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COVID-19
models
Commits
d5ae43b3
Commit
d5ae43b3
authored
Feb 04, 2021
by
Marek Ostaszewski
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Cleaned crosstalks code, Reactome added, new Cytoscape session file
parent
d9709d11
Pipeline
#37217
passed with stages
in 3 minutes and 17 seconds
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Resources/Crosstalks/C19DM_crosstalks_focused.cys
Resources/Crosstalks/C19DM_crosstalks_focused.cys
+0
-0
Resources/Crosstalks/find_crosstalks.R
Resources/Crosstalks/find_crosstalks.R
+148
-95
Resources/Crosstalks/map_groups.json
Resources/Crosstalks/map_groups.json
+81
-0
Resources/Crosstalks/minerva_access.R
Resources/Crosstalks/minerva_access.R
+0
-62
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Resources/Crosstalks/C19DM_crosstalks_focused.cys
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d5ae43b3
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Resources/Crosstalks/find_crosstalks.R
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d5ae43b3
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Resources/Crosstalks/map_groups.json
0 → 100644
View file @
d5ae43b3
{
"Virus replication cycle"
:
[
"WP4846"
,
"WP4799"
,
"Virus replication cycle"
,
"Nsp9 protein interactions"
,
"SARS-CoV-2 RTC and transcription"
,
"Nsp4 and Nsp6 protein interactions"
,
"E protein interactions"
,
"Orf3a protein interactions"
,
"R-HSA-9678110"
,
"R-HSA-9679504"
,
"R-HSA-9694514"
,
"R-HSA-9683701"
,
"R-HSA-9679509"
,
"R-HSA-9694614"
,
"R-HSA-9694676"
,
"R-HSA-9694682"
,
"R-HSA-9694635"
,
"R-HSA-9694322"
],
"ER stress and unfolded protein response"
:
[
"WP4861"
,
"WP5027"
,
"Endoplasmatic Reticulum stress"
,
"Orf10 Cul2 pathway"
],
"Autophagy and protein degradation"
:
[
"WP4860"
,
"WP4936"
,
"WP4863"
,
"Endoplasmatic Reticulum stress"
],
"Apoptosis pathway"
:
[
"WP4864"
,
"WP4877"
,
"WP5038"
,
"Apoptosis pathway"
,
"JNK pathway"
,
"Electron Transport Chain disruption"
],
"Renin-angiotensin system"
:
[
"WP4883"
,
"WP4965"
,
"WP4969"
,
"Renin-angiotensin pathway"
],
"Coagulopathy pathway"
:
[
"WP4927"
,
"Coagulation pathway"
],
"PAMP signalling"
:
[
"WP4912"
,
"PAMP signalling"
],
"Induction of interferons and the cytokine storm"
:
[
"WP4868"
,
"WP4880"
,
"WP4876"
,
"WP4884"
,
"WP4961"
,
"WP5039"
,
"Interferon 1 pathway"
,
"Interferon lambda pathway"
,
"TGFbeta signalling"
,
"NLRP3 inflammasome activation"
],
"Altered host metabolism"
:
[
"WP4853"
,
"WP4904"
,
"Kynurenine synthesis pathway"
,
"HMOX1 pathway"
,
"Nsp14 and metabolism"
,
"Pyrimidine deprivation"
],
"Other diagrams"
:
[
"WP4891"
,
"WP5017"
,
"overview"
]
}
Resources/Crosstalks/minerva_access.R
deleted
100644 → 0
View file @
d9709d11
##################################################
## Project: COVID-19 Disease Map
## Script purpose: Convenience functions for accessing the MINERVA Platform
## Date: 24.12.2020
## Author: Marek Ostaszewski
##################################################
library
(
httr
)
library
(
jsonlite
)
### A convenience function to handle API queries
ask_GET
<-
function
(
fask_url
,
verbose
=
F
)
{
if
(
verbose
)
{
message
(
URLencode
(
fask_url
))
}
resp
<-
httr
::
GET
(
url
=
URLencode
(
fask_url
),
httr
::
add_headers
(
'Content-Type'
=
"application/x-www-form-urlencoded"
))
if
(
httr
::
status_code
(
resp
)
==
200
)
{
return
(
httr
::
content
(
resp
,
as
=
"text"
))
}
return
(
NULL
)
}
### 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"
]
}
### The address of the latest (default) build
mnv_base
<-
paste0
(
map_api
,
"projects/"
,
project_id
,
"/"
)
message
(
paste0
(
"Asking for diagrams in: "
,
mnv_base
,
"models/"
))
### Get diagrams
models
<-
fromJSON
(
ask_GET
(
paste0
(
mnv_base
,
"models/"
)))
### Get elements of the chosen diagram
model_elements
<-
lapply
(
models
$
idObject
,
function
(
x
)
fromJSON
(
ask_GET
(
paste0
(
mnv_base
,
"models/"
,
x
,
"/"
,
"bioEntities/elements/?columns=id,name,type,references,elementId,complexId"
)),
flatten
=
F
))
### Request for reactions that have at least one top 10 element as participant
model_reactions
<-
lapply
(
models
$
idObject
,
function
(
x
)
fromJSON
(
ask_GET
(
paste0
(
mnv_base
,
"models/"
,
x
,
"/"
,
"bioEntities/reactions/?columns=modifiers,products,reactants"
)),
flatten
=
F
))
### Pack all into a list and return
return
(
list
(
models
=
models
,
map_elements
=
model_elements
,
map_reactions
=
model_reactions
))
}
### Get annotation of a given type, from element/reaction references
get_annotation
<-
function
(
freferences
,
ftype
)
{
sapply
(
freferences
,
function
(
x
)
{
ifelse
(
any
(
x
$
type
==
ftype
),
x
$
resource
[
x
$
type
==
ftype
],
NA
)
})
}
\ No newline at end of file
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