--- a/kegg_pathways_visualization.xml	Fri Nov 09 05:16:58 2018 -0500
+++ b/kegg_pathways_visualization.xml	Fri Nov 09 05:22:50 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="kegg_pathways_visualization" name="KEGG pathways" version="2018.11.09">
+<tool id="kegg_pathways_visualization" name="KEGG pathways" version="2018.11.09.1">
     <description>map visualisation (PathView)</description>
     <requirements>
         <requirement type="package" version="1.18.0">bioconductor-pathview</requirement>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/hsa_pathways.loc.sample	Fri Nov 09 05:22:50 2018 -0500
@@ -0,0 +1,330 @@
+#value	name
+hsa00010	Glycolysis / Gluconeogenesis
+hsa00020	Citrate cycle (TCA cycle)
+hsa00030	Pentose phosphate pathway
+hsa00040	Pentose and glucuronate interconversions
+hsa00051	Fructose and mannose metabolism
+hsa00052	Galactose metabolism
+hsa00053	Ascorbate and aldarate metabolism
+hsa00061	Fatty acid biosynthesis
+hsa00062	Fatty acid elongation
+hsa00071	Fatty acid degradation
+hsa00072	Synthesis and degradation of ketone bodies
+hsa00100	Steroid biosynthesis
+hsa00120	Primary bile acid biosynthesis
+hsa00130	Ubiquinone and other terpenoid-quinone biosynthesis
+hsa00140	Steroid hormone biosynthesis
+hsa00190	Oxidative phosphorylation
+hsa00220	Arginine biosynthesis
+hsa00230	Purine metabolism
+hsa00232	Caffeine metabolism
+hsa00240	Pyrimidine metabolism
+hsa00250	Alanine, aspartate and glutamate metabolism
+hsa00260	Glycine, serine and threonine metabolism
+hsa00270	Cysteine and methionine metabolism
+hsa00280	Valine, leucine and isoleucine degradation
+hsa00290	Valine, leucine and isoleucine biosynthesis
+hsa00310	Lysine degradation
+hsa00330	Arginine and proline metabolism
+hsa00340	Histidine metabolism
+hsa00350	Tyrosine metabolism
+hsa00360	Phenylalanine metabolism
+hsa00380	Tryptophan metabolism
+hsa00400	Phenylalanine, tyrosine and tryptophan biosynthesis
+hsa00410	beta-Alanine metabolism
+hsa00430	Taurine and hypotaurine metabolism
+hsa00440	Phosphonate and phosphinate metabolism
+hsa00450	Selenocompound metabolism
+hsa00471	D-Glutamine and D-glutamate metabolism
+hsa00472	D-Arginine and D-ornithine metabolism
+hsa00480	Glutathione metabolism
+hsa00500	Starch and sucrose metabolism
+hsa00510	N-Glycan biosynthesis
+hsa00511	Other glycan degradation
+hsa00512	Mucin type O-glycan biosynthesis
+hsa00514	Other types of O-glycan biosynthesis
+hsa00515	Mannose type O-glycan biosynthesis
+hsa00520	Amino sugar and nucleotide sugar metabolism
+hsa00524	Neomycin, kanamycin and gentamicin biosynthesis
+hsa00531	Glycosaminoglycan degradation
+hsa00532	Glycosaminoglycan biosynthesis
+hsa00533	Glycosaminoglycan biosynthesis
+hsa00534	Glycosaminoglycan biosynthesis
+hsa00561	Glycerolipid metabolism
+hsa00562	Inositol phosphate metabolism
+hsa00563	Glycosylphosphatidylinositol (GPI)-anchor biosynthesis
+hsa00564	Glycerophospholipid metabolism
+hsa00565	Ether lipid metabolism
+hsa00590	Arachidonic acid metabolism
+hsa00591	Linoleic acid metabolism
+hsa00592	alpha-Linolenic acid metabolism
+hsa00600	Sphingolipid metabolism
+hsa00601	Glycosphingolipid biosynthesis
+hsa00603	Glycosphingolipid biosynthesis
+hsa00604	Glycosphingolipid biosynthesis
+hsa00620	Pyruvate metabolism
+hsa00630	Glyoxylate and dicarboxylate metabolism
+hsa00640	Propanoate metabolism
+hsa00650	Butanoate metabolism
+hsa00670	One carbon pool by folate
+hsa00730	Thiamine metabolism
+hsa00740	Riboflavin metabolism
+hsa00750	Vitamin B6 metabolism
+hsa00760	Nicotinate and nicotinamide metabolism
+hsa00770	Pantothenate and CoA biosynthesis
+hsa00780	Biotin metabolism
+hsa00785	Lipoic acid metabolism
+hsa00790	Folate biosynthesis
+hsa00830	Retinol metabolism
+hsa00860	Porphyrin and chlorophyll metabolism
+hsa00900	Terpenoid backbone biosynthesis
+hsa00910	Nitrogen metabolism
+hsa00920	Sulfur metabolism
+hsa00970	Aminoacyl-tRNA biosynthesis
+hsa00980	Metabolism of xenobiotics by cytochrome P450
+hsa00982	Drug metabolism
+hsa00983	Drug metabolism
+hsa01040	Biosynthesis of unsaturated fatty acids
+hsa01100	Metabolic pathways
+hsa01200	Carbon metabolism
+hsa01210	2-Oxocarboxylic acid metabolism
+hsa01212	Fatty acid metabolism
+hsa01230	Biosynthesis of amino acids
+hsa01521	EGFR tyrosine kinase inhibitor resistance
+hsa01522	Endocrine resistance
+hsa01523	Antifolate resistance
+hsa01524	Platinum drug resistance
+hsa02010	ABC transporters
+hsa03008	Ribosome biogenesis in eukaryotes
+hsa03010	Ribosome
+hsa03013	RNA transport
+hsa03015	mRNA surveillance pathway
+hsa03018	RNA degradation
