{ "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/2007/06/19/quality-of-chemical-database.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/10.59350/49wqj-62k11", "url": "https://chem-bla-ics.linkedchemistry.info/2007/06/19/quality-of-chemical-database.html", "title": "Quality of Chemical Database", "content_html": "

Lately, Chemical blogspace has seen an interesting discussion on the quality of opendata and free chemical database (over\n32 free resources now ), such as the\nNMRShiftDB.org. For example, see Antony’s view on the NMRShiftDB\nand Robien’s analysis.

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Opendata makes such quality assurance possible, and I am happy that the NMRShiftDB was\nexplored like this; the found problems can be reported and corrected. If correcting them upstream is difficult, opendata allows\none to make a better derivative; that’s what opendata is about. For example, BioMeta\n(DOI:10.1186/1471-2105-7-517) took data from KEGG and corrected a lot of molecular\nproblems (like reaction balancing, stereo chemistry, etc).

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I have contributed almost 900 spectra to the NMRShiftDB, and I am sure I may have made a mistake here and there. But my submission is verified\nby a reviewer, and furthermore, users of the database can report inconsistencies via the NMRShiftDB.org website. Now, I have focused on uncommon\nNMR nuclei, like 11B, 195Pt and 29Si (see the stats),\nwhich tend to have only one peak. Nothing much that can go wrong; still, one or two errors were catched by the reviewer.

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Ensuring data quality

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Humans make errors, but not even only when data is entered; they make mistakes checking data too. Nothing much that can\nbe done about that, other than using computers to find patterns. This is exactly what Robien did: he used his software\nwhich implements common patterns to find entries in the database that did not comply to those patterns.

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Automated quality assurance requires a easy to use, machine-readable interface. For example, CMLRSS\n(DOI:10.1021/ci034244p) can be used for running new entries in databases\nagainst known patterns. But other interfaces are most welcome too. Rich recently\ndiscussed the new PUG interface ,\nwhich offers an interface to PubChem.

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German scientists offer a RDF interface to Wikipedia: DBPedia.\nInformal semantic markup in Wikipedia, such as the Infobox template,\nare used to create triples. It’s a shame that the ChemBox\nis not used yet, which would make detecting molecules in blogs \neven easier.

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References

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Apodaca, R. (2007). Hacking PubChem - Learning to Speak PUG. In Front Matter. Front Matter. https://doi.org/10.59350/zwnp1-qy767 CrossRef Scholia
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Apodaca, R. (2007). Thirty-Two Free Chemistry Databases. In Front Matter. Front Matter. https://doi.org/10.59350/jy0f5-7m219 CrossRef Scholia
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Murray-Rust, P., Rzepa, H. S., Williamson, M. J., & Willighagen, E. L. (2004). Chemical Markup, XML, and the World Wide Web. 5. Applications of Chemical Metadata in RSS Aggregators. Journal of Chemical Information and Computer Sciences, 44(2), 462–469. https://doi.org/10.1021/ci034244p CrossRef Scholia
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Ott, M. A., & Vriend, G. (2006). Correcting ligands, metabolites, and pathways. BMC Bioinformatics, 7(1). https://doi.org/10.1186/1471-2105-7-517 CrossRef Scholia
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", "summary": "Lately, Chemical blogspace has seen an interesting discussion on the quality of opendata and free chemical database (over 32 free resources now ), such as the NMRShiftDB.org. For example, see Antony’s view on the NMRShiftDB and Robien’s analysis.", "date_published": "2007-06-19T00:10:00+00:00", "date_modified": "2025-08-10T00:00:00+00:00", "tags": ["opendata","chemistry","pubchem","rdf","nmrshiftdb"], "_references": [ { "url": "https://doi.org/10.1186/1471-2105-7-517", "doi": "10.1186/1471-2105-7-517" } , { "url": "https://doi.org/10.1021/CI034244P", "doi": "10.1021/CI034244P" } , { "url": "https://doi.org/10.59350/jy0f5-7m219", "doi": "10.59350/jy0f5-7m219" } , { "url": "https://doi.org/10.59350/zwnp1-qy767", "doi": "10.59350/zwnp1-qy767" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }