Commit 121e6261 authored by Marek Ostaszewski's avatar Marek Ostaszewski
Browse files

Merge branch 'repo_update' into 'master'

formats in sbgn

See merge request !265
parents ea544ac4 3fdfb358
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
FAS/FASL_complex POSITIVE FADD
BAD/BBC3/BCL2L11_complex POSITIVE BAX
BCL2/MCL1/BCL2L1_complex POSITIVE BAD/BBC3/BCL2L11_complex
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
csa2 POSITIVE sa9
csa3 POSITIVE sa30
csa11 POSITIVE csa3
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
KNG1:KLKB1_complex POSITIVE Kininogen
KNG1:KLKB1_complex POSITIVE Kallikrein
KNG1:KLKB1_complex POSITIVE Bradykinin
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
csa11 POSITIVE sa250
csa11 POSITIVE sa251
csa11 POSITIVE sa402
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
EIF2-P:GDP_complex POSITIVE ATF4_rna
EIF2S1_phosphorylated POSITIVE EIF2-P:GDP_complex
EIF2S1_phosphorylated POSITIVE EIF2S1
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
path_0_csa33 POSITIVE path_0_sa106
path_0_sa87 POSITIVE path_0_csa33
path_0_sa87 POSITIVE path_0_sa90
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
Complex_1_complex POSITIVE Complex_1_complex
Complex_1_complex POSITIVE complex_2_complex_mitochondrial_matrix
Complex_1_complex POSITIVE complex_3_complex
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
csa20 POSITIVE csa20
csa20 POSITIVE csa24
csa20 POSITIVE csa34
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
histone_complex_Nucleus POSITIVE Chromatin_organization_phenotype
histone_complex_Nucleus POSITIVE histone_complex_Nucleus
BRD4 POSITIVE histone_complex_Nucleus
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
csa1 POSITIVE sa78
csa2 POSITIVE csa1
sa12 POSITIVE csa1
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
Nrf2/Maf_complex POSITIVE HMOX1_rna
NRF2_phosphorylated_Nucleus POSITIVE Nrf2/Maf_complex
NRF2_phosphorylated_Nucleus POSITIVE SLC40A1_rna
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
csa2 POSITIVE sa50
sa43 POSITIVE csa2
sa43 POSITIVE sa140
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
receptor_complex_complex_cell POSITIVE receptor_complex_complex_cell
receptor_complex_complex_cell POSITIVE receptor_complex_complex_cell
receptor_complex_complex_cell POSITIVE ISGF3_precursor_complex
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
csa10 POSITIVE csa9
csa10 POSITIVE csa11
csa10 POSITIVE csa12
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
IFNA1_IFNAR_complex POSITIVE JAK1_TYK2_complex
IFNAR_complex POSITIVE IFNA1_IFNAR_complex
IFNAR_complex POSITIVE IFNB1_IFNAR_complex
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
csa2 POSITIVE csa9
csa1 POSITIVE csa2
csa1 POSITIVE csa3
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
JNK_complex_Cytoplasm POSITIVE AP-1_complex
JNK_complex_Cytoplasm POSITIVE BCL2_phosphorylated
JNK_complex_Cytoplasm POSITIVE ATF2_phosphorylated
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
csa1 POSITIVE csa4
csa1 POSITIVE sa12
csa1 POSITIVE sa33
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
AHR/L-KYN_complex POSITIVE Regulatory_T-cell_generation_phenotype
L-Kynurenine_simple_molecule POSITIVE AHR/L-KYN_complex
L-Kynurenine_simple_molecule POSITIVE H2O_simple_molecule_Cytosol
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
csa2 POSITIVE sa35
sa17 POSITIVE csa2
sa17 POSITIVE sa10
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
Nsp3:Nsp4:Nsp6_complex POSITIVE Plasma_membrane_organization_phenotype
Nsp3 POSITIVE Nsp3:Nsp4:Nsp6_complex
Nsp6 POSITIVE Nsp3:Nsp4:Nsp6_complex
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
csa39 POSITIVE sa164
sa162 POSITIVE csa39
sa48 POSITIVE csa39
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
Nsp9_cytoplasm POSITIVE Fibrillincomp_complex
Nsp9_cytoplasm POSITIVE Nuclear_Pore_comp_complex
Nsp9_cytoplasm POSITIVE mibcomp_complex
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
a7c94 POSITIVE csa17
a7c94 POSITIVE csa21
a7c94 POSITIVE csa28
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
Cul2_ubiquitin_ligase_complex POSITIVE Zyg11B:EloBC_complex
Cul2_ubiquitin_ligase_complex POSITIVE Cul2_ubiquitin_ligase:Orf10_complex
Cul2_ubiquitin_ligase_complex POSITIVE Cul2_ubiquitin_ligase:substrate_complex_cytosol
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
csa5 POSITIVE csa2
csa5 POSITIVE csa35
csa5 POSITIVE csa4
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
Orf3a POSITIVE Hops_Complex_complex
Orf3a POSITIVE P65/P015_complex
Orf3a POSITIVE TRIM59
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
sa1 POSITIVE csa2
sa1 POSITIVE csa7
sa1 POSITIVE sa3
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
MYD88:IRAK:TRAF_complex POSITIVE IRF7_phosphorylated
MYD88:IRAK:TRAF_complex POSITIVE TRAF6_ubiquitinated
