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@prefix foaf: <http://xmlns.com/foaf/0.1/#term_> .
@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." .
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