NEUROSCIENCE INFORMATION FRAMEWORK

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The case of the missing research resources

Illuminating dark data, one antibody at a time

Image attributionwww.costaricantimes.com

History

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How much time do you spend tracking down antibodies??

Seems like a waste of timea robot should be able to do this

NIH thought the same, so they tasked the Neuroscience Information

Framework with looking into the feasibility of creating such a robot!

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The problem

Paz et al, J Neurosci, 2010

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Now, go find the antibody

http://www.millipore.com/searchsummary.do?tabValue=&q=gfap Nov 12, 2010

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What

URL?

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Jan 15, 2014

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scicrun.ch/resources Image attribution http://lifeasahuman.com/2011/arts-culture

The Literature

The internet

Classes of problems:• Insufficient data–Which of the 40 antibodies was used in

the paper?

• Time dependency of data– Of the 40 antibodies listed, are there

others that were sold last year that are no longer on the website?

• Vendor transition– If Millipore goes out of business

tomorrow, will anyone be able to reproduce the findings in the paper?

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Our survey• 1 Volume of the Journal of Neuroscience• 8 articles• 106 (95 unique) antibodies were identified• 52 did not contain enough information to

determine the catalog number• a few antibodies were identified with either a

clone number or a catalog number– Clone #’s are not unique

• supplier name and url were available in all but 26

• no antibodies had lot numbers associated

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If we can’t do it, neither can the robot

• Automated text mining tools were not deployed on this problem, because too few antibodies were able to be automatically identified

• We are asking authors to change their ways, instead!

• Almost all antibodies were identified with the company name, city and state, but the information is useless if the goal is to identify the antibody used

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Our solution: the antibodyregistry.org

• Gather all available data from vendors• Assign Unique Identifiers!• Keep unique identifiers stable over

years• Resolve identifiers • antibodyregistry.org/AB_12345

• Consolidate identifiers where possible• Ask authors to use them in papers

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neuinfo.org

Simple interface

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How do you ask authors to change their ways?Image attribution westislandgazette.com

The case of the meanest journal in the world, coincidentally having the lowest retraction rate

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The problem

is general across

multiple resource

types and

disciplines

Vasilevsky et al 2013

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Are we doomed

?

Image attributionwww.sodahead.com

Meet the Urban Lab

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Urban Lab Antibodies

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Urban Lab Antibodies in

Literature

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What can we Learn from the Urban Lab?

Many labs keep track of reagents

Authors don’t think about reagent provenance

gentle reminders?

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Editor’s Meetings 2012/2013 outcomes

Perform a pilot study with researchers, editors and publishers to make key resources more identifiable in the published literatureRequirements:Resources should be identifiable in such a way that they are:1 | Machine readable2 | Are available outside the paywall3 | Uniform across publishers and journals

Current work

1 | Establish Resource Identification in Neuroscience Literature (RINL) Group

2 | Ensure identifiers are available for all model organisms

3 | Establish a single website for obtaining identifiers

4 | Prepare instructions for authors

5 | Perform usability study within RINL group

☐in progress…

http://www.scicrun.ch/resources

antibodyregistry.org

25 Journals

4 publishe

rs1

set of author

guidelines

Start date

February!

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How can I help?

Join/Endorse Force11.org efforthttp://www.force11.org/node/4463

We also have a mailing list for the working group, keep tabs on us.

What does it take to participate?*instructions to authors text and sample

letters to authors available

Outside of the paywall? Will this need to go through major journal

restructuring? *No, RRID in the underutilized keyword field

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