Evidence map›Paper›PMID 40378136›Full record

ArticleGigaScience2025

A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications.

Jerven Bolleman, Vincent Emonet, Adrian Altenhoff, Amos Bairoch, Marie-Claude Blatter, Alan Bridge, Séverine Duvaud, Elisabeth Gasteiger, Dmitry Kuznetsov, Sébastien Moretti and 7 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in GigaScience, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

17 authors.

Jerven BollemanSIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.ORCID 0000-0002-7449-1266
Vincent EmonetSIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.ORCID 0000-0002-1501-1082
Adrian AltenhoffSIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.ORCID 0000-0001-7492-1273
Amos BairochSIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.ORCID 0000-0003-2826-6444
Marie-Claude BlatterSIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.ORCID 0000-0002-7474-1499
Alan BridgeSIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.ORCID 0000-0003-2148-9135
Séverine DuvaudSIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.ORCID 0000-0001-7892-9678
Elisabeth GasteigerSIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.ORCID 0000-0003-1829-162X
Dmitry KuznetsovSIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.ORCID 0000-0002-9972-947X
Sébastien MorettiSIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.ORCID 0000-0003-3947-488X
Pierre-Andre MichelSIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.ORCID 0000-0002-7023-1045
Anne MorgatSIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.ORCID 0000-0002-1216-2969
Marco PagniSIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.ORCID 0000-0001-9292-9463
Nicole RedaschiSIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.ORCID 0000-0001-8890-2268
Monique Zahn-ZabalSIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.ORCID 0000-0001-7961-6091
Tarcisio Mendes de FariasSIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.ORCID 0000-0002-3175-5372
Ana Claudia SimaSIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.ORCID 0000-0003-3213-4495

Funding

UniProt - Text Mining and Large Language models to Enhance Functional Annotation in UniProt of Protein Variants Associated with Alzheimer's DiseaseU24HG007822 · NHGRI · GEORGETOWN UNIVERSITY · PI Alex Bateman, Alan James Bridge · 2018 to 2026
$53.0M
National Institute of Allergy and Infectious DiseasesNCI NIH HHSNEI NIH HHSNHGRI NIH HHS U24 HG007822NIA NIH HHSNIDDK NIH HHSNIGMS NIH HHSNIH HHS U24HG007822SERI CHIST-ERA-22-ORD-09SERI HORIZON-INFRA-2024-EOSC-01-03SNF 20CH21_217482
6 · The paper itself

Abstract

backgroundIn recent decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased adoption in bioinformatics due to their advantages for representing data in a generic graph format. For example, yummydata.org catalogs more than 60 knowledge graphs accessible through SPARQL, a technical query language. Although SPARQL allows powerful, expressive queries, even across physically distributed knowledge graphs, formulating such queries is a challenge for most users. Therefore, to guide users in retrieving the relevant data, many of these resources provide representative examples. These examples can also be an important source of information for machine learning (for example, machine-learning algorithms for translating natural language questions to SPARQL), if a sufficiently large number of examples are provided and published in a common, machine-readable, and standardized format across different resources.

findingsWe introduce a large collection of human-written natural language questions and their corresponding SPARQL queries over federated bioinformatics knowledge graphs (KGs) collected for several years across different research groups at the SIB Swiss Institute of Bioinformatics. The collection comprises more than 1,000 example questions and queries, including almost 100 federated queries. We propose a methodology to uniformly represent the examples with minimal metadata, based on existing standards. Furthermore, we introduce an extensive set of open-source applications, including query graph visualizations and smart query editors, easily reusable by KG maintainers who adopt the proposed methodology.

conclusionsWe encourage the community to adopt and extend the proposed methodology, towards richer KG metadata and improved Semantic Web services. URL:  https://github.com/sib-swiss/sparql-examples.

Indexed as

Computational BiologyAlgorithmsHumansInformation Storage and RetrievalMachine LearningSoftwarefederated SPARQLknowledge graphsmetadataquery editorResource Description Framework (RDF)

Identifiers

PMID40378136
PMCPMC12083453

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.