Compartment harmonisatino, missed fixes

Curation/SARS-CoV-2 proteins/Nsp14/Nsp14_stable.xml

@@ -245,7 +245,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
 <celldesigner:compartmentAlias id="ca1" compartment="c1">
 <celldesigner:class>SQUARE</celldesigner:class>
 <celldesigner:bounds x="57.0" y="358.0" w="5937.0" h="2499.0"/>
-<celldesigner:namePoint x="2133.5" y="2813.5"/>
+<celldesigner:namePoint x="2143.5" y="2813.5"/>
 <celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
 <celldesigner:paint color="ffcccc00" scheme="Color"/>
 <celldesigner:info state="empty" angle="-1.5707963267948966"/>
@@ -253,7 +253,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
 <celldesigner:compartmentAlias id="ca2" compartment="c2">
 <celldesigner:class>SQUARE</celldesigner:class>
 <celldesigner:bounds x="1759.0" y="815.0" w="524.0" h="1050.0"/>
-<celldesigner:namePoint x="2169.0" y="1736.5"/>
+<celldesigner:namePoint x="2167.0" y="1736.5"/>
 <celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
 <celldesigner:paint color="ffcccc00" scheme="Color"/>
 <celldesigner:info state="empty" angle="-1.5707963267948966"/>
@@ -7427,17 +7427,26 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
 </listOfUnitDefinitions>
 <listOfCompartments>
 <compartment metaid="default" id="default" size="1" units="volume"/>
-<compartment metaid="c1" id="c1" name="cytosol" size="1" units="volume" outside="default">
+<compartment metaid="c1" id="c1" name="cell" size="1" units="volume" outside="default">
 <annotation>
 <celldesigner:extension>
-<celldesigner:name>cytosol</celldesigner:name>
+<celldesigner:name>cell</celldesigner:name>
 </celldesigner:extension>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<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>
+</rdf:RDF>
 </annotation>
 </compartment>
-<compartment metaid="c2" id="c2" name="Mitochondria" size="1" units="volume" outside="c1">
+<compartment metaid="c2" id="c2" name="GO:0005739" size="1" units="volume" outside="c1">
 <annotation>
 <celldesigner:extension>
-<celldesigner:name>Mitochondria</celldesigner:name>
+<celldesigner:name>GO:0005739</celldesigner:name>
 </celldesigner:extension>
 </annotation>
 </compartment>
@@ -13438,7 +13447,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
 <celldesigner:lineDirection index="4" value="vertical"/>
 </celldesigner:listOfLineDirection>
 </celldesigner:connectScheme>
-<celldesigner:editPoints>0.524279717818656,0.010754456757060993 0.5104648484058965,0.22407921327330094 0.9365342984514049,0.23477069667908435 0.9481905302011189,-5.025690818349915E-4</celldesigner:editPoints>
+<celldesigner:editPoints>0.524279717818656,0.010754456757060993 0.5104648484058965,0.22407921327330094 0.936534298451404,0.2347706966790839 0.9481905302011189,-5.025690818349915E-4</celldesigner:editPoints>
 <celldesigner:line width="1.0" color="ff000000" type="Straight"/>
 </celldesigner:reactantLink>
 </celldesigner:listOfReactantLinks>
@@ -14144,7 +14153,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
 <celldesigner:lineDirection index="2" value="horizontal"/>
 </celldesigner:listOfLineDirection>
 </celldesigner:connectScheme>
-<celldesigner:editPoints>0.24871404607137243,0.17422018637011227 0.5778782251199432,-0.29568950950756534</celldesigner:editPoints>
+<celldesigner:editPoints>0.24871404607137199,0.17422018637011227 0.5778782251199428,-0.29568950950756534</celldesigner:editPoints>
 <celldesigner:line width="1.0" color="ff000000" type="Straight"/>
 </celldesigner:reactantLink>
 <celldesigner:reactantLink reactant="s28" alias="sa134" targetLineIndex="-1,0">
@@ -14166,7 +14175,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
 <celldesigner:lineDirection index="2" value="horizontal"/>
 </celldesigner:listOfLineDirection>
 </celldesigner:connectScheme>
