pyobo 0.11.1__py3-none-any.whl → 0.12.0__py3-none-any.whl

pyobo/sources/__init__.py

@@ -3,10 +3,12 @@
 from class_resolver import ClassResolver
 
 from .antibodyregistry import AntibodyRegistryGetter
+from .bigg import BiGGCompartmentGetter, BiGGMetaboliteGetter, BiGGModelGetter, BiGGReactionGetter
 from .ccle import CCLEGetter
 from .cgnc import CGNCGetter
-from .chembl import ChEMBLCompoundGetter
+from .chembl import ChEMBLCompoundGetter, ChEMBLTargetGetter
 from .civic_gene import CIVICGeneGetter
+from .clinicaltrials import ClinicalTrialsGetter
 from .complexportal import ComplexPortalGetter
 from .conso import CONSOGetter
 from .cpt import CPTGetter
@@ -14,34 +16,38 @@ from .credit import CreditGetter
 from .cvx import CVXGetter
 from .depmap import DepMapGetter
 from .dictybase_gene import DictybaseGetter
-from .drugbank import DrugBankGetter
-from .drugbank_salt import DrugBankSaltGetter
+from .drugbank import DrugBankGetter, DrugBankSaltGetter
 from .drugcentral import DrugCentralGetter
 from .expasy import ExpasyGetter
 from .famplex import FamPlexGetter
 from .flybase import FlyBaseGetter
-from .geonames import GeonamesGetter
-from .gwascentral_phenotype import GWASCentralPhenotypeGetter
-from .gwascentral_study import GWASCentralStudyGetter
-from .hgnc import HGNCGetter
-from .hgncgenefamily import HGNCGroupGetter
-from .icd10 import ICD10Getter
-from .icd11 import ICD11Getter
+from .gard import GARDGetter
+from .geonames import GeonamesFeatureGetter, GeonamesGetter
+from .gtdb import GTDBGetter
+from .gwascentral import GWASCentralPhenotypeGetter, GWASCentralStudyGetter
+from .hgnc import HGNCGetter, HGNCGroupGetter
+from .icd import ICD10Getter, ICD11Getter
 from .interpro import InterProGetter
 from .itis import ITISGetter
 from .kegg import KEGGGeneGetter, KEGGGenomeGetter, KEGGPathwayGetter
 from .mesh import MeSHGetter
 from .mgi import MGIGetter
-from .mirbase import MiRBaseGetter
-from .mirbase_family import MiRBaseFamilyGetter
-from .mirbase_mature import MiRBaseMatureGetter
+from .mirbase import MiRBaseFamilyGetter, MiRBaseGetter, MiRBaseMatureGetter
 from .msigdb import MSigDBGetter
-from .ncbigene import NCBIGeneGetter
+from .ncbi import NCBIGCGetter, NCBIGeneGetter
+from .nih_reporter import NIHReporterGetter
+from .nlm import NLMCatalogGetter, NLMPublisherGetter
 from .npass import NPASSGetter
 from .omim_ps import OMIMPSGetter
 from .pathbank import PathBankGetter
-from .pfam import PfamGetter
-from .pfam_clan import PfamClanGetter
+from .pfam import PfamClanGetter, PfamGetter
+from .pharmgkb import (
+    PharmGKBChemicalGetter,
+    PharmGKBDiseaseGetter,
+    PharmGKBGeneGetter,
+    PharmGKBPathwayGetter,
+    PharmGKBVariantGetter,
+)
 from .pid import PIDGetter
 from .pombase import PomBaseGetter
 from .pubchem import PubChemCompoundGetter
@@ -51,15 +57,21 @@ from .rhea import RheaGetter
 from .ror import RORGetter
 from .selventa import SCHEMGetter, SCOMPGetter, SDISGetter, SFAMGetter
 from .sgd import SGDGetter
+from .signor import SignorGetter
 from .slm import SLMGetter
-from .umls import UMLSGetter
+from .umls import UMLSGetter, UMLSSTyGetter
+from .unimod import UnimodGetter
 from .uniprot import UniProtGetter, UniProtPtmGetter
 from .wikipathways import WikiPathwaysGetter
 from .zfin import ZFINGetter
-from ..struct import Obo
+from ..struct.struct import AdHocOntologyBase, Obo
 
 __all__ = [
     "AntibodyRegistryGetter",
+    "BiGGCompartmentGetter",
+    "BiGGMetaboliteGetter",
+    "BiGGModelGetter",
+    "BiGGReactionGetter",
     "CCLEGetter",
     "CGNCGetter",
     "CIVICGeneGetter",
@@ -67,6 +79,8 @@ __all__ = [
     "CPTGetter",
     "CVXGetter",
     "ChEMBLCompoundGetter",
+    "ChEMBLTargetGetter",
+    "ClinicalTrialsGetter",
     "ComplexPortalGetter",
     "CreditGetter",
     "DepMapGetter",
@@ -77,8 +91,11 @@ __all__ = [
     "ExpasyGetter",
     "FamPlexGetter",
     "FlyBaseGetter",
+    "GARDGetter",
+    "GTDBGetter",
     "GWASCentralPhenotypeGetter",
     "GWASCentralStudyGetter",
+    "GeonamesFeatureGetter",
     "GeonamesGetter",
     "HGNCGetter",
     "HGNCGroupGetter",
@@ -95,13 +112,22 @@ __all__ = [
     "MiRBaseFamilyGetter",
     "MiRBaseGetter",
     "MiRBaseMatureGetter",
+    "NCBIGCGetter",
     "NCBIGeneGetter",
+    "NIHReporterGetter",
+    "NLMCatalogGetter",
+    "NLMPublisherGetter",
     "NPASSGetter",
     "OMIMPSGetter",
     "PIDGetter",
     "PathBankGetter",
     "PfamClanGetter",
     "PfamGetter",
+    "PharmGKBChemicalGetter",
+    "PharmGKBDiseaseGetter",
+    "PharmGKBGeneGetter",
+    "PharmGKBPathwayGetter",
+    "PharmGKBVariantGetter",
     "PomBaseGetter",
     "PubChemCompoundGetter",
     "RGDGetter",
@@ -114,24 +140,21 @@ __all__ = [
     "SFAMGetter",
     "SGDGetter",
     "SLMGetter",
+    "SignorGetter",
     "UMLSGetter",
+    "UMLSSTyGetter",
     "UniProtGetter",
     "UniProtPtmGetter",
+    "UnimodGetter",
     "WikiPathwaysGetter",
     "ZFINGetter",
     "ontology_resolver",
 ]
 
-
-def _assert_sorted():
-    _sorted = sorted(__all__)
-    if _sorted != __all__:
-        raise ValueError(f"unsorted. should be:\n{_sorted}")
-
-
-_assert_sorted()
-del _assert_sorted
-
-ontology_resolver: ClassResolver[Obo] = ClassResolver.from_subclasses(base=Obo, suffix="Getter")
+ontology_resolver: ClassResolver[Obo] = ClassResolver.from_subclasses(
+    base=Obo,
+    suffix="Getter",
+    skip={AdHocOntologyBase},
+)
 for getter in list(ontology_resolver):
     ontology_resolver.synonyms[getter.ontology] = getter

pyobo/sources/antibodyregistry.py

@@ -1,15 +1,18 @@
-"""Converter for the Antibody Registry."""
+"""Converter for the Antibody Registry.
+
+TODO use API https://www.antibodyregistry.org/api/antibodies?page=1&size=100
+"""
 
 import logging
 from collections.abc import Iterable, Mapping
-from typing import Optional
 
 import pandas as pd
 from bioregistry.utils import removeprefix
 from tqdm.auto import tqdm
 
-from pyobo import Obo, Term
+from pyobo import Obo, Reference, Term
 from pyobo.api.utils import get_version
+from pyobo.struct.typedef import has_citation
 from pyobo.utils.path import ensure_df
 
 __all__ = [
@@ -23,7 +26,7 @@ URL = "http://antibodyregistry.org/php/fileHandler.php"
 CHUNKSIZE = 20_000
 
 
-def get_chunks(*, force: bool = False, version: Optional[str] = None) -> pd.DataFrame:
+def get_chunks(*, force: bool = False, version: str | None = None) -> pd.DataFrame:
     """Get the BioGRID identifiers mapping dataframe."""
     if version is None:
         version = get_version(PREFIX)
@@ -44,19 +47,15 @@ class AntibodyRegistryGetter(Obo):
     """An ontology representation of the Antibody Registry."""
 
     ontology = bioversions_key = PREFIX
+    typedefs = [has_citation]
 
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
         """Iterate over terms in the ontology."""
         return iter_terms(force=force, version=self._version_or_raise)
 
 
-def get_obo(*, force: bool = False) -> Obo:
-    """Get the Antibody Registry as OBO."""
-    return AntibodyRegistryGetter(force=force)
-
-
 # TODO there are tonnnnsss of mappings to be curated
-MAPPING: Mapping[str, Optional[str]] = {
+MAPPING: Mapping[str, str | None] = {
     "AMERICAN DIAGNOSTICA": None,  # No website
     "Biolegend": "biolegend",
     "Enzo Life Sciences": "enzo",
@@ -74,7 +73,7 @@ SKIP = {
 }
 
 
-def iter_terms(*, force: bool = False, version: Optional[str] = None) -> Iterable[Term]:
+def iter_terms(*, force: bool = False, version: str | None = None) -> Iterable[Term]:
     """Iterate over antibodies."""
     chunks = get_chunks(force=force, version=version)
     needs_curating = set()
@@ -98,7 +97,7 @@ def iter_terms(*, force: bool = False, version: Optional[str] = None) -> Iterabl
                     pubmed_id = pubmed_id.strip()
                     if not pubmed_id:
                         continue
-                    term.append_provenance(("pubmed", pubmed_id))
+                    term.append_provenance(Reference(prefix="pubmed", identifier=pubmed_id))
             yield term
 
 

pyobo/sources/bigg/__init__.py

@@ -0,0 +1,13 @@
+"""Converter for resources in BiGG."""
+
+from .bigg_compartment import BiGGCompartmentGetter
+from .bigg_metabolite import BiGGMetaboliteGetter
+from .bigg_model import BiGGModelGetter
+from .bigg_reaction import BiGGReactionGetter
+
+__all__ = [
+    "BiGGCompartmentGetter",
+    "BiGGMetaboliteGetter",
+    "BiGGModelGetter",
+    "BiGGReactionGetter",
+]

