pyobo 0.10.8__tar.gz → 0.10.9__tar.gz

{pyobo-0.10.8/src/pyobo.egg-info → pyobo-0.10.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyobo
-Version: 0.10.8
+Version: 0.10.9
 Summary: Handling and writing OBO
 Home-page: https://github.com/pyobo/pyobo
 Download-URL: https://github.com/pyobo/pyobo/releases
@@ -49,7 +49,7 @@ Requires-Dist: class_resolver
 Requires-Dist: psycopg2-binary
 Requires-Dist: drugbank_downloader
 Requires-Dist: chembl_downloader
-Requires-Dist: umls_downloader>=0.1.2
+Requires-Dist: umls_downloader>=0.1.3
 Requires-Dist: typing_extensions
 Provides-Extra: tests
 Requires-Dist: coverage; extra == "tests"

{pyobo-0.10.8 → pyobo-0.10.9}/docs/source/conf.py

@@ -58,7 +58,7 @@ author = "Charles Tapley Hoyt"
 #
 
 # The full version, including alpha/beta/rc tags.
-release = "0.10.8"
+release = "0.10.9"
 
 # The short X.Y version.
 parsed_version = re.match(

{pyobo-0.10.8 → pyobo-0.10.9}/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = pyobo
-version = 0.10.8
+version = 0.10.9
 description = Handling and writing OBO
 long_description = file: README.rst
 url = https://github.com/pyobo/pyobo
@@ -56,7 +56,7 @@ install_requires =
 	psycopg2-binary
 	drugbank_downloader
 	chembl_downloader
-	umls_downloader>=0.1.2
+	umls_downloader>=0.1.3
 	typing_extensions
 zip_safe = false
 include_package_data = True

{pyobo-0.10.8 → pyobo-0.10.9}/src/pyobo/api/hierarchy.py

@@ -168,14 +168,15 @@ def is_descendent(prefix, identifier, ancestor_prefix, ancestor_identifier) -> b
 @lru_cache()
 def get_descendants(
     prefix: str,
-    identifier: str,
+    identifier: Optional[str] = None,
     include_part_of: bool = True,
     include_has_member: bool = False,
     use_tqdm: bool = False,
     force: bool = False,
     **kwargs,
 ) -> Optional[Set[str]]:
-    """Get all of the descendants (children) of the term as CURIEs."""
+    """Get all the descendants (children) of the term as CURIEs."""
+    curie, prefix, identifier = _pic(prefix, identifier)
     hierarchy = get_hierarchy(
         prefix=prefix,
         include_has_member=include_has_member,
@@ -184,23 +185,32 @@ def get_descendants(
         force=force,
         **kwargs,
     )
-    curie = f"{prefix}:{identifier}"
     if curie not in hierarchy:
         return None
     return nx.ancestors(hierarchy, curie)  # note this is backwards
 
 
+def _pic(prefix, identifier=None) -> Tuple[str, str, str]:
+    if identifier is None:
+        curie = prefix
+        prefix, identifier = prefix.split(":")
+    else:
+        curie = f"{prefix}:{identifier}"
+    return curie, prefix, identifier
+
+
 @lru_cache()
 def get_children(
     prefix: str,
-    identifier: str,
+    identifier: Optional[str] = None,
     include_part_of: bool = True,
     include_has_member: bool = False,
     use_tqdm: bool = False,
     force: bool = False,
     **kwargs,
 ) -> Optional[Set[str]]:
-    """Get all of the descendants (children) of the term as CURIEs."""
+    """Get all the descendants (children) of the term as CURIEs."""
+    curie, prefix, identifier = _pic(prefix, identifier)
     hierarchy = get_hierarchy(
         prefix=prefix,
         include_has_member=include_has_member,
@@ -209,7 +219,6 @@ def get_children(
         force=force,
         **kwargs,
     )
-    curie = f"{prefix}:{identifier}"
     if curie not in hierarchy:
         return None
     return set(hierarchy.predecessors(curie))
@@ -228,14 +237,15 @@ def has_ancestor(prefix, identifier, ancestor_prefix, ancestor_identifier) -> bo
 @lru_cache()
 def get_ancestors(
     prefix: str,
-    identifier: str,
+    identifier: Optional[str] = None,
     include_part_of: bool = True,
     include_has_member: bool = False,
     use_tqdm: bool = False,
     force: bool = False,
     **kwargs,
 ) -> Optional[Set[str]]:
-    """Get all of the ancestors (parents) of the term as CURIEs."""
+    """Get all the ancestors (parents) of the term as CURIEs."""
+    curie, prefix, identifier = _pic(prefix, identifier)
     hierarchy = get_hierarchy(
         prefix=prefix,
         include_has_member=include_has_member,
@@ -244,7 +254,6 @@ def get_ancestors(
         force=force,
         **kwargs,
     )
-    curie = f"{prefix}:{identifier}"
     if curie not in hierarchy:
         return None
     return nx.descendants(hierarchy, curie)  # note this is backwards
@@ -252,7 +261,7 @@ def get_ancestors(
 
 def get_subhierarchy(
     prefix: str,
-    identifier: str,
+    identifier: Optional[str] = None,
     include_part_of: bool = True,
     include_has_member: bool = False,
     use_tqdm: bool = False,
@@ -260,6 +269,7 @@ def get_subhierarchy(
     **kwargs,
 ) -> nx.DiGraph:
     """Get the subhierarchy for a given node."""
+    curie, prefix, identifier = _pic(prefix, identifier)
     hierarchy = get_hierarchy(
         prefix=prefix,
         include_has_member=include_has_member,
@@ -271,7 +281,7 @@ def get_subhierarchy(
     logger.info(
         "getting descendants of %s:%s ! %s", prefix, identifier, get_name(prefix, identifier)
     )
-    curies = nx.ancestors(hierarchy, f"{prefix}:{identifier}")  # note this is backwards
+    curies = nx.ancestors(hierarchy, curie)  # note this is backwards
     logger.info("inducing subgraph")
     sg = hierarchy.subgraph(curies).copy()
     logger.info("subgraph has %d nodes/%d edges", sg.number_of_nodes(), sg.number_of_edges())

{pyobo-0.10.8 → pyobo-0.10.9}/src/pyobo/api/xrefs.py

@@ -142,7 +142,9 @@ def get_sssom_df(
         df = get_xrefs_df(prefix=prefix, **kwargs)
     rows: List[Tuple[str, ...]] = []
     with logging_redirect_tqdm():
-        for source_id, target_prefix, target_id in tqdm(df.values, unit="mapping", unit_scale=True):
+        for source_id, target_prefix, target_id in tqdm(
+            df.values, unit="mapping", unit_scale=True, desc=f"[{prefix}] SSSOM"
+        ):
             source = Reference(prefix=prefix, identifier=source_id)
             target = Reference(prefix=target_prefix, identifier=target_id)
 

{pyobo-0.10.8 → pyobo-0.10.9}/src/pyobo/getters.py

@@ -55,7 +55,7 @@ class UnhandledFormat(NoBuild):
 
 #: The following prefixes can not be loaded through ROBOT without
 #: turning off integrity checks
-REQUIRES_NO_ROBOT_CHECK = {"clo", "vo"}
+REQUIRES_NO_ROBOT_CHECK = {"clo", "vo", "orphanet.ordo", "orphanet"}
 
 
 @wrap_norm_prefix
@@ -117,7 +117,7 @@ def get_ontology(
 
     ontology_format, path = _ensure_ontology_path(prefix, force=force, version=version)
     if path is None:
-        raise NoBuild
+        raise NoBuild(prefix)
     elif ontology_format == "obo":
         pass  # all gucci
     elif ontology_format == "owl":

{pyobo-0.10.8 → pyobo-0.10.9}/src/pyobo/sources/__init__.py

@@ -8,6 +8,7 @@ from .antibodyregistry import AntibodyRegistryGetter
 from .ccle import CCLEGetter
 from .cgnc import CGNCGetter
 from .chembl import ChEMBLCompoundGetter
+from .civic_gene import CIVICGeneGetter
 from .complexportal import ComplexPortalGetter
 from .conso import CONSOGetter
 from .cpt import CPTGetter
@@ -38,6 +39,7 @@ from .mirbase_mature import MiRBaseMatureGetter
 from .msigdb import MSigDBGetter
 from .ncbigene import NCBIGeneGetter
 from .npass import NPASSGetter
+from .omim_ps import OMIMPSGetter
 from .pathbank import PathBankGetter
 from .pfam import PfamGetter
 from .pfam_clan import PfamClanGetter
@@ -61,6 +63,7 @@ __all__ = [
     "AntibodyRegistryGetter",
     "CCLEGetter",
     "CGNCGetter",
+    "CIVICGeneGetter",
     "CONSOGetter",
     "CPTGetter",
     "CVXGetter",
@@ -94,6 +97,7 @@ __all__ = [
     "MiRBaseMatureGetter",
     "NCBIGeneGetter",
     "NPASSGetter",
+    "OMIMPSGetter",
     "PIDGetter",
     "PathBankGetter",
     "PfamClanGetter",

{pyobo-0.10.8 → pyobo-0.10.9}/src/pyobo/sources/cgnc.py

@@ -69,7 +69,7 @@ def get_terms(force: bool = False) -> Iterable[Term]:
         term = Term.from_triple(
             prefix=PREFIX,
             identifier=cgnc_id,
-            name=name,
+            name=name if pd.notna(name) else None,
         )
         term.set_species(identifier="9031", name="Gallus gallus")
         if entrez_id and pd.notna(entrez_id):

pyobo-0.10.9/src/pyobo/sources/civic_gene.py

@@ -0,0 +1,55 @@
+# -*- coding: utf-8 -*-
+
+"""Converter for CiVIC Genes."""
+
+from typing import Iterable, Optional
+
+import pandas as pd
+
+from pyobo.struct import Obo, Reference, Term
+from pyobo.utils.path import ensure_df
+
+__all__ = [
+    "CIVICGeneGetter",
+]
+
+PREFIX = "civic.gid"
+URL = "https://civicdb.org/downloads/nightly/nightly-GeneSummaries.tsv"
+
+
+def _sort(_o, t):
+    return int(t.identifier)
+
+
+class CIVICGeneGetter(Obo):
+    """An ontology representation of CiVIC's gene nomenclature."""
+
+    bioversions_key = ontology = PREFIX
+    term_sort_key = _sort
+
+    def iter_terms(self, force: bool = False) -> Iterable[Term]:
+        """Iterate over gene terms for CiVIC."""
+        yield from get_terms(self.data_version, force=force)
+
+
+def get_terms(version: Optional[str] = None, force: bool = False) -> Iterable[Term]:
+    """Get CIVIC terms."""
+    # if version is not None:
+    #     version_dt: datetime.date = dateutil.parser.parse(version)
+    # else:
+    #     version_dt: datetime.date = datetime.today()
+    # version = version_dt.strftime("01-%b-%Y")
+    # version is like 01-Feb-2024
+    url = f"https://civicdb.org/downloads/{version}/{version}-GeneSummaries.tsv"
+    df = ensure_df(prefix=PREFIX, url=url, sep="\t", force=force, dtype=str, version=version)
+    for identifier, _, name, entrez_id, description, _last_review, _flag in df.values:
+        term = Term(
+            reference=Reference(prefix=PREFIX, identifier=identifier, name=name),
+            definition=description if pd.notna(description) else None,
+        )
+        term.append_exact_match(Reference(prefix="ncbigene", identifier=entrez_id))
+        yield term
+
+
+if __name__ == "__main__":
+    CIVICGeneGetter.cli()

{pyobo-0.10.8 → pyobo-0.10.9}/src/pyobo/sources/mesh.py

@@ -6,7 +6,7 @@ import datetime
 import itertools as itt
 import logging
 import re
-from typing import Any, Dict, Iterable, List, Mapping, Optional, Set, Tuple
+from typing import Any, Collection, Dict, Iterable, List, Mapping, Optional, Set, Tuple
 from xml.etree.ElementTree import Element
 
 from tqdm.auto import tqdm
@@ -19,6 +19,7 @@ from pyobo.utils.path import ensure_path, prefix_directory_join
 
 __all__ = [
     "MeSHGetter",
+    "get_mesh_category_curies",
 ]
 
 logger = logging.getLogger(__name__)
@@ -317,5 +318,32 @@ def _get_descriptor_qualifiers(descriptor: Element) -> List[Mapping[str, str]]:
     ]
 
 
+def get_mesh_category_curies(letter: str, skip: Optional[Collection[str]] = None) -> List[str]:
+    """Get the MeSH LUIDs for a category, by letter (e.g., "A").
+
+    :param letter: The MeSH tree, A for anatomy, C for disease, etc.
+    :param skip: An optional collection of MeSH tree codes to skip, such as "A03"
+    :returns: A list of MeSH CURIE strings for the top level of each MeSH tree.
+
+    .. seealso:: https://meshb.nlm.nih.gov/treeView
+    """
+    import bioversions
+
+    mesh_version = bioversions.get_version("mesh")
+    if mesh_version is None:
+        raise ValueError
+    tree_to_mesh = get_tree_to_mesh_id(mesh_version)
+    rv = []
+    for i in range(1, 100):
+        key = f"{letter}{i:02}"
+        if skip and key in skip:
+            continue
+        mesh_id = tree_to_mesh.get(key)
+        if mesh_id is None:
+            break
+        rv.append(f"mesh:{mesh_id}")
+    return rv
+
+
 if __name__ == "__main__":
     get_obo(force=True).write_default(force=True, write_obo=True)

{pyobo-0.10.8 → pyobo-0.10.9}/src/pyobo/sources/ncbigene.py

@@ -171,15 +171,17 @@ def get_terms(force: bool = False) -> Iterable[Term]:
             continue
         term = Term(
             reference=Reference(prefix=PREFIX, identifier=gene_id, name=symbol),
-            definition=description,
+            definition=description if pd.notna(description) else None,
         )
         term.set_species(identifier=tax_id)
         if pd.notna(xref_curies):
             for xref_curie in xref_curies.split("|"):
                 if xref_curie.startswith("EnsemblRapid"):
                     continue
-                if xref_curie.startswith("AllianceGenome"):
+                elif xref_curie.startswith("AllianceGenome"):
                     xref_curie = xref_curie[len("xref_curie") :]
+                elif xref_curie.startswith("nome:WB:"):
+                    xref_curie = xref_curie[len("nome:") :]
                 xref_prefix, xref_id = bioregistry.parse_curie(xref_curie)
                 if xref_prefix and xref_id:
                     term.append_xref(Reference(prefix=xref_prefix, identifier=xref_id))
@@ -187,7 +189,7 @@ def get_terms(force: bool = False) -> Iterable[Term]:
                     p = xref_curie.split(":")[0]
                     if p not in warning_prefixes:
                         warning_prefixes.add(p)
-                        tqdm.write(f"[{PREFIX}] unhandled xref prefix: {p}")
+                        tqdm.write(f"[{PREFIX}] unhandled prefix in xref: {xref_curie}")
         yield term
 
 

pyobo-0.10.9/src/pyobo/sources/omim_ps.py

@@ -0,0 +1,39 @@
+# -*- coding: utf-8 -*-
+
+"""Converter for OMIM Phenotypic Series."""
+
+import logging
+from typing import Iterable
+
+from bioversions.utils import get_soup
+
+from pyobo.struct import Obo, Term
+
+__all__ = [
+    "OMIMPSGetter",
+]
+
+
+logger = logging.getLogger(__name__)
+PREFIX = "omim.ps"
+URL = "https://omim.org/phenotypicSeriesTitles/all"
+
+
+class OMIMPSGetter(Obo):
+    """An ontology representation of OMIM Phenotypic Series."""
+
+    ontology = bioversions_key = PREFIX
+
+    def iter_terms(self, force: bool = False) -> Iterable[Term]:
+        """Iterate over terms in the ontology."""
+        soup = get_soup(URL, user_agent="Mozilla/5.0")
+        rows = soup.find(id="mimContent").find("table").find("tbody").find_all("tr")
+        for row in rows:
+            anchor = row.find("td").find("a")
+            name = anchor.text.strip()
+            identifier = anchor.attrs["href"][len("/phenotypicSeries/") :]
+            yield Term.from_triple(PREFIX, identifier, name)
+
+
+if __name__ == "__main__":
+    OMIMPSGetter.cli()

{pyobo-0.10.8 → pyobo-0.10.9}/src/pyobo/sources/umls/umls.py

@@ -7,12 +7,13 @@ Run with ``python -m pyobo.sources.umls``
 
 import itertools as itt
 import operator
-from typing import Iterable
+from collections import defaultdict
+from typing import Iterable, Mapping, Set
 
 import bioregistry
 import pandas as pd
 from tqdm.auto import tqdm
-from umls_downloader import open_umls
+from umls_downloader import open_umls, open_umls_semantic_types
 
 from pyobo import Obo, Reference, Synonym, SynonymTypeDef, Term
 
@@ -66,8 +67,20 @@ def get_obo() -> Obo:
     return UMLSGetter()
 
 
+def get_semantic_types() -> Mapping[str, Set[str]]:
+    """Get UMLS semantic types for each term."""
+    dd = defaultdict(set)
+    with open_umls_semantic_types() as file:
+        for line in tqdm(file, unit_scale=True):
+            cui, sty, _ = line.decode("utf8").split("|", 2)
+            dd[cui].add(sty)
+    return dict(dd)
+
+
 def iter_terms(version: str) -> Iterable[Term]:
     """Iterate over UMLS terms."""
+    semantic_types = get_semantic_types()
+
     with open_umls(version=version) as file:
         it = tqdm(file, unit_scale=True, desc="[umls] parsing")
         lines = (line.decode("utf-8").strip().split("|") for line in it)
@@ -118,6 +131,8 @@ def iter_terms(version: str) -> Iterable[Term]:
                 synonyms=synonyms,
                 xrefs=xrefs,
             )
+            for sty_id in semantic_types.get(cui, set()):
+                term.append_parent(Reference(prefix="sty", identifier=sty_id))
             yield term
 
 

pyobo-0.10.9/src/pyobo/sources/uniprot/uniprot.py

@@ -0,0 +1,181 @@
+# -*- coding: utf-8 -*-
+
+"""Converter for UniProt."""
+
+from operator import attrgetter
+from pathlib import Path
+from typing import Iterable, List, Optional, cast
+
+import bioversions
+from tqdm.auto import tqdm
+
+from pyobo import Obo, Reference
+from pyobo.constants import RAW_MODULE
+from pyobo.identifier_utils import standardize_ec
+from pyobo.struct import Term, derives_from, enables, from_species, participates_in
+from pyobo.struct.typedef import gene_product_of, located_in, molecularly_interacts_with
+from pyobo.utils.io import open_reader
+
+PREFIX = "uniprot"
+BASE_URL = "https://rest.uniprot.org/uniprotkb/stream"
+SEARCH_URL = "https://rest.uniprot.org/uniprotkb/search"
+QUERY = "(*) AND (reviewed:true)"
+FIELDS = [
+    "accession",
+    "id",
+    "organism_id",
+    "protein_name",
+    "ec",
+    "lit_pubmed_id",
+    "xref_pdb",
+    "xref_proteomes",
+    "xref_geneid",
+    "rhea",
+    "go_c",
+    "go_f",
+    "go_p",
+    "ft_binding",
+    "cc_function",
+]
+PARAMS = {
+    "compressed": "true",
+    "format": "tsv",
+    # "size": 10,  # only used with search
+    "query": QUERY,
+    "fields": FIELDS,
+}
+
+
+class UniProtGetter(Obo):
+    """An ontology representation of the UniProt database."""
+
+    bioversions_key = ontology = PREFIX
+    typedefs = [
+        from_species,
+        enables,
+        participates_in,
+        gene_product_of,
+        molecularly_interacts_with,
+        derives_from,
+    ]
+
+    def iter_terms(self, force: bool = False) -> Iterable[Term]:
+        """Iterate over terms in the ontology."""
+        yield from iter_terms(version=self._version_or_raise)
+
+
+def get_obo(force: bool = False) -> Obo:
+    """Get UniProt as OBO."""
+    return UniProtGetter(force=force)
+
+
+def iter_terms(version: Optional[str] = None) -> Iterable[Term]:
+    """Iterate over UniProt Terms."""
+    with open_reader(ensure(version=version)) as reader:
+        _ = next(reader)  # header
+        for (
+            uniprot_id,
+            accession,
+            taxonomy_id,
+            _name,  # this field should have the name, but it's a mismatch of random name annotations
+            ecs,
+            pubmeds,
+            pdbs,
+            proteome,
+            gene_id,
+            rhea_curies,
+            go_components,
+            go_functions,
+            go_processes,
+            bindings,
+            description,
+        ) in tqdm(reader, desc="Mapping UniProt", unit_scale=True):
+            if description:
+                description = description.removeprefix("FUNCTION: ")
+            term = Term(
+                reference=Reference(prefix=PREFIX, identifier=uniprot_id, name=accession),
+                definition=description or None,
+            )
+            term.set_species(taxonomy_id)
+            if gene_id:
+                term.append_relationship(
+                    gene_product_of, Reference(prefix="ncbigene", identifier=gene_id)
+                )
+
+            # TODO add type=Reference(prefix="xsd", identifier="boolean")
+            term.append_property("reviewed", "true")
+
+            for go_process_ref in _parse_go(go_processes):
+                term.append_relationship(participates_in, go_process_ref)
+            for go_function_ref in _parse_go(go_functions):
+                term.append_relationship(enables, go_function_ref)
+            for go_component_ref in _parse_go(go_components):
+                term.append_relationship(located_in, go_component_ref)
+
+            if proteome:
+                uniprot_proteome_id = proteome.split(":")[0]
+                term.append_relationship(
+                    derives_from,
+                    Reference(prefix="uniprot.proteome", identifier=uniprot_proteome_id),
+                )
+
+            if rhea_curies:
+                for rhea_curie in rhea_curies.split(" "):
+                    term.append_relationship(
+                        # FIXME this needs a different relation than enables
+                        #  see https://github.com/biopragmatics/pyobo/pull/168#issuecomment-1918680152
+                        enables,
+                        cast(Reference, Reference.from_curie(rhea_curie, strict=True)),
+                    )
+
+            if bindings:
+                binding_references = set()
+                for part in bindings.split(";"):
+                    part = part.strip()
+                    if part.startswith("/ligand_id"):
+                        curie = part.removeprefix('/ligand_id="').rstrip('"')
+                        binding_references.add(
+                            cast(Reference, Reference.from_curie(curie, strict=True))
+                        )
+                for binding_reference in sorted(binding_references, key=attrgetter("curie")):
+                    term.append_relationship(molecularly_interacts_with, binding_reference)
+
+            if ecs:
+                for ec in ecs.split(";"):
+                    term.append_relationship(
+                        enables, Reference(prefix="eccode", identifier=standardize_ec(ec))
+                    )
+            for pubmed in pubmeds.split(";"):
+                if pubmed:
+                    term.append_provenance(Reference(prefix="pubmed", identifier=pubmed.strip()))
+            for pdb in pdbs.split(";"):
+                if pdb:
+                    term.append_xref(Reference(prefix="pdb", identifier=pdb.strip()))
+            yield term
+
+
+def _parse_go(go_terms) -> List[Reference]:
+    rv = []
+    if go_terms:
+        for go_term in go_terms.split(";"):
+            go_id = go_term.rsplit("[GO:")[1].rstrip("]")
+            rv.append(Reference(prefix="go", identifier=go_id))
+    return rv
+
+
+def ensure(version: Optional[str] = None, force: bool = False) -> Path:
+    """Ensure the reviewed uniprot names are available."""
+    if version is None:
+        version = bioversions.get_version("uniprot")
+    return RAW_MODULE.ensure(
+        PREFIX,
+        version,
+        force=force,
+        name="reviewed.tsv.gz",
+        url=BASE_URL,  # switch to SEARCH_URL for debugging
+        download_kwargs={"backend": "requests", "params": PARAMS},
+    )
+
+
+if __name__ == "__main__":
+    UniProtGetter.cli()

{pyobo-0.10.8 → pyobo-0.10.9}/src/pyobo/struct/__init__.py

@@ -15,6 +15,7 @@ from .struct import (  # noqa: F401
 from .typedef import (  # noqa: F401
     RelationHint,
     TypeDef,
+    derives_from,
     enables,
     from_species,
     gene_product_member_of,

{pyobo-0.10.8 → pyobo-0.10.9}/src/pyobo/struct/struct.py

@@ -1023,7 +1023,7 @@ class Obo:
     def iterate_id_name(self, *, use_tqdm: bool = False) -> Iterable[Tuple[str, str]]:
         """Iterate identifier name pairs."""
         for term in self._iter_terms(use_tqdm=use_tqdm, desc=f"[{self.ontology}] getting names"):
-            if term.name:
+            if term.prefix == self.ontology and term.name:
                 yield term.identifier, term.name
 
     def get_id_name_mapping(self, *, use_tqdm: bool = False) -> Mapping[str, str]:

{pyobo-0.10.8 → pyobo-0.10.9}/src/pyobo/struct/typedef.py

@@ -205,6 +205,15 @@ has_participant = TypeDef(
     comment="Inverse of has participant",
     inverse=Reference(prefix=RO_PREFIX, identifier="0000056", name="participates in"),
 )
+derives_from = TypeDef(
+    reference=Reference(prefix=RO_PREFIX, identifier="0001000", name="derives from"),
+)
+molecularly_interacts_with = TypeDef(
+    reference=Reference(prefix=RO_PREFIX, identifier="0002436", name="molecularly interacts with"),
+)
+located_in = TypeDef(
+    reference=Reference(prefix=RO_PREFIX, identifier="0001025", name="located in"),
+)
 exact_match = TypeDef(
     reference=Reference(prefix="skos", identifier="exactMatch", name="exact match"),
 )