[open-science] PLOS ONE offers Registered Reports

Thu Jan 16 15:18:16 UTC 2020

Peter,

Thanks for your comments. A couple of thoughts/comments: Did you try extracting data from the PDF. Check out the same table in the pdf. It’s not a bitmap. You also asked if other organizations were involved in designing the structure of our preregistrations.  We follow the same conventions as other journals. The final published stage 2 article will look like a conventional Research Article at the journal, there will be no difference and it will be the same article type.

David Knutson
Sr. Communications Manager
651-260-8288

From: Peter Murray-Rust <pm286 at cam.ac.uk>
Sent: Wednesday, January 15, 2020 1:24 AM
To: David Knutson <dknutson at plos.org>
Cc: open-science at lists.okfn.org
Subject: Re: [open-science] PLOS ONE offers Registered Reports

On Tue, Jan 14, 2020 at 10:44 PM David Knutson <dknutson at plos.org<mailto:dknutson at plos.org>> wrote:
PLOS today announced that PLOS ONE<https://journals.plos.org/plosone/> will soon offer a new preregistration article type,<https://www.plos.org/preregistration> Registered Reports.
This is a useful step forward in principle.

However most reports of studies and reviews in the scholarly literature, including PLOS, are not machine-processable or validatable.  (I have looked at the first PLOS article I found and the tables are published as bitmaps doi: https://doi.org/10.1371/journal.pone.0226983.t001  It is important that machines can determine whether a preregistration is compliant and whether the ontology is Open. So I have some technical questions/suggestions:
* are there other bodies (e.g. scientific societies or other publishers) who have been involved in designing the structure and ontology of PLOS preregistrations? Without those we get a plethora of publisher-specific protocols, probably weakly designed.
* is there a published Open ontology/dictionary of terms and data description?
* are there semantic machine-accessible tools for validating subsequent reports against the preregistration ("did they do what they said they would")?
I spend a lot of time writing software to extract data from PDFs and bitmaps because the publication-process destroys most semantic data. It *is* possible to do a proper job as the International Union of Crystallography has done for 30 years with its CIF standard. (https://www.iucr.org/resources/cif)  - disclaimer, I am on the Advisory Ctte. The first step is publicly agreed ontology/metadata which I hope already exists.

--
"I always retain copyright in my papers, and nothing in any contract I sign with any publisher will override that fact. You should do the same".

Peter Murray-Rust
Reader Emeritus in Molecular Informatics
Unilever Centre, Dept. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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