+hsa03020	RNA polymerase
+hsa03022	Basal transcription factors
+hsa03030	DNA replication
+hsa03040	Spliceosome
+hsa03050	Proteasome
+hsa03060	Protein export
+hsa03320	PPAR signaling pathway
+hsa03410	Base excision repair
+hsa03420	Nucleotide excision repair
+hsa03430	Mismatch repair
+hsa03440	Homologous recombination
+hsa03450	Non-homologous end-joining
+hsa03460	Fanconi anemia pathway
+hsa04010	MAPK signaling pathway
+hsa04012	ErbB signaling pathway
+hsa04014	Ras signaling pathway
+hsa04015	Rap1 signaling pathway
+hsa04020	Calcium signaling pathway
+hsa04022	cGMP-PKG signaling pathway
+hsa04024	cAMP signaling pathway
+hsa04060	Cytokine-cytokine receptor interaction
+hsa04062	Chemokine signaling pathway
+hsa04064	NF-kappa B signaling pathway
+hsa04066	HIF-1 signaling pathway
+hsa04068	FoxO signaling pathway
+hsa04070	Phosphatidylinositol signaling system
+hsa04071	Sphingolipid signaling pathway
+hsa04072	Phospholipase D signaling pathway
+hsa04080	Neuroactive ligand-receptor interaction
+hsa04110	Cell cycle
+hsa04114	Oocyte meiosis
+hsa04115	p53 signaling pathway
+hsa04120	Ubiquitin mediated proteolysis
+hsa04122	Sulfur relay system
+hsa04130	SNARE interactions in vesicular transport
+hsa04136	Autophagy
+hsa04137	Mitophagy
+hsa04140	Autophagy
+hsa04141	Protein processing in endoplasmic reticulum
+hsa04142	Lysosome
+hsa04144	Endocytosis
+hsa04145	Phagosome
+hsa04146	Peroxisome
+hsa04150	mTOR signaling pathway
+hsa04151	PI3K-Akt signaling pathway
+hsa04152	AMPK signaling pathway
+hsa04210	Apoptosis
+hsa04211	Longevity regulating pathway
+hsa04213	Longevity regulating pathway
+hsa04215	Apoptosis
+hsa04216	Ferroptosis
+hsa04217	Necroptosis
+hsa04218	Cellular senescence
+hsa04260	Cardiac muscle contraction
+hsa04261	Adrenergic signaling in cardiomyocytes
+hsa04270	Vascular smooth muscle contraction
+hsa04310	Wnt signaling pathway
+hsa04330	Notch signaling pathway
+hsa04340	Hedgehog signaling pathway
+hsa04350	TGF-beta signaling pathway
+hsa04360	Axon guidance
+hsa04370	VEGF signaling pathway
+hsa04371	Apelin signaling pathway
+hsa04380	Osteoclast differentiation
+hsa04390	Hippo signaling pathway
+hsa04392	Hippo signaling pathway
+hsa04510	Focal adhesion
+hsa04512	ECM-receptor interaction
+hsa04514	Cell adhesion molecules (CAMs)
+hsa04520	Adherens junction
+hsa04530	Tight junction
+hsa04540	Gap junction
+hsa04550	Signaling pathways regulating pluripotency of stem cells
+hsa04610	Complement and coagulation cascades
+hsa04611	Platelet activation
+hsa04612	Antigen processing and presentation
+hsa04614	Renin-angiotensin system
+hsa04620	Toll-like receptor signaling pathway
+hsa04621	NOD-like receptor signaling pathway
+hsa04622	RIG-I-like receptor signaling pathway
+hsa04623	Cytosolic DNA-sensing pathway
+hsa04625	C-type lectin receptor signaling pathway
+hsa04630	Jak-STAT signaling pathway
+hsa04640	Hematopoietic cell lineage
+hsa04650	Natural killer cell mediated cytotoxicity
+hsa04657	IL-17 signaling pathway
+hsa04658	Th1 and Th2 cell differentiation
+hsa04659	Th17 cell differentiation
+hsa04660	T cell receptor signaling pathway
+hsa04662	B cell receptor signaling pathway
+hsa04664	Fc epsilon RI signaling pathway
+hsa04666	Fc gamma R-mediated phagocytosis
+hsa04668	TNF signaling pathway
+hsa04670	Leukocyte transendothelial migration
+hsa04672	Intestinal immune network for IgA production
+hsa04710	Circadian rhythm
+hsa04713	Circadian entrainment
+hsa04714	Thermogenesis
+hsa04720	Long-term potentiation
+hsa04721	Synaptic vesicle cycle
+hsa04722	Neurotrophin signaling pathway
+hsa04723	Retrograde endocannabinoid signaling
+hsa04724	Glutamatergic synapse
+hsa04725	Cholinergic synapse
+hsa04726	Serotonergic synapse
+hsa04727	GABAergic synapse
+hsa04728	Dopaminergic synapse
+hsa04730	Long-term depression
+hsa04740	Olfactory transduction
+hsa04742	Taste transduction
+hsa04744	Phototransduction
+hsa04750	Inflammatory mediator regulation of TRP channels
+hsa04810	Regulation of actin cytoskeleton
+hsa04910	Insulin signaling pathway
+hsa04911	Insulin secretion
+hsa04912	GnRH signaling pathway
+hsa04913	Ovarian steroidogenesis
+hsa04914	Progesterone-mediated oocyte maturation
+hsa04915	Estrogen signaling pathway
+hsa04916	Melanogenesis
+hsa04917	Prolactin signaling pathway
+hsa04918	Thyroid hormone synthesis
+hsa04919	Thyroid hormone signaling pathway
+hsa04920	Adipocytokine signaling pathway
+hsa04921	Oxytocin signaling pathway
+hsa04922	Glucagon signaling pathway
+hsa04923	Regulation of lipolysis in adipocytes
+hsa04924	Renin secretion
+hsa04925	Aldosterone synthesis and secretion
+hsa04926	Relaxin signaling pathway
+hsa04927	Cortisol synthesis and secretion
+hsa04928	Parathyroid hormone synthesis, secretion and action
+hsa04930	Type II diabetes mellitus
+hsa04931	Insulin resistance
+hsa04932	Non-alcoholic fatty liver disease (NAFLD)
+hsa04933	AGE-RAGE signaling pathway in diabetic complications
+hsa04934	Cushing's syndrome
+hsa04940	Type I diabetes mellitus
+hsa04950	Maturity onset diabetes of the young
+hsa04960	Aldosterone-regulated sodium reabsorption
+hsa04961	Endocrine and other factor-regulated calcium reabsorption
+hsa04962	Vasopressin-regulated water reabsorption
+hsa04964	Proximal tubule bicarbonate reclamation
+hsa04966	Collecting duct acid secretion
+hsa04970	Salivary secretion
+hsa04971	Gastric acid secretion
+hsa04972	Pancreatic secretion
+hsa04973	Carbohydrate digestion and absorption
+hsa04974	Protein digestion and absorption
+hsa04975	Fat digestion and absorption
+hsa04976	Bile secretion
+hsa04977	Vitamin digestion and absorption
+hsa04978	Mineral absorption
+hsa04979	Cholesterol metabolism
+hsa05010	Alzheimer's disease
+hsa05012	Parkinson's disease
+hsa05014	Amyotrophic lateral sclerosis (ALS)
+hsa05016	Huntington's disease
+hsa05020	Prion diseases
+hsa05030	Cocaine addiction
+hsa05031	Amphetamine addiction
+hsa05032	Morphine addiction
+hsa05033	Nicotine addiction
+hsa05034	Alcoholism
+hsa05100	Bacterial invasion of epithelial cells
+hsa05110	Vibrio cholerae infection
+hsa05120	Epithelial cell signaling in Helicobacter pylori infection
+hsa05130	Pathogenic Escherichia coli infection
+hsa05131	Shigellosis
+hsa05132	Salmonella infection
+hsa05133	Pertussis
+hsa05134	Legionellosis
+hsa05140	Leishmaniasis
+hsa05142	Chagas disease (American trypanosomiasis)
+hsa05143	African trypanosomiasis
+hsa05144	Malaria
+hsa05145	Toxoplasmosis
+hsa05146	Amoebiasis
+hsa05150	Staphylococcus aureus infection
+hsa05152	Tuberculosis
+hsa05160	Hepatitis C
+hsa05161	Hepatitis B
+hsa05162	Measles
+hsa05163	Human cytomegalovirus infection
+hsa05164	Influenza A
+hsa05165	Human papillomavirus infection
+hsa05166	HTLV-I infection
+hsa05167	Kaposi's sarcoma-associated herpesvirus infection
+hsa05168	Herpes simplex infection
+hsa05169	Epstein-Barr virus infection
+hsa05200	Pathways in cancer
+hsa05202	Transcriptional misregulation in cancer
+hsa05203	Viral carcinogenesis
+hsa05204	Chemical carcinogenesis
+hsa05205	Proteoglycans in cancer
+hsa05206	MicroRNAs in cancer
+hsa05210	Colorectal cancer
+hsa05211	Renal cell carcinoma
+hsa05212	Pancreatic cancer
+hsa05213	Endometrial cancer
+hsa05214	Glioma
+hsa05215	Prostate cancer
+hsa05216	Thyroid cancer
+hsa05217	Basal cell carcinoma
+hsa05218	Melanoma
+hsa05219	Bladder cancer
+hsa05220	Chronic myeloid leukemia
+hsa05221	Acute myeloid leukemia
+hsa05222	Small cell lung cancer
+hsa05223	Non-small cell lung cancer
+hsa05224	Breast cancer
+hsa05225	Hepatocellular carcinoma
+hsa05226	Gastric cancer
+hsa05230	Central carbon metabolism in cancer
+hsa05231	Choline metabolism in cancer
+hsa05310	Asthma
+hsa05320	Autoimmune thyroid disease
+hsa05321	Inflammatory bowel disease (IBD)
+hsa05322	Systemic lupus erythematosus
+hsa05323	Rheumatoid arthritis
+hsa05330	Allograft rejection
+hsa05332	Graft-versus-host disease
+hsa05340	Primary immunodeficiency
+hsa05410	Hypertrophic cardiomyopathy (HCM)
+hsa05412	Arrhythmogenic right ventricular cardiomyopathy (ARVC)
+hsa05414	Dilated cardiomyopathy (DCM)
+hsa05416	Viral myocarditis
+hsa05418	Fluid shear stress and atherosclerosis

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/mmu_pathways.loc.sample	Fri Nov 09 05:22:50 2018 -0500
@@ -0,0 +1,326 @@
+#value	name
+mmu00010	Glycolysis / Gluconeogenesis
+mmu00020	Citrate cycle (TCA cycle)
+mmu00030	Pentose phosphate pathway
+mmu00040	Pentose and glucuronate interconversions
+mmu00051	Fructose and mannose metabolism
+mmu00052	Galactose metabolism
+mmu00053	Ascorbate and aldarate metabolism
+mmu00061	Fatty acid biosynthesis
+mmu00062	Fatty acid elongation
+mmu00071	Fatty acid degradation
+mmu00072	Synthesis and degradation of ketone bodies
+mmu00100	Steroid biosynthesis
+mmu00120	Primary bile acid biosynthesis
+mmu00130	Ubiquinone and other terpenoid-quinone biosynthesis
+mmu00140	Steroid hormone biosynthesis
+mmu00190	Oxidative phosphorylation
+mmu00220	Arginine biosynthesis
+mmu00230	Purine metabolism
+mmu00232	Caffeine metabolism
+mmu00240	Pyrimidine metabolism
+mmu00250	Alanine, aspartate and glutamate metabolism
+mmu00260	Glycine, serine and threonine metabolism
+mmu00270	Cysteine and methionine metabolism
+mmu00280	Valine, leucine and isoleucine degradation
+mmu00290	Valine, leucine and isoleucine biosynthesis
+mmu00310	Lysine degradation
+mmu00330	Arginine and proline metabolism
+mmu00340	Histidine metabolism
+mmu00350	Tyrosine metabolism
+mmu00360	Phenylalanine metabolism
+mmu00380	Tryptophan metabolism
+mmu00400	Phenylalanine, tyrosine and tryptophan biosynthesis
+mmu00410	beta-Alanine metabolism
+mmu00430	Taurine and hypotaurine metabolism
+mmu00440	Phosphonate and phosphinate metabolism
+mmu00450	Selenocompound metabolism
+mmu00471	D-Glutamine and D-glutamate metabolism
+mmu00472	D-Arginine and D-ornithine metabolism
+mmu00480	Glutathione metabolism
+mmu00500	Starch and sucrose metabolism
+mmu00510	N-Glycan biosynthesis
+mmu00511	Other glycan degradation
+mmu00512	Mucin type O-glycan biosynthesis
+mmu00514	Other types of O-glycan biosynthesis
+mmu00515	Mannose type O-glycan biosynthesis
+mmu00520	Amino sugar and nucleotide sugar metabolism
+mmu00524	Neomycin, kanamycin and gentamicin biosynthesis
+mmu00531	Glycosaminoglycan degradation
+mmu00532	Glycosaminoglycan biosynthesis
+mmu00533	Glycosaminoglycan biosynthesis
+mmu00534	Glycosaminoglycan biosynthesis
+mmu00561	Glycerolipid metabolism
+mmu00562	Inositol phosphate metabolism
+mmu00563	Glycosylphosphatidylinositol (GPI)-anchor biosynthesis
+mmu00564	Glycerophospholipid metabolism
+mmu00565	Ether lipid metabolism
+mmu00590	Arachidonic acid metabolism
+mmu00591	Linoleic acid metabolism
+mmu00592	alpha-Linolenic acid metabolism
+mmu00600	Sphingolipid metabolism
+mmu00601	Glycosphingolipid biosynthesis
+mmu00603	Glycosphingolipid biosynthesis
+mmu00604	Glycosphingolipid biosynthesis
+mmu00620	Pyruvate metabolism
+mmu00630	Glyoxylate and dicarboxylate metabolism
+mmu00640	Propanoate metabolism
+mmu00650	Butanoate metabolism
+mmu00670	One carbon pool by folate
+mmu00730	Thiamine metabolism
+mmu00740	Riboflavin metabolism
+mmu00750	Vitamin B6 metabolism
+mmu00760	Nicotinate and nicotinamide metabolism
+mmu00770	Pantothenate and CoA biosynthesis
+mmu00780	Biotin metabolism
+mmu00785	Lipoic acid metabolism
+mmu00790	Folate biosynthesis
+mmu00830	Retinol metabolism
+mmu00860	Porphyrin and chlorophyll metabolism
+mmu00900	Terpenoid backbone biosynthesis
+mmu00910	Nitrogen metabolism
+mmu00920	Sulfur metabolism
+mmu00970	Aminoacyl-tRNA biosynthesis
+mmu00980	Metabolism of xenobiotics by cytochrome P450
+mmu00982	Drug metabolism
+mmu00983	Drug metabolism
+mmu01040	Biosynthesis of unsaturated fatty acids
+mmu01100	Metabolic pathways
+mmu01200	Carbon metabolism
+mmu01210	2-Oxocarboxylic acid metabolism
+mmu01212	Fatty acid metabolism
+mmu01230	Biosynthesis of amino acids
+mmu01521	EGFR tyrosine kinase inhibitor resistance
+mmu01522	Endocrine resistance
+mmu01523	Antifolate resistance
+mmu01524	Platinum drug resistance
+mmu02010	ABC transporters
+mmu03008	Ribosome biogenesis in eukaryotes
+mmu03010	Ribosome
+mmu03013	RNA transport
+mmu03015	mRNA surveillance pathway
+mmu03018	RNA degradation
+mmu03020	RNA polymerase
+mmu03022	Basal transcription factors
+mmu03030	DNA replication
+mmu03040	Spliceosome
+mmu03050	Proteasome
+mmu03060	Protein export
+mmu03320	PPAR signaling pathway
+mmu03410	Base excision repair
+mmu03420	Nucleotide excision repair
+mmu03430	Mismatch repair
+mmu03440	Homologous recombination
+mmu03450	Non-homologous end-joining
+mmu03460	Fanconi anemia pathway
+mmu04010	MAPK signaling pathway
+mmu04012	ErbB signaling pathway
+mmu04014	Ras signaling pathway
+mmu04015	Rap1 signaling pathway
+mmu04020	Calcium signaling pathway
+mmu04022	cGMP-PKG signaling pathway
+mmu04024	cAMP signaling pathway
+mmu04060	Cytokine-cytokine receptor interaction
+mmu04062	Chemokine signaling pathway
+mmu04064	NF-kappa B signaling pathway
+mmu04066	HIF-1 signaling pathway
+mmu04068	FoxO signaling pathway
+mmu04070	Phosphatidylinositol signaling system
+mmu04071	Sphingolipid signaling pathway
+mmu04072	Phospholipase D signaling pathway
+mmu04080	Neuroactive ligand-receptor interaction
+mmu04110	Cell cycle
+mmu04114	Oocyte meiosis
+mmu04115	p53 signaling pathway
+mmu04120	Ubiquitin mediated proteolysis
+mmu04122	Sulfur relay system
+mmu04130	SNARE interactions in vesicular transport
+mmu04136	Autophagy
+mmu04137	Mitophagy
+mmu04140	Autophagy
+mmu04141	Protein processing in endoplasmic reticulum
+mmu04142	Lysosome
+mmu04144	Endocytosis
+mmu04145	Phagosome
+mmu04146	Peroxisome
+mmu04150	mTOR signaling pathway
+mmu04151	PI3K-Akt signaling pathway
+mmu04152	AMPK signaling pathway
+mmu04210	Apoptosis
+mmu04211	Longevity regulating pathway
+mmu04213	Longevity regulating pathway
