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Commit 6199cfca authored by Aishwarya Alex's avatar Aishwarya Alex
Browse files

added mesh

parent 01d3530f
<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="ProjectLevelVcsManager" settingsEditedManually="false">
<OptionsSetting value="true" id="Add" />
<OptionsSetting value="true" id="Remove" />
<OptionsSetting value="true" id="Checkout" />
<OptionsSetting value="true" id="Update" />
<OptionsSetting value="true" id="Status" />
<OptionsSetting value="true" id="Edit" />
<ConfirmationsSetting value="0" id="Add" />
<ConfirmationsSetting value="0" id="Remove" />
</component>
<component name="ProjectRootManager" version="2" project-jdk-name="Python 2.7.10 (/usr/bin/python2.7)" project-jdk-type="Python SDK" />
<component name="masterDetails">
<states>
<state key="ScopeChooserConfigurable.UI">
<settings>
<splitter-proportions>
<option name="proportions">
<list>
<option value="0.2" />
</list>
</option>
</splitter-proportions>
</settings>
</state>
</states>
</component>
</project>
\ No newline at end of file
......@@ -2,7 +2,7 @@
<module type="PYTHON_MODULE" version="4">
<component name="NewModuleRootManager">
<content url="file://$MODULE_DIR$" />
<orderEntry type="inheritedJdk" />
<orderEntry type="jdk" jdkName="Python 2.7.10 (/usr/bin/python2.7)" jdkType="Python SDK" />
<orderEntry type="sourceFolder" forTests="false" />
</component>
<component name="TestRunnerService">
......
BTree Number Desc Ui Term
......@@ -34,26 +34,36 @@ def getReactionDict():
return reactionDict
def termToIdentifier(belnamespace,term):
if "GO" in belnamespace or belnamespace is "":
if "GO" in belnamespace:
term=getGoIDfromTerm(term)
if "CHEM" in belnamespace:
elif "CHEM" in belnamespace:
term=getChemicalIDfromTerm(term)
elif belnamespace is "":
return term
#Get GOID from reflect
def getGoIDfromTerm(term):
goID= term
print term
#print term
reflect_client = reflectclient.ReflectClient()
GOresult=reflect_client.get_entities(term, [EntityType.biological_process,EntityType.cellular_component,EntityType.molecular_function])
print GOresult
print len(GOresult)
if len(GOresult) >0:
goID=GOresult[0]['entities'][0]['identifier']
print goID
#print goID
return goID
def getIDandNamespacefromAbundance(term):
#check GO
reflect_client = reflectclient.ReflectClient()
GOresult = reflect_client.get_entities(term, [EntityType.biological_process, EntityType.cellular_component,
EntityType.molecular_function])
if len(GOresult) > 0:
goID = GOresult[0]['entities'][0]['identifier']
# print goID
#Get pubchemID from reflect
def getChemicalIDfromTerm(term):
chemID= term
......
proteinModification
abundance
element
degradation
transcriptionalActivity
list
complexAbundance
molecularActivity
reaction
reactants
translocation
cellSecretion
compositeAbundance
peptidaseActivity
catalyticActivity
kinaseActivity
phosphataseActivity
transportActivity
gtpBoundActivity
......@@ -13,4 +13,11 @@ PFR
SPAC
SFAM
SCOMP
GOBP
dbSNP
MESHCL
GOCCTERM
GO
catalyticActivity
peptidaseActivity
complexAbundance
abundance
SIMPLE_MOLECULE
PHENOTYPE
translocation
kinaseActivity
transcriptionalActivity
peptidaseActivity
molecularActivity
degradation
gtpBoundActivity
cellSurfaceExpression
translocation
list
phosphataseActivity
reaction
reactants
compositeAbundance
cellSecretion
transportActivity
causesNoChange
Complex
association
hasMembers
isA
subProcessOf
hasComponent
prognosticBiomarkerFor
hasComponents
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