Add Rhea (#95)

Closes #53

setup.cfg

@@ -33,6 +33,7 @@ classifiers =
     License :: OSI Approved :: MIT License
     Operating System :: OS Independent
     Programming Language :: Python
+    Programming Language :: Python :: 3.9
     Programming Language :: Python :: 3.8
     Programming Language :: Python :: 3.7
     Programming Language :: Python :: 3.6
@@ -59,8 +60,8 @@ install_requires =
     tabulate
     cachier
     pystow
-    bioversions
-    bioregistry
+    bioversions>=0.0.9
+    bioregistry>=0.0.10
     drugbank_downloader
 
 # Random options
@@ -132,6 +133,7 @@ pyobo.nomenclatures =
     pid.pathway      = pyobo.sources.pid:get_obo
     pubchem.compound = pyobo.sources.pubchem:get_obo
     reactome         = pyobo.sources.reactome:get_obo
+    rhea             = pyobo.sources.rhea:get_obo
     rgd              = pyobo.sources.rgd:get_obo
     sgd              = pyobo.sources.sgd:get_obo
     umls             = pyobo.sources.umls:get_obo

src/pyobo/sources/rhea.py

@@ -0,0 +1,102 @@
+# -*- coding: utf-8 -*-
+
+"""Converter for Rhea."""
+
+import logging
+from typing import Iterable
+
+import bioversions
+import pystow
+
+from pyobo.path_utils import ensure_df
+from pyobo.struct import Obo, Reference, Term, TypeDef
+
+logger = logging.getLogger(__name__)
+PREFIX = 'rhea'
+
+has_lr = TypeDef(Reference(PREFIX, 'has_lr_reaction'))
+has_rl = TypeDef(Reference(PREFIX, 'has_rl_reaction'))
+has_bi = TypeDef(Reference(PREFIX, 'has_bi_reaction'))
+
+
+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 iter_terms(version: str) -> Iterable[Term]:
+    """Iterate over terms in Rhea."""
+    terms = {}
+
+    directions = ensure_df(PREFIX, url='ftp://ftp.expasy.org/databases/rhea/tsv/rhea-directions.tsv', version=version)
+    for master, lr, rl, bi in directions.values:
+        terms[master] = Term(reference=Reference(PREFIX, master))
+        terms[lr] = Term(reference=Reference(PREFIX, lr))
+        terms[rl] = Term(reference=Reference(PREFIX, rl))
+        terms[bi] = Term(reference=Reference(PREFIX, bi))
+
+        terms[master].append_relationship(has_lr, terms[lr])
+        terms[master].append_relationship(has_rl, terms[rl])
+        terms[master].append_relationship(has_bi, terms[bi])
+        terms[lr].append_parent(terms[master])
+        terms[rl].append_parent(terms[master])
+        terms[bi].append_parent(terms[master])
+
+    hierarchy = ensure_df(PREFIX, url='ftp://ftp.expasy.org/databases/rhea/tsv/rhea-relationships.tsv', version=version)
+    for source, relation, target in hierarchy.values:
+        if relation != 'is_a':
+            raise ValueError(f'RHEA unrecognized relation: {relation}')
+        terms[source].append_parent(terms[target])
+
+    for xref_prefix, url in [
+        ('ecocyc', 'rhea2ecocyc'),
+        ('kegg.reaction', 'rhea2kegg_reaction'),
+        ('reactome', 'rhea2reactome'),
+        ('macie', 'rhea2macie'),
+        ('metacyc', 'rhea2metacyc'),
+    ]:
+        xref_df = ensure_df(PREFIX, url=f'ftp://ftp.expasy.org/databases/rhea/tsv/{url}.tsv', version=version)
+        for rhea_id, _, _, xref_id in xref_df.values:
+            if rhea_id not in terms:
+                logger.warning('[%s] could not find %s:%s for xref %s:%s', PREFIX, PREFIX, rhea_id, xref_prefix,
+                               xref_id)
+                continue
+            terms[rhea_id].append_xref(Reference(xref_prefix, xref_id))
+
+    # TODO are EC codes equivalent?
+    # TODO uniprot enabled by (RO:0002333)
+    # TODO names?
+
+    url = 'ftp://ftp.expasy.org/databases/rhea/rdf/rhea.rdf.gz'
+    graph = pystow.ensure_rdf('pyobo', 'raw', PREFIX, version, url=url)
+    result = graph.query('''
+    PREFIX rh:<http://rdf.rhea-db.org/>
+    SELECT ?reaction ?reactionId ?reactionLabel WHERE {
+      ?reaction rdfs:subClassOf rh:Reaction .
+      ?reaction rh:id ?reactionId .
+      ?reaction rdfs:label ?reactionLabel .
+    }
+    ''')
+    for _, identifier, name in result:
+        identifier = str(identifier)
+        if identifier not in terms:
+            logger.warning('isolated element in rdf: rhea:%s ! %s', identifier, name)
+            continue
+        terms[identifier].reference.name = name
+
+    # TODO participants?
+
+    yield from terms.values()
+
+
+if __name__ == '__main__':
+    get_obo().write_default(force=True, write_obo=True)