Identifying research resources should be easy

Anita Bandrowski, UCSD

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. 2011

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)…

…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, PeerJ, 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 partnersLed 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…

Resource IDs from NIF aggregated databases

•A single portal for authors

• >10 databases• One search interface• Simple directions• Prominent “Cite This” button

•Uniform format for citation across publishers

•Help desk for authors

RII Portal

http://scicrunch.com/resources

Current Progress• >150 articles have

appeared to date• 23 journals• >650 RRID’s

•3 removed by typesetting

•95% correct•14% false negative rate

• thousands of antibodies added from vendors, >200 added by individuals

• >90 software tools/databases were added to tool registry

Database available at: https://www.force11.org/node/5635

Chemicon – out of business, >8 yr

Millipore – just joined Merck, URL

still works

Millipore / Chemicon not a company

Authors cite ID properly

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1.0

Post-PilotPre-Pilot

Antibodies Organisms Tools

Increased identifiability of resources after the Resource Identification Initiative Pilot

Update of Vasilevsky et al, PeerJ, 2013

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

Utopia Tools

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

What Can YOU Do?

– Authors: Use IDs in the methods section of next paper. scicrun.ch/resources *it is really easy!*

– Reviewers: You are ‘super beings’, use your status to improve the literature!

– Antibody Vendors: Register your tools! Make it easy for authors to cite you in a uniform format. Display the “proper citation” format proudly on the tool home page.

– Editors: easy to join the RII, download a sample letter from Force11, modify and send to authors.

– Central instructions to authors have been updated at Springer and Elsevier, we are working on Wiley. Any help appreciated with others.

Questions or Complaints: abandrowski@ucsd.edu