Add BiGG Compartment

src/pyobo/sources/__init__.py

@@ -3,7 +3,7 @@
 from class_resolver import ClassResolver
 
 from .antibodyregistry import AntibodyRegistryGetter
-from .bigg import BiGGMetaboliteGetter, BiGGModelGetter, BiGGReactionGetter
+from .bigg import BiGGCompartmentGetter, BiGGMetaboliteGetter, BiGGModelGetter, BiGGReactionGetter
 from .ccle import CCLEGetter
 from .cgnc import CGNCGetter
 from .chembl import ChEMBLCompoundGetter
@@ -65,6 +65,7 @@
 
 __all__ = [
     "AntibodyRegistryGetter",
+    "BiGGCompartmentGetter",
     "BiGGMetaboliteGetter",
     "BiGGModelGetter",
     "BiGGReactionGetter",

src/pyobo/sources/bigg/__init__.py

@@ -1,10 +1,12 @@
 """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",

src/pyobo/sources/bigg/bigg_compartment.py

@@ -0,0 +1,85 @@
+"""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] = {
+    "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"),
+}
+"""
+MISSING:
+
+x peroxisome/glyoxysome
+im intermembrane space of mitochondria
+cx carboxyzome
+cm cytosolic membrane
+i inner mitochondrial compartment
+mm mitochondrial intermembrane
+w wildtype staph aureus
+"""
+
+
+class BiGGCompartmentGetter(Obo):
+    """An ontology representation of BiGG compartments."""
+
+    ontology = PREFIX
+    bioversions_key = "bigg"
+    idspaces = {
+        PREFIX: "http://bigg.ucsd.edu/compartments/",
+    }
+
+    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"})
+    for row in table.findAll("tr"):
+        cells = list(row.findAll("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()