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Aggregate retrieval of pyobo resources into one method
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@nanglo123
nanglo123 committed Jul 16, 2024
1 parent baeae10 commit d3ead11
Showing 1 changed file with 65 additions and 182 deletions.
247 changes: 65 additions & 182 deletions mira/dkg/construct.py
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Original file line number Diff line number Diff line change
Expand Up @@ -205,6 +205,60 @@ class NodeInfo(NamedTuple):
synonym_types: str


def extract_nodes_edges_from_pyobo_terms(term_getter, resource_prefix):
nodes, edges = [], []
if resource_prefix in {"geonames"}:
entity_type = "individual"
elif resource_prefix in {"ncit", "ncbitaxon", "eiffel", "cso"}:
entity_type = "class"
for term in tqdm(term_getter(), unit="term"):
nodes.append(
{
"id": term.curie,
"name": term.name,
"type": entity_type,
"description": term.definition if term.definition else "",
"obsolete": False if not term.is_obsolete else True,
"synonyms": [Synonym(value=syn._fp(),
type=f"{syn.type.reference.prefix}:"
f"{syn.type.reference.prefix}")
for syn in term.synonyms],
"alts": term.alt_ids,
"xrefs": [Xref(value=value, type=type) for value, type in
zip(term.xrefs, term.xref_types)],
"properties": dict(term.properties),
}
)
if resource_prefix != "eiffel":
for parent in term.get_relationships(part_of):
edges.append(
{
"source_curie": term.curie,
"target_curie": parent.curie,
"type": "part_of",
"pred": part_of.curie.lower(),
"source": resource_prefix,
"graph": resource_prefix,
"version": "",
}
)
else:
for typedef, object_references in term.relationships.items():
for object_reference in object_references:
edges.append(
{
"source_curie": term.curie,
"target_curie": object_reference.curie,
"type": typedef.name.replace(" ", "").lower(),
"pred": typedef.curie,
"source": "eiffel",
"graph": "eiffel",
"version": "",
}
)
return nodes, edges


def extract_probonto_nodes_edges():
probonto_nodes, probonto_edges = [], []
for term in tqdm(get_probonto_terms(), unit="term"):
Expand Down Expand Up @@ -272,186 +326,10 @@ def extract_probonto_nodes_edges():
return probonto_nodes, probonto_edges


def extract_geonames_nodes_edges():
geonames_nodes, geonames_edges = [], []
for term in tqdm(get_geonames_terms(), unit="term"):
geonames_nodes.append(
{
"id": term.curie,
"name": term.name,
"type": "individual",
"description": term.definition if term.definition else "",
"obsolete": False if not term.is_obsolete else True,
"synonyms": [Synonym(value=syn._fp(),
type=f"{syn.type.reference.prefix}:"
f"{syn.type.reference.prefix}")
for syn in term.synonyms],
"alts": term.alt_ids,
"xrefs": [Xref(value=value, type=type) for value, type in
zip(term.xrefs, term.xref_types)],
"properties": term.properties,
}
)
for parent in term.get_relationships(part_of):
geonames_edges.append(
{
"source_curie": term.curie,
"target_curie": parent.curie,
"type": "part_of",
"pred": part_of.curie.lower(),
"source": "geonames",
"graph": "geonames",
"version": "",
}
)
return geonames_nodes, geonames_edges


def extract_ncit_nodes_edges():
ncit_nodes, ncit_edges = [], []
for term in tqdm(get_ncit_subset(), unit="term"):
ncit_nodes.append(
{
"id": term.curie,
"name": term.name,
"type": "class",
"description": term.definition if term.definition else "",
"obsolete": False if not term.is_obsolete else True,
"synonyms": [Synonym(value=syn._fp(),
type=f"{syn.type.reference.prefix}:"
f"{syn.type.reference.prefix}")
for syn in term.synonyms],
"alts": term.alt_ids,
"xrefs": [Xref(value=value, type=type) for value, type in
zip(term.xrefs, term.xref_types)],
"properties": term.properties,
}
)
for parent in term.get_relationships(part_of):
ncit_edges.append(
{
"source_curie": term.curie,
"target_curie": parent.curie,
"type": "part_of",
"pred": part_of.curie.lower(),
"source": "ncit",
"graph": "ncit",
"version": "",
}
)
return ncit_nodes, ncit_edges


def extract_ncbitaxon_nodes_edges():
ncbitaxon_nodes, ncbitaxon_edges = [], []
for term in tqdm(get_ncbitaxon(), unit="term"):
ncbitaxon_nodes.append(
{
"id": term.curie,
"name": term.name,
"type": "class",
"description": term.definition if term.definition else "",
"obsolete": False if not term.is_obsolete else True,
"synonyms": [Synonym(value=syn._fp(),
type=f"{syn.type.reference.prefix}:"
f"{syn.type.reference.prefix}")
for syn in term.synonyms],
"alts": term.alt_ids,
"xrefs": [Xref(value=value, type=type) for value, type in
zip(term.xrefs, term.xref_types)],
"properties": term.properties,
}
)
for parent in term.get_relationships(part_of):
ncbitaxon_edges.append(
{
"source_curie": term.curie,
"target_curie": parent.curie,
"type": "part_of",
"pred": part_of.curie.lower(),
"source": "ncbitaxon",
"graph": "ncbitaxon",
"version": "",
}
)
return ncbitaxon_nodes, ncbitaxon_edges


def extract_eiffel_nodes_edges():
eiffel_nodes, eiffel_edges = [], []
for term in tqdm(get_eiffel_ontology_terms(), unit="term"):
eiffel_nodes.append(
{
"id": term.curie,
"name": term.name,
"type": "class",
"description": term.definition if term.definition else "",
"obsolete": False if not term.is_obsolete else True,
"synonyms": [Synonym(value=syn._fp(),
type=f"{syn.type.reference.prefix}:"
f"{syn.type.reference.prefix}")
for syn in term.synonyms],
"alts": term.alt_ids,
"xrefs": [Xref(value=value, type=type) for value, type in
zip(term.xrefs, term.xref_types)],
"properties": term.properties,
}
)
for typedef, object_references in term.relationships.items():
for object_reference in object_references:
eiffel_edges.append(
{
"source_curie": term.curie,
"target_curie": object_reference.curie,
"type": typedef.name.replace(" ", "").lower(),
"pred": typedef.curie,
"source": "eiffel",
"graph": "eiffel",
"version": "",
}
)
return eiffel_nodes, eiffel_edges


def extract_cso_nodes_edges():
cso_nodes, cso_edges = [], []
for term in get_cso_obo().iter_terms():
cso_nodes.append(
{
"id": term.curie,
"name": term.name,
"type": "class",
"description": term.definition if term.definition else "",
"obsolete": False if not term.is_obsolete else True,
"synonyms": [Synonym(value=syn._fp(),
type=f"{syn.type.reference.prefix}:"
f"{syn.type.reference.prefix}")
for syn in term.synonyms],
"alts": term.alt_ids,
"xrefs": [Xref(value=value, type=type) for value, type in
zip(term.xrefs, term.xref_types)],
"properties": term.properties,
}
)
for parent in term.get_relationship(part_of):
cso_edges.append(
{
"source_curie": term.curie,
"target_curie": parent.curie,
"type": "part_of",
"pred": part_of.curie.lower(),
"source": "cso",
"graph": "cso",
"version": "",
}
)
return cso_nodes, cso_edges


def extract_wikidata_nodes_edges():
wikidata_nodes, wikidata_edges = [], []
for wikidata_id, label, description, synonyms, xrefs in tqdm(
get_unit_terms(), unit="unit"):
get_unit_terms(), unit="unit"):
synonyms_list = [Synonym(value=value, type="") for value in synonyms]
xrefs_list = [Xref(id=_id, type="oboinowl:hasDbXref") for _id in xrefs]
wikidata_nodes.append(
Expand Down Expand Up @@ -502,15 +380,20 @@ def add_resource_to_dkg(resource_prefix: str):
if resource_prefix == "probonto":
return extract_probonto_nodes_edges()
elif resource_prefix == "geonames":
return extract_geonames_nodes_edges()
return extract_nodes_edges_from_pyobo_terms(get_geonames_terms,
"geonames")
elif resource_prefix == "ncit":
return extract_ncit_nodes_edges()
return extract_nodes_edges_from_pyobo_terms(get_ncit_subset,
"ncit")
elif resource_prefix == "ncbitaxon":
return extract_ncbitaxon_nodes_edges()
return extract_nodes_edges_from_pyobo_terms(get_ncbitaxon,
"ncbitaxon")
elif resource_prefix == "eiffel":
return extract_eiffel_nodes_edges()
return extract_nodes_edges_from_pyobo_terms(
get_eiffel_ontology_terms, "eiffel")
elif resource_prefix == "cso":
return extract_cso_nodes_edges()
return extract_nodes_edges_from_pyobo_terms(get_cso_obo(),
"cso")
elif resource_prefix == "wikidata":
# combine retrieval of wikidata constants and units
return extract_wikidata_nodes_edges()
Expand Down

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