diff --git a/modules/Data/Data.yaml b/modules/Data/Data.yaml index 2ee0e58a..da8861a4 100644 --- a/modules/Data/Data.yaml +++ b/modules/Data/Data.yaml @@ -6,22 +6,21 @@ enums: meaning: http://purl.obolibrary.org/obo/NCIT_C16723 behavior process: description: The action, reaction, or performance of an organism in response to external or internal stimuli. - meaning: hhttps://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=structural_variation clinical: description: Data related to patient diagnosis, demographics, exposures, laboratory tests, and family relationships - meaning: https://docs.gdc.cancer.gov/Encyclopedia/pages/Clinical_Data + source: https://docs.gdc.cancer.gov/Encyclopedia/pages/Clinical_Data demographics: description: The statistical characterization of human populations or segments of human populations (e.g., characterization by age, sex, race, or income). meaning: http://purl.obolibrary.org/obo/NCIT_C16495 particle characterization: - description: 'A series of analytical methods that provide information about entities such as composition, structure and defects. ' - meaning: https://ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C62317 + description: Data providing information about entities such as composition, structure and defects. + meaning: http://purl.obolibrary.org/obo/NCIT_C62317 drugCombinationScreen: description: Information on drug sensitivity of more than one compound - meaning: https://www.ncbi.nlm.nih.gov/pubmed/29344898 + source: https://www.ncbi.nlm.nih.gov/pubmed/29344898 isoformExpression: description: Expression of protein isoforms formed from alternative splicings or other post-translational modifications of a single gene through RNA splicing mechanisms. - meaning: https://en.wikipedia.org/wiki/Protein_isoform + source: https://en.wikipedia.org/wiki/Protein_isoform proteomics: description: Protein and peptide identification, especially in the study of whole proteomes of organisms. meaning: https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Ftopic_0121 @@ -30,10 +29,10 @@ enums: meaning: http://purl.obolibrary.org/obo/OMIABIS_0000060 kinomics: description: Kinomics is the study of protein kinases and protein kinase signaling. - meaning: http://www.kinomecore.com/what-is-kinomics/ + source: http://www.kinomecore.com/what-is-kinomics/ SomaticVariants: description: Called somatic variants - meaning: https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=simple_somatic_mutation + source: https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=simple_somatic_mutation Volume: description: The amount of three dimensional space occupied by an object or the capacity of a space or container. meaning: http://purl.obolibrary.org/obo/NCIT_C25335 @@ -42,15 +41,21 @@ enums: meaning: http://purl.obolibrary.org/obo/NCIT_C25447 drugScreen: description: Information on drug sensitivity and molecular markers of drug response - meaning: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531057/ + source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531057/ geneExpression: description: The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data. meaning: https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Ftopic_0203 AlignedReads: description: Aligned reads output from alignment workflows meaning: https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=aligned_reads + genomicFeatures: + description: Data of sequence feature (continuous extent of biological sequence) that is of genomic origin. + meaning: http://purl.obolibrary.org/obo/GENO_0000481 + see_also: gff3 (file format) genomicVariants: - description: Genomic alterations, including single nucleotide polymorphisms, short indels and structural variants. Use more specific term if possible, esp. if data is only of one specific subset. + description: > + Genomic alterations, including single nucleotide polymorphisms, short indels and structural variants. + Use more specific term if possible, esp. if data is only of one specific subset. meaning: https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Foperation_3227 raw counts: description: The number or amount of something. @@ -65,7 +70,8 @@ enums: description: Chromatin activity that allow access of condensed genomic DNA and potentially control gene expression. meaning: https://en.wikipedia.org/wiki/Chromatin_remodeling StructuralVariants: - description: Specifically genomic variants data classified as structural variants, which may be derived from specialized variant calling workflows + description: Genomic variants data that covers deletions, duplications, CNVs, insertions, inversions, and translocations, which may be derived from specialized variant calling workflows. + source: hhttps://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=structural_variation GermlineVariants: description: Called germline variants meaning: https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=simple_germline_variation @@ -74,7 +80,7 @@ enums: meaning: https://docs.gdc.cancer.gov/Data_Dictionary/viewer/#?view=table-definition-view&id=copy_number_variation image: description: Biological or biomedical data that has been rendered into an image. - meaning: https://www.ebi.ac.uk/ols/ontologies/edam/terms?iri=http%3A%2F%2Fedamontology.org%2Fdata_2968 + meaning: http://edamontology.org/data_2968 network: description: An interconnected system of things or people. meaning: http://purl.obolibrary.org/obo/NCIT_C61377 @@ -93,9 +99,15 @@ enums: meaning: http://purl.obolibrary.org/obo/NCIT_C25208 electrophysiology: description: Data generated from an electrophysiology assay. - meaning: http://purl.obolibrary.org/obo/ERO_0000564 + notes: + - ERO has been deprecated and direct URIs no longer work. + source: https://bioportal.bioontology.org/ontologies/ERO/?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FERO_0000564&jump_to_nav=true audio transcript: description: '' + dataIndex: + description: A data index is information used to help with retrieval of some other data, especially large-scale data that would benefit from such an index. Very common formats are .bai and .tbi. + meaning: http://edamontology.org/data_0955 + DataSubtype: permissible_values: