FALSE,https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h,fileFormat,,"","",img,Class,Data,File_Format,"","","","" sf,"Salmon’s main output is its quantification file. This file is a plain-text, tab-separated file with a single header line (which names all of the columns).","","",FALSE,https://salmon.readthedocs.io/en/latest/file_formats.html,fileFormat,,"","",sf,Class,Data,File_Format,"","","","" +tom,"The .tom format is a specialized 3D image export format from the Vectra medical imaging systems that can optionally preserve trimmings and/or landmarks.","","",FALSE,http://canfieldupgrade.com/assets/media/VECTRA-M3-User-Guide.pdf,fileFormat,,"","",tom,Class,Data,File_Format,"","","","" gene symbol,A unique gene name approved by an organism specific nomenclature committee.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C43568,curatedDataType,,,,Gene_Symbol,Class,Data,Metadata,,,, clinical data,Data obtained through patient examination or treatment.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C15783,curatedDataType,,,,Clinical_Curated_Data,Class,Data,Metadata,,,, gene function,A term that expresses the function of a gene product.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C48933,curatedDataType,,,,Gene_Function,Class,Data,Metadata,,,, @@ -661,7 +663,7 @@ programmingLanguage,A computer programming language,"Python, R, MATLAB, Java, C, runtimePlatform,"Runtime platform or script interpreter dependencies (e.g. Java v1, Python 2.3).",,,FALSE,Sage Bionetworks,,,,,runtimePlatform,Property,Data,annotationProperty,ngsParameter,,, documentation,URL to any documentation describing the resource and its use.,,,FALSE,Sage Bionetworks,,,,,documentation,Property,Data,annotationProperty,ngsParameter,,, resourceType,The type of resource being stored and annotated,"experimentalData, curatedData, result, tool, report, metadata, protocol",,TRUE,,sageCommunity,,,,resourceType,Property,Data,annotationProperty,,Resource,, -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","bash script,bedgraph,ai,idx,idat,bam,bai,excel,powerpoint,tif,png,doc,pdf,hdf,fasta,fastq,sam,vcf,bcf,maf,bed,chp,cel,sif,tsv,csv,txt,plink,bigwig,wiggle,gct,bgzip,zip,seg,html,mov,hyperlink,svs,md,flagstat,gtf,raw,msf,rmd,bed narrowPeak,bed broadPeak,bed gappedPeak,avi,pzfx,fig,xml,tar,R script,abf,bpm,dat,jpg,locs,Sentrix descriptor file,Python script,sav,gzip,sdf,RData,hic,ab1,7z,gff3,json,sqlite,svg,sra,recal,tranches,mtx,tagAlign,dup,DICOM,czi,mzML,SPAR,SDAT,nii,PAR,REC,hdr,img,sf,MATLAB script, MATLAB data",,TRUE,,sageCommunity,,,,fileFormat,Property,Data,annotationProperty,,File_Format,one, +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","bash script,bedgraph,ai,idx,idat,bam,bai,excel,powerpoint,tif,png,doc,pdf,hdf,fasta,fastq,sam,vcf,bcf,maf,bed,chp,cel,sif,tsv,csv,txt,plink,bigwig,wiggle,gct,bgzip,zip,seg,html,mov,hyperlink,svs,md,flagstat,gtf,raw,msf,rmd,bed narrowPeak,bed broadPeak,bed gappedPeak,avi,pzfx,fig,xml,tar,R script,abf,bpm,dat,jpg,locs,Sentrix descriptor file,Python script,sav,gzip,sdf,RData,hic,ab1,7z,gff3,json,sqlite,svg,sra,recal,tranches,mtx,tagAlign,dup,DICOM,czi,mzML,SPAR,SDAT,nii,PAR,REC,hdr,img,sf,MATLAB script, MATLAB data,tom",,TRUE,,sageCommunity,,,,fileFormat,Property,Data,annotationProperty,,File_Format,one, 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","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",,FALSE,,template,,,,progressReportNumber,DataProperty,Data,annotationProperty,,,one, comments,Brief free-text comments that may also be important to understanding the resource.,,,FALSE,Sage Bionetworks,experimentalData,,,,comments,DataProperty,Data,annotationProperty,,,many, Resource_id,A UUID for a Resource from the NF Research Tools Database,,,FALSE,Sage Bionetworks,dccProperty,,,,Resource_id,Property,Data,annotationProperty,dccProperty,,, diff --git a/NF.jsonld b/NF.jsonld index f9f1701e..9314eddd 100644 --- a/NF.jsonld +++ b/NF.jsonld @@ -3473,6 +3473,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:RiccardiandAblonscales", + "@type": "rdfs:Class", + "rdfs:comment": "The Riccardi and Ablon scales score severity and visibility of disease, respectively, and are commonly used as a combined assessment for NF1 patients in clinical settings. See https://doi.org/10.1001/archderm.137.11.1421 for example usage.", + "rdfs:label": "RiccardiandAblonscales", + "rdfs:subClassOf": [ + { + "@id": "bts:Assay" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Riccardi and Ablon scales", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Channel", "@type": "rdfs:Class", @@ -5465,6 +5482,9 @@ }, { "@id": "bts:MassivelyParallelReporterAssay" + }, + { + "@id": "bts:RiccardiandAblonscales" } ], "sms:displayName": "assay", @@ -14405,6 +14425,23 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:Tom", + "@type": "rdfs:Class", + "rdfs:comment": "The .tom format is a specialized 3D image export format from the Vectra medical imaging systems that can optionally preserve trimmings and/or landmarks.", + "rdfs:label": "Tom", + "rdfs:subClassOf": [ + { + "@id": "bts:FileFormat" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "tom", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Genesymbol", "@type": "rdfs:Class", @@ -15444,6 +15481,9 @@ }, { "@id": "bts:MATLABdata" + }, + { + "@id": "bts:Tom" } ], "sms:displayName": "fileFormat", diff --git a/docs/index.html b/docs/index.html index e48f2237..ba80239a 100644 --- a/docs/index.html +++ b/docs/index.html @@ -70,7 +70,7 @@ - + @@ -258,7 +258,7 @@

