identifying research resources should be easy anita bandrowski, representing the rii team
TRANSCRIPT
Identifying research resources should be easy
Anita Bandrowski, representing the
RII team
A SYSTEM TO IDENTIFY NOT JUST WHO PRODUCED A FINDING, BUT WHAT
PRODUCED IT
Faulty Antibodies Continue to Enter US and European Markets, Warns Top Clinical Chemistry Researcher-Genome Web Daily, October 11, 2013
“…of the findings in the literature about neuronal NF-κB are based on data garnered with antibodies that are not selective for the NF-κB …”
--Herkenham et al.
WHAT STUDIES USED MY MONOCLONAL MOUSE ANTIBODY AGAINST ACTIN IN
HUMANS?
The following antibodies were used for immunoblotting: -actin mAb (1:10,000 dilution, Sigma-Aldrich); -tubulin mAb (1:10,000, Abcam); T46 mAb (specific to tau 404–441, 1:1000, Invitrogen); Tau-5 mAb (human tau 218–225, 1:1000, BD Biosciences) (Porzig et al., 2007); AT8 mAb (phospho-tau Ser199, Ser202, and Thr205, 1:500, Innogenetics); PHF-1 mAb (phospho-tau Ser396 and Ser404, 1:250, gift from P. Davies); 12E8 mAb (phospho-tau Ser262 and Ser356, 1:1000, gift from P. Seubert); NMDA receptors 2A, 2B and 2D goat pAbs (C terminus, 1:1000, Santa Cruz Biotechnology)…
mAb=monoclonal antibody
…SURELY THIS YOU HAVE FOUND A TERRIBLE PAPER, THIS CAN’T BE THE NORM
Hypothesis: Resources in the published literature are not uniquely identifiable
Gather journal articles
5 domains:ImmunologyCell biologyNeuroscienceDevelopmental biologyGeneral biology
3 impact factors:HighMediumLow
84 Journals
238 papers
707 antibodies
104 cell lines
258 constructs
210 knockdown reagents
437 model organisms
Vasilevsky et al, PeerJ, 2013
The problem
is general across
multiple resource
types and
disciplines
Vasilevsky et al, Peer J 2013
RESOURCE IDENTIFICATION INITIATIVE
Two pre-meetings with editors and publishers Society for Neuroscience, 2012 NIH: June, 2013 Society for Neuroscience, 2013
Designed pilot project Entities Procedure Infrastructure
Established working group through FORCE11
Signed up partners Led by: Matt Brush, Nicole Vasilevsky, Anita Bandrowski
And more
https://www.force11.org/Resource_identification_initiative
PILOT PROJECT Authors to identify 3 types of
research resources: Software /databases Antibodies Model organisms
Include RRID in methods section Voluntary for authors Journals did not have to modify
their submission system Journals have flexibility in
implementation. Send request to author at: Submission During review After acceptance
Launched February 2014: 3 month commitment
and more…
RII PORTAL
A single portal for authors >10 databases One search interface Simple directions Big “Cite This”
button Uniform format for
citation Help desk for
authors
http://scicrun.ch/resources
WHAT STUDIES USED… •>100 articles have appeared to date
•15 journals
•630 RRID’s• 3 removed by
typesetting• 95% correct• 14% false negative
rate
•>200 antibodies were added
•>75 software tools/databases were added
Database available at: https://www.force11.org/node/5635
Antibodies Organisms Software0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
0.5423311475409840.593220338983051 0.573247727272727
0.856907894736842 0.848055252635405
0.723577235772358
Identifiability of research resources
Pre Pilot Post Pilot
Fra
cti
on I
denti
fied
An update of Vasilevsky et al.
WHAT CAN WE DO WITH AN RRID?
A resolver service has been created
3rd party tools are being created to provide linkage between resources and papers Utopia prototype ScienceDirect
http://scicrunch.com/resolver/RRID:nlx_144509
WHAT HAVE WE LEARNED?
Authors are willing to adopt new types of citations
Authors were fairly accurate at performing the task
RRID’s resolved by search engines without requiring specialized citation services
Citation drives registration Clear role for repositories as authorities
HOW CAN YOU HELP? Authors: Use IDs in YOUR next paper. At least 100 of your
friends already have. scicrun.ch/resources
Tool Makers: Register your tools! Make authors job easy. Display the proper citation format proudly.
Reviewer: Ask authors to put identifiers in their methods, you know they will do almost anything to get you off their back.
Editors: Still time to join the RII, go to Force11 to download a sample letter to authors.
Publishers: Central instructions to authors have been updated at Springer and Elsevier, where are yours?