+mmu04215	Apoptosis
+mmu04216	Ferroptosis
+mmu04217	Necroptosis
+mmu04218	Cellular senescence
+mmu04260	Cardiac muscle contraction
+mmu04261	Adrenergic signaling in cardiomyocytes
+mmu04270	Vascular smooth muscle contraction
+mmu04310	Wnt signaling pathway
+mmu04330	Notch signaling pathway
+mmu04340	Hedgehog signaling pathway
+mmu04350	TGF-beta signaling pathway
+mmu04360	Axon guidance
+mmu04370	VEGF signaling pathway
+mmu04371	Apelin signaling pathway
+mmu04380	Osteoclast differentiation
+mmu04390	Hippo signaling pathway
+mmu04392	Hippo signaling pathway
+mmu04510	Focal adhesion
+mmu04512	ECM-receptor interaction
+mmu04514	Cell adhesion molecules (CAMs)
+mmu04520	Adherens junction
+mmu04530	Tight junction
+mmu04540	Gap junction
+mmu04550	Signaling pathways regulating pluripotency of stem cells
+mmu04610	Complement and coagulation cascades
+mmu04611	Platelet activation
+mmu04612	Antigen processing and presentation
+mmu04614	Renin-angiotensin system
+mmu04620	Toll-like receptor signaling pathway
+mmu04621	NOD-like receptor signaling pathway
+mmu04622	RIG-I-like receptor signaling pathway
+mmu04623	Cytosolic DNA-sensing pathway
+mmu04625	C-type lectin receptor signaling pathway
+mmu04630	Jak-STAT signaling pathway
+mmu04640	Hematopoietic cell lineage
+mmu04650	Natural killer cell mediated cytotoxicity
+mmu04657	IL-17 signaling pathway
+mmu04658	Th1 and Th2 cell differentiation
+mmu04659	Th17 cell differentiation
+mmu04660	T cell receptor signaling pathway
+mmu04662	B cell receptor signaling pathway
+mmu04664	Fc epsilon RI signaling pathway
+mmu04666	Fc gamma R-mediated phagocytosis
+mmu04668	TNF signaling pathway
+mmu04670	Leukocyte transendothelial migration
+mmu04672	Intestinal immune network for IgA production
+mmu04710	Circadian rhythm
+mmu04713	Circadian entrainment
+mmu04714	Thermogenesis
+mmu04720	Long-term potentiation
+mmu04721	Synaptic vesicle cycle
+mmu04722	Neurotrophin signaling pathway
+mmu04723	Retrograde endocannabinoid signaling
+mmu04724	Glutamatergic synapse
+mmu04725	Cholinergic synapse
+mmu04726	Serotonergic synapse
+mmu04727	GABAergic synapse
+mmu04728	Dopaminergic synapse
+mmu04730	Long-term depression
+mmu04740	Olfactory transduction
+mmu04742	Taste transduction
+mmu04744	Phototransduction
+mmu04750	Inflammatory mediator regulation of TRP channels
+mmu04810	Regulation of actin cytoskeleton
+mmu04910	Insulin signaling pathway
+mmu04911	Insulin secretion
+mmu04912	GnRH signaling pathway
+mmu04913	Ovarian steroidogenesis
+mmu04914	Progesterone-mediated oocyte maturation
+mmu04915	Estrogen signaling pathway
+mmu04916	Melanogenesis
+mmu04917	Prolactin signaling pathway
+mmu04918	Thyroid hormone synthesis
+mmu04919	Thyroid hormone signaling pathway
+mmu04920	Adipocytokine signaling pathway
+mmu04921	Oxytocin signaling pathway
+mmu04922	Glucagon signaling pathway
+mmu04923	Regulation of lipolysis in adipocytes
+mmu04924	Renin secretion
+mmu04925	Aldosterone synthesis and secretion
+mmu04926	Relaxin signaling pathway
+mmu04927	Cortisol synthesis and secretion
+mmu04928	Parathyroid hormone synthesis, secretion and action
+mmu04930	Type II diabetes mellitus
+mmu04931	Insulin resistance
+mmu04932	Non-alcoholic fatty liver disease (NAFLD)
+mmu04933	AGE-RAGE signaling pathway in diabetic complications
+mmu04934	Cushing's syndrome
+mmu04940	Type I diabetes mellitus
+mmu04950	Maturity onset diabetes of the young
+mmu04960	Aldosterone-regulated sodium reabsorption
+mmu04961	Endocrine and other factor-regulated calcium reabsorption
+mmu04962	Vasopressin-regulated water reabsorption
+mmu04964	Proximal tubule bicarbonate reclamation
+mmu04966	Collecting duct acid secretion
+mmu04970	Salivary secretion
+mmu04971	Gastric acid secretion
+mmu04972	Pancreatic secretion
+mmu04973	Carbohydrate digestion and absorption
+mmu04974	Protein digestion and absorption
+mmu04975	Fat digestion and absorption
+mmu04976	Bile secretion
+mmu04977	Vitamin digestion and absorption
+mmu04978	Mineral absorption
+mmu04979	Cholesterol metabolism
+mmu05010	Alzheimer's disease
+mmu05012	Parkinson's disease
+mmu05014	Amyotrophic lateral sclerosis (ALS)
+mmu05016	Huntington's disease
+mmu05020	Prion diseases
+mmu05030	Cocaine addiction
+mmu05031	Amphetamine addiction
+mmu05032	Morphine addiction
+mmu05033	Nicotine addiction
+mmu05034	Alcoholism
+mmu05100	Bacterial invasion of epithelial cells
+mmu05132	Salmonella infection
+mmu05133	Pertussis
+mmu05134	Legionellosis
+mmu05140	Leishmaniasis
+mmu05142	Chagas disease (American trypanosomiasis)
+mmu05143	African trypanosomiasis
+mmu05144	Malaria