pyobo/sources/bigg/bigg_compartment.py

@@ -0,0 +1,81 @@
+"""Get compartments from BiGG."""
+
+from collections.abc import Iterable
+
+from bioversions.utils import get_soup
+
+from pyobo import Obo, Reference, Term
+
+__all__ = [
+    "BiGGCompartmentGetter",
+    "get_compartments",
+]
+
+DATA_URL = "http://bigg.ucsd.edu/compartments/"
+PREFIX = "bigg.compartment"
+GO_MAPPING: dict[str, Reference | None] = {
+    "c": Reference(prefix="go", identifier="0005829", name="cytosol"),
+    "e": Reference(prefix="go", identifier="0005615", name="extracellular space"),
+    "p": Reference(prefix="go", identifier="0042597", name="periplasmic space"),
+    "m": Reference(prefix="go", identifier="0005739", name="mitochondrion"),
+    "r": Reference(prefix="go", identifier="0005783", name="endoplasmic reticulum"),
+    "v": Reference(prefix="go", identifier="0005773", name="vacuole"),
+    "n": Reference(prefix="go", identifier="0005634", name="nucleus"),
+    "g": Reference(prefix="go", identifier="0005794", name="Golgi apparatus"),
+    "u": Reference(prefix="go", identifier="0009579", name="thylakoid"),
+    "l": Reference(prefix="go", identifier="0005764", name="lysosome"),
+    "h": Reference(prefix="go", identifier="0009507", name="chloroplast"),
+    "f": Reference(prefix="go", identifier="0005929", name="cilium"),
+    "s": Reference(prefix="go", identifier="1990413", name="eyespot apparatus"),
+    "um": Reference(prefix="go", identifier="0042651", name="thylakoid membrane"),
+    "y": Reference(prefix="go", identifier="0070069", name="cytochrome complex"),
+    # note that glyoxysome is a child class of peroxisome in GO
+    "x": Reference(prefix="go", identifier="0005777", name="peroxisome"),
+    "mm": Reference(prefix="go", identifier="0005743", name="mitochondrial inner membrane"),
+    "im": Reference(prefix="go", identifier="0005758", name="mitochondrial intermembrane space"),
+    "cx": None,  # missing for carboxyzome
+    "cm": None,  # missing for cytosolic membrane
+    "i": None,  # missing for inner mitochondrial compartment
+    "w": None,  # missing for wildtype staph aureus
+}
+
+
+class BiGGCompartmentGetter(Obo):
+    """An ontology representation of BiGG compartments."""
+
+    ontology = PREFIX
+    bioversions_key = "bigg"
+
+    def iter_terms(self, force: bool = False) -> Iterable[Term]:
+        """Iterate over terms in the ontology."""
+        return iterate_terms(force=force, version=self._version_or_raise)
+
+
+def get_compartments(*, force: bool = False, version: str | None = None) -> dict[str, str]:
+    """Get a dictionary of BiGG compartments."""
+    rv = {}
+    soup = get_soup(DATA_URL)
+    table = soup.find(**{"class": "myTable"})  # type:ignore[arg-type]
+    if table is None:
+        raise ValueError
+    for row in table.find_all("tr"):  # type:ignore[attr-defined]
+        cells = list(row.find_all("td"))
+        if not cells:
+            continue
+        identifier_cell, name_cell = cells
+        rv[identifier_cell.text] = name_cell.text
+    return rv
+
+
+def iterate_terms(*, force: bool = False, version: str | None = None) -> Iterable[Term]:
+    """Iterate over BiGG compartments."""
+    compartments = get_compartments(force=force, version=version)
+    for identifier, name in compartments.items():
+        term = Term.from_triple(PREFIX, identifier, name)
+        if go_component_ref := GO_MAPPING.get(identifier):
+            term.append_exact_match(go_component_ref)
+        yield term
+
+
+if __name__ == "__main__":
+    BiGGCompartmentGetter.cli()

pyobo/sources/bigg/bigg_metabolite.py

@@ -0,0 +1,229 @@
+"""Converter for metabolites in BiGG."""
+
+import logging
+import re
+from collections.abc import Iterable
+
+import bioregistry
+import pandas as pd
+from pydantic import ValidationError
+from tqdm import tqdm
+
+from pyobo.sources.bigg.bigg_compartment import GO_MAPPING
+from pyobo.struct import Obo, Reference, Term
+from pyobo.struct.typedef import located_in, participates_in
+from pyobo.utils.path import ensure_df
+
+__all__ = [
+    "BiGGMetaboliteGetter",
+]
+
+logger = logging.getLogger(__name__)
+
+PREFIX = "bigg.metabolite"
+URL = "http://bigg.ucsd.edu/static/namespace/bigg_models_metabolites.txt"
+PATTERN = re.compile("^[a-z_A-Z0-9]+$")
+
+MOLECULE = Term.from_triple("cob", "0000013", "molecule")
+
+
+class BiGGMetaboliteGetter(Obo):
+    """An ontology representation of BiGG Metabolites."""
+
+    ontology = PREFIX
+    bioversions_key = "bigg"
+    typedefs = [participates_in, located_in]
+    root_terms = [MOLECULE.reference]
+
+    def iter_terms(self, force: bool = False) -> Iterable[Term]:
+        """Iterate over terms in the ontology."""
+        return iterate_terms(force=force, version=self._version_or_raise)
+
+
+KEY_TO_PREFIX = {
+    "CHEBI": "chebi",
+    "Human Metabolome Database": "hmdb",
+    "LipidMaps": "lipidmaps",
+    "BioCyc": "biocyc",
+    "KEGG Compound": "kegg.compound",
+    "MetaNetX (MNX) Chemical": "metanetx.chemical",
+    "InChI Key": "inchikey",
+    "SEED Compound": "seed.compound",
+    "Reactome Compound": "reactome",
+    "KEGG Drug": "kegg.drug",
+    "KEGG Glycan": "kegg.glycan",
+    "MetaNetX (MNX) Equation": "metanetx.reaction",
+    "RHEA": "rhea",
+    "EC Number": "ec",
+    "SEED Reaction": "seed.reaction",
+    "Reactome Reaction": "reactome",
+    "KEGG Reaction": "kegg.reaction",
+}
+EXACTS = {"inchikey"}
+
+
+def _split(x) -> list[str]:
+    if pd.notna(x):
+        return [y.strip() for y in x.split(";")]
+    return []
+
+
+def iterate_terms(force: bool = False, version: str | None = None) -> Iterable[Term]:
+    """Iterate terms for BiGG Metabolite."""
+    bigg_df = ensure_df(
+        prefix=PREFIX,
+        url=URL,
+        force=force,
+        version=version,
+    )
+
+    for v in KEY_TO_PREFIX.values():
+        nmp = bioregistry.normalize_prefix(v)
+        if v != nmp:
+            raise ValueError(f"Normalize {v} to {nmp}")
+
+    universal_references: set[Reference] = set()
+    compartment_references: set[Reference] = set()
+
+    yield MOLECULE
+
+    # TODO there are duplicates on universal ID - this might be
+    # because the compartment ID is unique
+    for (
+        bigg_compartmental_id,
+        universal_bigg_id,
+        name,
+        model_list,
+        database_links,
+        old_bigg_ids,
+    ) in tqdm(
+        bigg_df.values,
+        unit_scale=True,
+        unit="metabolite",
+        desc=f"[{PREFIX}] processing",
+    ):
+        if not PATTERN.match(bigg_compartmental_id):
+            tqdm.write(f"[{PREFIX}] invalid BIGG ID: {bigg_compartmental_id}")
+            continue
+
+        universal_name = name.strip() if pd.notna(name) else None
+
+        _, _, compartment_letter = bigg_compartmental_id.rpartition("_")
+        compartment_reference = GO_MAPPING[compartment_letter] or Reference(
+            prefix="bigg.compartment", identifier=compartment_letter
+        )
+        compartment_references.add(compartment_reference)
+        compartment_name = (
+            f"{universal_name} (in {compartment_reference.name})" if universal_name else None
+        )
+
+        term = Term(
+            reference=Reference(
+                prefix=PREFIX,
+                identifier=bigg_compartmental_id,
+                name=compartment_name,
+            ),
+        )
+        term.append_relationship(located_in, compartment_reference)
+
+        if PATTERN.match(universal_bigg_id):
+            universal_reference = Reference(
+                prefix=PREFIX, identifier=universal_bigg_id, name=universal_name
+            )
+            term.append_parent(universal_reference)
+            universal_references.add(universal_reference)
+        else:
+            tqdm.write(f"[{PREFIX}] invalid universal BIGG ID: {bigg_compartmental_id}")
+
+        for old_bigg_id in _split(old_bigg_ids):
+            if old_bigg_id in {bigg_compartmental_id, universal_bigg_id}:
+                continue
+            if not PATTERN.match(old_bigg_id):
+                if not old_bigg_id.endswith("]"):
+                    # if it ends with ']' then it's a compartment identifier
+                    logger.debug(f"[{PREFIX}:{universal_bigg_id}] invalid alt ID: {old_bigg_id}")
+                continue
+            term.append_alt(Reference(prefix=PREFIX, identifier=old_bigg_id))
+        _parse_model_links(term, model_list)
+        _parse_dblinks(term, database_links)
+
+        yield term
+
+    for universal_reference in universal_references:
+        yield Term(reference=universal_reference).append_parent(MOLECULE)
+
+    for compartment in compartment_references:
+        yield Term(reference=compartment)
+
+
+def _parse_model_links(term: Term, model_list: str) -> None:
+    for model_id in _split(model_list):
+        try:
+            reference = Reference(prefix="bigg.model", identifier=model_id)
+        except ValidationError:
+            tqdm.write(f"[{term.curie}] invalid model reference: {model_id}")
+        else:
+            term.annotate_object(participates_in, reference)
+
+
+def _parse_dblinks(term: Term, database_links: str, property_map=None) -> None:
+    if not property_map:
+        property_map = {}
+
+    # there are duplicate xrefs, keep track
+    seen = set()
+
+    for dblink in _split(database_links):
+        key, _, identifier_url = dblink.strip().partition(":")
+        identifier_url = identifier_url.strip()
+        if not identifier_url:
+            continue
+
+        if identifier_url.startswith("http://identifiers.org/kegg.glycan/"):
+            prefix = "kegg.glycan"
+            identifier = identifier_url.removeprefix("http://identifiers.org/kegg.glycan/")
+        elif identifier_url.startswith("http://identifiers.org/kegg.drug/"):
+            prefix = "kegg.drug"
+            identifier = identifier_url.removeprefix("http://identifiers.org/kegg.drug/")
+        elif identifier_url.startswith("http://identifiers.org/kegg.reaction/"):
+            prefix = "kegg.reaction"
+            identifier = identifier_url.removeprefix("http://identifiers.org/kegg.reaction/")
+        else:
+            prefix_, identifier_ = bioregistry.parse_iri(identifier_url)
+            if not prefix_ or not identifier_:
+                tqdm.write(f"[{PREFIX}] failed to parse xref IRI: {identifier_url}")
+                continue
+            prefix, identifier = prefix_, identifier_
+        if prefix == "kegg":
+            prefix = "kegg.compound"
+        if prefix != KEY_TO_PREFIX.get(key):
+            tqdm.write(f"[{PREFIX}] mismatch between {prefix=} and {key=} - {identifier_url}")
+            continue
+        if prefix == "rhea" and "#" in identifier:
+            identifier = identifier.split("#")[0]
+
+        try:
+            reference = Reference(prefix=prefix, identifier=identifier)
+        except ValidationError:
+            tqdm.write(f"[{term.curie}] could not validate xref - {prefix}:{identifier}")
+            continue
+        # don't add self-reference
+        if reference.pair == term.pair:
+            continue
+
+        if reference in seen:
+            tqdm.write(f"[{term.curie}] got duplicate xref {reference}")
+            continue
+
+        seen.add(reference)
+
+        if prefix in property_map:
+            term.annotate_object(property_map[prefix], reference)
+        elif prefix in EXACTS:
+            term.append_exact_match(reference)
+        else:
+            term.append_xref(reference)
+
+
+if __name__ == "__main__":
+    BiGGMetaboliteGetter.cli()

