这应该可以满足您的需求...

This should do what you are looking for ...

from sqlalchemy import (Column, create_engine, Integer, ForeignKey, Unicode,
                        Enum)
from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy.orm import sessionmaker, relationship

Base = declarative_base()

class Gene(Base):
    __tablename__ = 'gene'

    id = Column(Integer, primary_key=True)
    name = Column(Unicode(64), unique=True)

    def __init__(self, name):
        self.name = name

class Experiment(Base):
    __tablename__ = 'experiment'

    id = Column(Integer, primary_key=True)

class Organ(Base):
    __tablename__ = 'organ'

    id = Column(Integer, primary_key=True)
    name = Column(Unicode(64), unique=True)

    def __init__(self, name):
        self.name = name

class Measurement(Base):
    __tablename__ = 'measurement'

    id = Column(Integer, primary_key=True)
    experiment_id = Column(Integer, ForeignKey(Experiment.id))
    gene_id = Column(Integer, ForeignKey(Gene.id))
    organ_id = Column(Integer, ForeignKey(Organ.id))

    # Add your measured values here
    expression = Column(Enum('UP', 'DOWN'))
    # ...

    experiment = relationship(Experiment, backref='measurements')
    gene = relationship(Gene, backref='measurements')
    organ = relationship(Organ, backref='measurements')

    def __repr__(self):
        return 'Experiment %d: %s, %s, %s' % (self.experiment.id,
                         self.gene.name, self.organ.name, self.expression)

if __name__ == '__main__':
    engine = create_engine('sqlite://')
    session = sessionmaker(engine)()
    Base.metadata.create_all(engine)

    #
    # Creating the data
    #

    x = Gene('Gene X')
    y = Gene('Gene Y')
    z = Gene('Gene Z')

    heart = Organ('Heart')
    lungs = Organ('Lungs')
    brain = Organ('Brain')

    session.add_all([x, y, z, heart, lungs, brain])
    session.commit()

    experiment_1 = Experiment()
    experiment_1.measurements.extend(
            [Measurement(gene_id=x.id, organ_id=heart.id, expression='UP'),
             Measurement(gene_id=x.id, organ_id=lungs.id, expression='UP'),
             Measurement(gene_id=x.id, organ_id=brain.id, expression='DOWN'),
             Measurement(gene_id=y.id, organ_id=brain.id, expression='UP'),
             Measurement(gene_id=z.id, organ_id=brain.id, expression='DOWN')])

    experiment_2 = Experiment()
    experiment_2.measurements.extend(
            [Measurement(gene_id=y.id, organ_id=lungs.id, expression='UP'),
             Measurement(gene_id=y.id, organ_id=lungs.id, expression='UP'),
             Measurement(gene_id=y.id, organ_id=brain.id, expression='UP'),
             Measurement(gene_id=x.id, organ_id=brain.id, expression='UP'),
             Measurement(gene_id=z.id, organ_id=heart.id, expression='UP')])

    session.add_all([experiment_1, experiment_2])
    session.commit()

    #
    # Querying the data
    #

    print('All measurements in the first experiment')
    experiment = session.query(Experiment).filter(Experiment.id == 1).one()
    for measurement in experiment.measurements:
        print(measurement)
    print('')

    print('All measurements of Gene X')
    gene_x = session.query(Gene).filter(Gene.name == 'Gene X').one()
    for measurement in gene_x.measurements:
        print(measurement)
    print('')

    print('All measurements of the brain')
    the_brain = session.query(Organ).filter(Organ.name == 'Brain').one()
    for measurement in the_brain.measurements:
        print(measurement)
    print('')