{ "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/2024/08/07/cito-updates.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/10.59350/8c1e7-8yp77", "url": "https://chem-bla-ics.linkedchemistry.info/2024/08/07/cito-updates.html", "title": "CiTO updates: Wakefield and WikiPathways", "content_html": "

This summer I am trying to finish up some smaller projects that I did not have time for to finish, with\nmixed successes. I am combing this with a nice Dutch staycation, and I already cycled in\nOverijssel and in south-west Friesland\nand learning about their histories.\nBut this post is about an update on my Citation Typing Ontology use cases. And I have to say,\na mention by Silvio Peroni is pretty awesome, thanks!

\n\n

First, the bad news. I still did not get around to the following to tasks I have. First, I need to write up a\nstep-by-step guide how to create CiTO nanopublications\nand matching draft article. Second, I still need to work out how to update the JATS workflow for\nCiTO annotation in BioHackrXiv.

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Wakefield

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Let’s first start with a dataset. Peroni mentioned a study they did (10.1007/S11192-021-04097-5)\ninto why the famous Wakefield paper\n(doi:10.1016/S0140-6736(97)11096-0) is cited. They published\ntheir data set on Zenodo (doi:10.5281/zenodo.13166142) with CCZero,\nso I imported it into Wikidata. Well, at least the citations\nof articles already in Wikidata. I used a Bacting (doi:10.21105/joss.02558)\nscript and it actually was quite short.\nIn the end, this added some 500 new citation intentions to Wikidata, now at almost 2000.\nThis is also the third dataset with explicit CiTO intention annotations (see also\nthis post).

\n\n

This is what the CiTO section of the Wakefield paper\nin Scholia (doi:10.1007/978-3-319-70407-4_36)\nnow looks like:

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WikiPathways

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A second thing I want to show is a potentional CiTO intention annotation dataset. Almost two years ago\nAlex Pico started a new WikiPathways\nfeature as part of the new website (doi:10.1093/NAR/GKAD960)):\na list of citations to specific pathways\n(in WikiPathways). Alex’ setup is fully automated and using PubMed Central\nand find mentions in figure captions:

\n\n

Beyond citations to previous WikiPathways journal articles, we have identified 1228 mentions of a total of 582\nunique WikiPathways pathway model identifiers, e.g. WP4846, in PubMedCentral articles over the past 13 years.

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The file format is a pretty basic YAML file:

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Additional mentions are found in the main text and tables in the article. These are not always picked up.\nThese can be added manually. Over the past months and the past two weeks particularly, I have been adding\nadditional mentions, not listed yet. We now passed 1500 mentions but I cannot easily give the other\nstatistics.

\n\n

BTW, anyone can add these citations with the ‘edit’ pencil and some Microsoft GitHub editing (but\nas far as I am concerned, please feel free to also just mention the paper on the\nWikiPathways Community Forum):

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So, in the next few days I plan to do two things: 1. generate RDF for the YAML file and make that part of the\nmonthly WikiPathways RDF release; 2. extract citations and\noffer this back to the OpenCitations project; and, 3. add the citations\ninto Wikidata. Of course, all with cito:usesDataFrom :)

\n\n

There is a fourth things that I am still thinking about. I can also use the above data the annotation\ncitations to the WikiPathways papers if they also mention a WikiPathways identifier as cito:usesDataFrom,\nbut I cannot fully oversee the implications of that. What do you think?

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References

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Agrawal, A., Balcı, H., Hanspers, K., Coort, S. L., Martens, M., Slenter, D. N., Ehrhart, F., Digles, D., Waagmeester, A., Wassink, I., Abbassi-Daloii, T., Lopes, E. N., Iyer, A., Acosta, J. M., Willighagen, L. G., Nishida, K., Riutta, A., Basaric, H., Evelo, C. T., … Pico, A. R. (2023). WikiPathways 2024: next generation pathway database. Nucleic Acids Research, 52(D1), D679–D689. https://doi.org/10.1093/nar/gkad960 CrossRef Scholia
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Heibi, I., & Peroni, S. (2020). Methodology data of “A qualitative and quantitative citation analysis toward retracted articles: a case of study” [Dataset]. Zenodo. https://doi.org/10.5281/ZENODO.13166142 CrossRef Scholia
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Heibi, I., & Peroni, S. (2021). A qualitative and quantitative analysis of open citations to retracted articles: the Wakefield 1998 et al.’s case. Scientometrics, 126(10), 8433–8470. https://doi.org/10.1007/s11192-021-04097-5 CrossRef Scholia
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Nielsen, F. Å., Mietchen, D., & Willighagen, E. (2017). Scholia, Scientometrics and Wikidata. In Lecture Notes in Computer Science (pp. 237–259). Springer International Publishing. https://doi.org/10.1007/978-3-319-70407-4_36 CrossRef Scholia
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Wakefield, A., Murch, S., Anthony, A., Linnell, J., Casson, D., Malik, M., Berelowitz, M., Dhillon, A., Thomson, M., Harvey, P., Valentine, A., Davies, S., & Walker-Smith, J. (1998). RETRACTED: Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children. The Lancet, 351(9103), 637–641. https://doi.org/10.1016/s0140-6736(97)11096-0 CrossRef Scholia
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Willighagen, E. (2021). Bacting: a next generation, command line version of Bioclipse. Journal of Open Source Software, 6(62), 2558. https://doi.org/10.21105/joss.02558 CrossRef Scholia
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", "summary": "This summer I am trying to finish up some smaller projects that I did not have time for to finish, with mixed successes. I am combing this with a nice Dutch staycation, and I already cycled in Overijssel and in south-west Friesland and learning about their histories. But this post is about an update on my Citation Typing Ontology use cases. And I have to say, a mention by Silvio Peroni is pretty awesome, thanks!", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/wakefieldCitations.png", "date_published": "2024-08-07T00:00:00+00:00", "date_modified": "2024-08-07T00:00:00+00:00", "tags": ["cito","wikipathways","wikidata"], "_references": [ { "url": "https://doi.org/10.1016/S0140-6736(97)11096-0", "doi": "10.1016/S0140-6736(97)11096-0" } , { "url": "https://doi.org/10.21105/JOSS.02558", "doi": "10.21105/JOSS.02558" } , { "url": "https://doi.org/10.1007/978-3-319-70407-4_36", "doi": "10.1007/978-3-319-70407-4_36" } , { "url": "https://doi.org/10.5281/ZENODO.13166142", "doi": "10.5281/ZENODO.13166142" } , { "url": "https://doi.org/10.1093/NAR/GKAD960", "doi": "10.1093/NAR/GKAD960" } , { "url": "https://doi.org/10.1007/S11192-021-04097-5", "doi": "10.1007/S11192-021-04097-5" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }