Revised dir structure

Merge branch 'master' into repo_update

Revised dir structure
Merge branch 'master' into repo_update
5d849b0e · Marek Ostaszewski · d63ba69c · b2fb54e6 · 5d849b0e · 5d849b0e
Commit 5d849b0e authored Feb 13, 2021 by Marek Ostaszewski
75 changed files
--- a/EUvsVirus/Covid19KG_Fraunhofer_Hipathia/.gitkeep
+++ b/EUvsVirus/Covid19KG_Fraunhofer_Hipathia/.gitkeep
--- a/EUvsVirus/GMLs_AF__four_maps/.gitkeep
+++ b/EUvsVirus/GMLs_AF__four_maps/.gitkeep
--- a/EUvsVirus/GMLs_AF__four_maps/Apoptosis.gml
+++ b/EUvsVirus/GMLs_AF__four_maps/Apoptosis.gml
--- a/EUvsVirus/GMLs_AF__four_maps/Apoptosis_AF.pdf
+++ b/EUvsVirus/GMLs_AF__four_maps/Apoptosis_AF.pdf
--- a/EUvsVirus/GMLs_AF__four_maps/ER-stress.gml
+++ b/EUvsVirus/GMLs_AF__four_maps/ER-stress.gml
--- a/EUvsVirus/GMLs_AF__four_maps/ER-stress_AF.pdf
+++ b/EUvsVirus/GMLs_AF__four_maps/ER-stress_AF.pdf
--- a/EUvsVirus/GMLs_AF__four_maps/Interferon.gml
+++ b/EUvsVirus/GMLs_AF__four_maps/Interferon.gml
--- a/EUvsVirus/GMLs_AF__four_maps/Interferon_AF.pdf
+++ b/EUvsVirus/GMLs_AF__four_maps/Interferon_AF.pdf
--- a/EUvsVirus/GMLs_AF__four_maps/PAMP.graphml
+++ b/EUvsVirus/GMLs_AF__four_maps/PAMP.graphml
--- a/EUvsVirus/GMLs_AF__four_maps/PAMP_AF.pdf
+++ b/EUvsVirus/GMLs_AF__four_maps/PAMP_AF.pdf
--- a/EUvsVirus/Hackathon workflow.png
+++ b/EUvsVirus/Hackathon workflow.png
--- a/EUvsVirus/Hipathia_maps/.gitkeep
+++ b/EUvsVirus/Hipathia_maps/.gitkeep
--- a/EUvsVirus/Hipathia_operableMaps/.gitkeep
+++ b/EUvsVirus/Hipathia_operableMaps/.gitkeep
--- a/EUvsVirus/Hipathia_operableMaps/hsaCovid19KG.att
+++ b/EUvsVirus/Hipathia_operableMaps/hsaCovid19KG.att
--- a/EUvsVirus/Hipathia_operableMaps/hsaCovid19KG.sif
+++ b/EUvsVirus/Hipathia_operableMaps/hsaCovid19KG.sif
--- a/EUvsVirus/MINERVA-API/ACE2-Spike-drugs.txt
+++ b/EUvsVirus/MINERVA-API/ACE2-Spike-drugs.txt
--- a/EUvsVirus/MINERVA-API/Apoptosis.txt
+++ b/EUvsVirus/MINERVA-API/Apoptosis.txt
--- a/EUvsVirus/MINERVA-API/ER stress.txt
+++ b/EUvsVirus/MINERVA-API/ER stress.txt
--- a/EUvsVirus/MINERVA-API/HCoVs ER stress (WP4869).txt
+++ b/EUvsVirus/MINERVA-API/HCoVs ER stress (WP4869).txt
--- a/EUvsVirus/MINERVA-API/HCoVs autophagy (WP4863).txt
+++ b/EUvsVirus/MINERVA-API/HCoVs autophagy (WP4863).txt
--- a/EUvsVirus/MINERVA-API/Ifn 2 pathway drug targets MINERVA.txt
+++ b/EUvsVirus/MINERVA-API/Ifn 2 pathway drug targets MINERVA.txt
--- a/EUvsVirus/MINERVA-API/Influenza-Cytokine-storm_Textmining_2018.gpml
+++ b/EUvsVirus/MINERVA-API/Influenza-Cytokine-storm_Textmining_2018.gpml
--- a/EUvsVirus/MINERVA-API/Interferon 2 pathway.txt
+++ b/EUvsVirus/MINERVA-API/Interferon 2 pathway.txt
--- a/EUvsVirus/MINERVA-API/Nsp14 and metabolism.txt
+++ b/EUvsVirus/MINERVA-API/Nsp14 and metabolism.txt
--- a/EUvsVirus/MINERVA-API/Nsp4 and Nsp6 interactions.txt
+++ b/EUvsVirus/MINERVA-API/Nsp4 and Nsp6 interactions.txt
--- a/EUvsVirus/MINERVA-API/Orf10 Cul2 pathway.txt
+++ b/EUvsVirus/MINERVA-API/Orf10 Cul2 pathway.txt
--- a/EUvsVirus/MINERVA-API/PAMP signaling.txt
+++ b/EUvsVirus/MINERVA-API/PAMP signaling.txt
--- a/EUvsVirus/MINERVA-API/Type I Ifn signaling (WP4868).txt
+++ b/EUvsVirus/MINERVA-API/Type I Ifn signaling (WP4868).txt
--- a/EUvsVirus/MINERVA-API/Virus replication cycle.txt
+++ b/EUvsVirus/MINERVA-API/Virus replication cycle.txt
--- a/EUvsVirus/MINERVA-API/drug_targets.R
+++ b/EUvsVirus/MINERVA-API/drug_targets.R
--- a/EUvsVirus/MINERVA-API/drug_targets/ACE2-Spike-drugs.txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/ACE2-Spike-drugs.txt
--- a/EUvsVirus/MINERVA-API/drug_targets/Apoptosis.txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/Apoptosis.txt
--- a/EUvsVirus/MINERVA-API/drug_targets/ER stress.txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/ER stress.txt
--- a/EUvsVirus/MINERVA-API/drug_targets/HCoVs ER stress (WP4869).txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/HCoVs ER stress (WP4869).txt
--- a/EUvsVirus/MINERVA-API/drug_targets/HCoVs autophagy (WP4863).txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/HCoVs autophagy (WP4863).txt
--- a/EUvsVirus/MINERVA-API/drug_targets/Interferon 2 pathway.txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/Interferon 2 pathway.txt
--- a/EUvsVirus/MINERVA-API/drug_targets/Nsp14 and metabolism.txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/Nsp14 and metabolism.txt
--- a/EUvsVirus/MINERVA-API/drug_targets/Nsp4 and Nsp6 interactions.txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/Nsp4 and Nsp6 interactions.txt
--- a/EUvsVirus/MINERVA-API/drug_targets/Orf10 Cul2 pathway.txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/Orf10 Cul2 pathway.txt
--- a/EUvsVirus/MINERVA-API/drug_targets/PAMP signaling.txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/PAMP signaling.txt
--- a/EUvsVirus/MINERVA-API/drug_targets/Type I Ifn signaling (WP4868).txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/Type I Ifn signaling (WP4868).txt
--- a/EUvsVirus/MINERVA-API/drug_targets/Virus replication cycle.txt
+++ b/EUvsVirus/MINERVA-API/drug_targets/Virus replication cycle.txt
--- a/EUvsVirus/MINERVA-API/element_jsons/ACE2-Spike-drugs_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/ACE2-Spike-drugs_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/Apoptosis_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/Apoptosis_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/ER stress_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/ER stress_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/HCoVs ER stress (WP4869)_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/HCoVs ER stress (WP4869)_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/HCoVs autophagy (WP4863)_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/HCoVs autophagy (WP4863)_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/HMOX1 pathway_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/HMOX1 pathway_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/Interferon 2 pathway_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/Interferon 2 pathway_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/Nsp14 and metabolism_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/Nsp14 and metabolism_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/Nsp4 and Nsp6 interactions_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/Nsp4 