NEUROSCIENCE INFORMATION FRAMEWORK antibodyregistry.org An
antibody registry for biological sciences Illuminating dark data,
one antibody at a time Image attribution
www.costaricantimes.com
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History antibodyregistry.org
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neuinfo.org How much time do you spend tracking down
antibodies?? Seems like a waste of time a 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
antibodyregistry.org
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Now, go find the antibody
http://www.millipore.com/searchsummary.do?tabValue=&q=gfaphttp://www.millipore.com/searchsummary.do?tabValue=&q=gfap
Nov 12, 2010
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What URL? antibodyregistry.org
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Jan 15, 2014
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antibodyregistry.org Image attribution
http://lifeasahuman.com/2011/arts-culture The Literature The
internet
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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? antibodyregistry.org
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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
antibodyregistry.org
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If we cant 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
antibodyregistry.org
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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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antibodyregistry.org How do you ask authors to change their
ways? Image attribution westislandgazette.com
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antibodyregistry.org The case of the meanest journal in the
world, coincidentally having the lowest retraction rate
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antibodyregistry.org The problem is general across multiple
resource types and disciplines Vasilevsky et al 2013
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antibodyregistry.org Are we doomed? Image attribution
www.sodahead.com
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antibodyregistry.org Meet the Urban Lab
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antibodyregistry.org Urban Lab Antibodies
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antibodyregistry.org Urban Lab Antibodies in Literature
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antibodyregistry.org What can we Learn from the Urban Lab? Many
labs keep track of reagents Authors dont think about reagent
provenance gentle reminders?
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Editors Meeting 2012 outcomes Perform a pilot study with
researchers, editors and publishers to make key resources more
identifiable in the published literature Requirements: Resources
should be identifiable in such a way that they are: 1 | Machine
readable 2 | Are available outside the paywall 3 | Uniform across
publishers and journals
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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
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antibodyregistry.org
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25 Journals 4 publishers 1 set of author guidelines Start date
February! 25 Journals 4 publishers 1 set of author guidelines Start
date February!
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antibodyregistry.org Can you help the Resource Identification
Initiative? Add antibody identifiers to your papers Press your
website? Join/Endorse Force11.org effort
http://www.force11.org/node/4463 Mirroring Identifiers at
ImmPort