From a4e2caef64becf3135bc972a2da261ee25deee07 Mon Sep 17 00:00:00 2001 From: Christina Conrad <114612268+cconrad8@users.noreply.github.com> Date: Wed, 29 Mar 2023 09:19:37 -0400 Subject: [PATCH 1/2] Update NF.csv --- NF.csv | 1 + 1 file changed, 1 insertion(+) diff --git a/NF.csv b/NF.csv index 0beaa330..61fa1050 100644 --- a/NF.csv +++ b/NF.csv @@ -276,6 +276,7 @@ image,Biological or biomedical data that has been rendered into an image.,"",ass geneExpression,The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data.,"",assay,FALSE,https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Ftopic_0203,dataType,,"","",Gene_Expression,Class,Data,Data_Class,"","","","" isoformExpression,Expression of protien isoforms formed from alternative splicings or other post-translational modifications of a single gene through RNA splicing mechanisms.,"",assay,FALSE,https://en.wikipedia.org/wiki/Protein_isoform,dataType,,"","",Isoform_Expression,Class,Data,Data_Class,"","","","" proteomics,"Protein and peptide identification, especially in the study of whole proteomes of organisms.","",assay,FALSE,https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Ftopic_0121,dataType,,"","",Proteomics,Class,Data,Data_Class,"","","","" +particle characterization,"A series of analytical methods that provide information about entities such as composition, structure and defects. ",,assay,FALSE,https://ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C62317,dataType,,,,Particle_Characterization,Class,Data,Data_Class,"","","","" kinomics,Kinomics is the study of protein kinases and protein kinase signaling.,"",assay,FALSE,http://www.kinomecore.com/what-is-kinomics/,dataType,,"","",Kinomics,Class,Data,Data_Class,"","","","" drugScreen,Information on drug sensitivity and molecular markers of drug response,"",assay,FALSE,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531057/,dataType,,"","",Drug_Screen,Class,Data,Data_Class,"","","","" drugCombinationScreen,Information on drug sensitivity of more than one compound,"","",FALSE,https://www.ncbi.nlm.nih.gov/pubmed/29344898,dataType,,"","",Drug_Combination_Screen,Class,Data,Data_Class,"","","","" From 0c6b783b85f693313e80a6853662bc28d9cd6952 Mon Sep 17 00:00:00 2001 From: Christina Conrad <114612268+cconrad8@users.noreply.github.com> Date: Wed, 29 Mar 2023 09:20:14 -0400 Subject: [PATCH 2/2] Update NF.csv --- NF.csv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/NF.csv b/NF.csv index 61fa1050..7b3d0d38 100644 --- a/NF.csv +++ b/NF.csv @@ -415,7 +415,7 @@ reference sequence,Syntactic sequences that has a role as reference of an annota dataSubtype,"Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata.","normalized, dataMatrix, raw, processed, metadata, representative",,TRUE,,experimentalData,,,,dataSubtype,Property,Data,annotationProperty,,Data_Level,one, metadataType,"For files of dataSubtype: metadata, a description of the type of metadata in the file.","individual, biospecimen, assay, data dictionary, manifest, protocol",,FALSE,,experimentalData,,,,metadataType,Property,Data,annotationProperty,,,, 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`.","Volume, Weight, Pharmacokinetic Study, genomicVariants,behavior process, metabolomics, image, geneExpression, isoformExpression, proteomics, particle characterization, kinomics, drugScreen, drugCombinationScreen, cellularPhysiology, chromatinActivity, surveyData, network, clinical, immunoassay, electrophysiology, raw counts, mask image,AlignedReads,SomaticVariants,AnnotatedSomaticVariants,StructuralVariants,GermlineVariants,AnnotatedGermlineVariants,characteristic",dataSubtype,TRUE,,experimentalData,,,,dataType,Property,Data,annotationProperty,,Data,one, -expressionUnit,Measure used for transcript expression quantification,"TPM,RPKM,FPKM,Counts,Other",,TRUE,,experimentalData,,,,expressionUnit,DataProperty,Data,annotationProperty,,,, +expressionUnit,Measure used for transcript expression quantification,"TPM,RPKM,FPKM,Counts,Other",,TRUE,,experimentalData,,,,expressionUnit,DataProperty,Data,annotationProperty,,, failedQC,"Whether the sample or data failed QC checks (Yes, No)","Yes, No",,TRUE,,experimentalData,,,,failedQC,DataProperty,Data,annotationProperty,,, Filename,The name of the file.,,"entityId,fileFormat",TRUE,Sage Bionetworks,NF,,,,fileName,Class,Data,annotationProperty,fileName,,one,Automatically filled when using the curator app. programmingLanguage,A computer programming language,"Python, R, MATLAB, Java, C, C++, C#, Javascript, bash",,FALSE,Sage Bionetworks,,,,,programmingLanguage,Property,Data,annotationProperty,ngsParameter,,,