Maryann E. Martone, Ph. D.Professor of Neuroscience, University of California, San

Diego

The Resource Identification Initiative

What research resources are used in biomedical research?◦ Resources = materials, organisms, tools, data,

services

What other published studies used this resource?

Two simple use cases

Our current system for publication and citation makes these two straightforward cases difficult

Access to Materials and Methods sections

Machine Readability◦ “We used the protocol of Martone et al., 1999”◦ Official mouse strain names not meant for computers

SMNΔ7tg/tg:Smn1−/−◦ Non-unique, common names for resources, e.g., Enzyme

Lack of Identifiers ****◦ Author doesn’t supply sufficient information to uniquely identify the

resource No stock numbers, catalog numbers, model numbers, or other uniquely

identifying information

Identifying Resources: Current problems

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)…

What studies used my monoclonal mouse antibody against actin in

humans?

mAb=monoclonal antibody

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

Needed: A 21st century citation 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. J Neuroinflammation 2011, 8:141

Two pre-meetings with editors and publishers◦ Society for Neuroscience◦ NIH: June, 2013

Designed pilot project◦ Entities◦ Procedure◦ Infrastructure

Established working group through FORCE11

Signed up partners

Resource Identification Initiative

Led by: Matt Brush, Nicole Vasilevsky, Anita Bandrowski

And more

https://www.force11.org/Resource_identification_initiative

ID’s should be:◦ Machine processible (i.e.,

unique identifier that resolves to a single resource)

◦ Outside of the paywall◦ Uniform across journals and

publishers Proof of principle

◦ What infrastructure would be needed?

◦ Will authors perform the task?◦ Can authors perform the task?◦ Will it be useful?

Resource Identification Initiative: Goals

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

Pilot Project

Launched February 2014: 3 month commitment

and more…

A single portal for authors◦ RRID’s = accession

numbers from authoritative database

◦ Identifiers were scattered over >10 different databases

◦ Very difficult to find the identifier in some cases

Uniform format for citation

Help desk for authors

Resource Identification Portal

http://scicrunch.com/resources

First results are in the literature

Google Scholar: Search RRID; select since 2014

What studies used…•80 articles have appeared to date•15 journals•Data set being made available to community•>500 RRID’s• 3 removed by

typesetting• 94% correct• 14% false negative

rate•>200 antibodies were added•>75 software tools/databases were added•~50 help requests

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

A resolver service has been created

3rd party tools are being created to provide linkage between resources and papers◦ Utopia prototype◦ Text mining tools

for assigning and validating RRID’s

What can we do with an RRID?

http://scicrunch.com/resolver/RRID:nlx_144509

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 have we learned?

What identifier systems should be used◦ Accession numbers vs DOI’s◦ Entities vs digital objects

Integrate with system for citation of data sets and more complex research objects

What entities should be identified?◦ All reagents and tools?◦ Governance

Machine actionability

Where should we go?

Join the Resource Identification Initiative!◦ Authors: Add ID’s to your papers◦ Journal Editors: It’s not too late to join!◦ Publishers: Use RRID’s to enhance the reading

experience Vendors:

◦ List your products in the Resource Registry◦ Include RRID’s in your catalog◦ Increase transparency!

What can you do now?