![\"\"](\"/assets/images/doiTagDelicious.png\")
On my way back from the Taverna workshop I visited Nature HQ, as\nIan reported about on Nascent. It was a (too) short\nmeeting, but very nice to meet Euan (finally; he wrote the\npostgenomic.com software which I use for Chemical blogspace),\nJoanna (whom I met in Chicago already, where she had\ntwo \npresentations ,\nand is responsible for Second Nature),\nIan (who works on Connotea,\nand commented on\nmy tagging molecule blog )\nand Ålf (who works on Scintilla) and\nbriefly Timo (who rules them all). BTW, I had a simple but delicious pasta.
\n\nFirst, let me note that if I would have to name a favorite molecule, and it was acetic acid,\nnot ascorbic acid. Reason why it would be my favorite is acetic acid was the first\norganic molecule I put in the Woordenboek Organische Chemie in 1995.
\n\nWe discussed a number of things, regarding the things we do. One of these was tagging molecules. Ian used\nhttp://rdf.openmolecules.net/?info:inchi/InChI=1/CH4/h1H4 instead of http://rdf.openmolecules.net/?InChI=1/CH4/h1H4.\nThe first was not yet picked up by rdf.openmolecules.net but I fixed that.
\n\nWe also discussed linking molecular structures with scientific literature. The discussions in blogspace of this week\nshow that doing that by using computer programs is not appreciated by publishers (see\nhere,\nhere ,\nhere ,\nhere ,\nhere, and\nhere )\n(The publishers seem to prefer to like to send of a PDF to India or China.)
\n\nI proposed that the InChI would be part of the publication, for all molecules mentioned in the article. If a\njournal can require exact bibliography and experimental section formats, they can certainly require InChIs too.\nThere are few programs left which cannot autogenerate an InChI, and the chemists draws the structures anyway.\nHowever, the software used in the editorial process does not support linking InChIs with a PDF (if that software\nwould have been opensource …).
\n\nSo, the best current option seems to be social tagging mechanisms, and this is what we talked about. Just use\nConnotea (or any other service) and tag your molecule with a DOI:
\n\n
and
\n\n![\"\"](\"/assets/images/connoteaTagDelicious1.png\")
This tagging is done manually. No machines involved in that. Nothing the publishers can do about this. No ChemRefer needed.\nBut this will allow us to start building a database with links between papers and molecules, which we badly need. BTW, we will\nnot have to start from scratch. The NMRShiftDB already contains many links, which is open data!
\n\nNow, you might notice the informal semantics of the doi: prefix. That’s something I hereby propose, as it allow\nservices to pick up the content more easily. You might also note the incorrect DOI in Connotea. The reason for\nthat is that Connotea does not yet support a ‘/’ in a tag. I\nreported that problem.