{ "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/2006/12/06/chemoblogs-2.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/gwy1n-1sc04", "url": "https://chem-bla-ics.linkedchemistry.info/2006/12/06/chemoblogs-2.html", "title": "Chemo::Blogs #2", "content_html": "

Because no one picked up my Chemo::Blogs suggestion, I will now\nofficially claim the blog series title. However, unlike the original Bio::Blogs series,\nI will not summarize interesting blogs, but just spam you with websites I recently marked as\ntoblog on del.icio.us.

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Semantics and Text Mining

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Evan Prodromou wrote about RDFa vs microformats.\nThe latter are commonly used in enhancing blog semantics , and\nfor example used by PostGenomic.com. While RDFa is more explicit, e.g. by using\nnamespaced markup, we have to wait until XHTML2 to see it working. I do not think chemists are using tags a log yet, but let me\npropose the following microformats: 1/CH4/h1H4 and\nmethane. Standard JavaScripts and CSS scripts will then do the rest. (Think: addressing newlines,\nauto googling-for-inchi, etc).

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The reason why using microformats is interesting, is text mining, of various kinds. Whether it is setting up a molecule-article\nlink database, or find hot molecules in blogspace ,\nadding semantics will help tools like OSCAR3 to mine chemistry .\nSome time ago OTMI was proposed by Nature ,\nand they now set up a dedicated web site to explain there view on text mining.\nZack Rosen has a good idea why RDF Semantic web research isn’t working.

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Blogspace

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There are a few new chemistry blogs I want to mention (and already added to Chemical blogspace ):\nChemBark, lirico which has an interesting\nchemoinformatics section, and The Curious Wavefunction.\nWorth reading indeed.

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Pierre’s YOKOFAKUN deserves a paragraph of his own. He recently blogged about\nbio2rdf which provides an RDF interface to biochemical knowledge\nvia Life Science Identifiers (LSID), OBOEdit\nwhich is a Java-based ontology editor, and Amadea\nwhich is a Taverna- and KNIME-like tool for setting up UNIX pipes.

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Online EMBL Symposium

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A few EMBL PhD students are having the First Online EMBL PhD Symposium (catchy name, or … ;)\nAnyway, discussions are held on IRC, and it has a rather interesting Web2.0 session. All\nmedia is available on the website but requires registration right now.\nAfter the conference it will become open access to all. Jean-Claude contributed\nThe UsefulChem Project: Open Source Chemistry Research using Blogs and Wikis to the\nParticipants’ Contributions section, and I had\na poster on Distributing molecular information over the Internet, discussing CMLRSS, blog aggregators, CML and other things.\nThe IRC session was logged and is available here.

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Literature

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Finally, I want to mention three recent articles. First one is a recent write up by Bourne and Friedberg about\nTen Simple Rules for Selecting a Postdoctoral Position (DOI: 10.1371/journal.pcbi.0020121).\nWith the end of my current postdoc position nearing, rather useful reading. Some time ago I blogged about a\nNew open access journal Source Code for Biology and Medicine ,\nand the journal is now up and running. Details can be read in the first editorial (DOI: 10.1186/1751-0473-1-1).\nThe third article I would like to mention is Scientific Software Development Is Not an Oxymoron by Baxter\n(DOI: 10.1371/journal.pcbi.0020087), though I do not think it has new insights.

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OK, this was a rather lengthy write up, but really needed to clean up my toblog section :)

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References

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Baxter, S. M., Day, S. W., Fetrow, J. S., & Reisinger, S. J. (2006). Scientific Software Development Is Not an Oxymoron. PLoS Computational Biology, 2(9), e87. https://doi.org/10.1371/journal.pcbi.0020087 CrossRef Scholia
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Bourne, P. E., & Friedberg, I. (2006). Ten Simple Rules for Selecting a Postdoctoral Position. PLoS Computational Biology, 2(11), e121. https://doi.org/10.1371/journal.pcbi.0020121 CrossRef Scholia
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Peterson, L. E., & Ifeachor, E. C. (2006). Welcome to Source Code for Biology and Medicine. Source Code for Biology and Medicine, 1(1). https://doi.org/10.1186/1751-0473-1-1 CrossRef Scholia
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", "summary": "Because no one picked up my Chemo::Blogs suggestion, I will now officially claim the blog series title. However, unlike the original Bio::Blogs series, I will not summarize interesting blogs, but just spam you with websites I recently marked as toblog on del.icio.us.", "date_published": "2006-12-06T00:00:00+00:00", "date_modified": "2025-02-16T00:00:00+00:00", "tags": ["blog","rdf","textmining","cb","rdfa"], "_references": [ { "url": "https://doi.org/10.1371/journal.pcbi.0020121", "doi": "10.1371/journal.pcbi.0020121" } , { "url": "https://doi.org/10.1186/1751-0473-1-1", "doi": "10.1186/1751-0473-1-1" } , { "url": "https://doi.org/10.1371/journal.pcbi.0020087", "doi": "10.1371/journal.pcbi.0020087" } ], "authors": [ { "name": "Egon Willighagen", "url": "https://orcid.org/0000-0001-7542-0286" } ] } ] }