NF Vocabulary / Schema

NF-OSI DCC

-

Last updated on 2022-04-08

+

Last updated on 2022-05-31

@@ -274,24 +274,24 @@

Assay Module

Assay

Terms
-
- +
+
Relations Graph

This partial graph view logically relates assays to metadata templates available at the NF Data Curator App. For example, assays under the classification of Imaging_Assay currently uses a generic Imaging_Assay_Template for annotation. More specialized templates may be made available as needed for specific assays.

-
- +
+

Platform

Terms
-
- +
+
Relations Graph
@@ -310,28 +310,28 @@

Parameters

NGS Parameter
Library Prep
-
- +
+
Library Prep Method
-
- +
+
Read Pair
-
- +
+
Read Pair Orientation
-
- +
+
Run Type
-
- +
+
@@ -342,8 +342,8 @@

Data Module

Data Type

Terms
-
- +
+
Relations Graph
@@ -368,8 +368,8 @@
Terms

(open) formats.

-
- +
+
Relations Graph
@@ -390,32 +390,32 @@

Biosample Module

Sex

Terms
-
- +
+

Species

Terms
-
- +
+

Diagnosis

Terms
-
- +
+

Genotype

Terms
-
- +
+

Data can be linked to specimen-level information such as sample site (the organ or body part), specimen tissue or cell type, tumor class (if specimen is a tumor), and specimen state.

@@ -426,21 +426,21 @@
Terms

Sample Site

Terms
-
- +
+

Sample Specimen

Tissue
-
- +
+
Cell / Cell Line
-
- +
+
@@ -455,8 +455,8 @@

Specimen State

Tumor Class

Terms
-
- +
+
@@ -466,13 +466,13 @@

Experiment Module

Gene Perturbation

Gene Perturbation Type
-
- +
+
Gene Perturbation Technology
-
- +
+
@@ -496,56 +496,56 @@

Annotation Templates

Templates for Assay Data

Genomics Assay
-
- +
+
Proteomics Assay
-
- +
+
Epigenetics Assay
-
- +
+
Imaging Assay
-
- +
+
MRI Assay
-
- +
+
Pharmacokinetics Assay
-
- +
+
Plate Based Reporter Assay
-
- +
+
Clinical Assay
-
- +
+

Other Templates

Patient Timepoints
-
- +
+
Source Code
-
- +
+
@@ -558,8 +558,8 @@

Reserved Properties

Terms
-
- +
+
diff --git a/docs/templates/Behavioral_Assay_Template.csv b/docs/templates/Behavioral_Assay_Template.csv index 95ab1a7e..257067d4 100644 --- a/docs/templates/Behavioral_Assay_Template.csv +++ b/docs/templates/Behavioral_Assay_Template.csv @@ -1,4 +1,5 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "Filename","The name of the file.","required","","Automatically filled when using the curator app." "resourceType","The type of resource being stored and annotated","required","#Resource","" "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","" diff --git a/docs/templates/Biospecimen_Template.csv b/docs/templates/Biospecimen_Template.csv index bc691158..8bc1c162 100644 --- a/docs/templates/Biospecimen_Template.csv +++ b/docs/templates/Biospecimen_Template.csv @@ -1,3 +1,4 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort." "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","","" diff --git a/docs/templates/Biospecimen_Template_Normalized.csv b/docs/templates/Biospecimen_Template_Normalized.csv index c9ab8633..1a1a4053 100644 --- a/docs/templates/Biospecimen_Template_Normalized.csv +++ b/docs/templates/Biospecimen_Template_Normalized.csv @@ -1,11 +1,12 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "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","","" "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." "aliquotID","A unique identifier (non-PII) that represents the aliquots used for e.g. replicate runs. This is linked to the specimenID. ","optional","","" "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","" "tissue","A tissue is a mereologically maximal collection of cells that together perform physiological function.","optional","#Tissue","" -"isCellLine","Boolean flag indicating whether or not sample source is a cell line. (Note: TRUE = Yes; FALSE = No)","optional","TRUE, FALSE","" -"isPrimaryCell","Boolean flag indicating whether or not cellType is primary (Note: TRUE = Yes; FALSE = No)","optional","TRUE, FALSE","" +"isCellLine","Whether or not sample source is a cell line (Yes; No)","optional","Yes, No","" +"isPrimaryCell","Whether or not cellType is primary (Yes; No)","optional","Yes, No","" "cellType","A cell type is a distinct morphological or functional form of cell.","optional","#Cell","" "tumorType","The type of tumor that the biospecimen used to generate the data were collected from.","optional","#Tumor","" "specimenPreparationMethod","Term that represents preservation of the sample before usage in, e.g. sequencing","optional","#Specimen_State","" diff --git a/docs/templates/Clinical_Assay_Template.csv b/docs/templates/Clinical_Assay_Template.csv index 3ff81efe..ddb3fb49 100644 --- a/docs/templates/Clinical_Assay_Template.csv +++ b/docs/templates/Clinical_Assay_Template.csv @@ -1,4 +1,5 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "Filename","The name of the file.","required","","Automatically filled when using the curator app." "resourceType","The type of resource being stored and annotated","required","#Resource","" "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","" diff --git a/docs/templates/Clinical_Assay_Template_Extended.csv b/docs/templates/Clinical_Assay_Template_Extended.csv index db54f15f..b465b9bb 100644 --- a/docs/templates/Clinical_Assay_Template_Extended.csv +++ b/docs/templates/Clinical_Assay_Template_Extended.csv @@ -1,4 +1,5 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "Filename","The name of the file.","required","","Automatically filled when using the curator app." "resourceType","The type of resource being stored and annotated","required","#Resource","" "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","" diff --git a/docs/templates/Epigenetics_Assay_Template.csv b/docs/templates/Epigenetics_Assay_Template.csv index ba6cb596..f2ac5400 100644 --- a/docs/templates/Epigenetics_Assay_Template.csv +++ b/docs/templates/Epigenetics_Assay_Template.csv @@ -1,4 +1,5 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "Filename","The