def __init__(self, download_path):
self.online_version = None
self.get_online_version()
self.version = Version('Entrez',
version=self.online_version,
download_path=download_path)
self.logged_version = self.version.last_logged_version()
self.download_path = download_path
def __init__(self, username, password):
self.online_version = None
self.get_online_version()
self.version = Version('DrugBank', version=self.online_version)
self.logged_version = self.version.last_logged_version()
self.interactions = self.drug_info = None
self.username = username
self.password = password
def __init__(self, username, password, download_path, tsv_file):
self.online_version = None
self.get_online_version()
self.version = Version('DrugBank',
version=self.online_version,
download_path=download_path)
self.logged_version = self.version.last_logged_version()
self.interactions = self.drug_info = None
self.username = username
self.password = password
self.download_path = download_path
self.tsv_file = tsv_file
def __init__(self):
# These were assembled from the original DGIdb identifiers
self.dgidb_go_terms = [{
"short_name": "Kinase",
"full_go_name": "KinaseActivity",
"human_readable": "Kinase",
"go_id": "GO0016301"
}, {
"short_name": "TyrosineKinase",
"full_go_name": "ProteinTyrosineKinaseActivity",
"human_readable": "Tyrosine Kinase",
"go_id": "GO0004713"
}, {
"short_name": "SerineThreonineKinase",
"full_go_name": "ProteinSerineThreonineKinaseActivity",
"human_readable": "Serine Threonine Kinase",
"go_id": "GO0004674"
}, {
"short_name": "ProteinPhosphatase",
"full_go_name": "PhospoproteinPhosphataseActivity",
"human_readable": "Protein Phosphatase",
"go_id": "GO0004721"
}, {
"short_name": "GProteinCoupledReceptor",
"full_go_name": "GpcrActivity",
"human_readable": "G Protein Coupled Receptor",
"go_id": "GO0004930"
}, {
"short_name": "NeutralZincMetallopeptidases",
"full_go_name": "MetallopeptidaseActivity",
"human_readable": "Neutral Zinc Metallopeptidase",
"go_id": "GO0008237"
}, {
"short_name": "ABCTransporter",
"full_go_name": "ABCTransporterActivity",
"human_readable": "ABC Transporter",
"go_id": "GO0042626"
}, {
"short_name": "RNADirectedDNAPolymerase",
"full_go_name": "RNADirectedDnaPolymeraseActivity",
"human_readable": "RNA Directed DNA Polymerase",
"go_id": "GO0003964"
}, {
"short_name": "Transporter",
"full_go_name": "TransporterActivity",
"human_readable": "Transporter",
"go_id": "GO0005215"
}, {
"short_name": "IonChannel",
"full_go_name": "IonChannelActivity",
"human_readable": "Ion Channel",
"go_id": "GO0005216"
}, {
"short_name": "NuclearHormoneReceptor",
"full_go_name": "LigandDependentNuclearReceptorActivity",
"human_readable": "Nuclear Hormone Receptor",
"go_id": "GO0004879"
}, {
"short_name": "LipidKinase",
"full_go_name": "LipidKinaseActivity",
"human_readable": "Lipid Kinase",
"go_id": "GO0001727"
}, {
"short_name": "Phospholipase",
"full_go_name": "PhospholipaseActivity",
"human_readable": "Phospholipase",
"go_id": "GO0004620"
}, {
"short_name": "ProteaseInhibitorActivity",
"full_go_name": "PeptidaseInhibitorActivity",
"human_readable": "Protease Inhibitor",
"go_id": "GO0030414"
}, {
"short_name": "DNARepair",
"full_go_name": "DnaRepair",
"human_readable": "DNA Repair",
"go_id": "GO0006281"
}, {
"short_name": "CellSurface",
"full_go_name": "CellSurface",
"human_readable": "Cell Surface",
"go_id": "GO0009986"
}, {
"short_name": "ExternalSideOfPlasmaMembrane",
"full_go_name": "ExternalSideOfPlasmaMembrane",
"human_readable": "External Side Of Plasma Membrane",
"go_id": "GO0009897"
}, {
"short_name": "GrowthFactor",
"full_go_name": "GrowthFactorActivity",
"human_readable": "Growth Factor",
"go_id": "GO0008083"
}, {
"short_name": "HormoneActivity",
"full_go_name": "HormoneActivity",
"human_readable": "Hormone Activity",
"go_id": "GO0005179"
}, {
"short_name": "TumorSuppressor",
"full_go_name": "RegulationOfCellCycle",
"human_readable": "Tumor Suppressor",
"go_id": "GO0051726"
}, {
"short_name": "TranscriptionFactorBinding",
"full_go_name": "TranscriptionFactorBinding",
"human_readable": "Transcription Factor Binding",
"go_id": "GO0008134"
}, {
"short_name": "TranscriptionFactorComplex",
"full_go_name": "TranscriptionFactorComplex",
"human_readable": "Transcription Factor Complex",
"go_id": "GO0005667"
}, {
"short_name": "HistoneModification",
"full_go_name": "HistoneModification",
"human_readable": "Histone Modification",
"go_id": "GO0016570"
}, {
"short_name": "DrugMetabolism",
"full_go_name": "DrugMetabolism",
"human_readable": "Drug Metabolism",
"go_id": "GO0017144"
}, {
"short_name": "DrugResistance",
"full_go_name": "ResponseToDrug",
"human_readable": "Drug Resistance",
"go_id": "GO0042493"
}, {
"short_name": "ProteaseActivity",
"full_go_name": "PeptidaseActivity",
"human_readable": "Protease",
"go_id": "GO0008233"
}]
#TODO: Use http://www.ebi.ac.uk/QuickGO/GHistory#info=2 for versioning.
self.version = Version('GO', append_date=True)
self.logged_version = self.version.last_logged_version()
self.rows = []
def __init__(self):
self.online_version = None
self.get_online_version()
self.version = Version('Entrez', version=self.online_version)
self.logged_version = self.version.last_logged_version()
def __init__(self):
self.online_version = None
self.get_online_version()
self.version = Version('DrugBank', version=self.online_version)
self.logged_version = self.version.last_logged_version()
self.interactions = self.drug_info = None