+mmu05145	Toxoplasmosis
+mmu05146	Amoebiasis
+mmu05150	Staphylococcus aureus infection
+mmu05152	Tuberculosis
+mmu05160	Hepatitis C
+mmu05161	Hepatitis B
+mmu05162	Measles
+mmu05163	Human cytomegalovirus infection
+mmu05164	Influenza A
+mmu05165	Human papillomavirus infection
+mmu05166	HTLV-I infection
+mmu05167	Kaposi's sarcoma-associated herpesvirus infection
+mmu05168	Herpes simplex infection
+mmu05169	Epstein-Barr virus infection
+mmu05200	Pathways in cancer
+mmu05202	Transcriptional misregulation in cancer
+mmu05203	Viral carcinogenesis
+mmu05204	Chemical carcinogenesis
+mmu05205	Proteoglycans in cancer
+mmu05206	MicroRNAs in cancer
+mmu05210	Colorectal cancer
+mmu05211	Renal cell carcinoma
+mmu05212	Pancreatic cancer
+mmu05213	Endometrial cancer
+mmu05214	Glioma
+mmu05215	Prostate cancer
+mmu05216	Thyroid cancer
+mmu05217	Basal cell carcinoma
+mmu05218	Melanoma
+mmu05219	Bladder cancer
+mmu05220	Chronic myeloid leukemia
+mmu05221	Acute myeloid leukemia
+mmu05222	Small cell lung cancer
+mmu05223	Non-small cell lung cancer
+mmu05224	Breast cancer
+mmu05225	Hepatocellular carcinoma
+mmu05226	Gastric cancer
+mmu05230	Central carbon metabolism in cancer
+mmu05231	Choline metabolism in cancer
+mmu05310	Asthma
+mmu05320	Autoimmune thyroid disease
+mmu05321	Inflammatory bowel disease (IBD)
+mmu05322	Systemic lupus erythematosus
+mmu05323	Rheumatoid arthritis
+mmu05330	Allograft rejection
+mmu05332	Graft-versus-host disease
+mmu05340	Primary immunodeficiency
+mmu05410	Hypertrophic cardiomyopathy (HCM)
+mmu05412	Arrhythmogenic right ventricular cardiomyopathy (ARVC)
+mmu05414	Dilated cardiomyopathy (DCM)
+mmu05416	Viral myocarditis
+mmu05418	Fluid shear stress and atherosclerosis

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/rno_pathways.loc.sample	Fri Nov 09 05:22:50 2018 -0500
@@ -0,0 +1,326 @@
+rno00010	Glycolysis / Gluconeogenesis
+rno00020	Citrate cycle (TCA cycle)
+rno00030	Pentose phosphate pathway
+rno00040	Pentose and glucuronate interconversions
+rno00051	Fructose and mannose metabolism
+rno00052	Galactose metabolism
+rno00053	Ascorbate and aldarate metabolism
+rno00061	Fatty acid biosynthesis
+rno00062	Fatty acid elongation
+rno00071	Fatty acid degradation
+rno00072	Synthesis and degradation of ketone bodies
+rno00100	Steroid biosynthesis
+rno00120	Primary bile acid biosynthesis
+rno00130	Ubiquinone and other terpenoid-quinone biosynthesis
+rno00140	Steroid hormone biosynthesis
+rno00190	Oxidative phosphorylation
+rno00220	Arginine biosynthesis
+rno00230	Purine metabolism
+rno00232	Caffeine metabolism
+rno00240	Pyrimidine metabolism
+rno00250	Alanine, aspartate and glutamate metabolism
+rno00260	Glycine, serine and threonine metabolism
+rno00270	Cysteine and methionine metabolism
+rno00280	Valine, leucine and isoleucine degradation
+rno00290	Valine, leucine and isoleucine biosynthesis
+rno00310	Lysine degradation
+rno00330	Arginine and proline metabolism
+rno00340	Histidine metabolism
+rno00350	Tyrosine metabolism
+rno00360	Phenylalanine metabolism
+rno00380	Tryptophan metabolism
+rno00400	Phenylalanine, tyrosine and tryptophan biosynthesis
+rno00410	beta-Alanine metabolism
+rno00430	Taurine and hypotaurine metabolism
+rno00440	Phosphonate and phosphinate metabolism
+rno00450	Selenocompound metabolism
+rno00471	D-Glutamine and D-glutamate metabolism
+rno00472	D-Arginine and D-ornithine metabolism
+rno00480	Glutathione metabolism
+rno00500	Starch and sucrose metabolism
+rno00510	N-Glycan biosynthesis
+rno00511	Other glycan degradation
+rno00512	Mucin type O-glycan biosynthesis
+rno00514	Other types of O-glycan biosynthesis
+rno00515	Mannose type O-glycan biosynthesis
+rno00520	Amino sugar and nucleotide sugar metabolism
+rno00524	Neomycin, kanamycin and gentamicin biosynthesis
+rno00531	Glycosaminoglycan degradation
+rno00532	Glycosaminoglycan biosynthesis
+rno00533	Glycosaminoglycan biosynthesis
+rno00534	Glycosaminoglycan biosynthesis
+rno00561	Glycerolipid metabolism
+rno00562	Inositol phosphate metabolism
+rno00563	Glycosylphosphatidylinositol (GPI)-anchor biosynthesis
+rno00564	Glycerophospholipid metabolism
+rno00565	Ether lipid metabolism
+rno00590	Arachidonic acid metabolism
+rno00591	Linoleic acid metabolism
+rno00592	alpha-Linolenic acid metabolism
+rno00600	Sphingolipid metabolism
+rno00601	Glycosphingolipid biosynthesis
+rno00603	Glycosphingolipid biosynthesis
+rno00604	Glycosphingolipid biosynthesis
+rno00620	Pyruvate metabolism
+rno00630	Glyoxylate and dicarboxylate metabolism
+rno00640	Propanoate metabolism
+rno00650	Butanoate metabolism
+rno00670	One carbon pool by folate
+rno00730	Thiamine metabolism
+rno00740	Riboflavin metabolism
+rno00750	Vitamin B6 metabolism
+rno00760	Nicotinate and nicotinamide metabolism
+rno00770	Pantothenate and CoA biosynthesis
+rno00780	Biotin metabolism
+rno00785	Lipoic acid metabolism
+rno00790	Folate biosynthesis
+rno00830	Retinol metabolism
+rno00860	Porphyrin and chlorophyll metabolism
+rno00900	Terpenoid backbone biosynthesis
+rno00910	Nitrogen metabolism
+rno00920	Sulfur metabolism
+rno00970	Aminoacyl-tRNA biosynthesis
+rno00980	Metabolism of xenobiotics by cytochrome P450
+rno00982	Drug metabolism
+rno00983	Drug metabolism
+rno01040	Biosynthesis of unsaturated fatty acids
+rno01100	Metabolic pathways
+rno01200	Carbon metabolism
+rno01210	2-Oxocarboxylic acid metabolism
+rno01212	Fatty acid metabolism
+rno01230	Biosynthesis of amino acids
+rno01521	EGFR tyrosine kinase inhibitor resistance
+rno01522	Endocrine resistance
+rno01523	Antifolate resistance
+rno01524	Platinum drug resistance
+rno02010	ABC transporters
+rno03008	Ribosome biogenesis in eukaryotes
+rno03010	Ribosome
+rno03013	RNA transport
+rno03015	mRNA surveillance pathway
+rno03018	RNA degradation
+rno03020	RNA polymerase
+rno03022	Basal transcription factors
+rno03030	DNA replication
+rno03040	Spliceosome
+rno03050	Proteasome
+rno03060	Protein export
+rno03320	PPAR signaling pathway
+rno03410	Base excision repair
+rno03420	Nucleotide excision repair
+rno03430	Mismatch repair
+rno03440	Homologous recombination
+rno03450	Non-homologous end-joining
+rno03460	Fanconi anemia pathway
+rno04010	MAPK signaling pathway
+rno04012	ErbB signaling pathway
+rno04014	Ras signaling pathway
+rno04015	Rap1 signaling pathway
+rno04020	Calcium signaling pathway
+rno04022	cGMP-PKG signaling pathway
+rno04024	cAMP signaling pathway
+rno04060	Cytokine-cytokine receptor interaction
+rno04062	Chemokine signaling pathway
+rno04064	NF-kappa B signaling pathway
+rno04066	HIF-1 signaling pathway
+rno04068	FoxO signaling pathway
+rno04070	Phosphatidylinositol signaling system
+rno04071	Sphingolipid signaling pathway
+rno04072	Phospholipase D signaling pathway
+rno04080	Neuroactive ligand-receptor interaction
+rno04110	Cell cycle
+rno04114	Oocyte meiosis
+rno04115	p53 signaling pathway
+rno04120	Ubiquitin mediated proteolysis
+rno04122	Sulfur relay system
+rno04130	SNARE interactions in vesicular transport
+rno04136	Autophagy
+rno04137	Mitophagy
+rno04140	Autophagy
+rno04141	Protein processing in endoplasmic reticulum
+rno04142	Lysosome
+rno04144	Endocytosis
+rno04145	Phagosome
+rno04146	Peroxisome
+rno04150	mTOR signaling pathway
+rno04151	PI3K-Akt signaling pathway
+rno04152	AMPK signaling pathway
+rno04210	Apoptosis
+rno04211	Longevity regulating pathway
+rno04213	Longevity regulating pathway
+rno04215	Apoptosis
+rno04216	Ferroptosis
+rno04217	Necroptosis
+rno04218	Cellular senescence
+rno04260	Cardiac muscle contraction
+rno04261	Adrenergic signaling in cardiomyocytes
+rno04270	Vascular smooth muscle contraction
+rno04310	Wnt signaling pathway
+rno04330	Notch signaling pathway
+rno04340	Hedgehog signaling pathway
+rno04350	TGF-beta signaling pathway
+rno04360	Axon guidance
+rno04370	VEGF signaling pathway
+rno04371	Apelin signaling pathway
+rno04380	Osteoclast differentiation
+rno04390	Hippo signaling pathway
+rno04392	Hippo signaling pathway
+rno04510	Focal adhesion
+rno04512	ECM-receptor interaction
+rno04514	Cell adhesion molecules (CAMs)
+rno04520	Adherens junction
+rno04530	Tight junction
+rno04540	Gap junction
+rno04550	Signaling pathways regulating pluripotency of stem cells
+rno04610	Complement and coagulation cascades
+rno04611	Platelet activation
+rno04612	Antigen processing and presentation
+rno04614	Renin-angiotensin system
+rno04620	Toll-like receptor signaling pathway
+rno04621	NOD-like receptor signaling pathway
+rno04622	RIG-I-like receptor signaling pathway
+rno04623	Cytosolic DNA-sensing pathway
+rno04625	C-type lectin receptor signaling pathway
+rno04630	JAK-STAT signaling pathway
+rno04640	Hematopoietic cell lineage
+rno04650	Natural killer cell mediated cytotoxicity
+rno04657	IL-17 signaling pathway
+rno04658	Th1 and Th2 cell differentiation
+rno04659	Th17 cell differentiation
+rno04660	T cell receptor signaling pathway
+rno04662	B cell receptor signaling pathway
+rno04664	Fc epsilon RI signaling pathway
+rno04666	Fc gamma R-mediated phagocytosis
+rno04668	TNF signaling pathway
+rno04670	Leukocyte transendothelial migration
+rno04672	Intestinal immune network for IgA production
+rno04710	Circadian rhythm