name of the file.","required","","Automatically filled when using the curator app." "resourceType","The type of resource being stored and annotated","required","#Resource","" "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","" diff --git a/docs/templates/Genomics_Assay_Template.csv b/docs/templates/Genomics_Assay_Template.csv index 393576e6..30a3d8b4 100644 --- a/docs/templates/Genomics_Assay_Template.csv +++ b/docs/templates/Genomics_Assay_Template.csv @@ -1,4 +1,5 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "Filename","The name of the file.","required","","Automatically filled when using the curator app." "resourceType","The type of resource being stored and annotated","required","#Resource","" "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","" diff --git a/docs/templates/Genomics_Assay_Template_Extended.csv b/docs/templates/Genomics_Assay_Template_Extended.csv index 46a1380e..26f47d82 100644 --- a/docs/templates/Genomics_Assay_Template_Extended.csv +++ b/docs/templates/Genomics_Assay_Template_Extended.csv @@ -1,4 +1,5 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "Filename","The name of the file.","required","","Automatically filled when using the curator app." "resourceType","The type of resource being stored and annotated","required","#Resource","" "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","" diff --git a/docs/templates/Genomics_Assay_Template_Normalized.csv b/docs/templates/Genomics_Assay_Template_Normalized.csv index 882d7cb3..4522eef4 100644 --- a/docs/templates/Genomics_Assay_Template_Normalized.csv +++ b/docs/templates/Genomics_Assay_Template_Normalized.csv @@ -1,4 +1,5 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "Filename","The name of the file.","required","","Automatically filled when using the curator app." "resourceType","The type of resource being stored and annotated","required","#Resource","" "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","" diff --git a/docs/templates/Imaging_Assay_Template.csv b/docs/templates/Imaging_Assay_Template.csv index a77ec0b9..c784c248 100644 --- a/docs/templates/Imaging_Assay_Template.csv +++ b/docs/templates/Imaging_Assay_Template.csv @@ -1,4 +1,5 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "Filename","The name of the file.","required","","Automatically filled when using the curator app." "resourceType","The type of resource being stored and annotated","required","#Resource","" "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","" diff --git a/docs/templates/Imaging_Assay_Template_Extended.csv b/docs/templates/Imaging_Assay_Template_Extended.csv index 6bba0538..9946b1ce 100644 --- a/docs/templates/Imaging_Assay_Template_Extended.csv +++ b/docs/templates/Imaging_Assay_Template_Extended.csv @@ -1,4 +1,5 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "Filename","The name of the file.","required","","Automatically filled when using the curator app." "resourceType","The type of resource being stored and annotated","required","#Resource","" "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","" diff --git a/docs/templates/Individual_Template.csv b/docs/templates/Individual_Template.csv index 88730186..af4c5dfb 100644 --- a/docs/templates/Individual_Template.csv +++ b/docs/templates/Individual_Template.csv @@ -1,4 +1,5 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort." "sex","Phenotypic expression of chromosomal makeup that defines a study subject as male, female, or other.","optional","#Sex","" "age","A numeric value representing age of the individual. Use with ageUnit.","optional","","" diff --git a/docs/templates/MRI_Assay_Template.csv b/docs/templates/MRI_Assay_Template.csv index 352d9547..c60e0933 100644 --- a/docs/templates/MRI_Assay_Template.csv +++ b/docs/templates/MRI_Assay_Template.csv @@ -1,4 +1,5 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "Filename","The name of the file.","required","","Automatically filled when using the curator app." "resourceType","The type of resource being stored and annotated","required","#Resource","" "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","" diff --git a/docs/templates/PDX_Genomics_Assay_Template.csv b/docs/templates/PDX_Genomics_Assay_Template.csv index 9896302b..773ca237 100644 --- a/docs/templates/PDX_Genomics_Assay_Template.csv +++ b/docs/templates/PDX_Genomics_Assay_Template.csv @@ -1,4 +1,5 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "Filename","The name of the file.","required","","Automatically filled when using the curator app." "resourceType","The type of resource being stored and annotated","required","#Resource","" "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","" diff --git a/docs/templates/Patient_Timepoints_Template.csv b/docs/templates/Patient_Timepoints_Template.csv index ad8e439c..58744d5b 100644 --- a/docs/templates/Patient_Timepoints_Template.csv +++ b/docs/templates/Patient_Timepoints_Template.csv @@ -1,3 +1,4 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "individualID","A unique identifier (non-PII) that represents the individual from which the data came. This could be a patient or animal ID.","optional","","Typically annotated with a single ID, but many allowed for, e.g. a clinical dataset that contains endpoint data for an entire cohort." "experimentalTimepoint","The numeric value indicating the time elapsed from the beginning of the experiment at which the specimen was collected. Use in tandem with timePointUnit","optional","","" diff --git a/docs/templates/Pharmacokinetics_Assay_Template.csv b/docs/templates/Pharmacokinetics_Assay_Template.csv index 6bba0538..9946b1ce 100644 --- a/docs/templates/Pharmacokinetics_Assay_Template.csv +++ b/docs/templates/Pharmacokinetics_Assay_Template.csv @@ -1,4 +1,5 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "Filename","The name of the file.","required","","Automatically filled when using the curator app." "resourceType","The type of resource being stored and annotated","required","#Resource","" "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","" diff --git a/docs/templates/Plate_Based_Reporter_Assay_Template.csv b/docs/templates/Plate_Based_Reporter_Assay_Template.csv index cb270893..ba435e78 100644 --- a/docs/templates/Plate_Based_Reporter_Assay_Template.csv +++ b/docs/templates/Plate_Based_Reporter_Assay_Template.csv @@ -1,4 +1,5 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "Filename","The name of the file.","required","","Automatically filled when using the curator app." "resourceType","The type of resource being stored and annotated","required","#Resource","" "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","" diff --git a/docs/templates/Proteomics_Assay_Template.csv b/docs/templates/Proteomics_Assay_Template.csv index 7113fa57..ba2950c4 100644 --- a/docs/templates/Proteomics_Assay_Template.csv +++ b/docs/templates/Proteomics_Assay_Template.csv @@ -1,4 +1,5 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "Filename","The name of the file.","required","","Automatically filled when using the curator app." "resourceType","The type of resource being stored and annotated","required","#Resource","" "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","" diff --git a/docs/templates/Protocol_Template.csv b/docs/templates/Protocol_Template.csv index 32661da3..d0d8c33c 100644 --- a/docs/templates/Protocol_Template.csv +++ b/docs/templates/Protocol_Template.csv @@ -1,4 +1,5 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "Filename","The name of the file.","required","","Automatically filled when using the curator app." "resourceType","The type of resource being stored and annotated","required","#Resource","" "author","The author of the resource; preferably use an ORCID ID, GitHub profile link, etc., if available and a text name if not.","optional","","" diff --git a/docs/templates/Source_Code_Template.csv b/docs/templates/Source_Code_Template.csv index 167a8b58..d76b5da6 100644 --- a/docs/templates/Source_Code_Template.csv +++ b/docs/templates/Source_Code_Template.csv @@ -1,4 +1,5 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "Filename","The name of the file.","required","","Automatically