This document discusses why journals should ask authors to include Research Resource Identifiers (RRIDs) in their manuscripts. RRIDs help answer questions about what antibodies, animals, cell lines, or software tools were used in a study and allow others to find papers that used the same resources. The document notes that RRIDs improve reproducibility by making materials and methods more transparent. It also discusses how RRIDs can help identify problematic resources like contaminated cell lines or antibodies that do not work or are no longer available. The document provides examples of journals that now require RRIDs and how compliance is implemented.

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. 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. What is reproducible science?
Step 1:
Materials
Step 2:
Methods

4. Step 1:
In
Practice

5. How common is this?
Papers are
currently poor at
identifying the
simplest part of
the paper, the
materials used
Vasilevsky 2013

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. RRIDs = Better papers
Bandrowski et al, 2015
Vasilevsky’s
analysis re-run
by Vasilevsky
for RRID pilot;
first 100 papers

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. 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. 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. Do we publish papers with
antibodies that don’t work?

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. Who does this?
Over 200 journals have RRID containing papers
across all major publishers
July 2016
Aug 2016
Oct 2016
Jun 2016

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