pyobo/sources/bigg/bigg_model.py

@@ -0,0 +1,46 @@
+"""Converter for models in BiGG."""
+
+import json
+import logging
+from collections.abc import Iterable
+
+from pyobo.resources.ncbitaxon import get_ncbitaxon_id
+from pyobo.struct import Obo, Term
+from pyobo.utils.path import ensure_path
+
+__all__ = [
+    "BiGGModelGetter",
+]
+
+logger = logging.getLogger(__name__)
+URL = "http://bigg.ucsd.edu/api/v2/models"
+PREFIX = "bigg.model"
+
+
+class BiGGModelGetter(Obo):
+    """An ontology representation of BiGG Models."""
+
+    ontology = PREFIX
+    bioversions_key = "bigg"
+
+    def iter_terms(self, force: bool = False) -> Iterable[Term]:
+        """Iterate over terms in the ontology."""
+        return iterate_terms(version=self._version_or_raise)
+
+
+def iterate_terms(version: str) -> Iterable[Term]:
+    """Iterate over BiGG Models."""
+    path = ensure_path(PREFIX, url=URL, version=version)
+    records = json.loads(path.read_text())["results"]
+    for record in records:
+        ncbitaxon_id = get_ncbitaxon_id(record["organism"])
+        term = Term.from_triple(PREFIX, record["bigg_id"])
+        if ncbitaxon_id:
+            term.set_species(ncbitaxon_id)
+        else:
+            logger.info("[%s] could not ground organism name: %s", term.curie, record["organism"])
+        yield term
+
+
+if __name__ == "__main__":
+    BiGGModelGetter.cli()

pyobo/sources/bigg/bigg_reaction.py

@@ -0,0 +1,77 @@
+"""Converter for BiGG."""
+
+from collections.abc import Iterable
+
+import pandas as pd
+from pydantic import ValidationError
+from tqdm import tqdm
+
+from pyobo.sources.bigg.bigg_metabolite import _parse_dblinks, _parse_model_links, _split
+from pyobo.struct import Obo, Reference, Term
+from pyobo.struct.typedef import enabled_by, participates_in
+from pyobo.utils.path import ensure_df
+
+__all__ = [
+    "BiGGReactionGetter",
+]
+
+PREFIX = "bigg.reaction"
+URL = "http://bigg.ucsd.edu/static/namespace/bigg_models_reactions.txt"
+PROPERTY_MAP = {"ec": enabled_by}
+
+
+class BiGGReactionGetter(Obo):
+    """An ontology representation of BiGG Reactions."""
+
+    ontology = PREFIX
+    bioversions_key = "bigg"
+    typedefs = [participates_in, enabled_by]
+
+    def iter_terms(self, force: bool = False) -> Iterable[Term]:
+        """Iterate over terms in the ontology."""
+        return iterate_terms(force=force, version=self._version_or_raise)
+
+
+def iterate_terms(force: bool = False, version: str | None = None) -> Iterable[Term]:
+    """Iterate terms for BiGG Reaction."""
+    bigg_reaction_df = ensure_df(
+        prefix=PREFIX,
+        url=URL,
+        force=force,
+        version=version,
+    )
+
+    for bigg_id, name, reaction_string, model_list, database_links, old_bigg_ids in tqdm(
+        bigg_reaction_df.values, unit_scale=True, unit="reaction", desc=f"[{PREFIX}] processing"
+    ):
+        if "(" in bigg_id:
+            tqdm.write(f"[{PREFIX}] identifier has open paren. can't encode in OWL: {bigg_id}")
+            continue
+
+        term = Term(
+            reference=Reference(
+                prefix=PREFIX, identifier=bigg_id, name=name if pd.notna(name) else None
+            ),
+            definition=reaction_string,
+        )
+        for old_bigg_id in _split(old_bigg_ids):
+            if old_bigg_id == bigg_id:
+                continue
+            if "(" in old_bigg_id:
+                continue
+            try:
+                alt_reference = Reference(prefix=PREFIX, identifier=old_bigg_id)
+            except ValidationError:
+                tqdm.write(f"[{term.curie}] had problematic alt reference: {old_bigg_id}")
+            else:
+                term.append_alt(alt_reference)
+        _parse_model_links(term, model_list)
+
+        # TODO make sure exact match goes to the bidirectional rhea reaction but not others
+        _parse_dblinks(term, database_links)
+
+        yield term
+
+
+if __name__ == "__main__":
+    BiGGReactionGetter.cli()