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chem-bla-ics

chem-bla-ics
Chemblaics (pronounced chem-bla-ics) is the science that uses open science and computers to solve problems in chemistry, biochemistry and related fields.
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SemwebChemistryChimieAnglais
Publié

Mike released Operator 0.8, which picks up RDF (RDFa en eRDF) from HTML pages, and adds actions to it. I blogged earlier about the beta and wrote a script for it for chemical RDFa. At this moment, Chemical blogspace and RDF for Molecular Space (see this blog) are using chemical RDFa to semantically markup molecular information. The new Operator release (download) has one notable API change: it now uses “RDF” as key for semantic information;

BlogChimieAnglais
Publié

Via SciFoo Planet (from Partial immortalization ) I learned about TouchGraph Google (Peter brought it into Chemical blogspace). It’s cool, though not open source. Here’s the touch graph for my blog: As you can see, plenty of blogspot bloggers around me, among which, in purple, Useful Chemistry. Funny thing is, each time I repeat the Google search, the output is different. Oh, and make sure to drag one of the halos around;

InchiSemwebChimieAnglais
Publié

Peter wondered if data should be stored centralized or decentralized, when Deepak blogged about Freebase and Metaweb. Now, I haven’t really looked into these two projects, but the question of centralized versus decentralized is interesting. It’s MySQL versus the world wide web; it’s the PubChem compound ID versus the InChI;

PublishingChemistryInchiChimieAnglais
Publié

Rich blogged about to Never Draw the Same Molecule Twice: Viewing Image Metadata in which he shows his molecular editor outputting images of molecular structure where the connectivity table of structure is embedded in the image. His molecular editor can read the image again, and will automatically pick up the embedded connection table. Noel showed that such can not only be done in Java, but in Python too.

BioinfoExcelChimieAnglais
Publié

Well, no wonder: Excel is meant to be used to process money flows. Anyway, greyarea pointed me to this nice blog item from March 2006. It discusses a 2004 article in BMC Bioinformatics Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics by Barry Zeeberg et al. (DOI:10.1186/1471-2105-5-80). Hence, the importance of semantics and proper markup languages.

ChemistryRdfInchiChimieAnglais
Publié

RDF might be the solution we are looking for to get a grip on the huge amount of information we are facing. microformats, and RDFa, are just solutions along the way, and Gleaning Resource Descriptions from Dialects of Languages (GRDDL) might be an important tool to get the web RDF-ied. One important aspect of RDF is that any resource has a unique URI.