{ "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/2022/08/01/biology-acps-lipids-cheminformatics-and.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/ab2rj-qdg37", "url": "https://chem-bla-ics.linkedchemistry.info/2022/08/01/biology-acps-lipids-cheminformatics-and.html", "title": "Biology, ACPs, lipids, cheminformatics, and Dagstuhl", "content_html": "

Already 3 months ago I visited Dagstuhl for the second time. The weather was much better than in the January right before\nthe start of the pandemic. The first I attended the Computational Metabolomics meeting, with the focus From Cheminformatics to Machine Learning, one\nof the things we concerned ourselves with was how to do computation with compound classes (see\nSection 3.6 and\nthis online book). We know how to handle\nSMILES and we know how to the substructure searching with SMARTS, but what if you have compound classes or lipid classes? Biology is a greasy business.

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From a WikiPathways there is additional complexity, with modified proteins involved in lipid metabolism, the acyl-carrier\nproteins. They look like this, and the R group is a protein:

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We have quite a few of them in WikiPathway and they also show up in ChEBI (and likely\nReactome), LIPID MAPS, and\nKEGG.

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During this years Dagstuhl we used up one session to continue working on it (report pending). Part of the results is that\nWikidata (see doi:10.7554/eLife.52614 and\ndoi:10.7554/eLife.70780) now has a property for CXSMILES.\nCDK 2.0 (doi:10.1186/s13321-017-0220-4) already supported CXSMILES and the above image is actually created with\nCDK Depict (thx to John!).

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So, that means I can now start adding all those ACPs to Wikidata :) Here’s hexadecanoyl-[acp]\n(or this Scholia page):

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References

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Rutz, A., Sorokina, M., Galgonek, J., Mietchen, D., Willighagen, E., Gaudry, A., Graham, J. G., Stephan, R., Page, R., Vondrášek, J., Steinbeck, C., Pauli, G. F., Wolfender, J.-L., Bisson, J., & Allard, P.-M. (2022). The LOTUS initiative for open knowledge management in natural products research. eLife, 11. https://doi.org/10.7554/elife.70780 CrossRef Scholia
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Waagmeester, A., Stupp, G., Burgstaller-Muehlbacher, S., Good, B. M., Griffith, M., Griffith, O. L., Hanspers, K., Hermjakob, H., Hudson, T. S., Hybiske, K., Keating, S. M., Manske, M., Mayers, M., Mietchen, D., Mitraka, E., Pico, A. R., Putman, T., Riutta, A., Queralt-Rosinach, N., … Su, A. I. (2020). Wikidata as a knowledge graph for the life sciences. eLife, 9. https://doi.org/10.7554/elife.52614 CrossRef Scholia
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Willighagen, E. L., Mayfield, J. W., Alvarsson, J., Berg, A., Carlsson, L., Jeliazkova, N., Kuhn, S., Pluskal, T., Rojas-Chertó, M., Spjuth, O., Torrance, G., Evelo, C. T., Guha, R., & Steinbeck, C. (2017). The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching. Journal of Cheminformatics, 9(1). https://doi.org/10.1186/s13321-017-0220-4 CrossRef Scholia
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", "summary": "Already 3 months ago I visited Dagstuhl for the second time. The weather was much better than in the January right before the start of the pandemic. The first I attended the Computational Metabolomics meeting, with the focus From Cheminformatics to Machine Learning, one of the things we concerned ourselves with was how to do computation with compound classes (see Section 3.6 and this online book). We know how to handle SMILES and we know how to the substructure searching with SMARTS, but what if you have compound classes or lipid classes? Biology is a greasy business.", "date_published": "2022-08-01T00:00:00+00:00", "date_modified": "2022-08-01T00:00:00+00:00", "tags": ["cdk","chebi","dagstuhl","epilipidnet","kegg","wikipathways","lipidmaps","metabolomics","smiles","wikidata","cxsmiles"], "_references": [ { "url": "https://doi.org/10.7554/ELIFE.52614", "doi": "10.7554/ELIFE.52614" } , { "url": "https://doi.org/10.7554/ELIFE.70780", "doi": "10.7554/ELIFE.70780" } , { "url": "https://doi.org/10.1186/S13321-017-0220-4", "doi": "10.1186/S13321-017-0220-4" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }