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COVID-19
models
Commits
ecd699d5
Commit
ecd699d5
authored
Jan 26, 2021
by
cylon-x
🤖
Browse files
Merge branch 'repo_update' of
https://git-r3lab.uni.lu/covid/models
into repo_update
parents
13467c79
0c51d734
Changes
7
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Curation/ER Stress/ER_Stress_stable.pdf
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Curation/SARS-CoV-2 proteins/Orf3b/Orf3b_0620_2020.xml
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ecd699d5
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...
Integration/MINERVA_access/get_drug_targets.R
View file @
ecd699d5
...
...
@@ -6,7 +6,7 @@
##################################################
### Helper functions to access and retrieve content from MINERVA-hosted diagrams
source
(
"minerva_access_functions.R"
)
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/"
...
...
@@ -18,5 +18,44 @@ refs <- lapply(map_components$map_elements, function(x) data.frame(id = x$id,
uniprot
=
get_annotation
(
x
$
references
,
"UNIPROT"
)))
names
(
refs
)
<-
map_components
$
models
$
name
### A helper function to retrieve one (first) element alias for all unique UniProts.
### The drug search API call is based on the alias of an element in the MINERVA project,
### while the drug targets are HGNC/UniProt based. Multiple aliases can point to the
### same HGNC/UniProt. To optimise drug requests, we take only one alias for
### each unique UniProt in a given diagram.
unique_drugs
<-
function
(
funiprot_references
)
{
frefs
<-
funiprot_references
[
!
is.na
(
funiprot_references
[,
"uniprot"
]),]
if
(
nrow
(
frefs
)
==
0
)
{
return
(
NULL
)
}
sapply
(
unique
(
frefs
[,
"uniprot"
]),
function
(
x
)
frefs
[
x
==
frefs
[,
"uniprot"
],
1
][
1
])
}
### Get the UniProt-alias mappings using the helper function
upd
<-
sapply
(
refs
,
unique_drugs
)
### Get the id of the default project
map_project
<-
paste0
(
map
,
"projects/"
,
get_default_project
(
map
),
"/"
)
### Lengthy calculation, ask for drug targets of all unique UniProt ids in every pathway
all_drugs
<-
c
()
### For each pathway
for
(
u
in
1
:
length
(
upd
))
{
if
(
!
is.null
(
upd
[[
u
]]))
{
message
(
paste0
(
"Processing diagram: "
,
map_components
$
models
$
name
[
u
]))
### For each UniProt id
for
(
p
in
1
:
length
(
upd
[[
u
]]))
{
### Add a row to the global table with pathway name, UniProt id and the drugs
### targeting the element alias associated with this UniProt
all_drugs
<-
rbind
(
all_drugs
,
c
(
pathway_name
=
map_components
$
models
$
name
[
u
],
uniprot
=
names
(
upd
[[
u
]])[
p
],
drugs
=
paste
(
fromJSON
(
ask_GET
(
paste0
(
map_project
,
"drugs:search?target=ALIAS:"
,
upd
[[
u
]][
p
])))
$
name
,
collapse
=
";"
)))
}
}
}
### Write down the table
write.table
(
all_drugs
,
file
=
"MINERVA_C19DM_drugs.tsv"
,
sep
=
"\t"
,
quote
=
F
,
col.names
=
T
,
row.names
=
F
)
message
(
"Done."
)
Integration/MINERVA_access/get_formats.R
0 → 100644
View file @
ecd699d5
##################################################
## 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
Integration/MINERVA_access/minerva_access_functions.R
View file @
ecd699d5
...
...
@@ -21,12 +21,17 @@ ask_GET <- function(fask_url, verbose = F) {
return
(
NULL
)
}
### Get the id of the default project for this MINERVA instance
get_default_project
<-
function
(
map_api
)
{
cfg
<-
fromJSON
(
ask_GET
(
paste0
(
map_api
,
"configuration/"
)))
return
(
cfg
$
options
[
cfg
$
options
$
type
==
"DEFAULT_MAP"
,
"value"
])
}
### Get the components of a given map/project on the MINERVA Platform
get_map_components
<-
function
(
map_api
,
project_id
=
NULL
)
{
if
(
is.null
(
project_id
))
{
### If project id not given, get configuration of the map, to obtain the latest (default) version
cfg
<-
fromJSON
(
ask_GET
(
paste0
(
map_api
,
"configuration/"
)))
project_id
<-
cfg
$
options
[
cfg
$
options
$
type
==
"DEFAULT_MAP"
,
"value"
]
project_id
<-
get_default_project
(
map_api
)
}
### The address of the latest (default) build
mnv_base
<-
paste0
(
map_api
,
"projects/"
,
project_id
,
"/"
)
...
...
Resources/Crosstalks/C19DM_crosstalks_focused.cys
0 → 100644
View file @
ecd699d5
File added
Resources/Crosstalks/find_crosstalks.R
View file @
ecd699d5
...
...
@@ -6,7 +6,7 @@
##################################################
### Helper functions to access and retrieve content from MINERVA-hosted diagrams
source
(
"minerva_access.R"
)
source
(
"
https://git-r3lab.uni.lu/covid/models/-/raw/master/Integration/MINERVA_access/
minerva_access
_functions
.R"
)
### For handling WikiPathway queries
library
(
rWikiPathways
)
...
...
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