New source: BiGG Models Metabolite Database

src/pyobo/sources/bigg.py

@@ -0,0 +1,61 @@
+# -*- coding: utf-8 -*-
+
+"""Converter for bigg."""
+
+from typing import Iterable, Optional
+
+import bioversions
+
+from pyobo.struct import Obo, Reference, SynonymTypeDef, Term, TypeDef
+
+from ..utils.path import ensure_df
+
+HEADER = ["bigg_id", "universal_bigg_id", "name", "model_list", "database_links", "old_bigg_ids"]
+PREFIX = "bigg.metabolite"
+
+URL = "http://bigg.ucsd.edu/static/namespace/bigg_models_metabolites.txt"
+
+alias_type = SynonymTypeDef(id="alias", name="alias")
+has_role = TypeDef(reference=Reference(prefix="bigg", identifier="has_role"))
+
+
+def get_obo(force: bool = False) -> Obo:
+    """Get bigg as OBO."""
+    version = bioversions.get_version("bigg")
+    # version = '1.2'
+    return Obo(
+        ontology=PREFIX,
+        name="bigg models metabolites database",
+        iter_terms=get_terms,
+        iter_terms_kwargs=dict(force=force, version=version),
+        typedefs=[has_role],
+        synonym_typedefs=[alias_type],
+        auto_generated_by=f"bio2obo:{PREFIX}",
+        data_version=version,
+    )
+
+
+def get_terms(force: bool = False, version: Optional[str] = None) -> Iterable[Term]:
+    bigg_df = ensure_df(
+        prefix=PREFIX,
+        url=URL,
+        sep="\t",
+        skiprows=18,
+        header=None,
+        names=HEADER,
+        usecols=["bigg_id", "name"],
+        force=force,
+        version=version,
+    )
+
+    for v in bigg_df.values:
+        bigg_id = v[0]
+        name = v[1]
+        term = Term(
+            reference=Reference(prefix=PREFIX, identifier=bigg_id, name=name),
+        )
+        yield term
+
+
+if __name__ == "__main__":
+    get_obo(force=True).cli()