+rno04713	Circadian entrainment
+rno04714	Thermogenesis
+rno04720	Long-term potentiation
+rno04721	Synaptic vesicle cycle
+rno04722	Neurotrophin signaling pathway
+rno04723	Retrograde endocannabinoid signaling
+rno04724	Glutamatergic synapse
+rno04725	Cholinergic synapse
+rno04726	Serotonergic synapse
+rno04727	GABAergic synapse
+rno04728	Dopaminergic synapse
+rno04730	Long-term depression
+rno04740	Olfactory transduction
+rno04742	Taste transduction
+rno04744	Phototransduction
+rno04750	Inflammatory mediator regulation of TRP channels
+rno04810	Regulation of actin cytoskeleton
+rno04910	Insulin signaling pathway
+rno04911	Insulin secretion
+rno04912	GnRH signaling pathway
+rno04913	Ovarian steroidogenesis
+rno04914	Progesterone-mediated oocyte maturation
+rno04915	Estrogen signaling pathway
+rno04916	Melanogenesis
+rno04917	Prolactin signaling pathway
+rno04918	Thyroid hormone synthesis
+rno04919	Thyroid hormone signaling pathway
+rno04920	Adipocytokine signaling pathway
+rno04921	Oxytocin signaling pathway
+rno04922	Glucagon signaling pathway
+rno04923	Regulation of lipolysis in adipocytes
+rno04924	Renin secretion
+rno04925	Aldosterone synthesis and secretion
+rno04926	Relaxin signaling pathway
+rno04927	Cortisol synthesis and secretion
+rno04928	Parathyroid hormone synthesis, secretion and action
+rno04930	Type II diabetes mellitus
+rno04931	Insulin resistance
+rno04932	Non-alcoholic fatty liver disease (NAFLD)
+rno04933	AGE-RAGE signaling pathway in diabetic complications
+rno04934	Cushing syndrome
+rno04940	Type I diabetes mellitus
+rno04950	Maturity onset diabetes of the young
+rno04960	Aldosterone-regulated sodium reabsorption
+rno04961	Endocrine and other factor-regulated calcium reabsorption
+rno04962	Vasopressin-regulated water reabsorption
+rno04964	Proximal tubule bicarbonate reclamation
+rno04966	Collecting duct acid secretion
+rno04970	Salivary secretion
+rno04971	Gastric acid secretion
+rno04972	Pancreatic secretion
+rno04973	Carbohydrate digestion and absorption
+rno04974	Protein digestion and absorption
+rno04975	Fat digestion and absorption
+rno04976	Bile secretion
+rno04977	Vitamin digestion and absorption
+rno04978	Mineral absorption
+rno04979	Cholesterol metabolism
+rno05010	Alzheimer disease
+rno05012	Parkinson disease
+rno05014	Amyotrophic lateral sclerosis (ALS)
+rno05016	Huntington disease
+rno05020	Prion diseases
+rno05030	Cocaine addiction
+rno05031	Amphetamine addiction
+rno05032	Morphine addiction
+rno05033	Nicotine addiction
+rno05034	Alcoholism
+rno05100	Bacterial invasion of epithelial cells
+rno05132	Salmonella infection
+rno05133	Pertussis
+rno05134	Legionellosis
+rno05140	Leishmaniasis
+rno05142	Chagas disease (American trypanosomiasis)
+rno05143	African trypanosomiasis
+rno05144	Malaria
+rno05145	Toxoplasmosis
+rno05146	Amoebiasis
+rno05150	Staphylococcus aureus infection
+rno05152	Tuberculosis
+rno05160	Hepatitis C
+rno05161	Hepatitis B
+rno05162	Measles
+rno05163	Human cytomegalovirus infection
+rno05164	Influenza A
+rno05165	Human papillomavirus infection
+rno05166	Human T-cell leukemia virus 1 infection
+rno05167	Kaposi sarcoma-associated herpesvirus infection
+rno05168	Herpes simplex infection
+rno05169	Epstein-Barr virus infection
+rno05170	Human immunodeficiency virus 1 infection
+rno05200	Pathways in cancer
+rno05202	Transcriptional misregulation in cancer
+rno05203	Viral carcinogenesis
+rno05204	Chemical carcinogenesis
+rno05205	Proteoglycans in cancer
+rno05206	MicroRNAs in cancer
+rno05210	Colorectal cancer
+rno05211	Renal cell carcinoma
+rno05212	Pancreatic cancer
+rno05213	Endometrial cancer
+rno05214	Glioma
+rno05215	Prostate cancer
+rno05216	Thyroid cancer
+rno05217	Basal cell carcinoma
+rno05218	Melanoma
+rno05219	Bladder cancer
+rno05220	Chronic myeloid leukemia
+rno05221	Acute myeloid leukemia
+rno05222	Small cell lung cancer
+rno05223	Non-small cell lung cancer
+rno05224	Breast cancer
+rno05225	Hepatocellular carcinoma
+rno05226	Gastric cancer
+rno05230	Central carbon metabolism in cancer
+rno05231	Choline metabolism in cancer
+rno05310	Asthma
+rno05320	Autoimmune thyroid disease
+rno05321	Inflammatory bowel disease (IBD)
+rno05322	Systemic lupus erythematosus
+rno05323	Rheumatoid arthritis
+rno05330	Allograft rejection
+rno05332	Graft-versus-host disease
+rno05340	Primary immunodeficiency
+rno05410	Hypertrophic cardiomyopathy (HCM)
+rno05412	Arrhythmogenic right ventricular cardiomyopathy (ARVC)
+rno05414	Dilated cardiomyopathy (DCM)
+rno05416	Viral myocarditis
+rno05418	Fluid shear stress and atherosclerosis