{ "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/2022/03/05/bridgedb-nwo-grant-update-1-first-steps.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/aegfe-5zc88", "url": "https://chem-bla-ics.linkedchemistry.info/2022/03/05/bridgedb-nwo-grant-update-1-first-steps.html", "title": "BridgeDb NWO grant update #1: first steps", "content_html": "

Last year, Denise, Tina, Marvin, and I received an NWO Open Science\ngrant (203.001.121) to improve the long running BridgeDb project, originally developed by Martijn van Iersel\n(see doi:10.1186/1471-2105-11-5). Helena joined our group as research software engineer and will work\npart-time on this grant. We started two weeks ago, so time for an update of results:

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It should be noted that FAIRplus has funded Chris’s team to work on identifier mapping too. Luc, Lucas, and now Tooba in our team have been working\non Ensembl-based gene/protein identifier mappings and FAIRplus Cookbook recipes.

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Not bad this progress in the first two weeks. We are ready now to start writing unit tests for much of the BridgeDb code. There were some, but a lot of code is used in production, but not formally tested. So far, the number of regressions due to updated libraries (dependencies) has been quite manageable. But with the work planned in this grant, we need more sustainable software, and therefore more unit testing. With the BridgeDb Webservice factored out, the code is compiling again and so is the code coverage testing.

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The BridgeDb Webservice itself needs a rewrite from scratch. At least the mapping between underlying code (which we can reuse) and the REST calls. The library we used here has never been updated and I spent last weekend figuring out how to change the code, but gave up after two days. Rewriting is faster.

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References

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van Iersel, M. P., Pico, A. R., Kelder, T., Gao, J., Ho, I., Hanspers, K., Conklin, B. R., & Evelo, C. T. (2010). The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC Bioinformatics, 11(1). https://doi.org/10.1186/1471-2105-11-5 CrossRef Scholia
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", "summary": "Last year, Denise, Tina, Marvin, and I received an NWO Open Science grant (203.001.121) to improve the long running BridgeDb project, originally developed by Martijn van Iersel (see doi:10.1186/1471-2105-11-5). Helena joined our group as research software engineer and will work part-time on this grant. We started two weeks ago, so time for an update of results:", "date_published": "2022-03-05T00:00:00+00:00", "date_modified": "2025-03-14T00:00:00+00:00", "tags": ["grant","bridgedb","openscience"], "_references": [ { "url": "https://doi.org/10.1186/1471-2105-11-5", "doi": "10.1186/1471-2105-11-5" } ], "_funding": [{"award": { "title" : "BridgeDb and Wikidata: a powerful combination generating interoperable open research", "uri" : "drc.filenumber:203001121" }, "funder": { "name": "Dutch Research Council", "ror": "04jsz6e67" } }], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }