RDF export & SPARQL queries

SPARQL is a query language used to retrieve and manipulate data stored in Resource Description Framework (RDF) format. In this tutorial, we demonstrate how lamindb registries can be queried with SPARQL.

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import warnings

warnings.filterwarnings("ignore")

# !pip install 'lamindb[aws,bionty]'
!lamin load laminlabs/cellxgene

→ connected lamindb: laminlabs/cellxgene

import bionty as bt

from rdflib import Graph, Literal, RDF, URIRef

Generally, we need to build a directed RDF Graph composed of triple statements. Such a graph statement is represented by:

1. a node for the subject

2. an arc that goes from a subject to an object for the predicate

3. a node for the object.

Each of the three parts can be identified by a URI.

We can use the DataFrame representation of lamindb registries to build a RDF graph.

Building a RDF graph

diseases = bt.Disease.df()
diseases.head()

→ connected lamindb: laminlabs/cellxgene

	uid	name	ontology_id	abbr	synonyms	description	source_id	run_id	created_at	created_by_id
id
769	1sfLCprL	clonal hematopoiesis	MONDO:0100542	None	None	None	NaN	27.0	2024-07-12 14:20:56.067237+00:00	1
767	7Zxvmde6	hereditary motor neuron disease	MONDO:0024257	None	genetic anterior horn cell disease|hereditary ...	An Instance Of Motor Neuron Disease That Is Ca...	49.0	27.0	2024-07-12 14:01:02.371130+00:00	1
766	3nbMYxeu	familial amyotrophic lateral sclerosis	MONDO:0005144	None	hereditary amyotrophic lateral sclerosis	An Instance Of Amyotrophic Lateral Sclerosis T...	49.0	27.0	2024-07-12 14:01:00.473714+00:00	1
765	4wI2szgu	basal cell neoplasm	MONDO:0020799	None	basal cell tumor	A Neoplastic Proliferation Of Basal Cells In T...	49.0	27.0	2024-07-12 14:00:59.087086+00:00	1
764	g0eRt9m2	scleroderma	MONDO:0019340	None	dermatosclerosis|scleroderma (disease)|sclerod...	Scleroderma Is A Rare Autoimmune Connective Ti...	49.0	27.0	2024-07-12 14:00:57.255644+00:00	1

We convert the DataFrame to RDF by generating triples.

rdf_graph = Graph()

namespace = URIRef("http://sparql-example.org/")

for _, row in diseases.iterrows():
    subject = URIRef(namespace + str(row["ontology_id"]))
    rdf_graph.add((subject, RDF.type, URIRef(namespace + "Disease")))
    rdf_graph.add((subject, URIRef(namespace + "name"), Literal(row["name"])))
    rdf_graph.add(
        (subject, URIRef(namespace + "description"), Literal(row["description"]))
    )

rdf_graph

<Graph identifier=N19fc43a14dff4a518bf7e771fc209ef7 (<class 'rdflib.graph.Graph'>)>

Now we can query the RDF graph using SPARQL for the name and associated description:

query = """
SELECT ?name ?description
WHERE {
  ?disease a <http://sparql-example.org/Disease> .
  ?disease <http://sparql-example.org/name> ?name .
  ?disease <http://sparql-example.org/description> ?description .
}
LIMIT 5
"""

for row in rdf_graph.query(query):
    print(f"Name: {row.name}, Description: {row.description}")

Name: clonal hematopoiesis, Description: None
Name: hereditary motor neuron disease, Description: An Instance Of Motor Neuron Disease That Is Caused By An Inherited Modification Of The Individual'S Genome.
Name: familial amyotrophic lateral sclerosis, Description: An Instance Of Amyotrophic Lateral Sclerosis That Is Caused By An Inherited Modification Of The Individual'S Genome.
Name: basal cell neoplasm, Description: A Neoplastic Proliferation Of Basal Cells In The Epidermis (Part Of The Skin) Or Other Anatomic Sites (Most Frequently The Salivary Glands). The Basal Cell Neoplastic Proliferation In The Epidermis Results In Basal Cell Carcinomas. The Basal Cell Neoplastic Proliferation In The Salivary Glands Can Be Benign, Resulting In Basal Cell Adenomas Or Malignant, Resulting In Basal Cell Adenocarcinomas.
Name: scleroderma, Description: Scleroderma Is A Rare Autoimmune Connective Tissue Disorder Characterized By Abnormal Hardening Of The Skin And, Sometimes, Other Organs. It Is Classified Into Two Main Forms: Localized Scleroderma And Systemic Sclerosis (Ssc), The Latter Comprising Three Subsets; Diffuse Cutaneous Ssc (Dcssc), Limited Cutaneous Ssc (Lcssc) And Limited Ssc (Lssc).