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

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Jerven Bolleman , Vincent Emonet , Adrian Altenhoff , Amos Bairoch , Marie-Claude Blatter , Alan Bridge , Séverine Duvaud , Elisabeth Gasteiger , Dmitry Kuznetsov , Sébastien Moretti , Pierre-André Michel , Anne Morgat , Marco Pagni , Nicole Redaschi , Monique Zahn‐Zabal , Tarcisio Mendes de Farias , Ana Claudia Sima ·

YOU? · · 2024 · Open Access · · DOI: https://doi.org/10.48550/arxiv.2410.06010

Background. In the last 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, if a sufficiently large number of examples are provided and published in a common, machine-readable and standardized format across different resources. Findings. We 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 1000 example questions and queries, including 65 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. Conclusions. We encourage the community to adopt and extend the proposed methodology, towards richer KG metadata and improved Semantic Web services.

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Computer science Information retrieval Data mining Knowledge graph Data science

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Type: preprint
Language: en
Landing Page: http://arxiv.org/abs/2410.06010
PDF: https://arxiv.org/pdf/2410.06010
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Cited By: 2
Related Works: 10
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DOI: https://doi.org/10.48550/arxiv.2410.06010

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

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Language: en

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Publication year: 2024

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Publication date: 2024-10-08

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Authors: Jerven Bolleman, Vincent Emonet, Adrian Altenhoff, Amos Bairoch, Marie-Claude Blatter, Alan Bridge, Séverine Duvaud, Elisabeth Gasteiger, Dmitry Kuznetsov, Sébastien Moretti, Pierre-André Michel, Anne Morgat, Marco Pagni, Nicole Redaschi, Monique Zahn‐Zabal, Tarcisio Mendes de Farias, Ana Claudia Sima

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Landing page: https://arxiv.org/abs/2410.06010

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Concepts: Computer science, Information retrieval, Data mining, Knowledge graph, Data science

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Cited by: 2

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Citations by year (recent): 2024: 2

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abstract_inverted_index.advantages	39
abstract_inverted_index.collection	140, 173
abstract_inverted_index.expressive	68
abstract_inverted_index.facilitate	26
abstract_inverted_index.physically	72
abstract_inverted_index.resources.	134
abstract_inverted_index.retrieving	90
abstract_inverted_index.standards.	201
abstract_inverted_index.structured	10
abstract_inverted_index.Background.	0
abstract_inverted_index.distributed	73
abstract_inverted_index.formulating	76
abstract_inverted_index.information	110
abstract_inverted_index.maintainers	223
abstract_inverted_index.methodology	189
abstract_inverted_index.open-source	209
abstract_inverted_index.Conclusions.	229
abstract_inverted_index.Furthermore,	202
abstract_inverted_index.methodology,	240
abstract_inverted_index.methodology.	228
abstract_inverted_index.representing	41
abstract_inverted_index.standardized	130
abstract_inverted_index.sufficiently	116
abstract_inverted_index.applications,	210
abstract_inverted_index.corresponding	148
abstract_inverted_index.human-written	142
abstract_inverted_index.yummydata.org	50
abstract_inverted_index.bioinformatics	35, 153
abstract_inverted_index.representative	99
abstract_inverted_index.visualizations	214
abstract_inverted_index.Bioinformatics.	171
abstract_inverted_index.machine-readable	128
abstract_inverted_index.interoperability.	27
cited_by_percentile_year
countries_distinct_count	0
institutions_distinct_count	17
citation_normalized_percentile