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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