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.

import warnings

warnings.filterwarnings("ignore")

# pip install 'lamindb[bionty]' rdflib
!lamin connect laminlabs/lamindata

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→ connected lamindb: laminlabs/lamindata
• to map a local dev directory, call: lamin settings set dev-dir .

import bionty as bt

from rdflib import Graph, Literal, RDF, URIRef

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→ connected lamindb: laminlabs/lamindata

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.to_dataframe()
diseases.head()

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! truncated query result to limit=100 Disease objects

	uid	name	ontology_id	abbr	synonyms	description	is_locked	created_at	branch_id	created_on_id	space_id	created_by_id	run_id	source_id
id
182	3lEY9l5KHXHvI6	precancerous condition	MONDO:0021074	None	precancerous condition|premalignant condition|...	A Pathological Process With Signs Indicating I...	False	2026-04-13 15:09:54.889610+00:00	1	1	1	9	6070.0	73
181	3UbujjzPMgLW9n	breast ductal adenocarcinoma	MONDO:0005590	None	ductal carcinoma of breast|mammary duct adenoc...	A Breast Carcinoma Arising From The Ducts. Whi...	False	2026-04-13 15:09:54.889610+00:00	1	1	1	9	6070.0	73
180	1yX8SwADeAa956	breast carcinoma	MONDO:0004989	None	mammary carcinoma|carcinoma of the breast|brea...	A Carcinoma That Arises From Epithelial Cells ...	False	2026-04-13 15:09:54.889610+00:00	1	1	1	9	6070.0	73
179	5BMsSAHuNlNkVR	breast adenocarcinoma	MONDO:0004988	None	adenocarcinoma of breast|adenocarcinoma of the...	A Carcinoma That Arises From Glandular Epithel...	False	2026-04-13 15:09:54.889610+00:00	1	1	1	9	6070.0	73
178	1vrnOyXFQ3Nd9W	breast carcinoma in situ	MONDO:0004658	None	stage 0 carcinoma of breast|non-infiltrating b...	A In Situ Carcinoma That Involves The Breast.	False	2026-04-13 15:09:54.889610+00:00	1	1	1	9	6070.0	73

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

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<Graph identifier=N0fcee6021b9c40b2a9aab3d826508d7e (<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}")

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Name: precancerous condition, Description: A Pathological Process With Signs Indicating It May Become Cancerous. Representative Examples Include Leukoplakia, Dysplastic Nevus, Actinic Keratosis, Xeroderma Pigmentosum, And Intraepithelial Neoplasia.
Name: breast ductal adenocarcinoma, Description: A Breast Carcinoma Arising From The Ducts. While Ductal Carcinomas Can Arise At Other Sites, This Term Is Universally Used To Refer To Carcinomas Of The Breast. Ductal Carcinomas Account For About Two Thirds Of All Breast Cancers. Two Types Of Ductal Carcinomas Have Been Described: Ductal Carcinoma In Situ (Dcis) And Invasive Ductal Carcinoma. The Latter Often Spreads To The Axillary Lymph Nodes And Other Anatomic Sites. The Two Forms Of Ductal Carcinoma Often Coexist.
Name: breast carcinoma, Description: A Carcinoma That Arises From Epithelial Cells Of The Breast
Name: breast adenocarcinoma, Description: A Carcinoma That Arises From Glandular Epithelial Cells Of The Breast
Name: breast carcinoma in situ, Description: A In Situ Carcinoma That Involves The Breast.