Source code for bio2bel_hmdb.models

# -*- coding: utf-8 -*-

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

from sqlalchemy import Column, Float, ForeignKey, Integer, String, Text
from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy.orm import relationship

from pybel.dsl import abundance, pathology, protein
from .constants import MODULE_NAME

HMDB_ID = 'HMDB'
HMDB_DISEASE = 'HMDB_D'
UNIPROT = 'UP'

Base = declarative_base()

METABOLITE_TABLE_NAME = f'{MODULE_NAME}_metabolite'
METABOLITE_SECONDARY_ACCESSION_TABLE_NAME = f'{MODULE_NAME}_metaboliteAccession'
METABOLITE_SYNONYM_TABLE_NAME = f'{MODULE_NAME}_metaboliteSynonym'
BIOFLUID_TABLE_NAME = f'{MODULE_NAME}_biofluid'
METABOLITE_BIOFLUID_TABLE_NAME = f'{MODULE_NAME}_metabolite_biofluid'
TISSUE_TABLE_NAME = f'{MODULE_NAME}_tissue'
METABOLITE_TISSUE_TABLE_NAME = f'{MODULE_NAME}_metabolite_tissue'
PATHWAY_TABLE_NAME = f'{MODULE_NAME}_pathway'
METABOLITE_PATHWAY_TABLE_NAME = f'{MODULE_NAME}_metabolite_pathway'
PROTEIN_TABLE_NAME = f'{MODULE_NAME}_protein'
METABOLITE_PROTEIN_TABLE_NAME = f'{MODULE_NAME}_metabolite_protein'
REFERENCE_TABLE_NAME = f'{MODULE_NAME}_reference'
METABOLITE_REFERENCE_TABLE_NAME = f'{MODULE_NAME}_metabolite_reference'
DISEASE_TABLE_NAME = f'{MODULE_NAME}_disease'
METABOLITE_DISEASE_REFERENCE_TABLE_NAME = f'{MODULE_NAME}_metabolite_disease'
CELLULAR_LOCATION_TABLE_NAME = f'{MODULE_NAME}_cellularLocation'
METABOLITE_CELLULAR_LOCATION_TABLE_NAME = f'{MODULE_NAME}_metabolite_cellularLocation'
BIOFUNCTION_TABLE_NAME = f'{MODULE_NAME}_biofunction'
METABOLITE_BIOFUNCTION_TABLE_NAME = f'{MODULE_NAME}_metabolite_biofunction'


class Metabolite(Base):
    """Table which stores the metabolites and all the information provided about them in HMDB."""

    __tablename__ = METABOLITE_TABLE_NAME

    id = Column(Integer, primary_key=True)
    version = Column(String(255), nullable=False, doc="Current version listing that metabolite")
    creation_date = Column(String(255), nullable=False, doc="Date when the metabolite was included into HMDB")
    update_date = Column(String(255), nullable=False, doc="Date when the entry was last updated")
    accession = Column(String(255), nullable=False, unique=True, doc="Accession ID for the metabolite")
    name = Column(String(255), nullable=True, doc="Name of the metabolite")
    description = Column(Text, nullable=True, doc="Description including some information about the metabolite")
    chemical_formula = Column(String(255), nullable=False, doc="Chemical formula of the metabolite")
    average_molecular_weight = Column(Float, nullable=True, doc="Average molecular weight of the metabolite")
    monisotopic_molecular_weight = Column(Float, nullable=True, doc="Monisotopic weight of the molecule")
    iupac_name = Column(Text, nullable=True, doc="IUPAC name of the metabolite")
    traditional_iupac = Column(Text, nullable=True, doc="")
    trivial = Column(String(255), nullable=True, doc="Trivial name of the metabolite")
    cas_registry_number = Column(String(255), nullable=True, doc="Cas registry number of the metabolite")
    smiles = Column(Text, nullable=True, doc="Smiles representation of the metabolite")
    inchi = Column(Text, nullable=True, doc="InChi of the metabolite")
    inchikey = Column(String(255), nullable=True, doc="InCHI key of the metabolite")
    state = Column(String(255), nullable=True, doc="Aggregate state of the metabolite")
    drugbank_id = Column(String(255), nullable=True, doc="DrugBank identifier of the metabolite")
    drugbank_metabolite_id = Column(String(255), nullable=True, doc="Drugbank metabolite ID of the metabolite")
    phenol_explorer_compound_id = Column(String(255), nullable=True,
                                         doc="Phenol explorer compound ID of the metabolite")
    phenol_explorer_metabolite_id = Column(String(255), nullable=True,
                                           doc="Phenol explorer metabolite ID of the metabolite")
    foodb_id = Column(String(255), nullable=True, doc="FooDB ID of the metabolite")
    knapsack_id = Column(String(255), nullable=True, doc="Knapsack ID of the metabolite")
    chemspider_id = Column(String(255), nullable=True, doc="Chemspider ID of the metabolite")
    kegg_id = Column(String(255), nullable=True, doc="KEGG ID of the metabolite")
    biocyc_id = Column(String(255), nullable=True, doc="BioCyc ID of the metabolite")
    bigg_id = Column(String(255), nullable=True, doc="Bigg ID of the metabolite")
    wikipedia = Column(String(255), nullable=True, doc="Wikipedia name of the metabolite")
    nugowiki = Column(String(255), nullable=True, doc="NukoWiki ID of the metabolite")
    metagene = Column(String(255), nullable=True, doc="Metagene ID of the metabolite")
    metlin_id = Column(String(255), nullable=True, doc="Metlin ID of the metabolite")
    pubchem_compound_id = Column(String(255), nullable=True, doc="PubChem compound ID of the metabolite")
    het_id = Column(String(255), nullable=True, doc="Het ID of the metabolite")
    chebi_id = Column(String(255), nullable=True, doc="ChEBI identifier of the metabolite")
    synthesis_reference = Column(Text, nullable=True, doc="Synthesis reference citation of the metabolite")

    def __repr__(self):
        return f'<Metabolite hmdb:{self.accession} ! {self.name}>'

    def serialize_to_bel(self) -> abundance:
        """Function to serialize a metabolite object to a PyBEL node data dictionary."""
        return abundance(
            namespace=HMDB_ID,
            name=self.name,
            identifier=self.accession,
        )


class SecondaryAccession(Base):
    """Table storing the different synonyms of metabolites."""

    __tablename__ = METABOLITE_SECONDARY_ACCESSION_TABLE_NAME

    id = Column(Integer, primary_key=True)

    secondary_accession = Column(String(255), nullable=False, unique=True,
                                 doc="Other accession numbers for the metabolite")

    metabolite_id = Column(Integer, ForeignKey("{}.id".format(METABOLITE_TABLE_NAME)))
    metabolite = relationship(Metabolite, backref="accessions")


class MetaboliteSynonym(Base):
    """Table storing the synonyms of metabolites."""

    __tablename__ = METABOLITE_SYNONYM_TABLE_NAME

    id = Column(Integer, primary_key=True)

    synonym = Column(String(255), nullable=False, unique=True, doc="Synonym for the metabolite")

    metabolite_id = Column(Integer, ForeignKey("{}.id".format(METABOLITE_TABLE_NAME)))
    metabolite = relationship(Metabolite, backref="synonyms")


class Biofluid(Base):
    """Table storing the different biofluids."""

    __tablename__ = BIOFLUID_TABLE_NAME

    id = Column(Integer, primary_key=True)
    biofluid = Column(String(255), nullable=False, unique=True, doc="Name of the biofluid")


class MetaboliteBiofluid(Base):
    """Table representing the Metabolite and Biofluid relations."""

    __tablename__ = METABOLITE_BIOFLUID_TABLE_NAME

    id = Column(Integer, primary_key=True)

    metabolite_id = Column(Integer, ForeignKey("{}.id".format(METABOLITE_TABLE_NAME)))
    metabolite = relationship(Metabolite, backref="biofluids")

    biofluid_id = Column(Integer, ForeignKey("{}.id".format(BIOFLUID_TABLE_NAME)))
    biofluid = relationship(Biofluid, backref="metabolites")


class Tissue(Base):
    """Table storing the different tissues."""

    __tablename__ = TISSUE_TABLE_NAME

    id = Column(Integer, primary_key=True)
    tissue = Column(String(255), nullable=False, unique=True, doc="Tissue type")


class MetaboliteTissue(Base):
    """Table storing the different relations between tissues and metabolites"""
    __tablename__ = "metabolite_tissues"

    id = Column(Integer, primary_key=True)

    metabolite_id = Column(Integer, ForeignKey("{}.id".format(METABOLITE_TABLE_NAME)))
    metabolite = relationship(Metabolite, backref="tissues")

    tissue_id = Column(Integer, ForeignKey("{}.id".format(TISSUE_TABLE_NAME)))
    tissue = relationship(Tissue, backref="metabolites")


class Pathway(Base):
    """Table storing the different tissues."""

    __tablename__ = PATHWAY_TABLE_NAME

    id = Column(Integer, primary_key=True)

    name = Column(String(255), nullable=True, unique=True, doc="Name of the pathway.")

    smpdb_id = Column(String(255), nullable=True, unique=False, doc="SMPDB identifier of the pathway.")
    kegg_map_id = Column(String(255), nullable=True, unique=False, doc="KEGG Map identifier of the pathway.")


class MetabolitePathway(Base):
    """Table storing the different relations between pathways and metabolites."""

    __tablename__ = METABOLITE_PATHWAY_TABLE_NAME

    id = Column(Integer, primary_key=True)

    metabolite_id = Column(Integer, ForeignKey("{}.id".format(METABOLITE_TABLE_NAME)))
    metabolite = relationship(Metabolite, backref="pathways")

    pathway_id = Column(Integer, ForeignKey("{}.id".format(PATHWAY_TABLE_NAME)))
    pathway = relationship(Pathway, backref="metabolites")


class Protein(Base):
    """Table to store the protein information."""

    __tablename__ = PROTEIN_TABLE_NAME

    id = Column(Integer, primary_key=True)
    protein_accession = Column(String(255), nullable=False, unique=True, doc="HMDB accession number for the protein")
    name = Column(String(255), nullable=False)
    uniprot_id = Column(String(255), nullable=True, doc="UniProt identifier of the protein")
    gene_name = Column(String(255), nullable=True, doc="Gene name of the protein coding gene")
    protein_type = Column(String(255), nullable=True, doc="Protein type like 'enzyme' etc.")

    def serialize_to_bel(self) -> protein:
        """Function to serialize a protein object to a PyBEL node data dictionary."""
        return protein(namespace=UNIPROT, name=str(self.uniprot_id))


class MetaboliteProtein(Base):
    """Table representing the many to many relationship between metabolites and proteins."""

    __tablename__ = METABOLITE_PROTEIN_TABLE_NAME

    id = Column(Integer, primary_key=True)

    metabolite_id = Column(Integer, ForeignKey("{}.id".format(METABOLITE_TABLE_NAME)))
    metabolite = relationship(Metabolite, backref="proteins")

    protein_id = Column(Integer, ForeignKey("{}.id".format(PROTEIN_TABLE_NAME)))
    protein = relationship(Protein, backref="metabolites")


class Reference(Base):
    """Table storing literature references."""

    __tablename__ = REFERENCE_TABLE_NAME

    id = Column(Integer, primary_key=True)

    pubmed_id = Column(String(255), nullable=True, unique=True, doc="PubMed identifier of the article")
    reference_text = Column(Text, nullable=False, unique=True, doc="Citation of the reference article")

    def __repr__(self):
        return f'<Reference pmid:{self.pubmed_id}>'


class MetaboliteReference(Base):
    """Table representing the many to many relationship between metabolites and references."""

    __tablename__ = METABOLITE_REFERENCE_TABLE_NAME

    id = Column(Integer, primary_key=True)

    metabolite_id = Column(Integer, ForeignKey("{}.id".format(METABOLITE_TABLE_NAME)))
    metabolite = relationship(Metabolite, backref="references")

    reference_id = Column(Integer, ForeignKey("{}.id".format(REFERENCE_TABLE_NAME)))
    reference = relationship(Reference, backref="metabolites")


class Disease(Base):
    """Table storing the diseases and their ids."""

