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-rw-r--r--schema/gn-curation-metadata.ttl19
-rw-r--r--schema/mapping.ttl164
-rw-r--r--schema/species.ttl38
3 files changed, 207 insertions, 14 deletions
diff --git a/schema/gn-curation-metadata.ttl b/schema/gn-curation-metadata.ttl
new file mode 100644
index 0000000..1286453
--- /dev/null
+++ b/schema/gn-curation-metadata.ttl
@@ -0,0 +1,19 @@
+@prefix gn:   <http://rdf.genenetwork.org/v1/id/> .
+@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#> .
+@prefix owl:  <http://www.w3.org/2002/07/owl#> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+
+gnt:editorial_status rdf:type owl:DatatypeProperty ;
+    rdfs:label "editorial status" ;
+    rdfs:comment "Curation and lifecycle status of a GN entity." .
+
+gnt:obsolete rdf:type skos:Concept ;
+    skos:prefLabel "obsolete" ;
+    skos:definition "Data retained for historical reasons but known to be incomplete, low-quality, or not scientifically useful." .
+
+gnt:deprecated rdf:type skos:Concept ;
+    skos:prefLabel "deprecated" ;
+    skos:definition "Data that should no longer be exposed in primary user interfaces." .
diff --git a/schema/mapping.ttl b/schema/mapping.ttl
new file mode 100644
index 0000000..5249526
--- /dev/null
+++ b/schema/mapping.ttl
@@ -0,0 +1,164 @@
+@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." .
diff --git a/schema/species.ttl b/schema/species.ttl
index 60ebd17..c66dda0 100644
--- a/schema/species.ttl
+++ b/schema/species.ttl
@@ -2,48 +2,58 @@
 
 @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 
-@prefix wd: <http://www.wikidata.org/entity/> .
 @prefix gn: <http://rdf.genenetwork.org/v1/id/> .
 @prefix gnt: <http://rdf.genenetwork.org/v1/term/> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
+@prefix wd: <http://www.wikidata.org/entity/> .
+
+
+gnt:has_wikidata_link a owl:ObjectProperty ;
+    rdfs:label "has Wikidata link" ;
+    rdfs:comment "Associates a GeneNetwork resource with its corresponding canonical entity in Wikidata." ;
+    rdfs:subPropertyOf skos:exactMatch ;
+    rdfs:range owl:Thing .
 
 # sorted on short names:
 #
-gn:Arabidopsis_thaliana rdf:isDefinedBy wd:Q158695 ;
+gn:Arabidopsis_thaliana gnt:has_wikidata_link wd:Q158695 ;
                         gnt:shortName "arabidopsis" .
 
-gn:Hordeum_vulgare rdf:isDefinedBy wd:Q11577 ;
+gn:Hordeum_vulgare gnt:has_wikidata_link wd:Q11577 ;
                gnt:shortName "barley" .
 
-gn:Glossophaga_soricina rdf:isDefinedBy wd:Q304929 ;
+gn:Glossophaga_soricina gnt:has_wikidata_link wd:Q304929 ;
                         gnt:shortName "bat" .
 
-gn:Drosophila_melanogaster rdf:isDefinedBy wd:Q130888 ;
+gn:Drosophila_melanogaster gnt:has_wikidata_link wd:Q130888 ;
 			   gnt:shortName "drosophila" .
 
-gn:Homo_sapiens rdf:isDefinedBy wd:Q15978631 ;
+gn:Homo_sapiens gnt:has_wikidata_link wd:Q15978631 ;
   	       gnt:shortName "human" .
 
 # Monkey
-# gn:Macaca_mulatta rdf:isDefinedBy wd:Q156606 ;
+# gn:Macaca_mulatta gnt:has_wikidata_link wd:Q156606 ;
 # 		  gnt:shortName "macaca" .
-gn:Macaca_nemestrina rdf:isDefinedBy wd:Q618026 ;
+gn:Macaca_nemestrina gnt:has_wikidata_link wd:Q618026 ;
   		     gnt:shortName "macaca" .
 
-gn:Mus_musculus rdf:isDefinedBy wd:Q83310 ;
+gn:Mus_musculus gnt:has_wikidata_link wd:Q83310 ;
 		gnt:shortName "mouse" .
 
-gn:Oryzias_latipes rdf:isDefinedBy wd:Q1142975 ;
+gn:Oryzias_latipes gnt:has_wikidata_link wd:Q1142975 ;
   		   gnt:shortName "medaka" .
 
-gn:Populus_trichocarpa rdf:isDefinedBy wd:Q149382 ;
+gn:Populus_trichocarpa gnt:has_wikidata_link wd:Q149382 ;
 		       gnt:shortName "poplar" .
 
-gn:Rattus_norvegicus rdf:isDefinedBy wd:Q184224 ;
+gn:Rattus_norvegicus gnt:has_wikidata_link wd:Q184224 ;
 		     gnt:shortName "rat" .
 
-gn:Glycine_max rdf:isDefinedBy wd:Q11006 ;
+gn:Glycine_max gnt:has_wikidata_link wd:Q11006 ;
 	       gnt:shortName "soybean" .
 
-gn:Solanum_lycopersicum rdf:isDefinedBy wd:Q23501 ;
+gn:Solanum_lycopersicum gnt:has_wikidata_link wd:Q23501 ;
 			gnt:shortName "tomato" .
generated by cgit-pink 1.4.1 (git 2.36.1) at 2026-02-08 18:37:24 +0000