pyobo 0.12.2__py3-none-any.whl → 0.12.3__py3-none-any.whl

pyobo/struct/obograph/reader.py

@@ -0,0 +1,242 @@
+"""Import of OBO Graph JSON."""
+
+import logging
+from pathlib import Path
+
+import curies
+import obographs
+from curies import Converter
+from curies.vocabulary import SynonymScope, synonym_scopes
+from obographs import (
+    Graph,
+    NodeType,
+    StandardizedGraph,
+    StandardizedMeta,
+    StandardizedNode,
+    StandardizedSynonym,
+)
+
+from pyobo import Obo, Reference, StanzaType, Synonym, Term, TypeDef
+from pyobo.identifier_utils import get_converter
+from pyobo.struct import Annotation, OBOLiteral, make_ad_hoc_ontology
+from pyobo.struct import vocabulary as v
+from pyobo.struct.typedef import has_ontology_root_term
+
+__all__ = [
+    "from_node",
+    "from_obograph",
+    "from_standardized_graph",
+    "read_obograph",
+]
+
+logger = logging.getLogger(__name__)
+
+
+def read_obograph(
+    prefix: str, path: str | Path, *, converter: Converter | None = None, strict: bool = False
+) -> Obo:
+    """Read an OBO Graph JSON file using :func:`obographs.read` then process into a PyOBO structure."""
+    graph = obographs.read(path, squeeze=True)
+    return from_obograph(prefix=prefix, graph=graph, converter=converter, strict=strict)
+
+
+def from_obograph(
+    prefix: str, graph: Graph, *, converter: Converter | None = None, strict: bool = False
+) -> Obo:
+    """Parse a raw OBO Graph JSON into a PyOBO structure."""
+    if converter is None:
+        converter = get_converter()
+    standardized_graph = graph.standardize(converter, strict=strict)
+    return from_standardized_graph(prefix, standardized_graph)
+
+
+def from_standardized_graph(prefix: str, graph: StandardizedGraph) -> Obo:
+    """Generate an OBO data structure from OBO Graph JSON."""
+    terms: dict[Reference, Term] = {}
+    typedefs: dict[Reference, TypeDef] = {}
+    for node in graph.nodes:
+        stanza = from_node(node)
+        match stanza:
+            case Term():
+                terms[stanza.reference] = stanza
+            case TypeDef():
+                typedefs[stanza.reference] = stanza
+
+    for edge in graph.edges:
+        s, p, o = (Reference.from_reference(r) for r in (edge.subject, edge.predicate, edge.object))
+        if s in terms:
+            stanza = terms[s]
+            stanza.append_relationship(p, o)
+        elif s in typedefs:
+            stanza = typedefs[s]
+            stanza.append_relationship(p, o)
+
+    root_terms: list[Reference] = []
+    property_values = []
+    auto_generated_by: str | None = None
+    if graph.meta:
+        for prop in graph.meta.properties or []:
+            predicate = Reference.from_reference(prop.predicate)
+            if predicate == has_ontology_root_term:
+                if isinstance(prop.value, str):
+                    raise TypeError
+                else:
+                    root_terms.append(Reference.from_reference(prop.value))
+            elif predicate == v.obo_autogenerated_by:
+                if not isinstance(prop.value, str):
+                    raise TypeError
+                auto_generated_by = prop.value
+            # TODO specific subsetdef, imports
+            else:
+                property_values.append(
+                    Annotation(
+                        predicate=predicate,
+                        # TODO obographs are limited by ability to specify datatype?
+                        value=OBOLiteral.string(prop.value)
+                        if isinstance(prop.value, str)
+                        else Reference.from_reference(prop.value),
+                    )
+                )
+
+    for equivalent_node_set in graph.equivalent_node_sets:
+        equivalent_reference = Reference.from_reference(equivalent_node_set.node)
+        if equivalent_reference in terms:
+            for equivalent in equivalent_node_set.equivalents:
+                terms[equivalent_reference].append_equivalent_to(
+                    Reference.from_reference(equivalent)
+                )
+        elif equivalent_reference in typedefs:
+            for equivalent in equivalent_node_set.equivalents:
+                typedefs[equivalent_reference].append_equivalent_to(
+                    Reference.from_reference(equivalent)
+                )
+        else:
+            logger.warning(
+                "unknown reference node in equivalent_node_set: %s", equivalent_reference.curie
+            )
+
+    for _domain_range_axiom in graph.domain_range_axioms or []:
+        p = Reference.from_reference(_domain_range_axiom.predicate)
+        if p not in typedefs:
+            continue
+        # the OBO Graph model allows for multiple ranges
+        # or domains, but OBO only one.
+        if _domain_range_axiom.ranges:
+            typedefs[p].range = Reference.from_reference(_domain_range_axiom.ranges[0])
+        if _domain_range_axiom.domains:
+            typedefs[p].domain = Reference.from_reference(_domain_range_axiom.domains[0])
+
+    for _property_chain_axiom in graph.property_chain_axioms:
+        p = Reference.from_reference(_property_chain_axiom.predicate)
+        if p not in typedefs or not _property_chain_axiom.chain:
+            continue
+        # TODO check if its also transitive_over and/or equivalent_to_chain
+        typedefs[p].holds_over_chain.append(
+            [Reference.from_reference(r) for r in _property_chain_axiom.chain]
+        )
+
+    for _logical_definition_axiom in graph.logical_definition_axioms:
+        pass  # TODO
+
+    return make_ad_hoc_ontology(
+        _ontology=prefix,
+        _name=graph.name,
+        terms=list(terms.values()),
+        _typedefs=list(typedefs.values()),
+        _root_terms=root_terms,
+        _property_values=property_values,
+        _data_version=graph.version or (graph.meta.version_iri if graph.meta is not None else None),
+        _auto_generated_by=auto_generated_by,
+    )
+
+
+#: A mapping between OBO Graph JSON node types and OBO stanza types
+MAPPING: dict[NodeType, StanzaType] = {
+    "CLASS": "Term",
+    "INDIVIDUAL": "Instance",
+    "PROPERTY": "TypeDef",
+}
+
+
+def from_node(node: StandardizedNode) -> Term | TypeDef:
+    """Generate a term from a node."""
+    if node.type == "PROPERTY":
+        return _from_property(node)
+    return _from_term(node)
+
+
+def _from_term(node: StandardizedNode) -> Term:
+    term = Term(
+        reference=_get_ref(node),
+        type=MAPPING[node.type] if node.type else "Term",
+    )
+    if node.meta is not None:
+        _process_term_meta(node.meta, term)
+    return term
+
+
+def _from_property(node: StandardizedNode) -> TypeDef:
+    typedef = TypeDef(
+        reference=_get_ref(node),
+        is_metadata_tag=node.property_type == "ANNOTATION",
+    )
+    if node.meta is not None:
+        _process_typedef_meta(node.meta, typedef)
+    return typedef
+
+
+def _get_ref(node: StandardizedNode) -> Reference:
+    return Reference(
+        prefix=node.reference.prefix,
+        identifier=node.reference.identifier,
+        name=node.label,
+    )
+
+
+def _process_term_meta(meta: StandardizedMeta, term: Term) -> None:
+    """Process the ``meta`` object associated with a term node."""
+    if meta.definition:
+        term.definition = meta.definition.value
+        for definition_xref in meta.definition.xrefs or []:
+            term.append_definition_xref(definition_xref)
+
+    if meta.subsets:
+        term.subsets.extend(Reference.from_reference(r) for r in meta.subsets)
+
+    for xref in meta.xrefs or []:
+        term.append_xref(xref.reference)
+
+    for synonym in meta.synonyms or []:
+        if s := _from_synonym(synonym):
+            term.append_synonym(s)
+
+    for comment in meta.comments or []:
+        term.append_comment(comment)
+
+    if meta.deprecated:
+        term.is_obsolete = True
+
+    for prop in meta.properties or []:
+        match prop.value:
+            case Reference():
+                term.annotate_object(prop.predicate, prop.value)
+            case str():
+                # note, OBO Graph format does not allow for annotating data type
+                term.annotate_literal(prop.predicate, OBOLiteral.string(prop.value))
+
+
+REV_SYNONYM_SCOPE: dict[curies.Reference, SynonymScope] = {v: k for k, v in synonym_scopes.items()}
+
+
+def _from_synonym(syn: StandardizedSynonym) -> Synonym | None:
+    return Synonym(
+        name=syn.text,
+        specificity=REV_SYNONYM_SCOPE[syn.predicate],
+        type=Reference.from_reference(syn.type) if syn.type is not None else None,
+        provenance=[Reference.from_reference(r) for r in syn.xrefs or []],
+    )
+
+
+def _process_typedef_meta(meta: StandardizedMeta, typedef: TypeDef) -> None:
+    """Process the ``meta`` object associated with a property node."""
+    # TODO everything else is in here

pyobo/struct/obograph/utils.py

@@ -0,0 +1,47 @@
+"""Testing utilities."""
+
+import unittest
+from typing import cast
+
+from curies import Reference
+from obographs import StandardizedGraph, StandardizedMeta
+
+__all__ = [
+    "assert_graph_equal",
+]
+
+
+def assert_graph_equal(
+    test_case: unittest.TestCase, expected: StandardizedGraph, actual: StandardizedGraph
+) -> None:
+    """Assert two graphs are equal."""
+    if expected.meta is not None:
+        test_case.assertIsNotNone(actual.meta)
+        test_case.assertEqual(
+            expected.meta.model_dump(exclude_unset=True, exclude_none=True, exclude_defaults=True),
+            cast(StandardizedMeta, actual.meta).model_dump(
+                exclude_unset=True, exclude_none=True, exclude_defaults=True
+            ),
+        )
+
+    # strip out extra info
+    for node in actual.nodes:
+        node.reference = Reference.from_reference(node.reference)
+
+    test_case.assertEqual(
+        {node.reference.curie: node for node in expected.nodes},
+        {node.reference.curie: node for node in actual.nodes},
+    )
+    test_case.assertEqual(
+        {node.as_str_triple(): node for node in expected.edges},
+        {node.as_str_triple(): node for node in actual.edges},
+    )
+    excludes = {"nodes", "edges", "meta"}
+    test_case.assertEqual(
+        expected.model_dump(
+            exclude_none=True, exclude_unset=True, exclude_defaults=True, exclude=excludes
+        ),
+        actual.model_dump(
+            exclude_none=True, exclude_unset=True, exclude_defaults=True, exclude=excludes
+        ),
+    )

pyobo/struct/struct.py

@@ -22,7 +22,7 @@ import curies
 import networkx as nx
 import pandas as pd
 import ssslm
-from curies import ReferenceTuple
+from curies import Converter, ReferenceTuple
 from curies import vocabulary as _cv
 from more_click import force_option, verbose_option
 from tqdm.auto import tqdm
@@ -84,6 +84,7 @@ __all__ = [
     "Synonym",
     "SynonymTypeDef",
     "Term",
+    "TypeDef",
     "abbreviation",
     "acronym",
     "make_ad_hoc_ontology",
@@ -91,9 +92,6 @@ __all__ = [
 
 logger = logging.getLogger(__name__)
 
-#: This is what happens if no specificity is given
-DEFAULT_SPECIFICITY: _cv.SynonymScope = "RELATED"
-
 #: Columns in the SSSOM dataframe
 SSSOM_DF_COLUMNS = [
     "subject_id",
@@ -104,7 +102,6 @@ SSSOM_DF_COLUMNS = [
     "confidence",
     "contributor",
 ]
-UNSPECIFIED_MATCHING_CURIE = "sempav:UnspecifiedMatching"
 FORMAT_VERSION = "1.4"
 
 
@@ -153,14 +150,14 @@ class Synonym(HasReferencesMixin):
     def _sort_key(self) -> tuple[str, _cv.SynonymScope, str]:
         return (
             self.name,
-            self.specificity or DEFAULT_SPECIFICITY,
+            self.specificity or _cv.DEFAULT_SYNONYM_SCOPE,
             self.type.curie if self.type else "",
         )
 
     @property
     def predicate(self) -> curies.NamedReference:
         """Get the specificity reference."""
-        return _cv.synonym_scopes[self.specificity or DEFAULT_SPECIFICITY]
+        return _cv.synonym_scopes[self.specificity or _cv.DEFAULT_SYNONYM_SCOPE]
 
     def to_obo(
         self,
@@ -189,7 +186,7 @@ class Synonym(HasReferencesMixin):
         elif self.type is not None:
             # it's not valid to have a synonym type without a specificity,
             # so automatically assign one if we'll need it
-            x = f"{x} {DEFAULT_SPECIFICITY}"
+            x = f"{x} {_cv.DEFAULT_SYNONYM_SCOPE}"
 
         # Add on the synonym type, if exists
         if self.type is not None:
@@ -429,9 +426,8 @@ class Term(Stanza):
         if self.definition:
             yield f"def: {self._definition_fp()}"
         # 7
-        for x in self.get_property_values(v.comment):
-            if isinstance(x, OBOLiteral):
-                yield f'comment: "{x.value}"'
+        for comment in self.get_comments():
+            yield f'comment: "{comment}"'
         # 8
         yield from _reference_list_tag("subset", self.subsets, ontology_prefix)
         # 9
@@ -723,17 +719,11 @@ class Obo:
         """Iterate over terms in this ontology."""
         raise NotImplementedError
 
-    def get_graph(self):
-        """Get an OBO Graph object."""
-        from ..obographs import graph_from_obo
-
-        return graph_from_obo(self)
-
-    def write_obograph(self, path: str | Path) -> None:
+    def write_obograph(self, path: str | Path, *, converter: Converter | None = None) -> None:
         """Write OBO Graph json."""
-        graph = self.get_graph()
-        with safe_open(path, read=False) as file:
-            file.write(graph.model_dump_json(indent=2, exclude_none=True, exclude_unset=True))
+        from . import obograph
+
+        obograph.write_obograph(self, path, converter=converter)
 
     @classmethod
     def cli(cls, *args, default_rewrite: bool = False) -> Any:
@@ -1642,13 +1632,13 @@ class Obo:
     #############
 
     def iterate_edges(
-        self, *, use_tqdm: bool = False
+        self, *, use_tqdm: bool = False, include_xrefs: bool = True
     ) -> Iterable[tuple[Stanza, TypeDef, Reference]]:
         """Iterate over triples of terms, relations, and their targets."""
         _warned: set[ReferenceTuple] = set()
         typedefs = self._index_typedefs()
         for stanza in self._iter_stanzas(use_tqdm=use_tqdm, desc=f"[{self.ontology}] edge"):
-            for predicate, reference in stanza._iter_edges():
+            for predicate, reference in stanza._iter_edges(include_xrefs=include_xrefs):
                 if td := self._get_typedef(stanza, predicate, _warned, typedefs):
                     yield stanza, td, reference
 

pyobo/struct/struct_utils.py

@@ -231,6 +231,8 @@ class Stanza(Referenced, HasReferencesMixin):
     ) -> None:
         self._axioms[_property_resolve(p, o)].append(annotation)
 
+    # TODO check different usages of this
+
     def append_equivalent(
         self,
         reference: ReferenceHint,
@@ -242,6 +244,15 @@ class Stanza(Referenced, HasReferencesMixin):
             stanza_type_to_eq_prop[self.type], reference, annotations=annotations
         )
 
+    def append_equivalent_to(
+        self, reference: ReferenceHint, *, annotations: Iterable[Annotation] | None = None
+    ) -> Self:
+        """Append to the "equivalent to" list."""
+        reference = _ensure_ref(reference)
+        self.equivalent_to.append(reference)
+        self._extend_annotations(stanza_type_to_eq_prop[self.type], reference, annotations)
+        return self
+
     def append_xref(
         self,
         reference: ReferenceHint,
@@ -317,15 +328,6 @@ class Stanza(Referenced, HasReferencesMixin):
         self.union_of.append(_ensure_ref(reference))
         return self
 
-    def append_equivalent_to(
-        self, reference: ReferenceHint, *, annotations: Iterable[Annotation] | None = None
-    ) -> Self:
-        """Append to the "equivalent to" list."""
-        reference = _ensure_ref(reference)
-        self.equivalent_to.append(reference)
-        self._extend_annotations(stanza_type_to_eq_prop[self.type], reference, annotations)
-        return self
-
     def _iterate_intersection_of_obo(self, *, ontology_prefix: str) -> Iterable[str]:
         for element in sorted(self.intersection_of, key=self._intersection_of_key):
             match element:
@@ -679,14 +681,18 @@ class Stanza(Referenced, HasReferencesMixin):
         """Add a comment property."""
         return self.annotate_string(v.comment, value, annotations=annotations, language=language)
 
+    def get_comments(self) -> list[str]:
+        """Get all comment strings."""
+        return [x.value for x in self.get_property_values(v.comment) if isinstance(x, OBOLiteral)]
+
     @property
     def alt_ids(self) -> Sequence[Reference]:
         """Get alternative terms."""
         return tuple(self.get_property_objects(v.alternative_term))
 
-    def get_edges(self) -> list[tuple[Reference, Reference]]:
+    def get_edges(self, *, include_xrefs: bool = True) -> list[tuple[Reference, Reference]]:
         """Get edges."""
-        return list(self._iter_edges())
+        return list(self._iter_edges(include_xrefs=include_xrefs))
 
     def _iter_parents(self) -> Iterable[tuple[Reference, Reference]]:
         parent_prop = stanza_type_to_prop[self.type]
@@ -702,7 +708,7 @@ class Stanza(Referenced, HasReferencesMixin):
                 case (predicate, target):
                     yield predicate, target
 
-    def _iter_edges(self) -> Iterable[tuple[Reference, Reference]]:
+    def _iter_edges(self, *, include_xrefs: bool = True) -> Iterable[tuple[Reference, Reference]]:
         # The following are "object" properties, meaning
         # they're part of the definition of the object
         yield from self.iterate_relations()
@@ -715,8 +721,10 @@ class Stanza(Referenced, HasReferencesMixin):
         for subset in self.subsets:
             yield v.in_subset, subset
         yield from self.iterate_object_properties()
-        for xref_reference in self.xrefs:
-            yield v.has_dbxref, xref_reference
+
+        if include_xrefs:
+            for xref_reference in self.xrefs:
+                yield v.has_dbxref, xref_reference
 
         # TODO disjoint_from
 

pyobo/struct/typedef.py

@@ -294,6 +294,10 @@ has_end_date = TypeDef(
 has_title = TypeDef(reference=v.has_title, is_metadata_tag=True)
 has_license = TypeDef(reference=v.has_license, is_metadata_tag=True)
 has_description = TypeDef(reference=v.has_description, is_metadata_tag=True)
+obo_autogenerated_by = TypeDef(reference=v.obo_autogenerated_by, is_metadata_tag=True)
+obo_has_format_version = TypeDef(reference=v.obo_has_format_version, is_metadata_tag=True)
+obo_is_metadata_tag = TypeDef(reference=v.obo_is_metadata_tag, is_metadata_tag=True)
+obo_has_id = TypeDef(reference=v.obo_has_id, is_metadata_tag=True)
 
 in_subset = TypeDef(reference=v.in_subset, is_metadata_tag=True)
 has_term_editor = TypeDef(reference=v.has_term_editor, is_metadata_tag=True)

pyobo/struct/vocabulary.py

@@ -47,6 +47,13 @@ has_dbxref = _c(_v.has_dbxref)
 
 in_subset = _c(_v.obo_in_subset)
 has_obo_namespace = _c(_v.obo_has_namespace)
+obo_is_metadata_tag = Reference(
+    prefix="oboinowl", identifier="is_metadata_tag", name="is metadata tag"
+)
+obo_has_id = Reference(prefix="oboinowl", identifier="id", name="has ID")
+obo_has_format_version = Reference(
+    prefix="oboinowl", identifier="hasOBOFormatVersion", name="has OBO format version"
+)
 obo_autogenerated_by = _c(_v.obo_autogenerated_by)
 obo_creation_date = _c(_v.obo_creation_date)
 

pyobo/version.py

@@ -12,7 +12,7 @@ __all__ = [
     "get_version",
 ]
 
-VERSION = "0.12.2"
+VERSION = "0.12.3"
 
 
 def get_git_hash() -> str:

{pyobo-0.12.2.dist-info → pyobo-0.12.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyobo
-Version: 0.12.2
+Version: 0.12.3
 Summary: A python package for handling and generating OBO
 Keywords: snekpack,cookiecutter,ontologies,biomedical ontologies,life sciences,natural sciences,bioinformatics,cheminformatics,Open Biomedical Ontologies,OBO
 Author: Charles Tapley Hoyt
@@ -45,7 +45,7 @@ Requires-Dist: zenodo-client>=0.3.6
 Requires-Dist: class-resolver>=0.6.0
 Requires-Dist: psycopg2-binary
 Requires-Dist: pydantic>=2.0
-Requires-Dist: curies>=0.10.13
+Requires-Dist: curies>=0.10.17
 Requires-Dist: curies-processing>=0.1.0
 Requires-Dist: python-dateutil
 Requires-Dist: networkx>=3.4
@@ -56,6 +56,7 @@ Requires-Dist: clinicaltrials-downloader>=0.0.2
 Requires-Dist: nih-reporter-downloader>=0.0.1
 Requires-Dist: typing-extensions
 Requires-Dist: rdflib
+Requires-Dist: obographs>=0.0.8
 Requires-Dist: ssslm[gilda] ; extra == 'gilda'
 Requires-Dist: ssslm[gilda-slim] ; extra == 'gilda-slim'
 Maintainer: Charles Tapley Hoyt

{pyobo-0.12.2.dist-info → pyobo-0.12.3.dist-info}/RECORD

@@ -1,5 +1,5 @@
 pyobo/.DS_Store,sha256=00b8c741cd5b001c03c1a582f55bfbcda0ad16f0e55019d64f93241b74991980,8196
-pyobo/__init__.py,sha256=0d90185e6e3aa041ccc27c68226c45e456e39369328e3db17706d65b52015819,3439
+pyobo/__init__.py,sha256=ae0b55a37ac88a8423fd32252683d3447102bcce078fe4c2a418f78196e9d648,3434
 pyobo/__main__.py,sha256=70e610d8e10bc45fbd4fa9ee67dc672d2bbd6cb1e4e9e8a7aec4a8cfb11c0fd3,83
 pyobo/api/__init__.py,sha256=259870a4519a6baa5df1180378837e67c688e8ecbe46e9a3d4a90e6435c79e1d,2955
 pyobo/api/alts.py,sha256=478b3162574616f2827bd73107f80f5dfdaf5971eaf6c6813109109dba89e522,3032
@@ -21,10 +21,10 @@ pyobo/cli/database_utils.py,sha256=8d0eea4a0fa8664f90f910b5db536451ba9778d8342bc
 pyobo/cli/lookup.py,sha256=1b11bbe771979c345ff8df494562919900b95e237c7c437997595ee42de31c76,9163
 pyobo/cli/utils.py,sha256=9e6b57b311b44d61088e321efa387f6aacebd3d6d337bf8d1c589fb871b3304d,1738
 pyobo/constants.py,sha256=c1ffa4f12c1ddee556adf728ef4ac51da44f228fe6fca9b58b9ab8f263acc87b,5112
-pyobo/getters.py,sha256=0d9a129a46213f3657cb80d7a70a73aa24567644a1d9090c57f09c67cb86921a,17375
+pyobo/getters.py,sha256=0bbd39aeba8b4511230ebadd209b2c9c64b117f81d80e1a1327230a068a13eeb,17618
 pyobo/gilda_utils.py,sha256=b9384002b00b48dcc98be86b47d954bed41c8b9548c380aaab62fa9ad929d0aa,1990
-pyobo/identifier_utils/__init__.py,sha256=ef7bbb0ffb088daa04ee79446bafc8a5ee1d404e347e637361b835879755dea2,753
-pyobo/identifier_utils/api.py,sha256=c308dc9f48753d14084d19362f08003f822c2e495fe0badd9b9d3bc176fbaba1,9215
+pyobo/identifier_utils/__init__.py,sha256=8921c06613b0a9666662939fa5734bb8aa2e4988fb652562697ec1179b93f2ca,793
+pyobo/identifier_utils/api.py,sha256=b65d99d4b8d223341d7d3bd4b7bc2e41ce7b52e218b0779b90bacde6a9beaa61,9247
 pyobo/identifier_utils/relations/__init__.py,sha256=2961f492b8530a678a9e010887b5530c3de1cc2df8f294e210a18dbb748d01db,159
 pyobo/identifier_utils/relations/api.py,sha256=c625bca0f09379ba7ef544d05aaf4b998ee9798945a90f3b98b6d763ef9d36df,5764
 pyobo/identifier_utils/relations/data.json,sha256=88b6ce5fb632faa389b512b68f1b73acdd54b552a1aaa8043430eb5e0020a0bc,113169
@@ -35,11 +35,8 @@ pyobo/mocks.py,sha256=8f9e392bd3ff0cfb0306e6070eb8724cb8e694fa0d951744b5c4652e15
 pyobo/ner/__init__.py,sha256=0199b704f1235184d521069034823c3d9960ff6756205c299649b87a4bbd4041,153
 pyobo/ner/api.py,sha256=b34309833eac8f5dea881d531323bf682f35d377e09d807066ba1183282964dc,2167
 pyobo/ner/normalizer.py,sha256=4e90d93801877f72f2fab8069db986e79cc749533a068a8b07a9d7c9e37cb9c2,954
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 pyobo/plugins.py,sha256=c04afe369c99ed9eae12bd2e18334e7972ce199a2419b166a377becf63cd2893,1232
 pyobo/py.typed,sha256=e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855,0
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 pyobo/resource_utils.py,sha256=6e5a1229b1df30bcf4841f009213247cb386ab0e85c8ef02114e8b360d0f54c9,4406
 pyobo/resources/__init__.py,sha256=43d9e293b1e0a4808238dec610aa5bc37cfd64833b345270a063697a9927da70,38
 pyobo/resources/ncbitaxon.py,sha256=92484774b0f45247cb4090b34e3851a5c175dde2da03e472d891c9953968116b,1979
@@ -49,7 +46,7 @@ pyobo/resources/ro.tsv,sha256=62f9412cf00acb6c38221798ccef68c75620e9690774c57331
 pyobo/resources/so.py,sha256=4bebe643b2fc009134f057c6543209a8d40d68b3d49ae27a1c2e45e2158732b0,1466
 pyobo/resources/so.tsv,sha256=50964a153100bff5eccd861bba7e167fa6f88e8bc38d229cd51591411713cc3c,82068
 pyobo/sources/README.md,sha256=0296f0a48da16d8422c3837a284fd5000a5f3a64d01e47936eb34413121b5f82,901
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 pyobo/sources/agrovoc.py,sha256=489b1b27b2adc5d2541bd4629a66f609f2dfce92bd78eccfd30c79f608feeace,787
 pyobo/sources/antibodyregistry.py,sha256=3726d4ccf1286e7e73aebd6252f0bc67d72ea83103335bb4eec8d5d540037664,3353
 pyobo/sources/bigg/__init__.py,sha256=e292beef5071d08bfddcfaa665e714297f4b71aa5b5bdc26ef304df6f85ba582,349
@@ -74,7 +71,7 @@ pyobo/sources/cvx.py,sha256=97d0acbae76bf54ca8d0f35c8c94db346eb610e51cac05688a3d
 pyobo/sources/depmap.py,sha256=7f05bfd54901e49b6c797c137dbd017e32ef626fb17feb17c1feb368f2a4960f,3585
 pyobo/sources/dictybase_gene.py,sha256=78bbde62732e26cd92c2d287ca3e34b678e9f058f2d72157a0f0e8b9bd5d6164,2672
 pyobo/sources/drugbank/__init__.py,sha256=880b2dbd9419d3525c25e0089b606727ddb7501be2f1a490e2d1158440e8540a,178
-pyobo/sources/drugbank/drugbank.py,sha256=eb2fc65b2d43ac54c0c81fefb0701b1326411027cf3cfb5eac7534df925cb33c,10899
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 pyobo/sources/drugbank/drugbank_salt.py,sha256=69b565fe280b7a698cc3850b8b7fc8b5381f09aab7bb26e3aa7b13f5187b0b59,1646
 pyobo/sources/drugcentral.py,sha256=9fb9bbcbaf0b3c494163dde2e627a6695366ca1c74cb7293efd2419871a610a1,4047
 pyobo/sources/expasy.py,sha256=25f116d229b5c25858db82add7a037e8c5b405e40dbfd76d3ff67a1f581c8755,11053
@@ -90,7 +87,7 @@ pyobo/sources/go.py,sha256=cd72c37dca9b894eb43371540adab37cfcd8a07952be4533000f1
 pyobo/sources/gtdb.py,sha256=ab420486568c8ad1d6a39200cb6979f2e5cc2d67a40addeb2303a60ecb031138,5221
 pyobo/sources/gwascentral/__init__.py,sha256=55d1c8801551fb7e81ee02ee851e175795179ff120359d3e8b583d36384e8d8d,231
 pyobo/sources/gwascentral/gwascentral_phenotype.py,sha256=4af302177b18a9cdc5e6735709fefa033221353ebdf191c79d3a4ed0819fb7ca,1788
-pyobo/sources/gwascentral/gwascentral_study.py,sha256=bddb3b20e2374cc3ff14601aba36c17466897d46f1d086bf75ecf62992263bd9,2657
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 pyobo/sources/hgnc/__init__.py,sha256=d5084cec674febf03108ccda073da4dd244b9034ce912da15213cc2c44d21963,157
 pyobo/sources/hgnc/hgnc.py,sha256=f05121570f4e4b06f4d70bbf6950363349a726de22c6f2ed5e3e43411591bf95,16377
 pyobo/sources/hgnc/hgncgenefamily.py,sha256=e3e8d0b750d59a7da3d0ac2b100e248e8dad51af54c045405a12704e36db20cd,3710
@@ -98,6 +95,7 @@ pyobo/sources/icd/__init__.py,sha256=0eb65597be8ff1eb2c278b6564f71ab8556b5d59082
 pyobo/sources/icd/icd10.py,sha256=61ab55ce0af6dbd27f59e25c6b8150007a96af1edcecde1f1db85bd5c4354de5,2587
 pyobo/sources/icd/icd11.py,sha256=5b6e59f8028cfbd41f860151d1164514be2653a50078c0fc8748c20b815ee11b,4867
 pyobo/sources/icd/icd_utils.py,sha256=8fbc63228bd61b4f86c47eee5d6ad76433b52d7132a3fe0275680f4874c85c96,4525
+pyobo/sources/intact.py,sha256=7e78d9e164acadf67b6df963a4c58116d4861a4e959aef0fb1d7d1f6c6f15cfe,2497
 pyobo/sources/interpro.py,sha256=d6d99771293946b8228fbd35183aa845b77f7c46af1e5f3f03a6887f92ba10b1,4809
 pyobo/sources/itis.py,sha256=6b1d54c40ece2a97176c497aaa3113fbf78ea32845e918fc76de4a1bf254dbbf,2876
 pyobo/sources/kegg/__init__.py,sha256=8553f4b6ec15a6234c8a416ffdb34faf3b98bfe1c0d7f6cf742bcdc7e7e6e458,219
@@ -169,19 +167,26 @@ pyobo/ssg/base.html,sha256=fef95d5026be80bd984cd63a1a002ec4d4f74e06840f9f39bc5fe
 pyobo/ssg/index.html,sha256=da62c16a198f7ad2468599c5d7e4da4d7b81e02a18a25a59da741a579746e676,4346
 pyobo/ssg/term.html,sha256=b522c82774980d37ad2bd8361280cacaee1a1dc855a351145e4fda62119e38aa,3869
 pyobo/ssg/typedef.html,sha256=2ab76acc1eb18edebcf5b1b7dc3dba00bfb5d49aef36e124a3134d23e106f938,2038
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 pyobo/struct/functional/__init__.py,sha256=d536edb7fe86a1aad19607df3dea62b49dd0b4bb2b30f31b8431a842700a499e,32
 pyobo/struct/functional/dsl.py,sha256=780b4e5616b8dc823cee610945a95ffa109aa43287992dd4dd51511c461f96fb,101183
 pyobo/struct/functional/macros.py,sha256=cc654f131fa685d4afc87d8c7b5e8565da1b789dd5d73045a77b3e033a8ced52,13785
 pyobo/struct/functional/obo_to_functional.py,sha256=785c46fdb00dc45f3903f67ad24ae4fcb6d187ce48208373fc9d42833a85f6b8,13273
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 pyobo/struct/functional/utils.py,sha256=73e5c6d9227b0a162dcfb294dcad05f93ea870c8d87af7a2d16c6591f9249ad1,3487
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 pyobo/struct/reference.py,sha256=4fc7d3b665cd18c8dfbbb2b8b49de4bc30a8e101d14ff26bf5f88e9c562bc2d3,11735
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 pyobo/struct/utils.py,sha256=ce4a4e138d894087e4374adce6a34434ad375482a691fff9eed1e88cc24aef56,906
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 pyobo/utils/__init__.py,sha256=08035263cbc6abfeaff2b5a159121d9e4f96a392c0d91f568e0d67a9b5aa2cec,17
 pyobo/utils/cache.py,sha256=136ccd03b82afd534699a36bad129e5f3e73aba5c3184fb93d5a24af30d99227,3098
 pyobo/utils/io.py,sha256=fa0cb5a8633a6c9fb95eb2f74e08fbf69acc4fc229b89c18dd233921b80378a9,5100
@@ -189,9 +194,9 @@ pyobo/utils/iter.py,sha256=ad845b6da1491f131a134c94fab419a026a0608aed7afd3db98d2
 pyobo/utils/misc.py,sha256=99d1f6e88b48d3f0cdbd7fff8a908556bf949278fcf0ef639e5cc8a421d0f4db,2684
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 pyobo/utils/path.py,sha256=cc37f10de8e0ef90a6063cc2b1c5d1b0993e41649536f04bfddc892d61a3bc4f,3398
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