filled when using the curator app." "resourceType","The type of resource being stored and annotated","required","#Resource","" "programmingLanguage","A computer programming language","optional","Python, R, MATLAB, Java, C, C++, C#, Javascript, bash","" diff --git a/docs/templates/Update_Milestone_Report.csv b/docs/templates/Update_Milestone_Report.csv index 47d982e2..ab02359f 100644 --- a/docs/templates/Update_Milestone_Report.csv +++ b/docs/templates/Update_Milestone_Report.csv @@ -1,4 +1,5 @@ "Field","Description","Required","ControlledVocab","Note" +"Component","Category of metadata manifest; provide the same one for all items/rows.","required","","" "Filename","The name of the file.","required","","Automatically filled when using the curator app." "resourceType","The type of resource being stored and annotated","required","#Resource","" "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","" diff --git a/modules/Assay/Assay.csv b/modules/Assay/Assay.csv index 5c56efe0..8694593e 100644 --- a/modules/Assay/Assay.csv +++ b/modules/Assay/Assay.csv @@ -87,3 +87,4 @@ compoundScreen,,,,FALSE,,assay,,,,Compound_Screen,Class,Assay,Assay,Drug_Screen, array,,,,FALSE,,assay,,,,Array,Class,Assay,Assay,Assay,,, Single Cell RNA Sequencing,A procedure that can determine the nucleotide sequence for all of the RNA transcripts in an amplified nucleotide sample that was derived from a single cell.,,,FALSE,http://purl.obolibrary.org/obo/NCIT_C171152,assay,,,,ScRNA_Seq,Class,Assay,Assay,RNA-Seq,,, Massively Parallel Reporter Assay,An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences.,,,FALSE,http://purl.obolibrary.org/obo/OBI_0002675,assay,,,,Massively_Parallel_Reporter_Assay,Class,Assay,Assay,Reporter_Gene_Assay,,, +Riccardi and Ablon scales,"The Riccardi and Ablon scales score severity and visibility of disease, respectively, and are commonly used as a combined assessment for NF1 patients in clinical settings. See https://doi.org/10.1001/archderm.137.11.1421 for example usage.",,,FALSE,https://doi.org/10.1001/archderm.137.11.1421,assay,,,,Riccardi_Ablon_Scales,Class,Assay,Assay,Clinical_Assay,,, diff --git a/modules/Assay/annotationProperty.csv b/modules/Assay/annotationProperty.csv index afaaee90..ed1086cf 100644 --- a/modules/Assay/annotationProperty.csv +++ b/modules/Assay/annotationProperty.csv @@ -1,6 +1,6 @@ Attribute,Description,Valid Values,DependsOn,Required,Source,Parent,Properties,DependsOn Component,Validation Rules,.ID,.Type,.Module,.Root,.SubOf,.Range,.Cardinality,.EditorNote 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, 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",,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, 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",,TRUE,,experimentalData,,,,assayType,Property,Assay,annotationProperty,,Assay,one, platform,"A sequencing platform, microscope, spectroscope/plate reader, or other platform for collecting data. ","HiSeq3000, HiSeq2500, HiSeq4000, NextSeq500, HiSeq2000, MiSeq, Zeiss LSM 980, Affy5.0, Affy6.0, PacBioRSII, GAIIx, Illumina_HumanOmni1-Quadv1.0, Illumina_1M, Illumina_h650, Illumina_Omni2pt5M, Illumina_Omni5M, Illumina MouseWG-6 v2.0 expression beadchip, Perlegen300Karray, Agilent44Karray, IlluminaWholeGenomeDASL, IlluminaHumanHap300, NanostringnCounter, LTQOrbitrapXL, IlluminaHumanMethylation450, Illumina Infinium MethylationEPIC BeadChip, AffymetrixU133AB, Affymetrix Human Gene 1.0 ST Array, AffymetrixU133Plus2, HiSeqX, Bionano Irys, Infinium HumanOmniExpressExome, NextSeq 550, NextSeq 1000, NextSeq 2000, PacBio Sequel IIe System, PacBio Sequel II System, NanostringGeoMx, LI-COR Odyssey CLx, Spectramax M Series, Olympus DP80, Orbitrap Fusion Lumos Tribrid, Illumina NovaSeq 6000, Chromium X,EnVision 2103 Multiplate Reader",,FALSE,https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=read_group&anchor=platform,experimentalData,,,,platform,Property,Assay,annotationProperty,,Platform,, libraryID,,,,TRUE,,experimentalData,,,,libraryID,Property,Assay,annotationProperty,,,, assayTarget,The HUGO gene symbol that represents the target