{ "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/2025/08/06/archiving-but-not-really.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/vwd81-p8z85", "url": "https://chem-bla-ics.linkedchemistry.info/2025/08/06/archiving-but-not-really.html", "title": "Archiving, but not really", "content_html": "

Mike Taylor wrote up a post about the various things a journal article is doing,\nthe first being a scientific report. We put a lot of money in establishing a scientific track record. In the past 30 years\nhow we publish our research and how we archive it has changed significantly. If you read my blog more often, you know I have\nbeen critical of the performance of many publishers. Springer Nature was so disappointing that after 5 years I\nstepped down\nas Editor-in-Chief (of two) of the Journal of Cheminformatics.\nThere is so much that must be done better.

\n\n

But in the most recent iteration, triggered by some work for WikiPathways, I was using\nEurope PMC to find articles that\nmention WikiPathways and then search in the full text for the string WP, as a trigger for the possible mention of\nWikiPathways pathway identifiers, which look like WP4846. The use of compact (resource) identifiers\n(see doi:10.1038/sdata.2018.29) is minimal, but at least some articles use identifiers.

\n\n

That allows me to extend our WikiPathways knowledge graph of articles citing specific pathways.\nAt the time of writing, we collected 2509 citations from 440 different articles to 883 different pathways. Now,\nI want to blog about that more, but it’s related to an observation.

\n\n

Information loss

\n

Now, back in the late ninities I learned about GNU/Linux and after playing with Red Hat and Suse, I settled for Debian.\nOne of the things I learned is that, generally, information corruption (like data loss) is an absolute red flag, a no-go,\na total showstopper.

\n\n

And then we have this in publishing, the one area where data corruption must also be a no-go:

\n\n

\"\"

\n\n

In this image, the left side shows a screenshot of the publisher version of the article and on the right side\nthe version in Pubmed Central (PMC). PMC has been an important project to archive full text versions of articles:

\n\n
\n

11.2 million articles are archived in PMC.

\n
\n\n

So, this is really bad! The archived version is not really useful. As a human I already struggle to read the\ndegraded image, let alone an algorithm.

\n\n

Does that matter? Yes, projects like the awesome\nPathway Figure OCR (see doi:10.1186/s13059-020-02181-2)\ndepend on images to be FAIR enough to extract information. (Side note: yes, these images should be vector\ngraphics, but commercial publishers decided about twenty years ago that they could not care enough.)

\n\n

At this moment, I do not know where the information is lost. Maybe PubMed Central is storing the images in a low\nresolution. Maybe the publisher provides PMC with a low resolution image. But to me, this must be solved as soon\nas possible. This is utterly unacceptable.

\n\n

I wonder what the authors of the article (doi:10.1186/s13287-025-04166-z)\nI took as example think of this.

\n\n

References

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Hanspers, K., Riutta, A., Summer-Kutmon, M., & Pico, A. R. (2020). Pathway information extracted from 25 years of pathway figures. Genome Biology, 21(1). https://doi.org/10.1186/s13059-020-02181-2 [cito:citesAsRecommendedReading] CrossRef Scholia
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Taylor, M. (2025). Journal articles are trying to do six things at once — no wonder they’re unreadable. In Front Matter. Front Matter. https://doi.org/10.59350/svpow.24000 [cito:citesAsRecommendedReading] CrossRef Scholia
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Wimalaratne, S. M., Juty, N., Kunze, J., Janée, G., McMurry, J. A., Beard, N., Jimenez, R., Grethe, J. S., Hermjakob, H., Martone, M. E., & Clark, T. (2018). Uniform resolution of compact identifiers for biomedical data. Scientific Data, 5(1). https://doi.org/10.1038/sdata.2018.29 [cito:obtainsBackgroundFrom] CrossRef Scholia
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Yuan, F., Liu, J., Zhong, L., Liu, P., Li, T., Yang, K., Gao, W., Zhang, G., Sun, J., & Zou, X. (2025). Enhanced therapeutic effects of hypoxia-preconditioned mesenchymal stromal cell-derived extracellular vesicles in renal ischemic injury. Stem Cell Research & Therapy, 16(1). https://doi.org/10.1186/s13287-025-04166-z [cito:describes] CrossRef Scholia
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", "summary": "Mike Taylor wrote up a post about the various things a journal article is doing, the first being a scientific report. We put a lot of money in establishing a scientific track record. In the past 30 years how we publish our research and how we archive it has changed significantly. If you read my blog more often, you know I have been critical of the performance of many publishers. Springer Nature was so disappointing that after 5 years I stepped down as Editor-in-Chief (of two) of the Journal of Cheminformatics. There is so much that must be done better.", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/imageResolutionLoss.png", "date_published": "2025-08-06T00:00:00+00:00", "date_modified": "2025-08-06T00:00:00+00:00", "tags": ["publishing","europepmc"], "_references": [ { "url": "https://doi.org/10.59350/svpow.24000", "doi": "10.59350/svpow.24000" , "cito": [ "citesAsRecommendedReading" ] } , { "url": "https://doi.org/10.1186/s13059-020-02181-2", "doi": "10.1186/s13059-020-02181-2" , "cito": [ "citesAsRecommendedReading" ] } , { "url": "https://doi.org/10.1186/s13287-025-04166-z", "doi": "10.1186/s13287-025-04166-z" , "cito": [ "describes" ] } , { "url": "https://doi.org/10.1038/sdata.2018.29", "doi": "10.1038/sdata.2018.29" , "cito": [ "obtainsBackgroundFrom" ] } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }