NEUROSCIENCE INFORMATION FRAMEWORK antibodyregistry.org An antibody registry for biological sciences Illuminating dark data, one antibody at a time Image attribution

History antibodyregistry.org

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!

The problem Paz et al, J Neurosci, 2010 antibodyregistry.org

Now, go find the antibody Nov 12, 2010

What URL? antibodyregistry.org

Jan 15, 2014

antibodyregistry.org Image attribution 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? antibodyregistry.org

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

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 antibodyregistry.org

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

neuinfo.org Simple interface

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

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

antibodyregistry.org The problem is general across multiple resource types and disciplines Vasilevsky et al 2013

antibodyregistry.org Are we doomed? Image attribution

antibodyregistry.org Meet the Urban Lab

antibodyregistry.org Urban Lab Antibodies

antibodyregistry.org Urban Lab Antibodies in Literature

antibodyregistry.org What can we Learn from the Urban Lab? Many labs keep track of reagents Authors don’t think about reagent provenance gentle reminders?

Editor’s 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

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…

antibodyregistry.org

25 Journals 4 publishers 1 set of author guidelines Start date February! 25 Journals 4 publishers 1 set of author guidelines Start date February!

antibodyregistry.org Can you help the Resource Identification Initiative? Add antibody identifiers to your papers Press – your website? Join/Endorse Force11.org effort Mirroring Identifiers at ImmPort