Manager¶
The Manager is a key component of HMDB. This class is used to create, populate and query the local HMDB version.
-
class
bio2bel_hmdb.manager.
Manager
(*args, **kwargs)[source]¶ Metabolite-proteins and metabolite-disease associations.
-
get_hmdb_accession
()[source]¶ Create a list of all HMDB metabolite identifiers present in the database.
Return type: list
-
get_hmdb_diseases
()[source]¶ Create a list of all disease names present in the database.
Return type: list
-
get_metabolite_by_accession
(hmdb_metabolite_accession: str) → Optional[bio2bel_hmdb.models.Metabolite][source]¶ Query the constructed HMDB database and extract a metabolite object.
Parameters: hmdb_metabolite_accession – HMDB metabolite identifier Example:
>>> import bio2bel_hmdb >>> manager = bio2bel_hmdb.Manager() >>> manager.get_metabolite_by_accession("HMDB00072")
-
get_reference_by_pubmed_id
(pubmed_id: str) → Optional[bio2bel_hmdb.models.Reference][source]¶ Get a reference by its PubMed identifier if it exists.
Parameters: pubmed_id – The PubMed identifier to search
-
populate
(source: Optional[str] = None, map_dis: bool = True, group_size: int = 500000)[source]¶ Populate the database with the HMDB data.
Parameters: - source – Path to an .xml file. If None the whole HMDB will be downloaded and used for population.
- map_dis – Should diseases be mapped?
-
query_disease_associated_metabolites
(disease_name: str) → List[bio2bel_hmdb.models.Metabolite][source]¶ Query function that returns a list of metabolite-disease interactions, which are associated to a disease.
Parameters: disease_name – HMDB disease name
-
query_metabolite_associated_diseases
(hmdb_metabolite_id: str) → List[bio2bel_hmdb.models.Disease][source]¶ Query the constructed HMDB database to get the metabolite associated disease relations for BEL enrichment
Parameters: hmdb_metabolite_id – HMDB metabolite identifier
-
query_metabolite_associated_proteins
(hmdb_metabolite_id: str) → Optional[List[bio2bel_hmdb.models.Protein]][source]¶ Query the constructed HMDB database to get the metabolite associated protein relations for BEL enrichment
Parameters: hmdb_metabolite_id – HMDB metabolite identifier
-
query_protein_associated_metabolites
(uniprot_id)[source]¶ Query function that returns a list of metabolite-disease interactions, which are associated to a disease.
Parameters: uniprot_id (str) – uniprot identifier of a protein for which the associated metabolite relations should be outputted Return type: list
-