Upload
maryann-martone
View
147
Download
5
Tags:
Embed Size (px)
DESCRIPTION
Presentation on the Resource Identification Pilot Project, an initiative to develop a machine-processable citation system for key research resources used in scientific studies
Citation preview
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?