{ "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/2006/09/08/chemical-archeology-oscar3-to.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/am2k8-ygc58", "url": "https://chem-bla-ics.linkedchemistry.info/2006/09/08/chemical-archeology-oscar3-to.html", "title": "Chemical Archeology: OSCAR3 to NMRShiftDB.org", "content_html": "

Chemical Archeology (see Christoph’s comment) is the\nprocess of extracting chemical information from old journal articles. Some time ago,\nPeter Corbett from the group of Peter Murray-Rust\nvisited the CUBIC to talk to us about\nOscar3 which can do just that. That day, we already\nhooked OPSIN into Bioclipse .

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Oscar3, however, is capable of more than the name2structure of OPSIN (see also\n10.1039/b411033a; it can take a plain text file with an experimental section\nwith details on the synthesis of small organic compounds, and analyze the chemistry in that. This functionality has been\navailable as an RSC authoring tool\nfor some time now (see also 10.1039/b411699m). Unfortunately, what publisher put\nonline (PDF and HTML) is much more difficult to process with Oscar3: those formats are often optimized for display,\nnot for machine processing. The HTML can be cleaned up, but there is no general approach.

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Christoph Steinbeck is going to present at the\nupcoming ACS meeting\nthe use of Oscar3 for extraction of NMR spectra from old journal article, in preperation for submission to the\nNMRShiftDB.org (see the abstract\nof CINF 101).

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Since the full Oscar3 was not hooked into Bioclipse yet, I had some work to do. It took me\nsome time to figure out how to properly configure Oscar3, and what additional things I had to do to clean up the HTML\nused by publishers to get Oscar3 to extract NMR spectra (thanx to PeterC for hints!). I also had to tweak the Oscar3\ncode itself here and there, but that’s what opensource is about :) (Peter, if you are reading this: I have a number\nof patches for the Oscar3 code in bc_oscar;\nlet me know if you’re interested in them.)

\n\n

This is the end result:

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\"\"

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Note especially the hierarchy in the resource navigator on the left. The misc folder contains all the chemistry found in the article. But more importantly is that for six molecules it fully detected he experimental section! For 3-(2-Oxocyclooctanyl)-3-phenylpropan-1-al (InChI=1/C17H22O2/c18-13-12-15(14-8-4-3-5-9-14)16-10-6-1-2-7-11-17(16)19/h3-5,8-9,13,15-16H,1-2,6-7,10-12H2) it derived the molecular structure (with OPSIN), and a few spectra: H-NMR, high-resolution MS and IR.

\n\n

So, if you attend the ACS meeting: make sure to visit Christoph’s CINF 101 presentation!

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References

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Adams, S. E., Goodman, J. M., Kidd, R. J., McNaught, A. D., Murray-Rust, P., Norton, F. R., Townsend, J. A., & Waudby, C. A. (2004). Experimental data checker: better information for organic chemists. Organic &  Biomolecular Chemistry, 2(21), 3067. https://doi.org/10.1039/b411699m CrossRef Scholia
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Townsend, J. A., Adams, S. E., Waudby, C. A., de Souza, V. K., Goodman, J. M., & Murray-Rust, P. (2004). Chemical documents: machine understanding and automated information extraction. Organic &  Biomolecular Chemistry, 2(22), 3294. https://doi.org/10.1039/b411033a CrossRef Scholia
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", "summary": "Chemical Archeology (see Christoph’s comment) is the process of extracting chemical information from old journal articles. Some time ago, Peter Corbett from the group of Peter Murray-Rust visited the CUBIC to talk to us about Oscar3 which can do just that. That day, we already hooked OPSIN into Bioclipse .", "image": "https://chem-bla-ics.linkedchemistry.info/assets/images/oscar1.png", "date_published": "2006-09-08T00:00:00+00:00", "date_modified": "2025-02-16T00:00:00+00:00", "tags": ["oscar","bioclipse","acs","chemistry","textmining","nmrshiftdb"], "_references": [ { "url": "https://doi.org/10.1039/b411033a", "doi": "10.1039/b411033a" } , { "url": "https://doi.org/10.1039/b411699m", "doi": "10.1039/b411699m" } ], "_citations": [ { "url": "https://doi.org/10.1186/1758-2946-3-37", "doi": "10.1186/1758-2946-3-37" , "cito": [ "citesForInformation" ] } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }