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diff --git a/schema/mapping.ttl b/schema/mapping.ttl new file mode 100644 index 0000000..e56d028 --- /dev/null +++ b/schema/mapping.ttl @@ -0,0 +1,164 @@ +@prefix foaf: <http://xmlns.com/foaf/0.1/> . +@prefix gn: <http://rdf.genenetwork.org/v1/id/> . +@prefix gnc: <http://rdf.genenetwork.org/v1/category/> . +@prefix gnt: <http://rdf.genenetwork.org/v1/term/> . +@prefix skos: <http://www.w3.org/2004/02/skos/core#> . +@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . +@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . + +gn:mapping_method_qtlreaper + skos:definition "Rapidly scan microarray expression data for QTLs" ; + foaf:homepage <https://github.com/genenetwork/QTLReaper> . + +gn:mapping_method_Rqtl + skos:definition "R/qtl is an extension library for the R statistics system. It is used to analyze experimental crosses for identifying genes contributing to variation in quantitative traits (so-called quantitative trait loci, QTLs). Using a hidden Markov model, R/qtl estimates genetic maps, to identify genotyping errors, and to perform single-QTL and two-QTL, two-dimensional genome scans." ; + foaf:homepage <https://rqtl.org/> . + +gn:mapping_method_HappyR + skos:definition "Haplotype-based QTL mapping method, often used for multiparent populations." . + +gn:mapping_method_PLINK + skos:definition + "Genome-wide association and population-based linkage analysis tool." . + +gn:mapping_method_FastMap + skos:definition + "Efficient mapping algorithm optimized for large datasets." . + +################################################################# +# Normalization / Averaging Method Concept Scheme +################################################################# + +gn:avg_method_MAS5 + skos:definition + "Affymetrix Microarray Suite 5 normalization method." . + +gn:avg_method_PDNN + skos:definition + "Probe-level normalization method that models sequence-dependent hybridization effects in microarray data." . + +gn:avg_method_RMA + skos:definition + "Robust Multi-array Average normalization for microarray data." . + +gn:avg_method_dChip + skos:definition + "Model-based normalization and expression summarization method for microarray data using probe-level intensity modeling." . + +gn:avg_method_GCRMA + skos:definition + "GC-content adjusted RMA normalization method." . + +gn:avg_method_Herit + skos:definition + "Method that estimates heritability by partitioning phenotypic variance into genetic and environmental components." . + +gn:avg_method_Rank + skos:definition + "Normalization method that transforms values based on their rank order within a dataset." . + +gn:avg_method_RankInv + skos:definition + "Normalization method that applies an inverse rank transformation to enforce a uniform distribution of values." . + +gn:avg_method_LOESS + skos:definition + "Locally estimated scatterplot smoothing normalization." . + +gn:avg_method_LOESS_NB + skos:definition + "LOESS-based normalization method that corrects systematic biases without assuming a parametric noise model." . + + +gn:avg_method_QUANT + skos:definition + "Quantile normalization method that forces all samples to share the same empirical distribution." . + +gn:avg_method_QUANT_NB + skos:definition + "Quantile normalization method applied without background correction or parametric noise assumptions." . + +gn:avg_method_RSN + skos:definition + "Robust spline normalization method that adjusts microarray data to remove systematic technical variation." . + +gn:avg_method_RSN_NB + skos:definition + "Robust spline normalization method applied without background correction or parametric noise assumptions." . + +gn:avg_method_Sscore + skos:definition + "Statistical scoring method for identifying significant gene expression changes in microarray data." . + +gn:avg_method_mlratio + skos:definition + "Method calculating the log-ratio of expression values between two conditions for microarray analysis." . + +gn:avg_method_VST + skos:definition + "Variance stabilizing transformation for RNA-seq count data to reduce heteroscedasticity." . + +gn:avg_method_RPN + skos:definition + "Robust Probe Normalization method for microarray data to adjust probe-level intensities." . + + +gn:TPM_Log2 + skos:definition + "Transcripts Per Million normalized expression values, log2 transformed." . + +gn:avg_method_RPKM + skos:definition + "Reads Per Kilobase Million normalization for RNA-seq data." . + +gn:avg_method_RNA_seq + skos:definition + "Normalization pipeline applied to RNA sequencing datasets." . + +gn:avg_method_SRM + skos:definition + "Normalization method for targeted proteomics using Selected Reaction Monitoring." . + +gn:avg_method_SWATH + skos:definition + "Normalization and quantification method for SWATH-MS proteomics data." . + +gn:avg_method_RPKM_log2 + skos:definition + "Log2-transformed Reads Per Kilobase per Million mapped reads for RNA-seq data." . + +gn:avg_method_Sesame + skos:definition + "Normalization method for Illumina methylation arrays using the Sesame pipeline." . + +gn:avg_method_TPM_Log2 + skos:definition + "Log2-transformed Transcripts Per Million for RNA-seq expression quantification." . + +gn:avg_method_rlog + skos:definition + "Regularized log transformation for RNA-seq count data to stabilize variance." . + +gn:avg_method_edgeR + skos:definition + "Normalization and differential expression analysis method for RNA-seq using edgeR." . + +gn:avg_method_minfi + skos:definition + "Normalization pipeline for Illumina methylation arrays using the minfi Bioconductor package." . + +gn:avg_method_2Z_8 + skos:definition + "Microarray normalization method that applies a 2Z+8 transformation to expression values." . + +gn:avg_method_Log2 + skos:definition + "Simple log2 transformation applied to expression values to reduce skew and stabilize variance." . + +gn:avg_method_DESeq2_rlog2 + skos:definition + "Regularized log transformation from the DESeq2 RNA-seq workflow." . + +gn:avg_method_N_A + skos:definition + "Indicates that no normalization or averaging method applies." . |