def __init__(self, biosettings, db_set, id=9):
bioloader.BioLoader.__init__(self,
biosettings,
id,
dbsettings_in=db_set)
biosettings.LoadAliases()
self.entityLookup = dict()
def __init__(self, biosettings, id=12):
bioloader.BioLoader.__init__(self, biosettings, id)
biosettings.LoadAliases()
self.ambiguousUni = set(
) #Keep up with ambiguous UniProt IDs that were encountered
self.missingUni = set(
) #Keep up with missing UniProt IDs that were encountered
def __init__(self, biosettings, id=15):
bioloader.BioLoader.__init__(self, biosettings, id)
self.biosettings.PurgeGroupData(id)
biosettings.LoadAliases()
self.kb = bioloader.KnowledgeBase(id, "PharmGKB",
"Pharmacogenomics Knowledge Base")
self.pathwayGroups = bioloader.Pathway(self.kb.groupTypeID, id + 1,
"Pathways", "PharmGKB Pathways")
self.kb.AddPathway(self.pathwayGroups, "PharmGKB Pathway")
self.pathways = []
#self.diseaseGroups = bioloader.KnowledgeBase(id+1, "PharmGKB-Diseases", "Pharmacogenomics Knowledge Base (Disease)")
self.diseaseGroups = bioloader.Pathway(
self.kb.groupTypeID, id + 2, "Diseases",
"PharmGKB Disease Associations")
self.kb.AddPathway(self.diseaseGroups, "PharmGKB Disease")
#self.drugGroups = bioloader.KnowledgeBase(id+2, "PharmGKB-Drugs", "Pharmacogenomics Knowledge Base (Drug)")
self.drugGroups = bioloader.Pathway(self.kb.groupTypeID, id + 3,
"Drugs",
"PharmGKB Drug Associations")
self.kb.AddPathway(self.drugGroups, "PharmGKB Drug")
self.gkbentities = dict()
self.gkbentities["Gene"] = dict()
self.gkbentities["Drug"] = dict()
self.gkbentities["Disease"] = dict()
def __init__(self, biosettings, id=13):
bioloader.BioLoader.__init__(self, biosettings, id)
biosettings.LoadAliases()
self.missingUni = set()
self.ambiguousUni = set()
self.observedIDs = set(
) # Just to see if there are any groups that are more than pairs
def __init__(self, biosettings, id=4):
bioloader.BioLoader.__init__(self, biosettings, id, "pfam")
biosettings.LoadAliases()
self.associations = dict()
self.submetas = dict()
submetaNames = ["Domain", "Family", "Motif", "Repeat"]
subID = id + 1
self.pfLookup = dict()
for name in submetaNames:
self.submetas[name] = PFamMetaGroup(id, subID, name,
"PFam:%s" % name)
subID += 1
def __init__(self, biosettings, id=1):
bioloader.BioLoader.__init__(self, biosettings, id)
biosettings.LoadAliases()
self.terms = dict() #term_id -> GoTerm
def __init__(self, biosettings, id=3):
bioloader.BioLoader.__init__(self, biosettings, id)
biosettings.LoadAliases()
def __init__(self, biosettings, id=15): bioloader.BioLoader.__init__(self, biosettings, id) biosettings.LoadAliases() self.kb = bioloader.KnowledgeBase(id, "PharGKB", "Pharmacogenomics Knowledge Base") self.pathways = []
def __init__(self, biosettings, id=2):
bioloader.BioLoader.__init__(self, biosettings, id, "KEGG")
biosettings.LoadAliases()
self.srv = Client("http://soap.genome.jp/KEGG.wsdl").service
def __init__(self, biosettings):
bioloader.BioLoader.__init__(self, biosettings, 0, "ncbi")
biosettings.LoadAliases()
self.newAliasList = dict()