Identifying research resources should be easy Anita Bandrowski, representing the RII team.

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?

[email protected]