pyobo 0.12.4__py3-none-any.whl → 0.12.5__py3-none-any.whl

pyobo/sources/chembl/chembl_tissue.py

@@ -0,0 +1,70 @@
+"""Converter for ChEMBL tissues."""
+
+import logging
+from collections.abc import Iterable
+
+import chembl_downloader
+
+from pyobo.struct import Obo, Reference, Term
+from pyobo.struct.typedef import exact_match
+
+__all__ = [
+    "ChEMBLTissueGetter",
+]
+
+logger = logging.getLogger(__name__)
+
+PREFIX = "chembl.tissue"
+QUERY = """\
+SELECT
+    CHEMBL_ID,
+    PREF_NAME,
+    UBERON_ID,
+    EFO_ID,
+    BTO_ID,
+    CALOHA_ID
+FROM TISSUE_DICTIONARY
+"""
+
+
+class ChEMBLTissueGetter(Obo):
+    """An ontology representation of ChEMBL tissues."""
+
+    ontology = PREFIX
+    bioversions_key = "chembl"
+    typedefs = [exact_match]
+
+    def iter_terms(self, force: bool = False) -> Iterable[Term]:
+        """Iterate over terms in the ontology."""
+        return iter_terms(version=self._version_or_raise)
+
+
+def iter_terms(version: str | None = None) -> Iterable[Term]:
+    """Iterate over ChEMBL tissue terms."""
+    with chembl_downloader.cursor(version=version) as cursor:
+        cursor.execute(QUERY)
+        for chembl_id, name, uberon, efo, bto, caloha in cursor.fetchall():
+            term = Term(
+                reference=Reference(prefix=PREFIX, identifier=chembl_id, name=name),
+            )
+            if uberon:
+                term.append_exact_match(
+                    Reference(prefix="uberon", identifier=uberon.removeprefix("UBERON:"))
+                )
+            if efo:
+                term.append_exact_match(
+                    Reference(
+                        prefix="efo", identifier=efo.removeprefix("EFO:").removeprefix("EFO;")
+                    )
+                )
+            if bto:
+                term.append_exact_match(
+                    Reference(prefix="bto", identifier=bto.removeprefix("BTO:"))
+                )
+            if caloha:
+                term.append_exact_match(Reference(prefix="caloha", identifier=caloha))
+            yield term
+
+
+if __name__ == "__main__":
+    ChEMBLTissueGetter.cli()

pyobo/sources/clinicaltrials.py

@@ -27,49 +27,48 @@ HAS_INTERVENTION = TypeDef(
     is_metadata_tag=True,
 )
 
-STUDY_TERM = Term(reference=default_reference(PREFIX, "study", name="study"))
+INVESTIGATION_TERM = Term(
+    reference=Reference(prefix="obi", identifier="0000066", name="investigation")
+)
 
-CLINICAL_TRIAL_TERM = Term(
-    reference=default_reference(PREFIX, "clinical-trial", name="clinical trial")
-).append_parent(STUDY_TERM)
+OBSERVATIONAL_INVESTIGATION_TERM = Term(
+    reference=Reference(prefix="obi", identifier="0003693", name="observational investigation")
+).append_parent(INVESTIGATION_TERM)
 
-INTERVENTIONAL_CLINICAL_TRIAL_TERM = Term(
-    reference=default_reference(
-        PREFIX, "interventional-clinical-trial", name="interventional clinical trial"
-    )
-).append_parent(CLINICAL_TRIAL_TERM)
+CLINICAL_INVESTIGATION_TERM = Term(
+    reference=Reference(prefix="obi", identifier="0003697", name="clinical investigation")
+).append_parent(INVESTIGATION_TERM)
+
+CLINICAL_TRIAL_TERM = Term(
+    reference=Reference(prefix="obi", identifier="0003699", name="clinical trial")
+).append_parent(CLINICAL_INVESTIGATION_TERM)
 
 RANDOMIZED_INTERVENTIONAL_CLINICAL_TRIAL_TERM = Term(
-    reference=default_reference(
-        PREFIX,
-        "randomized-interventional-clinical-trial",
-        name="randomized interventional clinical trial",
+    reference=Reference(
+        prefix="obi",
+        identifier="0004001",
+        name="randomized clinical trial",
     )
-).append_parent(INTERVENTIONAL_CLINICAL_TRIAL_TERM)
+).append_parent(CLINICAL_TRIAL_TERM)
 
 NON_RANDOMIZED_INTERVENTIONAL_CLINICAL_TRIAL_TERM = Term(
-    reference=default_reference(
-        PREFIX,
-        "non-randomized-interventional-clinical-trial",
-        name="non-randomized interventional clinical trial",
-    )
-).append_parent(INTERVENTIONAL_CLINICAL_TRIAL_TERM)
-
-OBSERVATIONAL_CLINICAL_TRIAL_TERM = Term(
-    reference=default_reference(
-        PREFIX, "observational-clinical-trial", name="observational clinical trial"
+    reference=Reference(
+        prefix="obi",
+        identifier="0004002",
+        name="non-randomized clinical trial",
     )
 ).append_parent(CLINICAL_TRIAL_TERM)
 
+# TODO request OBI term
 EXPANDED_ACCESS_STUDY_TERM = Term(
     reference=default_reference(PREFIX, "expanded-access-study", name="expanded access study")
-).append_parent(STUDY_TERM)
+).append_parent(INVESTIGATION_TERM)
 
 TERMS = [
-    STUDY_TERM,
+    INVESTIGATION_TERM,
+    CLINICAL_INVESTIGATION_TERM,
+    OBSERVATIONAL_INVESTIGATION_TERM,
     CLINICAL_TRIAL_TERM,
-    OBSERVATIONAL_CLINICAL_TRIAL_TERM,
-    INTERVENTIONAL_CLINICAL_TRIAL_TERM,
     EXPANDED_ACCESS_STUDY_TERM,
     RANDOMIZED_INTERVENTIONAL_CLINICAL_TRIAL_TERM,
     NON_RANDOMIZED_INTERVENTIONAL_CLINICAL_TRIAL_TERM,
@@ -79,13 +78,13 @@ TERMS = [
 # types in ClinicalTrials.gov. See summary script at
 # https://gist.github.com/cthoyt/12a3cb3c63ad68d73fe5a2f0d506526f
 PARENTS: dict[tuple[str | None, str | None], Term] = {
-    ("INTERVENTIONAL", None): INTERVENTIONAL_CLINICAL_TRIAL_TERM,
-    ("INTERVENTIONAL", "NA"): INTERVENTIONAL_CLINICAL_TRIAL_TERM,
+    ("INTERVENTIONAL", None): CLINICAL_TRIAL_TERM,
+    ("INTERVENTIONAL", "NA"): CLINICAL_TRIAL_TERM,
     ("INTERVENTIONAL", "RANDOMIZED"): RANDOMIZED_INTERVENTIONAL_CLINICAL_TRIAL_TERM,
     ("INTERVENTIONAL", "NON_RANDOMIZED"): NON_RANDOMIZED_INTERVENTIONAL_CLINICAL_TRIAL_TERM,
-    ("OBSERVATIONAL", None): OBSERVATIONAL_CLINICAL_TRIAL_TERM,
+    ("OBSERVATIONAL", None): OBSERVATIONAL_INVESTIGATION_TERM,
     ("EXPANDED_ACCESS", None): EXPANDED_ACCESS_STUDY_TERM,
-    (None, None): STUDY_TERM,
+    (None, None): INVESTIGATION_TERM,
 }
 
 
@@ -95,7 +94,7 @@ class ClinicalTrialsGetter(Obo):
     ontology = PREFIX
     dynamic_version = True
     typedefs = [has_contributor, INVESTIGATES_CONDITION, HAS_INTERVENTION]
-    root_terms = [STUDY_TERM.reference]
+    root_terms = [INVESTIGATION_TERM.reference]
 
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
         """Iterate over terms for studies."""

pyobo/sources/complexportal.py

@@ -57,6 +57,7 @@ SPECIES = [
 DTYPE = {
     "taxonomy_id": str,
 }
+ROOT = Reference(prefix="go", identifier="0032991", name="macromolecular complex")
 
 
 def _parse_members(s) -> list[tuple[Reference, str]]:
@@ -157,10 +158,12 @@ class ComplexPortalGetter(Obo):
 
     bioversions_key = ontology = PREFIX
     typedefs = [from_species, has_part, has_citation]
+    root_terms = [ROOT]
 
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
         """Iterate over terms in the ontology."""
-        return get_terms(version=self._version_or_raise)
+        yield Term(reference=ROOT)
+        yield from get_terms(version=self._version_or_raise)
 
 
 def get_df(version: str, force: bool = False) -> pd.DataFrame:
@@ -232,6 +235,7 @@ def get_terms(version: str, force: bool = False) -> Iterable[Term]:
             definition=definition.strip() if pd.notna(definition) else None,
             synonyms=[Synonym(name=alias) for alias in aliases],
         )
+        term.append_parent(ROOT)
         for reference, note in xrefs:
             if note == "identity":
                 term.append_xref(reference)

pyobo/sources/hgnc/hgnc.py

@@ -7,6 +7,7 @@ import typing
 from collections import Counter, defaultdict
 from collections.abc import Iterable
 
+import pydantic
 from tabulate import tabulate
 from tqdm.auto import tqdm
 
@@ -280,7 +281,7 @@ def get_terms(version: str | None = None, force: bool = False) -> Iterable[Term]
                 continue  # only add concrete annotations
             term.append_relationship(
                 gene_product_member_of,
-                Reference(prefix="ec", identifier=ec_code),
+                Reference(prefix="ec", identifier=ec_code.strip()),
             )
         for rna_central_ids in entry.pop("rna_central_id", []):
             for rna_central_id in rna_central_ids.split(","):
@@ -314,7 +315,7 @@ def get_terms(version: str | None = None, force: bool = False) -> Iterable[Term]
             )
         for mgi_curie in entry.pop("mgd_id", []):
             if not mgi_curie.startswith("MGI:"):
-                tqdm.write(f"hgnc:{identifier} had bad MGI CURIE: {mgi_curie}")
+                tqdm.write(f"[hgnc:{identifier}] had bad MGI CURIE: {mgi_curie}")
                 continue
             mgi_id = mgi_curie[len("MGI:") :]
             if not mgi_id:
@@ -335,7 +336,7 @@ def get_terms(version: str | None = None, force: bool = False) -> Iterable[Term]
                     Reference(prefix="iuphar.ligand", identifier=iuphar[len("ligandId:") :])
                 )
             else:
-                tqdm.write(f"unhandled IUPHAR: {iuphar}")
+                tqdm.write(f"[hgnc:{identifier}] unhandled IUPHAR: {iuphar}")
 
         for lrg_info in entry.pop("lsdb", []):
             if lrg_info.startswith("LRG_"):
@@ -360,9 +361,15 @@ def get_terms(version: str | None = None, force: bool = False) -> Iterable[Term]
                 xref_identifiers = [i.strip(".") for i in xref_identifiers]
 
             if len(xref_identifiers) == 1:
-                term.append_exact_match(
-                    Reference(prefix=xref_prefix, identifier=str(xref_identifiers[0]))
-                )
+                try:
+                    xref = Reference(prefix=xref_prefix, identifier=str(xref_identifiers[0]))
+                except pydantic.ValidationError:
+                    tqdm.write(
+                        f"[hgnc:{identifier}] had bad {key} xref: {xref_prefix}:{xref_identifiers[0]}"
+                    )
+                    continue
+                else:
+                    term.append_exact_match(xref)
             else:
                 for xref_identifier in xref_identifiers:
                     term.append_xref(Reference(prefix=xref_prefix, identifier=str(xref_identifier)))

pyobo/sources/iana_media_type.py

@@ -0,0 +1,100 @@
+"""An ontology representation of IANA media types (i.e. MIME types).
+
+.. seealso:: https://www.iana.org/assignments/media-types/media-types.xhtml
+"""
+
+from collections.abc import Iterable
+
+from pyobo import Obo, Reference, Term, default_reference
+from pyobo.struct.typedef import term_replaced_by
+from pyobo.utils.path import ensure_df
+
+__all__ = ["IANAGetter"]
+
+PREFIX = "iana.mediatype"
+ROOT = Term.from_triple(prefix="dcterms", identifier="MediaType", name="media type")
+
+#: The top-level types listed on https://www.iana.org/assignments/media-types/media-types.xhtml
+MEDIA_TYPE_GROUPS = [
+    "application",
+    "audio",
+    "font",
+    "haptics",
+    "image",
+    "message",
+    "model",
+    "multipart",
+    "text",
+    "video",
+]
+
+GROUP_TO_CSV = {
+    media_type_group: (
+        f"https://www.iana.org/assignments/media-types/{media_type_group}.csv",
+        Term(reference=default_reference(PREFIX, media_type_group, media_type_group)).append_parent(
+            ROOT
+        ),
+    )
+    for media_type_group in MEDIA_TYPE_GROUPS
+}
+
+
+class IANAGetter(Obo):
+    """An ontology representation of IANA media types (i.e. MIME types)."""
+
+    ontology = bioregistry_key = PREFIX
+    name = "IANA Media Types"
+    dynamic_version = True
+    root_terms = [t.reference for _, (_, t) in sorted(GROUP_TO_CSV.items())]
+    typedefs = [
+        term_replaced_by,
+    ]
+
+    def iter_terms(self, force: bool = False) -> Iterable[Term]:
+        """Iterate over terms in the ontology."""
+        return get_terms()
+
+
+def get_terms() -> list[Term]:
+    """Get IANA Media Type terms."""
+    terms: dict[str, Term] = {}
+    forwards: dict[Term, str] = {}
+    for key, (url, parent) in GROUP_TO_CSV.items():
+        df = ensure_df(PREFIX, url=url, sep=",")
+        terms[key] = parent
+        for name, identifier, references in df.values:
+            if "OBSOLE" in name or "DEPRECATED" in name:
+                is_obsolete = True
+            else:
+                is_obsolete = None
+            term = Term(
+                reference=Reference(prefix=PREFIX, identifier=identifier, name=name),
+                is_obsolete=is_obsolete,
+            ).append_parent(parent)
+            for reference in _process_references(references):
+                term.append_see_also_uri(reference)
+            terms[identifier.casefold()] = term
+
+            if "in favor of" in name:
+                _, _, new = name.partition("in favor of ")
+                forwards[term] = new.casefold().strip().rstrip(")").strip()
+
+    for old, new in forwards.items():
+        if new == "vnd.afpc.afplinedata":
+            new = "application/vnd.afpc.afplinedata"
+        old.append_replaced_by(terms[new].reference)
+
+    return list(terms.values())
+
+
+def _process_references(cell: str) -> list[str]:
+    rv = []
+    for part in cell.split("]["):
+        part = part.strip("[").strip("]")
+        if part.startswith("RFC"):
+            rv.append(f"https://www.iana.org/go/rfc{part.removeprefix('RFC')}")
+    return rv
+
+
+if __name__ == "__main__":
+    IANAGetter.cli()

pyobo/sources/mesh.py

@@ -10,12 +10,12 @@ from pathlib import Path
 from typing import Any
 from xml.etree.ElementTree import Element
 
+import bioversions
 from lxml import etree
 from tqdm.auto import tqdm
 
-from pyobo.api.utils import safe_get_version
 from pyobo.identifier_utils import standardize_ec
-from pyobo.struct import Obo, Reference, Synonym, Term
+from pyobo.struct import Obo, Reference, Synonym, Term, default_reference
 from pyobo.utils.cache import cached_json, cached_mapping
 from pyobo.utils.path import ensure_path, prefix_directory_join
 
@@ -31,6 +31,37 @@ PREFIX = "mesh"
 NOW_YEAR = str(datetime.datetime.now().year)
 CAS_RE = re.compile(r"^\d{1,7}\-\d{2}\-\d$")
 UNII_RE = re.compile(r"[0-9A-Za-z]{10}$")
+SUPPLEMENT_PARENT = default_reference(
+    prefix=PREFIX, identifier="supplemental-record", name="supplemental records"
+)
+
+#: A mapping from tree header letters to labels
+#:
+#: .. seealso:: https://meshb-prev.nlm.nih.gov/treeView
+TREE_HEADER_TO_NAME = {
+    "A": "Anatomy",
+    "B": "Organisms",
+    "C": "Diseases",
+    "D": "Chemicals and Drugs",
+    "E": "Analytical, Diagnostic and Therapeutic Techniques, and Equipment",
+    "F": "Psychiatry and Psychology",
+    "G": "Phenomena and Processes",
+    "H": "Disciplines and Occupations",
+    "I": "Anthropology, Education, Sociology, and Social Phenomena",
+    "J": "Technology, Industry, and Agriculture",
+    "K": "Humanities",
+    "L": "Information Science",
+    "M": "Named Groups",
+    "N": "Health Care",
+    "V": "Publication Characteristics",
+    "Z": "Geographicals",
+}
+
+#: A mapping from tree header letters to term objects
+TREE_HEADERS: dict[str, Reference] = {
+    letter: default_reference(prefix=PREFIX, identifier=letter, name=name)
+    for letter, name in TREE_HEADER_TO_NAME.items()
+}
 
 
 def _get_xml_root(path: Path) -> Element:
@@ -46,13 +77,20 @@ class MeSHGetter(Obo):
     """An ontology representation of the Medical Subject Headings."""
 
     ontology = bioversions_key = PREFIX
+    root_terms = [
+        SUPPLEMENT_PARENT,
+        *TREE_HEADERS.values(),
+    ]
 
     def _get_version(self) -> str | None:
         return NOW_YEAR
 
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
         """Iterate over terms in the ontology."""
-        return get_terms(version=self._version_or_raise, force=force)
+        yield Term(reference=SUPPLEMENT_PARENT)
+        for x in TREE_HEADERS.values():
+            yield Term(reference=x)
+        yield from get_terms(version=self._version_or_raise, force=force)
 
 
 def get_tree_to_mesh_id(version: str) -> Mapping[str, str]:
@@ -74,21 +112,21 @@ def get_tree_to_mesh_id(version: str) -> Mapping[str, str]:
     return _inner()
 
 
-def get_terms(version: str, force: bool = False) -> Iterable[Term]:
+def get_terms(version: str, *, force: bool = False) -> Iterable[Term]:
     """Get MeSH OBO terms."""
     mesh_id_to_term: dict[str, Term] = {}
 
-    descriptors = ensure_mesh_descriptors(version=version, force=force)
+    descriptor_records = ensure_mesh_descriptors(version=version, force=force)
     supplemental_records = ensure_mesh_supplemental_records(version=version, force=force)
 
-    for entry in itt.chain(descriptors, supplemental_records):
-        identifier = entry["identifier"]
-        name = entry["name"]
-        definition = entry.get("scope_note")
+    for descriptor_record in itt.chain(descriptor_records, supplemental_records):
+        identifier = descriptor_record["identifier"]
+        name = descriptor_record["name"]
+        definition = descriptor_record.get("scope_note")
 
         xrefs: list[Reference] = []
         synonyms: set[str] = set()
-        for concept in entry["concepts"]:
+        for concept in descriptor_record["concepts"]:
             synonyms.add(concept["name"])
             for term in concept["terms"]:
                 synonyms.add(term["name"])
@@ -102,11 +140,23 @@ def get_terms(version: str, force: bool = False) -> Iterable[Term]:
             xrefs=xrefs,
         )
 
-    for entry in descriptors:
-        mesh_id_to_term[entry["identifier"]].parents = [
-            mesh_id_to_term[parent_descriptor_id].reference
-            for parent_descriptor_id in entry["parents"]
-        ]
+    for descriptor_record in descriptor_records:
+        term = mesh_id_to_term[descriptor_record["identifier"]]
+        for parent_descriptor_id in descriptor_record["parents"]:
+            term.append_parent(mesh_id_to_term[parent_descriptor_id])
+
+        # This takes care of terms that don't have any parents like
+        # Body Regions (https://meshb.nlm.nih.gov/record/ui?ui=D001829),
+        # which have the tree code A01 and need to point to a made-up
+        # term for "A"
+        for top_level_letter in descriptor_record["top_levels"]:
+            term.append_parent(TREE_HEADERS[top_level_letter])
+
+    # MeSH supplementary records' identifiers start with "C"
+    # and do not have a hierarchy assigned to them
+    for supplemental_record in supplemental_records:
+        term = mesh_id_to_term[supplemental_record["identifier"]]
+        term.append_parent(SUPPLEMENT_PARENT)
 
     return mesh_id_to_term.values()
 
@@ -153,7 +203,7 @@ def ensure_mesh_supplemental_records(version: str, force: bool = False) -> list[
     return _inner()  # type:ignore
 
 
-def get_descriptor_records(element: Element, id_key: str, name_key) -> list[dict[str, Any]]:
+def get_descriptor_records(element: Element, id_key: str, name_key: str) -> list[dict[str, Any]]:
     """Get MeSH descriptor records."""
     logger.info("extract MeSH descriptors, concepts, and terms")
 
@@ -164,7 +214,7 @@ def get_descriptor_records(element: Element, id_key: str, name_key) -> list[dict
     logger.debug(f"got {len(rv)} descriptors")
 
     # cache tree numbers
-    tree_number_to_descriptor_ui = {
+    tree_number_to_descriptor_ui: dict[str, str] = {
         tree_number: descriptor["identifier"]
         for descriptor in rv
         for tree_number in descriptor["tree_numbers"]
@@ -173,26 +223,29 @@ def get_descriptor_records(element: Element, id_key: str, name_key) -> list[dict
 
     # add in parents to each descriptor based on their tree numbers
     for descriptor in rv:
+        top_levels = set()
         parents_descriptor_uis = set()
         for tree_number in descriptor["tree_numbers"]:
             try:
                 parent_tn, _self_tn = tree_number.rsplit(".", 1)
             except ValueError:
-                logger.debug("No dot for %s", tree_number)
-                continue
-
-            parent_descriptor_ui = tree_number_to_descriptor_ui.get(parent_tn)
-            if parent_descriptor_ui is not None:
-                parents_descriptor_uis.add(parent_descriptor_ui)
+                # e.g., this happens for A01 (Body Regions)
+                # https://meshb.nlm.nih.gov/record/ui?ui=D001829
+                top_levels.add(tree_number[0])
             else:
-                logger.debug("missing tree number: %s", parent_tn)
+                parent_descriptor_ui = tree_number_to_descriptor_ui.get(parent_tn)
+                if parent_descriptor_ui is not None:
+                    parents_descriptor_uis.add(parent_descriptor_ui)
+                else:
+                    tqdm.write(f"missing tree number: {parent_tn}")
 
