http://www.elsevier.com/about/content-innovation/minimal-data-standards

 

Please let us know if this needs to be significantly updated. We seem to be converging on a set of formats.

Thanks to Elena, our press release is live!!!

Elsevier and the Neuroscience Information Framework Work Together to Improve Reporting of Research in Neuroscience Literature!

http://www.elsevier.com/about/press-releases/science-and-technology/else...

 

http://online.wsj.com/article/PR-CO-20131107-910427.html

Thank you Francis Collins for including the work of this group in your thinking about improving reproducibility of pre-clinical research!

http://www.nature.com/news/policy-nih-plans-to-enhance-reproducibility-1...

http://blogs.biomedcentral.com/bmcblog/2014/02/03/the-force-11-resource-...

 

http://www.abc27.com/story/24630272/antibodies-onlinecom-supports-the-re...

http://finance.yahoo.com/news/antibodies-online-com-supports-identificat...

http://www.cbs8.com/story/24630272/antibodies-onlinecom-supports-the-res...

http://www.digitaljournal.com/pr/1719352

http://www.prnewswire.co.uk/news-releases/antibodies-onlinecom-supports-...

http://article.wn.com/view/2014/02/04/antibodiesonlinecom_Supports_the_R...

 

 

http://blog.f1000research.com/2014/01/31/resource-identification-initiat...

http://www.biotechniques.com/multimedia/archive/00231/BTN_A_000114143_O_...

As of yesterday this was true for two papers, now we have 3!

Looks like the Journal of Comparative Neurology and PeerJ contain the first RRIDs to come out. This is a great week!

Looking forward to many more in the coming weeks.

 

My Blog on the subject: http://blog.neuinfo.org/index.php/essays/rrids-are-in-the-wild-thanks-to...

http://onlinelibrary.wiley.com/enhanced/doi/10.1002/cne.23585/

Thanks to 15 journals (and counting) we have reached 100 articles that contain RRIDs.

 

Other statistics:

 # of RRIDs total 630

# of RRIDs that are correct 605

% of RRIDs that are correct 95%

most common research resource is RRID: nif-0000-30467 with 20 papers

   *if you want to know which research resource it is, you are just going to have to go to google scholar and find out!*

http://blogs.plos.org/biologue/2015/01/29/introducing-research-resource-...

Hi All,

Here are the blog and the instructions to authors from Frontiers group.

http://www.frontiersin.org/news/Frontiers_supports_the_Resource_Identifi...

http://www.frontiersin.org/neuroscience/authorguidelines#_ResourceIdenti...

 

You can also retweet this https://twitter.com/Loop_Network/status/573444912810737664

This is a cool benchmark:

We just hit the 50th journal that now contains at least 1 paper with an RRID, doubling the original number of journals that signed up to participate in the pilot.

...and that journal is: Alcohol Clinical Experimental Research.

pubmed.gov/25916839

http://www.nature.com/news/researchers-argue-for-standard-format-to-cite...

 

Best line: One format to rule them all!

Love it, just hope we don't need to be thrown down into lava at some point.

Check out the following

Editorial: http://www.genomebiology.com/2015/16/1/141

Blog: http://blogs.biomedcentral.com/bmcblog/2015/07/23/reproducibility-going/

Check list: http://www.biomedcentral.com/bmcneurosci/authors/instructions/minimum_st...

 

Ok PLoS you are up next ... will you up the anty?

Hi Folks, just saw an independent confirmation from a friend (author who shall remain nameless until her paper is published) that Cell Press is delivering on their promise to add RRIDs to relevant resources.

Woohooo!

Nice piece from Phil, explaining the data commons. http://www.nature.com/nature/journal/v527/n7576_supp/full/527S16a.html "First, each research object in the commons — for example, data, software, narratives or papers — must be uniquely identified, sharable (taking into account privacy issues), and resolvable to its source by using a common identifier." - Agreed!

https://www.faseb.org/Portals/2/PDFs/opa/2016/FASEB_Enhancing%20Research... "...To achieve uniform reporting of research findings, FASEB recommends that investigators, funding agencies, and journals adopt best practices for experiments using antibodies...."

We need to think and digest. How can RII help? http://arxiv.org/abs/1602.02296

Thanks to our friends at NIDA, we have the some rather strongly worded text, supporting RRIDs, now in the inboxes of all current and former NIDA grantees. SciCrunch: A resource for Enhancing Reproducibility Through Rigor and Transparency https://www.force11.org/blog/nida-supports-scicrunch-and-rrids-making-re...

Thanks to Christophe Bernard, spearheading this effort eNeuro, the premier open access journal at the Society for Neuroscience, has started asking for RRIDs. Read all about it: http://eneuro.org/content/3/2/ENEURO.0046-16.2016

Thanks to Colleen Hammer all products are identified with RRIDs on the website and in Material Data Sheets. This is exactly what we need from all manufacturers of products. http://immunostar.com/latest-news/

Thanks to Katharine Miller, RRIDs are discussed along side, BioSharing, DataMed, and CEDAR!

http://bcr.org/content/data%E2%80%99s-identity-crisis-struggle-name-it-d...

Read all about it: Practical steps towards reproducibility:

http://dx.doi.org/10.1016/j.neuron.2016.04.030

 

http://www.nature.com/news/365-days-the-science-events-that-shaped-2015-...

Please take a look at the instructions to authors (oh go on, I know you have never done it before....)

http://submit.elifesciences.org/html/elife_author_instructions.html

"To help promote the identification, discovery, and reuse of key research resources, we encourage you to include Research Resource Identifiers (RRIDs) within the Materials and Methods section to identify the model organisms, cells lines, antibodies, and tools (such as software or databases) you have used (e.g.RRID:AB_2178887 for an antibody, RRID:MGI:3840442 for an organism, RRID:CVCL_1H60 for a cell line, and RRID:SCR_007358 for a tool). The RRID Portal lists existing RRIDs, and instructions for creating a new one if an RRID matching the resource does not already exist."

Instructions to authors at the Journal of Neuroscience have just been updated to include a clear, short instructions for authors 

http://www.jneurosci.org/site/misc/ifa_organization.xhtml

 

http://www.economist.com/news/science-and-technology/21702166-two-studie...

 

Would it not be nice to figure out which software tool was being used in each of those studies so that we could quickly figure out which ones are likely experiencing this 70% false positive rate? Yes, yes it would. Just another reason to use RRIDs!

 

"...Since all the “participants” in these newly conducted trials were, in fact, controls in the original trials, there ought to have been no discernible signal. All would presumably have been thinking about something, but since they were idling rather than performing a specific task there should have been no discernible distinction between those categorised as controls and those used as subjects. In many cases, though, that is not what the analysis suggested. The software spat out false positives—claiming a signal where there was none—up to 70% of the time.

False positives can never be eliminated entirely. But the scientific standard used in this sort of work is to have only one chance in 20 that a result could have arisen by chance. The problem, says Dr Eklund, lies with erroneous statistical assumptions built into the algorithms. And in the midst of their inspection, his team turned up another flaw: a bug in one of the three software packages that was also generating false positives all on its own."

 

http://biomethods.oxfordjournals.org/content/manuscript-preparation#RRID

Welcome to the family Biology Methods and Protocols.

 

Additional protocols:

http://www.genetex.com/web/Protocol/Protocols.aspx

 

 

We have great news about the Endocrinology Society journal

They have updated the instructions to authors as follows, more to come!:

http://press.endocrine.org/page/endoita#mozTocId290874

"Antibody Table

It is the policy of Endocrinology to require authors using antibodies for immunohistochemistry, immunocytochemistry, western blots, immunoblots, immunoneutralization, or related methodology, to submit an Antibody table. This table should be numbered to indicate its position in the sequence of tables in the article (e.g. Table 1). In the Methods section, describe appropriate positive or negative controls, antibody validation, lot number, and provide references. Beginning in September 2016, authors should also ascertain whether the antibody has a Research Resource Identifier (RRID) by consulting the Antibody Registry and include this information, if available, in the Methods section and/or the Antibody table of the original submission. If there is not an RRID, authors are required to register the antibody and obtain one no later than the revision stage of submission. For more information, see the editorial Antibody Validation Requirements for Articles Published in Endocrinology and the Resource Identification Portal.

- See more at: http://press.endocrine.org/page/endoita#mozTocId290874"

This is really exciting, several papers have already come out in this new format. 

It is everything we wanted, transparent, structured, filled with good information for finding materials!

http://dx.doi.org/10.1016/j.cell.2016.08.021

 

http://www.sciencedirect.com/science/article/pii/S009286741631011X

http://www.sciencedirect.com/science/article/pii/S0092867416309953

http://www.sciencedirect.com/science/article/pii/S0092867416309321

 

 

http://us8.campaign-archive2.com/?u=9938fea8603b684592ae3da72&id=9a1fd0e21e

..."The Table allows for linking to reagent databases such as the Resource Identification Initiative’s RRID. In addition, the methods section will have no size limit and, more importantly, will NOT count against a word count. Cell suggests that “[t]he presence of these sections helps authors to report and readers to easily appreciate how the studies follow guidelines from the NIH Rigor and Reproducibility initiative” as well as the ARRIVE and TOP guidelines. "

http://www.eurekalert.org/pub_releases/2016-08/cp-cpt082516.php

"We are emboldened by the opportunity to be pioneers, and to extend what we do best--publishing the highest quality of science--to the methods section"

Nature Methods just published a paper entitled "a proposal for validation of antibodies", by the members of the International Working Group on Antibody Validation. 

The pillars of validation include something near and dear to our hearts here at RII, identification of antibodies, i.e., that RRIDs should be included. 

http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3995.html

Yes, you read this correctly, Thermo Fisher Scientific, one of the biggest antibody companies will validate all products according to the IWGAV outlined standards. 

http://www.businesswire.com/news/home/20160905005488/en/Thermo-Fisher-Sc...

Check out each BioLegend page showing the citation format for each product, using RRIDs! 

This is great news for validation of methods. Thank you BioLegend for helping authors do the right thing. 

http://www.genengnews.com/gen-articles/research-antibody-reproducibility...

 

http://www.ebiotrade.com/newsf/2016-9/201698122024832.htm

 

http://www.labnews.co.uk/interviews/guestbook/antibody-crisis-order-chao...

Update to instructions to authors is working, the first 5 papers are out!

https://wellcomeopenresearch.org/for-authors/article-guidelines/research...

Check out "talkin' immunology"

http://www.biolegend.com/newsdetail/rigor-and-transparency-in-reproducib...

This is the final report from the 2016 Asilomar meeting, which established among many other things, consensus from the antibody validation community including companies and researchers that RRIDs solve one of the validation problems, transparency. 

https://www.gbsi.org/gbsi-content/uploads/2016/12/Workshop-Report_12-15-...

Multiple solutions are needed to improve antibody reproducibility issues according to this article, but all solutions include RRIDs!

http://www.biocompare.com/333120-The-Antibody-Crisis-An-Ongoing-Discussion/

http://biorxiv.org/content/early/2017/02/16/109017

RRIDs are part of the solution, not the percipitate!

Chemistry also dealing with reproducibility and nomenclature problems! Great read!

https://www.chemistryworld.com/news/taking-on-chemistrys-reproducibility...

http://blog.benchsci.com/2017/03/31/reproducibility-in-science-how-prope...

..."An even better citation method that is gaining momentum with scientists was created by the Research Resource Initiative. This initiative was launched with the intention of creating a resource to standardize the citation of biomedical resources based on the references in which they were generated or used."

Thank you PLoS, apparently I completely missed this blog post.

http://blogs.plos.org/plos/2016/09/riding-a-wave-towards-improved-truth-...

Please see instructions to authors!

http://www.fasebj.org/site/misc/rc.xhtml

 

http://www.biotechniques.com/multimedia/archive/00254/Instructions_for_A...