{ "version": "https://jsonfeed.org/version/1.1", "title": "chem-bla-ics", "description": "Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.", "home_page_url": "https://chem-bla-ics.linkedchemistry.info/", "feed_url": "https://chem-bla-ics.linkedchemistry.info/2026/05/30/new-paper-pybiodatafuse.json", "icon": "https://chem-bla-ics.linkedchemistry.info/assets/images/chem-bla-ics_logo.png", "language": "en", "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286", "_orcid": "0000-0001-7542-0286" } ], "items": [ { "id": "https://doi.org/10.59350/7n2bs-zsm80", "url": "https://chem-bla-ics.linkedchemistry.info/2026/05/30/new-paper-pybiodatafuse.html", "title": "New paper: pyBiodatafuse: Extending interoperability of data using modular queries across biomedical resources", "content_html": "

The number of data and knowledge source relevant to your biological or chemical question\nincreases every year. They all come with different API and different data models. These\nneed to be documented and mapped. What better way to do that than actually do that and\nthen use that. I never asked, but I can imagine that was the original idea of Tooba\nand Yojana. At the very least, it demonstrates the level of interoperability we need\nin the life sciences.

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In a recent paper, Yojana Gadiya,\nJavier Millán Acosta, and\nTooba Abbassi-Daloii led a project called\nBioDataFuse (worked on at the biohackathons of ELIXIR in 2023\nand 2024\nand of SWAT4HCLS in 2024\nand 2025) and the matching Python package,\npyBiodatafuse\n(doi:10.1093/bioinformatics/btag064).

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With a group of researchers from The Netherlands, Switzerland, Czech Republic, and\nthe USA, multiple databases are wrapped in a uniform data model. The package\nallows the generation of a graph across the imported databases which can then\nbe further analyzed and visualized. This is an example (RDF) graph that was generated:

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Seeing this kind of interoperability brings back good memories.

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Congrats to all authors!

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References

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Acosta, J. M., Kawashima, S., Katayama, T., Bolleman, J., Martinat, D., Detering, H., Gayo, J. E. L., Gadiya, Y., & Abbassi-Daloii, T. (2025). BioHackEU24 report: Expanding FAIR database integration through elucidation and transformation of underlying graph schemas. Center for Open Science. https://doi.org/10.37044/osf.io/ptmg5_v1 CrossRef Scholia
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Gadiya, Y., Ammar, A., Willighagen, E., Martinat, D., Sima, A. C., Balci, H., & Abbassi-Daloii, T. (2023). BioHackEU23 report: Extending interoperability of experimental data using modular queries across biomedical resources. Center for Open Science. https://doi.org/10.37044/osf.io/mhsqp CrossRef Scholia
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Gadiya, Y., Millán Acosta, J., Ammar, A., Adriaque Lozano, A., Wetstede, D., Martinát, D., Sima, A. C., Mei, H., Willighagen, E., & Abbassi-Daloii, T. (2026). pyBiodatafuse: extending interoperability of data using modular queries across biomedical resources. Bioinformatics, 42(3). https://doi.org/10.1093/bioinformatics/btag064 CrossRef Scholia
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", "summary": "The number of data and knowledge source relevant to your biological or chemical question increases every year. They all come with different API and different data models. These need to be documented and mapped. What better way to do that than actually do that and then use that. I never asked, but I can imagine that was the original idea of Tooba and Yojana. At the very least, it demonstrates the level of interoperability we need in the life sciences.", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/pyBiodatafuseGraph.png", "date_published": "2026-05-30T00:00:00+00:00", "date_modified": "2026-05-30T00:00:00+00:00", "tags": ["python","data"], "_references": [ { "url": "https://doi.org/10.1093/BIOINFORMATICS/BTAG064", "doi": "10.1093/BIOINFORMATICS/BTAG064" } , { "url": "https://doi.org/10.37044/OSF.IO/MHSQP", "doi": "10.37044/OSF.IO/MHSQP" } , { "url": "https://doi.org/10.37044/OSF.IO/PTMG5_V1", "doi": "10.37044/OSF.IO/PTMG5_V1" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }