{ "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/2023/05/12/paper-extending-inherited-metabolic.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/xc7pj-vph59", "url": "https://chem-bla-ics.linkedchemistry.info/2023/05/12/paper-extending-inherited-metabolic.html", "title": "Paper: "Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations"", "content_html": "

When I joined the BiGCaT research group in 2012 I was particularly interested in the open science approach of WikiPathways.\nAs a chemist by training and researcher in cheminformatics, metabolites and their metabolic reactions took my particular\ninterest. I am happy that I have been able to fund Denise’s research project. And thanks Denise for this very exciting research.\nI know it’s just a first step, and far more translational steps are needed, but I for one am very exciting to bridge molecular\ninfo to clinical outcomes.

\n\n

In this study, Denise explored how we can take advantage from molecular pathway databases to link biomarker information:\n“Our framework integrates literature and expert knowledge into machine-readable pathway models, including relevant urine\nbiomarkers and their interactions. The clinical data of 16 previously diagnosed patients with various pyrimidine and urea\ncycle disorders were visualized on the top 3 relevant pathways. Two expert laboratory scientists evaluated the resulting\nvisualizations to derive a diagnosis” (doi:10.1186/s13023-023-02683-9).

\n\n

Figure 4 shows how such a visualization of those biomarker interactions can look like:

\n\n

\"\"

\n\n

And I am hugely proud of the open science approach, from GitHub repo, open source\nR code, SPARQL queries. Thank you, Denise! And thanks to Dr Laura Steinbusch\nfor this nice collaboration! Further acks in the article.

\n\n

References

\n
\n
Slenter, D. N., Hemel, I. M. G. M., Evelo, C. T., Bierau, J., Willighagen, E. L., & Steinbusch, L. K. M. (2023). Extending inherited metabolic disorder diagnostics with biomarker interaction visualizations. Orphanet Journal of Rare Diseases, 18(1). https://doi.org/10.1186/s13023-023-02683-9 CrossRef Scholia
\n
", "summary": "When I joined the BiGCaT research group in 2012 I was particularly interested in the open science approach of WikiPathways. As a chemist by training and researcher in cheminformatics, metabolites and their metabolic reactions took my particular interest. I am happy that I have been able to fund Denise’s research project. And thanks Denise for this very exciting research. I know it’s just a first step, and far more translational steps are needed, but I for one am very exciting to bridge molecular info to clinical outcomes.", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/13023_2023_2683_Fig4_HTML.png", "date_published": "2023-05-12T00:00:00+00:00", "date_modified": "2023-05-12T00:00:00+00:00", "tags": ["metabolomics","rdf","sparql","wikipathways"], "_references": [ { "url": "https://doi.org/10.1186/S13023-023-02683-9", "doi": "10.1186/S13023-023-02683-9" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }