Meetings
BioHackSWAT4HCLS 2025
BioHackathon Europe 2024
3rd BioHackathon Germany
DBCLS BioHackathon 2024
ELIXIR INTOXICOM
Recent preprints
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Expanding data on cultivation media and microbial traits
The standardization and integration of cultivation media data are essential for advancing microbial research and enabling AI-based predictions of optimal growth conditions. This study addresses the challenges of data fragmentation by aligning terminologies and mapping ingredients between two prominent databases: MediaDive (DSMZ) and TogoMedium (DBCLS). We successfully linked 870 ingredients, expanded the Growth Media Ontology (GMO), and prepared data for media similarity calculations, thereby enhancing the interoperability of these resources. Additionally, we developed the first version of a BacDive RDF knowledge graph, incorporating mapping rules for 24 key entities and materializing the data in turtle format to facilitate integration into broader knowledge networks. We also propose a novel process for the standardized registration of media recipes by depositors, ensuring that these recipes can be cited and shared consistently. Together, these efforts contribute to the creation of a more cohesive and accessible microbial data ecosystem, supporting future research and innovation. -
Revisiting SRAmetadb.sqlite
The SRAmetadb.sqlite database, which compiles Sequence Read Archive (SRA) metadata into an offline SQLite format, has been a crucial resource for bioinformatics tools like the SRAdb R package and the pysradb. Despite its utility, the database has not been regularly updated, with the last refresh occurring in late 2023. Moreover, no public tools exist to rebuild or update this database. This report introduces an open-source pipeline developed during the 2024 international biohackaton, designed to generate and update a similar SRAmetadb.sqlite database from SRA metadata, addressing the gap left by the lack of recent updates.The SRAmetadb.sqlite database’s value extends beyond its original use cases, offering potential integration with other tools such as DuckDB and programmatically accessing from custom scripts. The proposed pipeline introduces features like the generation of metadata subsets, enabling researchers to focus on specific species. It also offers offline access to SRA metadata, significantly enhancing query speed and efficiency. This adaptability is particularly relevant as new use cases emerge, including applications in large language models (LLMs) and Retrieval-Augmented Generation (RAG).This pipeline prioritizes low resource usage and ease of maintenance. It is not intended as a direct replacement for the original SRAmetadb.sqlite but seeks to maintain compatibility while exploring the benefits of modern SQLite features. By providing this tool as an open-source resource, the project encourages community involvement to ensure its ongoing development and relevance in the evolving landscape of bioinformatics research. -
DBCLS BioHackathon 2024 Report for Project: Human Glycome Atlas
As part of BioHackathon 2024, we here report on our analysis of tools reviewed by this group to implement a new knowledgebase called TOHSA for the Human Glycome Atlas (HGA) Project. In particular, we focus on the experiences of the integration process of the QLever framework, a promising Semantic Web tool for handling “Triple Stores” and SPARQL technologies in the scope of creating a reliable and performant Semantic Knowledge-Base (Infrastructure and Portal) for TOHSA. QLever highlights the ongoing relevance and potential of these technologies to deliver scalable and reliable solutions. It was nice to see that “Triple Stores” and SPARQL technology implementations and developments for the community are ongoing and that progressively useful and performant and scalable/reliable, open-source software is being implemented. And we did a general revision and comparison of relevant Semantic Web Frameworks for our use-case. -
The Plant Breeding Ontology (PBO): towards an ontology for the plant breeding community
The need of standardizing the language used within a community has been recognized as one of the major components to enable a better integration of data as well as their further analysis. The plant breeding community makes use of a very specialized language, which has been evolving according to the new technologies and needs of their final users (e.g. farmers). That community is disparate all over the world. Therefore, a translation of the most common used terms has always been a key asset to accomplish their objectives as well as the ones of their collaborators. Here, we present PBO (Plant Breeding Ontology), an ontology for the plant breeding community which captures more than 2200 entries where 80 represent the core terms. PBO has translations in 8 different languages: English (main language), Spanish, French, Dutch, German, Japanese, Catalan and Thai, as well as their definitions, synonyms, derived terms and samples of their usage. PBO has been built partially manually and semiautomatically. -
DBCLS BioHackathon 2024 report: Everything about workflow and container
Workflow engines are now widely used for genome analysis workflows.On the other hand, there are still difficulties to build and execute their workflows in various aspects.Here are examples of such difficulties:How to develop our workflows in workflow languages such as Common Workflow Language (CWL), Snakemake, Nextflow, and others?How to integrate our workflows with containers such as Docker, Singularity, and Podman?How to integrate our workflows with job schedulers such as Slurm and GridEngine?Our group solved these problems with the following activities. First, we cooperated with other groups to develop their workflows, and to make their workflows integrated with containers.Second, we developed and improved workflow ecosystems to remove the barriers to develop and execute their workflows. Ecosystems include workflow executors, specifications of workflow languages, and workflow-related tools.This paper reports what we did during the DBCLS BioHackathon 2024. -
Ontologies for single-cell experiments
Research data management is becoming increasingly important in the scientific community. Acritical challenge in this field is making research data FAIR (findable, accessible, interoperableand reusable, (Wilkinson et al., 2016)). Metadata plays a vital role in this challenge as it allowsresearchers to accurately understand and recreate experiments. To tackle this challenge, variousapproaches are being taken towards this goal, including the development of domain-overarchingand domain-specific standards.In the different scientific communities, multiple general, as well as domain-specific minimuminformation standards have been developed, such as MIAPPE (Ćwiek-Kupczyńska, 2016), theminimum information about a plant phenotyping experiment, MIAME (H. Brazma A., 2001),the minimum information about a microarray experiment, and MINSEQE (B. Brazma A., 2012),the minimum information about a high-throughput sequencing experiment. These standards aredesigned to describe specific types of experiments. Recently, a minimum information standardfor single-cell experiments, minSCe (Minimum Information about a Single-Cell Experiment),has been introduced (Füllgrabe et al., 2020). However, it is not yet widely applied.Minimum information standards are an important part of the solution and should be built upon.In addition, the use of controlled vocabularies and ontology terms is also essential. Ontologyterms have a persistent identifier, an expressive name and a curated definition. Using theseterms enables different researchers to understand and recreate annotated experiments. In thisBioHackathon Europe project, we propose to expand biological, experimental and technicalmetadata schema as well as ontologies for single-cell experiments across domains with a focuson transcriptomics. This will facilitate the sharing and reuse of single-cell data and promotecollaboration among researchers in different domains. Our goal is to improve data managementpractices and enhance the reproducibility of single-cell research. -
An analysis of sex ratios using a biodiversity data cube
This investigation uses biodiversity data cubes derived from the datasets mobilised by the Global Biodiversity Information Facility (GBIF), to conduct an analysis of sex ratios of ducks across Europe. Encompassing over 4 million occurrences extracted from nearly 5000 datasets, this study elucidates sex distribution patterns across various species, focussing on temporal and spatial dynamics. The aim of this study is to highlight the availability of open sex data and its potential usefulness in research and monitoring of sex ratios of wild organisms, particularly in sexual dimorphic species.