1. NEUROSCIENCE INFORMATION FRAMEWORK scicrun.ch/resources The case of the missing research resources Illuminating dark data, one antibody at a time Image attribution www.costaricantimes.com

2. History scicrun.ch/resources

3. 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! scicrun.ch/resources

4. The problem Paz et al, J Neurosci, 2010 scicrun.ch/resources

5. 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 scicrun.ch/resources

6. What URL? scicrun.ch/resources

7. Jan 15, 2014 scicrun.ch/resources

8. Image attribution http://lifeasahuman.com/2011/arts-culture The Literature The internet

9. 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? scicrun.ch/resources

10. 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 scicrun.ch/resources

11. 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 scicrun.ch/resources

12. 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 scicrun.ch/resources

13. neuinfo.org Simple interface

14. scicrun.ch/resources How do you ask authors to change their ways? Image attribution westislandgazette.com

15. The case of the meanest journal in the world, coincidentally having the lowest retraction rate scicrun.ch/resources

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

17. scicrun.ch/resources Are we doomed? Image attribution www.sodahead.com

18. Meet the Urban Lab scicrun.ch/resources

19. Urban Lab Antibodies scicrun.ch/resources

20. Urban Lab Antibodies in Literature scicrun.ch/resources

21. What can we Learn from the Urban Lab? Many labs keep track of reagents Authors don’t think about reagent provenance gentle reminders? scicrun.ch/resources

22. Editor’s Meetings 2012/2013 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

23. 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

24. antibodyregistry.org

25. 25 Journals 4 publishers 1 set of author guidelines Start date February! 25 Journals 4 publishers 1 set of author guidelines Start date February! scicrun.ch/resources

26. How can I help? Join/Endorse Force11.org effort http://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 scicrun.ch/resources