{ "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/2006/12/10/including-smiles-cml-and-inchi-in.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/wpaxr-93167", "url": "https://chem-bla-ics.linkedchemistry.info/2006/12/10/including-smiles-cml-and-inchi-in.html", "title": "Including SMILES, CML and InChI in blogs", "content_html": "

The blogs ChemBark and KinasePro have been discussing\nthe use of SMILES, CML and InChI in Chemical Blogspace (with 70 chemistry blogs now!).\nChemists seem to prefer SMILES over InChI, while there is\ninterest in moving towards CML too.\nPeter commented.

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Any incorporation of content other than images and free text requires some HTML knowledge, but this can be rather limited.\nIt is up to us chemoinformaticians to write good documentation on how to do things; so here is a first go.

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Including CML in blogs and other RSS feeds

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I blogged about including CML in blogs \nlast February, and can generally refer to this article published last year: Chemical markup, XML, and the World Wide Web. 5.\nApplications of chemical metadata in RSS aggregators (PMID:15032525,\nDOI:10.1021/ci034244p). Basically, it just comes down to putting the CML code into\nthe HTML version of your blog content, though I appreciate the need for plugins.

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Including SMILES, CAS and InChI in blogs

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Including SMILES is much easier as it is plain text, and has the advantage over InChI that it is much more readable.\nChris wondered in the KinasePro blog on how to tag SMILES, while Paul\ndid the same on ChemBark about CAS numbers.

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Now, users of PostGenomic.com know how to add markup to their blogs\nto get PostGenomic index discussed literature, website and conferences. Something similar is easily done for chemistry\nthings too, as I showed in Hacking InChI support into postgenomic.com \n(which was put on lower priority because of finishing my PhD). PostGenomic.com basically uses microformats, which I\nblogged about just a few days ago in Chemo::Blogs #2 ,\nwhere I suggested the use of <span class=\"chemicalcompound\">asperin</span>.

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And this is the way SMILES, CAS and InChI’s can be tagged on blogs. The <span> element is HTML code to indicate\na bit of similar content in HTML, and can, among many other things, be formatted differently than other text. However,\nthis can also be used to add semantics in a relatively cheap, but accepted, way. [Microformats](http://microformats.org/\n are formalized just by use, so whatever we, as chemistry bloggers, use will become the de facto standard. Here are my suggestions:

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The RDFa alternative

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The future, however, might use RDFa over microformats, so here are the RDFa equivalents:

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which requires you to register the namespace xmlns:chem=\"http://www.blueobelisk.org/chemistryblogs/\" somewhere though.\nFormally, the URN for this namespace needs to be formalized; Peter, would the Blue Obelisk\nbe the platform to do this? BTW, this is more advanced, and currently does not have practical advantages over the use of\nmicroformats.

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References

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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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", "summary": "The blogs ChemBark and KinasePro have been discussing the use of SMILES, CML and InChI in Chemical Blogspace (with 70 chemistry blogs now!). Chemists seem to prefer SMILES over InChI, while there is interest in moving towards CML too. Peter commented.", "date_published": "2006-12-10T00:00:00+00:00", "date_modified": "2024-12-29T00:00:00+00:00", "tags": ["cml","inchi","blog","cb","microformat","rdf","html","rdfa"], "_references": [ { "url": "https://doi.org/10.1021/CI034244P", "doi": "10.1021/CI034244P" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }