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Added stringdb ppis
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@jmillanacosta
jmillanacosta committed Sep 20, 2024
1 parent 5cafc7b commit 80f7cdd
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Showing 3 changed files with 100 additions and 14 deletions.
24 changes: 18 additions & 6 deletions examples/rdf_example.ipynb
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Expand Up @@ -11,9 +11,20 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 1,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/usr/lib/python3/dist-packages/requests/__init__.py:87: RequestsDependencyWarning: urllib3 (1.26.5) or chardet (5.2.0) doesn't match a supported version!\n",
" warnings.warn(\"urllib3 ({}) or chardet ({}) doesn't match a supported \"\n",
"/home/javi/.local/lib/python3.10/site-packages/tqdm/auto.py:21: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
" from .autonotebook import tqdm as notebook_tqdm\n"
]
}
],
"source": [
"import os\n",
"os.chdir(os.path.abspath(os.path.join(os.getcwd(), \"..\", \"src\")))\n",
Expand Down Expand Up @@ -478,7 +489,7 @@
{
"data": {
"text/plain": [
"<Graph identifier=N74599b16fd6b4ce9a22505dfc2c04af3 (<class 'rdflib.graph.Graph'>)>"
"<Graph identifier=N43623688e92d42b7a107c39a97ccfa75 (<class 'rdflib.graph.Graph'>)>"
]
},
"execution_count": 6,
Expand All @@ -492,7 +503,7 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 7,
"metadata": {},
"outputs": [
{
Expand Down Expand Up @@ -75921,7 +75932,7 @@
"<https://biodatafuse.org/example/score/001621/9/HTR3A_C0041696> a obo:NCIT_C25338 ;\n",
" sio:has_value 6e-01 .\n",
"\n",
"<https://biodatafuse.org/example/test.owl> dcterms:created \"2024-09-20T12:03:58.779325+00:00\"^^xsd:dateTime ;\n",
"<https://biodatafuse.org/example/test.owl> dcterms:created \"2024-09-20T13:21:14.649645+00:00\"^^xsd:dateTime ;\n",
" dcterms:creator <https://orcid.org/0000-0002-4166-7093> ;\n",
" dcterms:identifier <https://biodatafuse.org/example/test.owl> .\n",
"\n",
Expand Down Expand Up @@ -76350,7 +76361,8 @@
" obo:OMIM_620369,\n",
" obo:UMLS_C5830501 .\n",
"\n",
"<https://www.uniprot.org/uniprotkb/P35499> sio:SIO_000068 <https://biodatafuse.org/example/inhibition/P35499_3676> .\n",
"<https://www.uniprot.org/uniprotkb/P35499> a obo:NCIT_C17021 ;\n",
" sio:SIO_000068 <https://biodatafuse.org/example/inhibition/P35499_3676> .\n",
"\n",
"<https://www.wikipathways.org/pathways/WP2118> a obo:PW_0000001 ;\n",
" rdfs:label \"Arrhythmogenic right ventricular cardiomyopathy\"^^xsd:string ;\n",
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13 changes: 7 additions & 6 deletions src/pyBiodatafuse/constants.py
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Expand Up @@ -489,13 +489,14 @@
"gene_expression_value_node": f"{NAMESPACE_BINDINGS['sio']}SIO_001077",
"anatomical_entity_node": f"{NAMESPACE_BINDINGS['sio']}UBERON_0001062",
"tested_substance_node": "http://www.bioassayontology.org/bao#BAO_0003059",
"source_database" : f"{NAMESPACE_BINDINGS['sio']}SIO_000750",
"experimental_process_node" : f"{NAMESPACE_BINDINGS['obo']}EFO_0002694",
"source_database": f"{NAMESPACE_BINDINGS['sio']}SIO_000750",
"experimental_process_node": f"{NAMESPACE_BINDINGS['obo']}EFO_0002694",
"pathway_node": f"{NAMESPACE_BINDINGS['obo']}PW_0000001",
"adverse_event_node" : f"{NAMESPACE_BINDINGS['obo']}OAE_0000001",
"ensemble" : "http://identifiers.org/ensembl/",
"ncbi_disease" : "https://www.ncbi.nlm.nih.gov/medgen/",
"article" : f"{NAMESPACE_BINDINGS['obo']}IAO:0000013",
"adverse_event_node": f"{NAMESPACE_BINDINGS['obo']}OAE_0000001",
"ensemble": "http://identifiers.org/ensembl/",
"ncbi_disease": "https://www.ncbi.nlm.nih.gov/medgen/",
"article": f"{NAMESPACE_BINDINGS['obo']}IAO:0000013",
"protein_node": "http://purl.obolibrary.org/obo/NCIT_C17021",
}

## PREDICATES
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77 changes: 75 additions & 2 deletions src/pyBiodatafuse/graph/rdf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -871,7 +871,79 @@ def add_transporter_inhibitor_node(g: Graph, transporter_inhibitor_data:dict, ba
URIRef("https://purl.obolibrary.org/GO_0032410"),
)
)

g.add(
(
URIRef(f"https://www.uniprot.org/uniprotkb/{uniprot_trembl_id}"),
RDF.type,
URIRef(NODE_TYPES['protein_node']),
)
)

def add_ppi_data(g: Graph, entry: dict, base_uri: str, new_uris:dict)->URIRef:
"""Add a protein protein interaction node
:param g: RDFLib graph
:entry: the ppi dictionary
:base_uri: the base URI for the project
:new_uris: dictionary with project node URIs
Returns a ppi node
"""
stringdb_link_to = entry.get('stringdb_link_to', None)
ensembl = entry.get('stringdb_link_to', None)
score = entry.get('score', None)
try:
score = int(score)
# Nodes
ppi_node = URIRef(base_uri + f"inhibition/{stringdb_link_to}_{ensembl}")
g.add(
(
ppi_node,
RDF.type,
URIRef("http://purl.obolibrary.org/obo/NCIT_C18469"),
)
)

g.add(
(
URIRef(f"https://www.uniprot.org/uniprotkb/{stringdb_link_to}"),
RDF.type,
URIRef(NODE_TYPES['protein_node']),
)
)
g.add(
(
URIRef(f"https://www.uniprot.org/uniprotkb/{stringdb_link_to}"),
URIRef(PREDICATES['sio_is_part_of']),
ppi_node,
)
)
g.add(
(
URIRef(f"http://identifiers.org/ensembl/{ensembl}"),
URIRef(PREDICATES['sio_is_part_of']),
ppi_node,
)
)
g.add(
(
URIRef(f"http://identifiers.org/ensembl/{ensembl}"),
RDF.type,
URIRef(NODE_TYPES['gene_node']),
)
)
score_node = URIRef(f"{new_uris['score_base_node']}/{stringdb_link_to}_{ensembl}")
g.add((score_node, RDF.type, URIRef(NODE_TYPES["score_node"])))
g.add(
(
score_node,
URIRef(NAMESPACE_BINDINGS["sio"] + "has_value"),
Literal(score, datatype=XSD.double),
)
)
return ppi_node
except:
return None

def generate_rdf(
df: pd.DataFrame, base_uri: str, version_iri: str, author: str, orcid: str, metadata: dict
) -> Graph:
Expand Down Expand Up @@ -1016,7 +1088,8 @@ def generate_rdf(
if transporter_inhibitor_data:
for entry in transporter_inhibitor_data:
add_transporter_inhibitor_node(g, entry, base_uri)

if stringdb_data:
add_ppi_data(g, entry, base_uri, new_uris)
# Add metadata to the RDF graph
add_metadata(
g=g,
Expand Down

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