def get_obo() -> Obo:
"""Get ITIS as OBO."""
return Obo(
ontology=PREFIX,
name='Integrated Taxonomic Information System',
iter_terms=iter_terms,
auto_generated_by=f'bio2obo:{PREFIX}',
)
def get_obo() -> Obo:
"""Get KEGG Genome as OBO."""
return Obo(
ontology=KEGG_GENOME_PREFIX,
iter_terms=iter_terms,
name='KEGG Genome',
auto_generated_by=f'bio2obo:{KEGG_GENOME_PREFIX}',
)
def get_obo() -> Obo:
"""Get the ComplexPortal OBO."""
return Obo(
ontology=PREFIX,
name='Complex Portal',
data_version=VERSION,
iter_terms=get_terms,
typedefs=[from_species, has_part],
auto_generated_by=f'bio2obo:{PREFIX}',
)
def get_obo() -> Obo:
"""Get GWAS Central Studies as OBO."""
return Obo(
name="GWAS Central Phenotype",
ontology=PREFIX,
iter_terms=iter_terms,
iter_terms_kwargs=dict(version=VERSION),
data_version=VERSION,
auto_generated_by=f"bio2obo:{PREFIX}",
)
def get_obo() -> Obo:
"""Get DrugCentral OBO."""
version = bioversions.get_version(PREFIX)
return Obo(
ontology=PREFIX,
name='DrugCentral',
data_version=version,
iter_terms=iter_terms,
iter_terms_kwargs=dict(version=version),
auto_generated_by=f'bio2obo:{PREFIX}',
)
def get_obo() -> Obo:
"""Get KEGG Genome as OBO."""
version = bioversions.get_version("kegg")
return Obo(
ontology=KEGG_GENOME_PREFIX,
iter_terms=iter_terms,
iter_terms_kwargs=dict(version=version),
name="KEGG Genome",
data_version=version,
auto_generated_by=f"bio2obo:{KEGG_GENOME_PREFIX}",
)
def get_obo() -> Obo:
"""Return ChEMBL as OBO."""
version = bioversions.get_version('chembl')
return Obo(
ontology='chembl.compound',
name='ChEMBL',
data_version=version,
iter_terms=iter_terms,
iter_terms_kwargs=dict(version=version),
auto_generated_by=f'bio2obo:{PREFIX}',
)
def get_obo():
"""Get GWAS Central Studies as OBO."""
return Obo(
ontology=PREFIX,
name="GWAS Central Study",
iter_terms=iterate_terms,
iter_terms_kwargs=dict(version=VERSION),
data_version=VERSION,
typedefs=[has_part],
auto_generated_by=f"bio2obo:{PREFIX}",
)
def get_obo() -> Obo:
"""Return ChEMBL as OBO."""
version = bioversions.get_version("chembl")
return Obo(
ontology="chembl.compound",
name="ChEMBL",
data_version=version,
iter_terms=iter_terms,
iter_terms_kwargs=dict(version=version),
auto_generated_by=f"bio2obo:{PREFIX}",
)
def get_obo() -> Obo:
"""Get Rhea as OBO."""
version = bioversions.get_version(PREFIX)
return Obo(
ontology=PREFIX,
name='Rhea',
iter_terms=iter_terms,
iter_terms_kwargs=dict(version=version),
data_version=version,
auto_generated_by=f'bio2obo:{PREFIX}',
typedefs=[has_lr, has_bi, has_rl],
)
def get_obo(skip_missing: bool = True) -> Obo:
"""Get KEGG Pathways as OBO."""
version = bioversions.get_version('kegg')
return Obo(
ontology=KEGG_PATHWAY_PREFIX,
iter_terms=iter_terms,
iter_terms_kwargs=dict(skip_missing=skip_missing, version=version),
name='KEGG Pathways',
typedefs=[from_kegg_species, from_species, species_specific, has_part],
auto_generated_by=f'bio2obo:{KEGG_PATHWAY_PREFIX}',
data_version=version,
)
def get_obo(force: bool = False) -> Obo:
"""Get FamPlex as OBO."""
version = get_commit('sorgerlab', 'famplex')
return Obo(
ontology=PREFIX,
name='FamPlex',
iter_terms=get_terms,
iter_terms_kwargs=dict(version=version, force=force),
data_version=version,
typedefs=[has_member, has_part, is_a, part_of],
auto_generated_by=f'bio2obo:{PREFIX}',
)
def get_obo() -> Obo:
"""Get the ComplexPortal OBO."""
version = bioversions.get_version(PREFIX)
return Obo(
ontology=PREFIX,
name="Complex Portal",
data_version=version,
iter_terms=get_terms,
iter_terms_kwargs=dict(version=version),
typedefs=[from_species, has_part],
auto_generated_by=f"bio2obo:{PREFIX}",
)