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Why should Journals ask fo RRIDs?

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Slide about RRIDs for Journals and Publishers.

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Why should Journals ask fo RRIDs?

  1. 1. Why should Journals ask for RRIDs? It answers two questions: Which antibodies (or mice, cell lines) are used in this paper? What other papers use this antibody? RRIDs are in use for Antibodies, Animals, Cell Lines and Software tools. Questions: Anita Bandrowski PhD. abandrowski@ucsd.edu
  2. 2. Quality of published research is in question Solving quality: mandates and solutions NIH NOT-OD-16-011 Journals RRIDs Societies FASEB Guidelines Non-Profits TOP Guidelines Reproducibility of science is important Transparency in science is achievable
  3. 3. What is reproducible science? Step 1: Materials Step 2: Methods
  4. 4. Step 1: In Practice
  5. 5. How common is this? Papers are currently poor at identifying the simplest part of the paper, the materials used Vasilevsky 2013
  6. 6. Resource IDs from NIF aggregated databases •A single portal for authors •>25 authoritative databases (stock center IDs are RRIDs) •One search interface •Simple directions •Prominent “Cite This” button •Help desk (well used!) • Response time is 1 business day or less One Portal simplifies authors job http://scicrunch.org/resources author searches for an antibody / mouse author copies ”Cite This” text into manuscript Paper is Published
  7. 7. RRIDs = Better papers Bandrowski et al, 2015 Vasilevsky’s analysis re-run by Vasilevsky for RRID pilot; first 100 papers
  8. 8. RRIDs are Persistent Unique IDentifiers 1)  The data set itself and the sources for the data are covered by a CC0 license, that is, the data set is freely available for others to take up should any source fail.  This practice is recommended by Geoffrey Bilder of Cross Ref to ensure that key infrastructure is portable.  
 2)  Unlike DOI’s or PURL’s, which absolutely have to resolve to the entity that they point to, RRIDs reference metadata about physical things in the world. That is, RRID’s only point to metadata about the thing, not the thing itself (mouse, antibody).  Because the RRID’s are in the text next to the snippet of information that identifies them, you would in the future be able to identify the resource and a full set of metadata about them without any special infrastructure just from the literature itself.  As a whole, publishers and libraries are committed to preserving the scientific literature.     3)  We are planning to ensure that copies of landing pages for research resources referenced in the literature are placed in the internet archive.  Should any source disappear, the current resolvers (identifiers.org, CDL’s and SciCrunch’s) can point to these pages. 
  9. 9. When is RRID critical? …78 widely used cell lines that turned out to be overgrown with other cells… Slides presented at SfN: NIH led Rigor and Transparency Session Nov 2016
  10. 10. RRID shows problem resources Is the cell line I am about to publish contaminated? • Comment “Problematic cell line: Contaminated” • Data is derived from ICLAC list of contaminated cell lines, and it is curated / updated by Cellosaurus • Contamination noted in 714 common cell lines Not all vendors report contamination on their website, note ATCC & ECACC do for 1-5c-4
  11. 11. Do we publish papers with antibodies that don’t work?
  12. 12. Instruction to authors: How to authenticate antibodies? • Based on Uhlen et al, 2016 (Nat Methods) • Checking with the antibodyregistry.org • catalog number and clone ID may be different, if RRID is the same = same product • Chose antibodies that that have been validated by manufacturer for your application • Chose antibodies with independent validation: • ENCODE / ScienceExchange • RRID publications • Original manufacturers (in progress of adding this tag) • If no validation data is available, require full validation “discontinued 2016 due to animal welfare concerns” “Originating Manufacturer of this product; Tested applications: WB/ ELISA” “ENCODE PROJECT External validation DATA SET is released” ISO 9001: 2008 and ISO 13485: 2003 Validated by ScienceExchange no validation data or MDS available from vendor Example comments on antibody records:
  13. 13. Who does this?
 Over 200 journals have RRID containing papers across all major publishers July 2016 Aug 2016 Oct 2016 Jun 2016
  14. 14. What does compliance look like in a journal?
 *typesetting instructions in eLife provide links Identifiers.org and CDL’s n2T resolvers back scicrunch resolution services

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