-<celldesigner:editPoints>0.18779772750950408,0.08147600907220998 0.346206746071963,-0.2836480813416351</celldesigner:editPoints>
+<celldesigner:editPoints>0.18779772750950363,0.0814760090722082 0.34620674607196256,-0.2836480813416351</celldesigner:editPoints>
 <celldesigner:line width="1.0" color="ff000000" type="Straight"/>
 </celldesigner:reactantLink>
 </celldesigner:listOfReactantLinks>
@@ -16227,7 +16236,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
 </celldesigner:linkTarget>
 <celldesigner:line width="1.0" color="ff000000"/>
 </celldesigner:modification>
-<celldesigner:modification type="INHIBITION" modifiers="s132" aliases="sa213" targetLineIndex="-1,7" editPoints="0.48838794429575216,0.09570106029903513 0.5253656507051687,-0.09300600273284232">
+<celldesigner:modification type="INHIBITION" modifiers="s132" aliases="sa213" targetLineIndex="-1,7" editPoints="0.48838794429575927,0.09570106029903513 0.5253656507051758,-0.09300600273284232">
 <celldesigner:connectScheme connectPolicy="square">
 <celldesigner:listOfLineDirection>
 <celldesigner:lineDirection index="0" value="horizontal"/>
@@ -18423,7 +18432,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
 </celldesigner:linkTarget>
 <celldesigner:line width="1.0" color="ff000000"/>
 </celldesigner:modification>
-<celldesigner:modification type="CATALYSIS" modifiers="s165" aliases="sa290" targetLineIndex="-1,7" editPoints="0.3912819121836151,0.2711735917785134 0.7157445105009046,-0.19700011595237044">
+<celldesigner:modification type="CATALYSIS" modifiers="s165" aliases="sa290" targetLineIndex="-1,7" editPoints="0.39128191218360797,0.2711735917785134 0.7157445105008975,-0.19700011595237044">
 <celldesigner:connectScheme connectPolicy="square">
 <celldesigner:listOfLineDirection>
 <celldesigner:lineDirection index="0" value="horizontal"/>
@@ -18947,7 +18956,7 @@ Metabolic interactions of the SARS-CoV-2 Nsp14 with the human galactose, nicotin
 </celldesigner:connectScheme>
 <celldesigner:line width="1.0" color="ff000000"/>
 <celldesigner:listOfModification>
-<celldesigner:modification type="CATALYSIS" modifiers="s75" aliases="sa275" targetLineIndex="-1,2" editPoints="0.3752999022833716,-0.22561476254875856 0.6407574258721684,0.21596176169013148">
+<celldesigner:modification type="CATALYSIS" modifiers="s75" aliases="sa275" targetLineIndex="-1,2" editPoints="0.37529990228337695,-0.22561476254875856 0.6407574258721738,0.21596176169013148">
 <celldesigner:connectScheme connectPolicy="square">
 <celldesigner:listOfLineDirection>
 <celldesigner:lineDirection index="0" value="vertical"/>

Integration/MINERVA_access/minerva_access_functions.R

@@ -28,7 +28,9 @@ get_default_project <- function(map_api) {
 }
 
 ### 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 project id not given, get configuration of the map, to obtain the latest (default) version
     project_id <- get_default_project(map_api)
@@ -41,18 +43,19 @@ get_map_components <- function(map_api, project_id = NULL) {
   ### Get diagrams
   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
   model_elements <- lapply(models$idObject, 
                            function(x)
-                             fromJSON(ask_GET(paste0(mnv_base,"models/",x,"/",
-                                                     "bioEntities/elements/?columns=id,name,type,references,elementId,complexId")),
+                             fromJSON(ask_GET(paste0(mnv_base,"models/",x,"/","bioEntities/elements/",e_columns)),
                                       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")),
+                              fromJSON(ask_GET(paste0(mnv_base,"models/",x,"/","bioEntities/elements/",r_columns)),
                                        flatten = F))
   ### Pack all into a list and return
   return(list(models = models, map_elements = model_elements, map_reactions = model_reactions))