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COVID-19
models
Commits
acb9d8a3
Commit
acb9d8a3
authored
Feb 23, 2021
by
Marek Ostaszewski
Browse files
Compartment harmonisatino, missed fixes
parent
be673a43
Changes
3
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Curation/Pyrimidine deprivation/Pyrimidine_deprivation_stable.xml
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acb9d8a3
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Curation/SARS-CoV-2 proteins/Nsp14/Nsp14_stable.xml
View file @
acb9d8a3
...
@@ -245,7 +245,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
...
@@ -245,7 +245,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
<celldesigner:compartmentAlias id="ca1" compartment="c1">
<celldesigner:compartmentAlias id="ca1" compartment="c1">
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...
@@ -253,7 +253,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
...
@@ -253,7 +253,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
<celldesigner:compartmentAlias id="ca2" compartment="c2">
<celldesigner:compartmentAlias id="ca2" compartment="c2">
<celldesigner:class>SQUARE</celldesigner:class>
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...
@@ -7427,17 +7427,26 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
...
@@ -7427,17 +7427,26 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
</listOfUnitDefinitions>
</listOfUnitDefinitions>
<listOfCompartments>
<listOfCompartments>
<compartment metaid="default" id="default" size="1" units="volume"/>
<compartment metaid="default" id="default" size="1" units="volume"/>
<compartment metaid="c1" id="c1" name="c
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<rdf:Description rdf:about="#c1">
<bqbiol:is>
<rdf:Bag>
<rdf:li rdf:resource="urn:miriam:obo.go:GO%3A0005737"/>
</rdf:Bag>
</bqbiol:is>
</rdf:Description>
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</annotation>
</annotation>
</compartment>
</compartment>
...
@@ -13438,7 +13447,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
...
@@ -13438,7 +13447,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
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...
@@ -14144,7 +14153,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
...
@@ -14144,7 +14153,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
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...
@@ -14166,7 +14175,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
...
@@ -14166,7 +14175,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
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...
@@ -16227,7 +16236,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
...
@@ -16227,7 +16236,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
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...
@@ -18423,7 +18432,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
...
@@ -18423,7 +18432,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
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...
@@ -18947,7 +18956,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
...
@@ -18947,7 +18956,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
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...
...
Integration/MINERVA_access/minerva_access_functions.R
View file @
acb9d8a3
...
@@ -28,7 +28,9 @@ get_default_project <- function(map_api) {
...
@@ -28,7 +28,9 @@ get_default_project <- function(map_api) {
}
}
### Get the components of a given map/project on the MINERVA Platform
### Get the components of a given map/project on the MINERVA Platform
get_map_components
<-
function
(
map_api
,
project_id
=
NULL
)
{
get_map_components
<-
function
(
map_api
,
project_id
=
NULL
,
e_columns
=
""
,
r_columns
=
""
)
{
if
(
is.null
(
project_id
))
{
if
(
is.null
(
project_id
))
{
### If project id not given, get configuration of the map, to obtain the latest (default) version
### If project id not given, get configuration of the map, to obtain the latest (default) version
project_id
<-
get_default_project
(
map_api
)
project_id
<-
get_default_project
(
map_api
)
...
@@ -41,18 +43,19 @@ get_map_components <- function(map_api, project_id = NULL) {
...
@@ -41,18 +43,19 @@ get_map_components <- function(map_api, project_id = NULL) {
### Get diagrams
### Get diagrams
models
<-
fromJSON
(
ask_GET
(
paste0
(
mnv_base
,
"models/"
)))
models
<-
fromJSON
(
ask_GET
(
paste0
(
mnv_base
,
"models/"
)))
if
(
e_columns
!=
""
)
{
e_columns
<-
paste0
(
"?columns="
,
e_columns
)
}
if
(
r_columns
!=
""
)
{
r_columns
<-
paste0
(
"?columns="
,
r_columns
)
}
### Get elements of the chosen diagram
### Get elements of the chosen diagram
model_elements
<-
lapply
(
models
$
idObject
,
model_elements
<-
lapply
(
models
$
idObject
,
function
(
x
)
function
(
x
)
fromJSON
(
ask_GET
(
paste0
(
mnv_base
,
"models/"
,
x
,
"/"
,
fromJSON
(
ask_GET
(
paste0
(
mnv_base
,
"models/"
,
x
,
"/"
,
"bioEntities/elements/"
,
e_columns
)),
"bioEntities/elements/?columns=id,name,type,references,elementId,complexId"
)),
flatten
=
F
))
flatten
=
F
))
### Request for reactions that have at least one top 10 element as participant
### Request for reactions that have at least one top 10 element as participant
model_reactions
<-
lapply
(
models
$
idObject
,
model_reactions
<-
lapply
(
models
$
idObject
,
function
(
x
)
function
(
x
)
fromJSON
(
ask_GET
(
paste0
(
mnv_base
,
"models/"
,
x
,
"/"
,
fromJSON
(
ask_GET
(
paste0
(
mnv_base
,
"models/"
,
x
,
"/"
,
"bioEntities/elements/"
,
r_columns
)),
"bioEntities/reactions/?columns=modifiers,products,reactants"
)),
flatten
=
F
))
flatten
=
F
))
### Pack all into a list and return
### Pack all into a list and return
return
(
list
(
models
=
models
,
map_elements
=
model_elements
,
map_reactions
=
model_reactions
))
return
(
list
(
models
=
models
,
map_elements
=
model_elements
,
map_reactions
=
model_reactions
))
...
...
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