-        descriptor["parents"] = list(parents_descriptor_uis)
+        descriptor["parents"] = sorted(parents_descriptor_uis)
+        descriptor["top_levels"] = sorted(top_levels)
 
     return rv
 
 
-def get_scope_note(descriptor_record) -> str | None:
+def get_scope_note(descriptor_record: Mapping[str, Any] | list[Mapping[str, Any]]) -> str | None:
     """Get the scope note from the preferred concept in a term's record."""
     if isinstance(descriptor_record, dict):
         # necessary for pre-2023 data
@@ -221,7 +274,7 @@ def get_descriptor_record(
     """
     concepts = get_concept_records(element)
     scope_note = get_scope_note(concepts)
-    rv = {
+    rv: dict[str, Any] = {
         "identifier": element.findtext(id_key),
         "name": element.findtext(name_key),
         "tree_numbers": sorted(
@@ -298,7 +351,7 @@ def get_term_records(element: Element) -> list[Mapping[str, Any]]:
     return [get_term_record(term) for term in element.findall("TermList/Term")]
 
 
-def get_term_record(element) -> Mapping[str, Any]:
+def get_term_record(element: Element) -> Mapping[str, Any]:
     """Get a single MeSH term record."""
     return {
         "term_ui": element.findtext("TermUI"),
@@ -363,7 +416,7 @@ def get_mesh_category_references(
         https://meshb.nlm.nih.gov/treeView
     """
     if version is None:
-        version = safe_get_version("mesh")
+        version = bioversions.get_version("mesh", strict=True)
     tree_to_mesh = get_tree_to_mesh_id(version=version)
     rv = []
     for i in range(1, 100):

pyobo/sources/reactome.py

@@ -22,6 +22,7 @@ __all__ = [
 logger = logging.getLogger(__name__)
 
 PREFIX = "reactome"
+ROOT = Reference(prefix="pw", identifier="0000001", name="pathway")
 
 
 # TODO alt ids https://reactome.org/download/current/reactome_stable_ids.txt
@@ -32,10 +33,12 @@ class ReactomeGetter(Obo):
 
     ontology = bioversions_key = PREFIX
     typedefs = [from_species, has_participant, has_citation]
+    root_terms = [ROOT]
 
     def iter_terms(self, force: bool = False) -> Iterable[Term]:
         """Iterate over terms in the ontology."""
-        return iter_terms(version=self._version_or_raise, force=force)
+        yield Term(reference=ROOT)
+        yield from iter_terms(version=self._version_or_raise, force=force)
 
 
 def ensure_participant_df(version: str, force: bool = False) -> pd.DataFrame:
@@ -87,6 +90,10 @@ def iter_terms(version: str, force: bool = False) -> Iterable[Term]:
     for parent_id, child_id in hierarchy_df.values:
         terms[child_id].append_parent(terms[parent_id])
 
+    for term in terms.values():
+        if not term.parents:
+            term.append_parent(ROOT)
+
     uniprot_pathway_df = ensure_participant_df(version=version, force=force)
     for uniprot_id, reactome_id in tqdm(
         uniprot_pathway_df.values,
@@ -102,7 +109,7 @@ def iter_terms(version: str, force: bool = False) -> Iterable[Term]:
             reference = Reference(prefix="uniprot.isoform", identifier=uniprot_id)
         else:
             reference = Reference(prefix="uniprot", identifier=uniprot_id)
-        terms[reactome_id].append_relationship(has_participant, reference)
+        terms[reactome_id].annotate_object(has_participant, reference)
 
     chebi_pathway_url = f"https://reactome.org/download/{version}/ChEBI2Reactome_All_Levels.txt"
     chebi_pathway_df = ensure_df(
@@ -122,7 +129,7 @@ def iter_terms(version: str, force: bool = False) -> Iterable[Term]:
         if reactome_id not in terms:
             tqdm.write(f"{reactome_id} appears in chebi participants file but not pathways file")
             continue
-        terms[reactome_id].append_relationship(
+        terms[reactome_id].annotate_object(
             has_participant, Reference(prefix="chebi", identifier=chebi_id)
         )