MYD88 POSITIVE MYD88:IRAK:TRAF_complex
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
csa56 POSITIVE sa255
csa56 POSITIVE sa337
sa77 POSITIVE csa56
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
IFNB1_space_expression_space_complex_complex POSITIVE IFNA1_rna
IFNB1_space_expression_space_complex_complex POSITIVE IFNB1_rna
NF-kB_complex POSITIVE IFNB1_space_expression_space_complex_complex
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
csa8 POSITIVE sa88
csa8 POSITIVE sa89
csa19 POSITIVE csa8
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
Replication_space_transcription_space_complex_space__complex_double_space_membrane_space_vesicle_space_(DMV)_space_(builds_space_membrane_space_network_space_from_space_ER_space_membrane_space_and_space_accumulates_space_at_space_perinuclear_space_regions POSITIVE CoV_space_poly-br_merase_space_complex_complex_double_space_membrane_space_vesicle_space_(DMV)_space_(builds_space_membrane_space_network_space_from_space_ER_space_membrane_space_and_space_accumulates_space_at_space_perinuclear_space_regions
Replication_space_transcription_space_complex_space__complex_double_space_membrane_space_vesicle_space_(DMV)_space_(builds_space_membrane_space_network_space_from_space_ER_space_membrane_space_and_space_accumulates_space_at_space_perinuclear_space_regions POSITIVE complex_complex_double_space_membrane_space_vesicle_space_(DMV)_space_(builds_space_membrane_space_network_space_from_space_ER_space_membrane_space_and_space_accumulates_space_at_space_perinuclear_space_regions
Replication_space_transcription_space_complex_space__complex_double_space_membrane_space_vesicle_space_(DMV)_space_(builds_space_membrane_space_network_space_from_space_ER_space_membrane_space_and_space_accumulates_space_at_space_perinuclear_space_regions POSITIVE (+)gRNA_space_(including_space_ORF1a_space_ORF1b)_gene_double_space_membrane_space_vesicle_space_(DMV)_space_(builds_space_membrane_space_network_space_from_space_ER_space_membrane_space_and_space_accumulates_space_at_space_perinuclear_space_regions
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
glyph2 POSITIVE glyph4
glyph2 POSITIVE glyph6
glyph2 POSITIVE glyph17
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
AGTR1_cytoplasm POSITIVE ACE2:AGTR1_complex
AGTR1_cytoplasm POSITIVE AGTR1_cytoplasm_active
ACE2_cytoplasm POSITIVE ACE2:AGTR1_complex
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
sa26 POSITIVE csa4
sa26 POSITIVE sa102
sa30 POSITIVE csa4
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
SMAD1/5/8_complex POSITIVE Modulation_Cell_Cycle_phenotype
BAMBI NEGATIVE SMAD1/5/8_complex
BAMBI NEGATIVE SMAD2/3_complex
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
csa3 POSITIVE sa55
sa33 NEGATIVE csa3
sa33 NEGATIVE csa5
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
ACE2:SPIKE_complex_complex_EPITHELIAL_CELL POSITIVE Nucleocapsid_complex_SARS-CoV-2
ACE2_EPITHELIAL_CELL POSITIVE ACE2:SPIKE_complex_complex_EPITHELIAL_CELL
S_SARS-CoV-2 POSITIVE ACE2:SPIKE_complex_complex_EPITHELIAL_CELL
......
# Generated by CaSQ v0.9.3
# Generated by CaSQ v0.9.5
csa430 POSITIVE csa357
sa1462 POSITIVE csa430
sa1859 POSITIVE csa430
......
##################################################
## Project: COVID-19 Disease Map
## Script purpose: Get different formats of the MINERVA diagrams
## Date: 25.01.2021
## Author: Marek Ostaszewski
##################################################
### Helper functions to access and retrieve content from MINERVA-hosted diagrams
source("https://git-r3lab.uni.lu/covid/models/-/raw/master/Integration/MINERVA_access/minerva_access_functions.R")
### The address of the COVID-19 Disease Map in MINERVA
map <- "https://covid19map.elixir-luxembourg.org/minerva/api/"
library(jsonlite)
### Get config to obtain the default map and different format handlers
cfg <- fromJSON(ask_GET(paste0(map, "configuration/")))
### Get the default (most recent) project id
project_id <- cfg$options[cfg$options$type == "DEFAULT_MAP","value"]
### The address of the latest (default) build
mnv_base <- paste0(map, "projects/",project_id,"/")
### Get model information
models <- fromJSON(ask_GET(paste0(mnv_base, "models/")))
### Format handler;
### see cfg$modelFormats for available handlers, we will use the SBGNML handler
this_handler <- with(cfg$modelFormats, handler[name == "SBGN-ML"])
this_extension <- with(cfg$modelFormats, extension[name == "SBGN-ML"])
### Iterate over all model ids, get them in the format defined by the handler and add the handler-associated extension
for(i in 1:nrow(models)) {
lines <- ask_GET(paste0(mnv_base, "models/", models$idObject[i],":downloadModel?handlerClass=",this_handler))
cat(lines, file = paste0(models$name[i], ".", this_extension))
}
message("Done.")
\ No newline at end of file
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