Models

The data model for the local HMDB version consists of 22 different tables that represent the relations found in the original HMDB data.

class bio2bel_hmdb.models.Biofluid(**kwargs)

Table storing the different biofluids.

biofluid

Name of the biofluid

class bio2bel_hmdb.models.Biofunction(**kwargs)

Table for storing the ‘biofunctions’ annotations

class bio2bel_hmdb.models.CellularLocation(**kwargs)

Table for storing the cellular location GO annotations

class bio2bel_hmdb.models.Disease(**kwargs)

Table storing the diseases and their ids.

dion

Disease Ontology name for this disease. Found using string matching

hpo

Human Phenotype Ontology name for this disease. Found using string matching

mesh_diseases

MeSH Disease name for this disease. Found using string matching

name

Name of the disease

omim_id

OMIM identifier associated with the disease

serialize_to_bel() → pybel.dsl.node_classes.Pathology

Function to serialize a disease object to a PyBEL node data dictionary.

class bio2bel_hmdb.models.Metabolite(**kwargs)

Table which stores the metabolites and all the information provided about them in HMDB.

accession

Accession ID for the metabolite

average_molecular_weight

Average molecular weight of the metabolite

bigg_id

Bigg ID of the metabolite

biocyc_id

BioCyc ID of the metabolite

cas_registry_number

Cas registry number of the metabolite

chebi_id

ChEBI identifier of the metabolite

chemical_formula

Chemical formula of the metabolite

chemspider_id

Chemspider ID of the metabolite

creation_date

Date when the metabolite was included into HMDB

description

Description including some information about the metabolite

drugbank_id

DrugBank identifier of the metabolite

drugbank_metabolite_id

Drugbank metabolite ID of the metabolite

foodb_id

FooDB ID of the metabolite

het_id

Het ID of the metabolite

inchi

InChi of the metabolite

inchikey

InCHI key of the metabolite

iupac_name

IUPAC name of the metabolite

kegg_id

KEGG ID of the metabolite

knapsack_id

Knapsack ID of the metabolite

metagene

Metagene ID of the metabolite

metlin_id

Metlin ID of the metabolite

monisotopic_molecular_weight

Monisotopic weight of the molecule

name

Name of the metabolite

nugowiki

NukoWiki ID of the metabolite

phenol_explorer_compound_id

Phenol explorer compound ID of the metabolite

phenol_explorer_metabolite_id

Phenol explorer metabolite ID of the metabolite

pubchem_compound_id

PubChem compound ID of the metabolite

serialize_to_bel() → pybel.dsl.node_classes.Abundance

Function to serialize a metabolite object to a PyBEL node data dictionary.

smiles

Smiles representation of the metabolite

state

Aggregate state of the metabolite

synthesis_reference

Synthesis reference citation of the metabolite

trivial

Trivial name of the metabolite

update_date

Date when the entry was last updated

version

Current version listing that metabolite

wikipedia

Wikipedia name of the metabolite

class bio2bel_hmdb.models.MetaboliteBiofluid(**kwargs)

Table representing the Metabolite and Biofluid relations.

class bio2bel_hmdb.models.MetaboliteBiofunction(**kwargs)

Table storing the many to many relations between metabolites and cellular location GO annotations

class bio2bel_hmdb.models.MetaboliteCellularLocation(**kwargs)

Table storing the many to many relations between metabolites and cellular location GO annotations

class bio2bel_hmdb.models.MetaboliteDiseaseReference(**kwargs)

Table storing the relations between disease and metabolite

class bio2bel_hmdb.models.MetabolitePathway(**kwargs)

Table storing the different relations between pathways and metabolites.

class bio2bel_hmdb.models.MetaboliteProtein(**kwargs)

Table representing the many to many relationship between metabolites and proteins.

class bio2bel_hmdb.models.MetaboliteReference(**kwargs)

Table representing the many to many relationship between metabolites and references.

class bio2bel_hmdb.models.MetaboliteSynonym(**kwargs)

Table storing the synonyms of metabolites.

synonym

Synonym for the metabolite

class bio2bel_hmdb.models.MetaboliteTissue(**kwargs)

Table storing the different relations between tissues and metabolites

class bio2bel_hmdb.models.Pathway(**kwargs)

Table storing the different tissues.

kegg_map_id

KEGG Map identifier of the pathway.

name

Name of the pathway.

smpdb_id

SMPDB identifier of the pathway.

class bio2bel_hmdb.models.PropertyKinds(**kwargs)

Table storing the ‘kind’ of chemical properties e.g. logP.

Not used for BEL enrichment

kind

the ‘kind’ of chemical properties e.g. logP, melting point etc

class bio2bel_hmdb.models.PropertySource(**kwargs)

Table storing the sources of properties e.g. software like ‘ALOGPS’.

Not used for BEL enrichment

class bio2bel_hmdb.models.PropertyValues(**kwargs)

Table storing the values of chemical properties.

Not used for BEL enrichment

value

value of a chemical property (e.g. logp) that will be linked to the properts and metabolites

class bio2bel_hmdb.models.Protein(**kwargs)

Table to store the protein information.

gene_name

Gene name of the protein coding gene

protein_accession

HMDB accession number for the protein

protein_type

Protein type like ‘enzyme’ etc.

serialize_to_bel() → pybel.dsl.node_classes.Protein

Function to serialize a protein object to a PyBEL node data dictionary.

uniprot_id

UniProt identifier of the protein

class bio2bel_hmdb.models.Reference(**kwargs)

Table storing literature references.

pubmed_id

PubMed identifier of the article

reference_text

Citation of the reference article

class bio2bel_hmdb.models.SecondaryAccession(**kwargs)

Table storing the different synonyms of metabolites.

secondary_accession

Other accession numbers for the metabolite

class bio2bel_hmdb.models.Tissue(**kwargs)

Table storing the different tissues.

tissue

Tissue type