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