analyte assayed.,,,FALSE,Sage Bionetworks,experimentalData,,,,assayTarget,Property,Assay,annotationProperty,,,, diff --git a/modules/Data/File_Format.csv b/modules/Data/File_Format.csv index 190d9652..0a9b1a58 100644 --- a/modules/Data/File_Format.csv +++ b/modules/Data/File_Format.csv @@ -89,3 +89,4 @@ REC,This is yet another MRI image format generated by Philips scanners. It is an hdr,"MRI Header file, as in the NIFTI-1 Analyze 7.5 format","","",FALSE,https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h,fileFormat,,"","",hdr,Class,Data,File_Format,"","","","" img,"MRI Data file, as in the NIFTI-1 Analyze 7.5 format","","",FALSE,https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h,fileFormat,,"","",img,Class,Data,File_Format,"","","","" sf,"Salmon’s main output is its quantification file. This file is a plain-text, tab-separated file with a single header line (which names all of the columns).","","",FALSE,https://salmon.readthedocs.io/en/latest/file_formats.html,fileFormat,,"","",sf,Class,Data,File_Format,"","","","" +tom,"The .tom format is a specialized 3D image export format from the Vectra medical imaging systems that can optionally preserve trimmings and/or landmarks.","","",FALSE,http://canfieldupgrade.com/assets/media/VECTRA-M3-User-Guide.pdf,fileFormat,,"","",tom,Class,Data,File_Format,"","","","" diff --git a/modules/Data/annotationProperty.csv b/modules/Data/annotationProperty.csv index 1cfbaeb1..e86cea5a 100644 --- a/modules/Data/annotationProperty.csv +++ b/modules/Data/annotationProperty.csv @@ -11,7 +11,7 @@ programmingLanguage,A computer programming language,"Python, R, MATLAB, Java, C, runtimePlatform,"Runtime platform or script interpreter dependencies (e.g. Java v1, Python 2.3).",,,FALSE,Sage Bionetworks,,,,,runtimePlatform,Property,Data,annotationProperty,ngsParameter,,, documentation,URL to any documentation describing the resource and its use.,,,FALSE,Sage Bionetworks,,,,,documentation,Property,Data,annotationProperty,ngsParameter,,, resourceType,The type of resource being stored and annotated,"experimentalData, curatedData, result, tool, report, metadata, protocol",,TRUE,,sageCommunity,,,,resourceType,Property,Data,annotationProperty,,Resource,, -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","bash script,bedgraph,ai,idx,idat,bam,bai,excel,powerpoint,tif,png,doc,pdf,hdf,fasta,fastq,sam,vcf,bcf,maf,bed,chp,cel,sif,tsv,csv,txt,plink,bigwig,wiggle,gct,bgzip,zip,seg,html,mov,hyperlink,svs,md,flagstat,gtf,raw,msf,rmd,bed narrowPeak,bed broadPeak,bed gappedPeak,avi,pzfx,fig,xml,tar,R script,abf,bpm,dat,jpg,locs,Sentrix descriptor file,Python script,sav,gzip,sdf,RData,hic,ab1,7z,gff3,json,sqlite,svg,sra,recal,tranches,mtx,tagAlign,dup,DICOM,czi,mzML,SPAR,SDAT,nii,PAR,REC,hdr,img,sf,MATLAB script, MATLAB data",,TRUE,,sageCommunity,,,,fileFormat,Property,Data,annotationProperty,,File_Format,one, +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","bash script,bedgraph,ai,idx,idat,bam,bai,excel,powerpoint,tif,png,doc,pdf,hdf,fasta,fastq,sam,vcf,bcf,maf,bed,chp,cel,sif,tsv,csv,txt,plink,bigwig,wiggle,gct,bgzip,zip,seg,html,mov,hyperlink,svs,md,flagstat,gtf,raw,msf,rmd,bed narrowPeak,bed broadPeak,bed gappedPeak,avi,pzfx,fig,xml,tar,R script,abf,bpm,dat,jpg,locs,Sentrix descriptor file,Python script,sav,gzip,sdf,RData,hic,ab1,7z,gff3,json,sqlite,svg,sra,recal,tranches,mtx,tagAlign,dup,DICOM,czi,mzML,SPAR,SDAT,nii,PAR,REC,hdr,img,sf,MATLAB script, MATLAB data,tom",,TRUE,,sageCommunity,,,,fileFormat,Property,Data,annotationProperty,,File_Format,one, 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","1, 2, 3, 4, 5, 6, 7, 8, 9, 10, Not Applicable",,FALSE,,template,,,,progressReportNumber,DataProperty,Data,annotationProperty,,,one, comments,Brief free-text comments that may also be important to understanding the resource.,,,FALSE,Sage Bionetworks,experimentalData,,,,comments,DataProperty,Data,annotationProperty,,,many, Resource_id,A UUID for a Resource from the NF Research Tools Database,,,FALSE,Sage Bionetworks,dccProperty,,,,Resource_id,Property,Data,annotationProperty,dccProperty,,,