Meetings

Recent preprints

• Apr 4, 2023

  Enabling profile updates through the Data Discovery Engine (DDE)

  Bioschemas is a grassroots community effort to improve FAIRness of resources in the Life sciences by defining specific Life Science metadata schemas and exposing that metadata from resources that have adopted it. Now that some initial types have been adopted directly into schema.org, an improved mechanism is required to reignite community engagement and encourage profile development. The current process for creating or updating Bioschemas profiles and types is technical and convoluted which creates accessibility issues that can hamper community participation. As adoption of Bioschemas grows and more of the Life Science community considers contributing specific types and profiles, a more accessible creation/modification process is necessary to avoid a loss in engagement. To address this issue, and to drive further Bioschemas adoption, the community has exploited the Data Discovery Engine (DDE) for profile and type development. DDE provides a schema registry and user-friendly tools for creating and editing schemas. The goal of this project is to update existing Bioschemas community profiles in a targeted and crowd-sourced manner, add new profiles as required, and to ensure the documentation is fit for purpose to enable further Bioschemas contributions, at scale. 1 minute read
• Mar 15, 2023

  Comparison of orthology finding tools using plant genes

  Orthology finding tools are valuable for analyzing biological data from multiple species and predicting the functions of uncharacterized genes. Although several tools are available for this purpose, the characteristics of their results for plant genes are not well compared. In this hackathon, we examined three tools (OMA, OrthoDB, and Ensembl Plants) by extracting ortholog pairs between Arabidopsis and soybean and analyzing each result, focusing on five plant genes with varying degrees of conservation. We observed that changes in the taxonomic ranges of OMA and OrthoDB affected ortholog detection, and the range of ortholog detection across the three tools was inconsistent, suggesting the importance of comparing multiple tools to obtain more accurate information on orthologs. less than 1 minute read
• Feb 23, 2023

  Streamlining data brokering from Research Data Management platforms to ELIXIR Repositories

  Mobilizing data from data producers to data deposition databases is an integral service that research data management (RDM) platforms could offer. However, brokering the heterogeneous mixture of scientific data requires systems that are compatible with the diverse (meta)data models of the different RDM platforms, and diverse submission routes of different domain/techniques-specific repositories.Existing tools for brokering of research (meta)data in life sciences often are technique or domain specific and aimed at only one specific deposition database at a time, which does not reflect the way scientific projects are often conducted. As a result, infrastructure providers or research laboratories have to invest resources in manual curation and mapping of (meta)data in order to help researchers deposit their outputs into specialized repositories.This BioHackathon 2022 project specifically focused on designing and implementing a prototype of a data brokering system from ISA-JSON to multiple ELIXIR Deposition Databases, starting with the European Nucleotide Archive (ENA). Specifically, we started from a ISA-JSON file exported from the DataHub, a metadata management platform (an instance of the FAIRDOM-SEEK software) which uses the well-established ISA (Investigation Study Assay) framework to describe multi-omics metadata and link to the location of data files.During this project we performed a high-level mapping of the ISA-JSON schema to the ENA XML files necessary for metadata submission. We also described a flexible, sustainable and domain/technique-agnostic brokering strategy from ISA-JSON to multiple ELIXIR deposition databases and developed a prototype of an EBI multi-repositories converter tool. 1 minute read
• Feb 21, 2023

  Executing workflows in the cloud with WESkit

  With the exponential increase in genomic data, analyzing and processing large datasets has become a challenging task in healthcare. To address this issue, the Global Alliance for Genomics and Health (GA4GH) has proposed a set of community standards for enabling the adoption of FAIR principles for data, software, and infrastructure. These standards promote the concept of sending analysis and processing workflows to the data rather than transferring large datasets, thereby increasing efficiency and data security. In this paper, we present the outcomes of the ELIXIR Biohackathon 2021 project, where we worked on our software WESkit, which implements the GA4GH WES standard for running Snakemake and Nextflow workflows. During the hackathon, we implemented basic GA4GH TRS support, deployed a cloud platform, and added S3 support for downloading result files. less than 1 minute read
• Feb 16, 2023

  An evaluation of EDAM coverage in the Tools Ecosystem and prototype integration of Galaxy and WorkflowHub systems

  Here we report the results of a project started at the BioHackathon Europe 2022. Its goals were to cross-compare and analyze the metadata centralized in the Tools Ecosystem, and linked to the EDAM ontology, as well as to explore methods for connecting tools used in registered Galaxy workflows (i.e. WorkflowHub entries) to the annotations available in bio.tools. less than 1 minute read
• Feb 10, 2023

  Empowering the community with notebooks for bespoke microbiome analyses

  MGnify is EMBL-EBI’s metagenomics resource. MGnify’s recently launched Notebook Server provides an online Jupyter Lab environment for users to explore programmatic access to MGnify’s datasets using Python or R. Here, we report several developments to the Notebook Server completed during the BioHackathon Europe 2022. The developments range from establishing an instance of the notebooks on the Galaxy platform, to adding new notebooks and Jupyter UI extensions enabling more users to perform downstream analysis tasks on MGnify’s extensive metagenomics datasets. less than 1 minute read
• Feb 3, 2023

  CiTO support for BioHackrXiv

  In this paper we present the work executed on BioHackrXiv during the international ELIXIR BioHackathon in Barcelona, Spain, 2021. less than 1 minute read