and Nsp6 interactions_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/Orf10 Cul2 pathway_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/Orf10 Cul2 pathway_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/PAMP signaling_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/PAMP signaling_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/RTC and transcription_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/RTC and transcription_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/Type I Ifn signaling (WP4868)_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/Type I Ifn signaling (WP4868)_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/Virus replication cycle_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/Virus replication cycle_annotations.json
--- a/EUvsVirus/MINERVA-API/element_jsons/overview_annotations.json
+++ b/EUvsVirus/MINERVA-API/element_jsons/overview_annotations.json
--- a/EUvsVirus/MINERVA-API/generate_SBML.R
+++ b/EUvsVirus/MINERVA-API/generate_SBML.R
--- a/EUvsVirus/MINERVA-API/hackathon_covid19_map_v3-elementExport.txt
+++ b/EUvsVirus/MINERVA-API/hackathon_covid19_map_v3-elementExport.txt
--- a/EUvsVirus/MINERVA-API/map_cytstorm.txt
+++ b/EUvsVirus/MINERVA-API/map_cytstorm.txt
--- a/EUvsVirus/MINERVA-API/overlays/all_MINERVA_targets.txt
+++ b/EUvsVirus/MINERVA-API/overlays/all_MINERVA_targets.txt
--- a/EUvsVirus/MINERVA-API/overlays/eNIOS_downregulated_genes.txt
+++ b/EUvsVirus/MINERVA-API/overlays/eNIOS_downregulated_genes.txt
--- a/EUvsVirus/MINERVA-API/overlays/eNIOS_drug_targets.txt
+++ b/EUvsVirus/MINERVA-API/overlays/eNIOS_drug_targets.txt
--- a/EUvsVirus/MINERVA-API/overlays/eNIOS_upregulated_genes.txt
+++ b/EUvsVirus/MINERVA-API/overlays/eNIOS_upregulated_genes.txt
--- a/EUvsVirus/MINERVA-API/overlays/textmining_drug_targets.txt
+++ b/EUvsVirus/MINERVA-API/overlays/textmining_drug_targets.txt
--- a/EUvsVirus/MergedModels/.gitkeep
+++ b/EUvsVirus/MergedModels/.gitkeep
--- a/EUvsVirus/MergedModels/Apoptosis_VS_SSA_AN_drugs_mirna.xml
+++ b/EUvsVirus/MergedModels/Apoptosis_VS_SSA_AN_drugs_mirna.xml
--- a/EUvsVirus/MergedModels/COVID19_PAMP_signaling_drugs_mirna.xml
+++ b/EUvsVirus/MergedModels/COVID19_PAMP_signaling_drugs_mirna.xml
--- a/EUvsVirus/MergedModels/ER_Stress_drugs_mirna.xml
+++ b/EUvsVirus/MergedModels/ER_Stress_drugs_mirna.xml
--- a/EUvsVirus/MergedModels/Interferon2_drugs_mirna.xml
+++ b/EUvsVirus/MergedModels/Interferon2_drugs_mirna.xml
--- a/EUvsVirus/Overlays_Updated_Vid/.gitkeep
+++ b/EUvsVirus/Overlays_Updated_Vid/.gitkeep
--- a/EUvsVirus/Overlays_Updated_Vid/ER_stress_drugs_enios.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/ER_stress_drugs_enios.txt
--- a/EUvsVirus/Overlays_Updated_Vid/ER_stress_text_mining_drugs.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/ER_stress_text_mining_drugs.txt
--- a/EUvsVirus/Overlays_Updated_Vid/InterferonEniosListWithDrug.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/InterferonEniosListWithDrug.txt
--- a/EUvsVirus/Overlays_Updated_Vid/InterferonTextMiningListWithDrug.txt
+++ b/EUvsVirus/Overlays_Updated_Vid/InterferonTextMiningListWithDrug.txt