@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." .