Tobias Kind has asked (Comment to Nature Protocols: How much can we re-use?) why shouldn’t require chemists to submit data…
Hi Peter,
making chemistry data machine-readable is not the business of the publisher! It’s the business of the chemists themselves and it should be a requirement from editorial boards and reviewers. If chemists have to submit molecular structures and chemical property data before publication (a common fact for modern life sciences – compared to old-style chemistry) there would be no need to run any hamburger to cow algorithm like OSRA, Kekule, CLiDE, ChemOCR or Oscar. Beware(!), these are all sophisticated algorithms but their use could be avoided for new publications if raw data + metadata is directly submitted to a not yet functioning international open data chemistry repository. You can check out GenBank “Many journals require submission of sequence information to a database prior to publication so that an accession number may appear in the paper.” http://www.ncbi.nlm.nih.gov/Genbank/ As long we keep reviewing journals without requesting that molecular structures and metadata and spectra and molecular property data are made publicly available and as long we serve in editorial boards of journals which don’t require submission of original molecule data and other molecular property data in machine readable format its our own fault. All this will be a painful process but it will come; it’s also a process of teaching the young chemists. The upcoming ticket system for chemistry publications requiring a accession number for each publication will be nice topic for the BlueObelisk; Don’t you think so, or is that too radical for youhttp://blueobelisk.sourceforge.net/wiki/index.php/Open_Data_in_Chemistry
Kind regards
Tobias Kind
fiehnlab.ucdavis.edu
No, not too radical at all. Max Planck wrote: Scientific theories don’t change because old scientists change their minds; they change because old scientists die. And that’s the case here.
But I am not radical enough to hasten the death literally, so how do we ensure that old chemists die metaphorically? Note that I don’t want chemistry to die, and it will survive elsewhere – in biology, materials science, neuroscience and even computing. But many chemists are doing a good job of destroying the current edifice with their lack of interest in the current century’s informatics, their closed access publishing, their corralled information which is sold rather than freed, their lack of multidisciplinary collaborations. Of course there are exceptions, but if you look at eScience, publishing, informatics where is mainstream chemistry?
So we’ll devise methods and protocols elsewhere. The biologists have taken over the chemical ontosphere – we use Pubchem and ChEBI, created by and for biosciences. They’ll create the bits of the chemical semantic web they need – and I’ll be happy for that
No, it’s not the role of the publishers to convert data, and I didn’t mean to suggest it. The publishers should be the servants of the community and the community should ask them to police deposition of semantic documents. There is, I think, an interim period when we need messy measures such as converting legacy to show the way forward. OSRA, reverse-hamburgers and the rest are simply to prove the semantics, show the value. We know that all we have to do is invest in authoring tools and require them. Very shortly we’ll let you know what we are doing in that area.