    __tablename__ = DISEASE_TABLE_NAME

    id = Column(Integer, primary_key=True)
    name = Column(String(255), nullable=False, unique=True, doc="Name of the disease")
    omim_id = Column(String(255), nullable=True, doc="OMIM identifier associated with the disease")
    dion = Column(String(255), nullable=True, doc="Disease Ontology name for this disease. Found using string matching")
    hpo = Column(String(255), nullable=True,
                 doc="Human Phenotype Ontology name for this disease. Found using string matching")
    mesh_diseases = Column(String(255), nullable=True,
                           doc="MeSH Disease name for this disease. Found using string matching")

    def __repr__(self):
        return f'<Disease name={self.name}>'

    def serialize_to_bel(self) -> pathology:
        """Function to serialize a disease object to a PyBEL node data dictionary."""
        return pathology(namespace=HMDB_DISEASE, name=str(self.name))


class MetaboliteDiseaseReference(Base):
    """Table storing the relations between disease and metabolite"""

    __tablename__ = METABOLITE_DISEASE_REFERENCE_TABLE_NAME

    id = Column(Integer, primary_key=True)

    metabolite_id = Column(Integer, ForeignKey("{}.id".format(METABOLITE_TABLE_NAME)))
    metabolite = relationship(Metabolite, backref="diseases")

    disease_id = Column(Integer, ForeignKey("{}.id".format(DISEASE_TABLE_NAME)))
    disease = relationship(Disease, backref="metabolites")

    reference_id = Column(Integer, ForeignKey("{}.id".format(REFERENCE_TABLE_NAME)))
    reference = relationship(Reference, backref="diseases")

    def __repr__(self):
        return f'{self.metabolite} and {self.disease} from {self.reference}'


class CellularLocation(Base):
    """Table for storing the cellular location GO annotations"""

    __tablename__ = CELLULAR_LOCATION_TABLE_NAME

    id = Column(Integer, primary_key=True)
    cellular_location = Column(String(255), nullable=False, unique=True)


class MetaboliteCellularLocation(Base):
    """Table storing the many to many relations between metabolites and cellular location GO annotations"""

    __tablename__ = METABOLITE_CELLULAR_LOCATION_TABLE_NAME

    id = Column(Integer, primary_key=True)

    metabolite_id = Column(Integer, ForeignKey("{}.id".format(METABOLITE_TABLE_NAME)))
    metabolite = relationship(Metabolite, backref="cellular_locations")

    cellular_location_id = Column(Integer, ForeignKey("{}.id".format(CELLULAR_LOCATION_TABLE_NAME)))
    cellular_location = relationship(CellularLocation, backref="metabolites")


class Biofunction(Base):
    """Table for storing the 'biofunctions' annotations"""

    __tablename__ = BIOFUNCTION_TABLE_NAME

    id = Column(Integer, primary_key=True)
    biofunction = Column(String(255), nullable=False, unique=True)


class MetaboliteBiofunction(Base):
    """Table storing the many to many relations between metabolites and cellular location GO annotations"""

    __tablename__ = METABOLITE_BIOFUNCTION_TABLE_NAME

    id = Column(Integer, primary_key=True)

    metabolite_id = Column(Integer, ForeignKey("{}.id".format(METABOLITE_TABLE_NAME)))
    metabolite = relationship(Metabolite, backref="biofunctions")

    biofunctions_id = Column(Integer, ForeignKey("{}.id".format(BIOFUNCTION_TABLE_NAME)))
    biofunction = relationship(Biofunction, backref="metabolites")


class PropertyValues(Base):
    """Table storing the values of chemical properties.

    Not used for BEL enrichment
    """

    __tablename__ = "property_values"

    id = Column(Integer, primary_key=True)
    value = Column(String(255), nullable=False, unique=True,
                   doc="value of a chemical property (e.g. logp) that will be linked to the properts and metabolites")


class PropertyKinds(Base):
    """Table storing the 'kind' of chemical properties e.g. logP.

    Not used for BEL enrichment
    """

    __tablename__ = "property_kinds"

    id = Column(Integer, primary_key=True)
    kind = Column(String(255), nullable=False, unique=True,
                  doc="the 'kind' of chemical properties e.g. logP, melting point etc")


class PropertySource(Base):
    """Table storing the sources of properties e.g. software like 'ALOGPS'.

    Not used for BEL enrichment
    """

    __tablename__ = "property_source"

    id = Column(Integer, primary_key=True)
    source = Column(String(255), nullable=False, unique=True)