Persuading a community to deposit Open Data

Typed in support of a community that cares passionately into Arcturus

I recently blogged about how a community wanted access to raw experimental data:

They begged the authors, database, publishers, etc. to ensure that data was published as soon as the publication appeared.

Here’s the reply from the database. It gives a balanced account of how it requires continual effort to achieve routine deposition of effort. They outline the key forces: the community, the journal/editors, the funders. The good news is that in favourable cases the process has speeded up considerably – we can measure in years not decades. And we all agree that it’s not trivial to do this. Communities are resistant. But the process is autocatalytic – the more frequently we see a community adopting Open Data, the more rapidly the other communities will be encouraged and learn from this. And we believe it’s possible to create useful general guidelines – there is nothing special about protein data.

Read it carefully and replace ${cryoEM} by your own discipline. Try “proteomics”. If you don’t know about this, read the next blog.

Subject: Re: electron microscopy: where open access fails
From: Cathy Lawson cathy {- dot -} lawson {- at -} RUTGERS {- dot -} EDU
Date: 2010-05-21

Dear Filip, CCP4BB, 3DEM, and PDB-L list members,

Thank you for your enthusiastic showing of community support for mandatory deposition of cryoEM maps to EMDB and for their timely release.

The two year hold is available to EMDB depositors for just one practical reason: it encourages deposition of maps that we would probably otherwise not be getting at all (and those experiments would thus never be falsifiable). Until journals and major funding agencies make deposition and immediate release mandatory, we have to compromise. A large number of petition signatures ( ) will certainly help us to solidify our case.

It is easy to forget that it was not until 1989 (17 years after the PDB began collecting X-ray structures) that community-set guidelines were published for X-ray crystallography coordinate deposition, and several more years before the journals required deposition as a prerequisite for publication. Structure factor deposition only became mandatory in 2008. These policies emerged from cooperative action by the community of experimentalists and interestingly included a petition that was led by Fred Richards. The same process will be effective for the EM community.


The team

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