PomBase: a Global Core Biodata Resource—growth, collaboration, and sustainability

PomBase: a Global Core Biodata Resource—growth, collaboration, and sustainability

2024 | Kim M. Rutherford, Manuel Lera-Ramirez, Valerie Wood
PomBase, the model organism database for fission yeast, has been awarded Global Core Biodata Resource (GCBR) status by the Global Biodata Coalition. This recognition highlights its role as a comprehensive, FAIR-compliant resource that supports research in fission yeast and the broader scientific community. Over the past two years, PomBase has continued to grow and improve, with a significant increase in curated data, reaching 392,000 statements as of November 2023. The database provides detailed curation, standardization, and integration of information from thousands of experiments, offering a repository for molecular data at the gene and protein level. It also includes sophisticated query tools, organism and domain-level overviews, and support for functional inferences. PomBase's curated resources have been used in numerous studies, including those related to epigenetic pathways, translational control, nuclear membrane integrity, and the role of inositol pyrophosphate in RNA processing. The database also extends its reach beyond fission yeast by disseminating curated knowledge to other biological databases and supporting functional inferences for conserved gene functions in other species, including humans. PomBase has been recognized for its scientific quality, comprehensivity, and contributions to accelerating science. It has also made significant progress in collaboration with other biodata resources, sharing data and software, and contributing to global standards. The database has been used to curate over 23,000 standardized annotations from directed gene-specific hypothesis-driven experiments. It has also been involved in collaborative projects, such as the community curation project, which empowers authors to FAIRify their data and knowledge derived from in-depth hypothesis-driven research. PomBase has also contributed to quality control by reviewing existing annotations for consistency and accuracy, and by providing one of the largest contributions to the correction of manual and electronically inferred GO annotations. The database has also developed a generic pipeline to validate and correct the protein residue positions referred to by alleles and protein modifications. Despite these achievements, defining metrics for impact remains challenging. However, PomBase's role in connecting research communities and supporting discovery is vital. The database has been used in innovative ways by key scientific investigations, and its value is demonstrated through testimonials and use cases from user surveys. Looking ahead, PomBase aims to continue building richer, more comprehensive connections among curated data of all types. It is also working with AI and ML communities to support the application of machine-based methods, and to improve the specificity of curated data. The database is committed to maintaining its role as a reliable source of comprehensive, quality-controlled, curated knowledge derived from both large- and small-scale S. pombe experiments.PomBase, the model organism database for fission yeast, has been awarded Global Core Biodata Resource (GCBR) status by the Global Biodata Coalition. This recognition highlights its role as a comprehensive, FAIR-compliant resource that supports research in fission yeast and the broader scientific community. Over the past two years, PomBase has continued to grow and improve, with a significant increase in curated data, reaching 392,000 statements as of November 2023. The database provides detailed curation, standardization, and integration of information from thousands of experiments, offering a repository for molecular data at the gene and protein level. It also includes sophisticated query tools, organism and domain-level overviews, and support for functional inferences. PomBase's curated resources have been used in numerous studies, including those related to epigenetic pathways, translational control, nuclear membrane integrity, and the role of inositol pyrophosphate in RNA processing. The database also extends its reach beyond fission yeast by disseminating curated knowledge to other biological databases and supporting functional inferences for conserved gene functions in other species, including humans. PomBase has been recognized for its scientific quality, comprehensivity, and contributions to accelerating science. It has also made significant progress in collaboration with other biodata resources, sharing data and software, and contributing to global standards. The database has been used to curate over 23,000 standardized annotations from directed gene-specific hypothesis-driven experiments. It has also been involved in collaborative projects, such as the community curation project, which empowers authors to FAIRify their data and knowledge derived from in-depth hypothesis-driven research. PomBase has also contributed to quality control by reviewing existing annotations for consistency and accuracy, and by providing one of the largest contributions to the correction of manual and electronically inferred GO annotations. The database has also developed a generic pipeline to validate and correct the protein residue positions referred to by alleles and protein modifications. Despite these achievements, defining metrics for impact remains challenging. However, PomBase's role in connecting research communities and supporting discovery is vital. The database has been used in innovative ways by key scientific investigations, and its value is demonstrated through testimonials and use cases from user surveys. Looking ahead, PomBase aims to continue building richer, more comprehensive connections among curated data of all types. It is also working with AI and ML communities to support the application of machine-based methods, and to improve the specificity of curated data. The database is committed to maintaining its role as a reliable source of comprehensive, quality-controlled, curated knowledge derived from both large- and small-scale S. pombe experiments.
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