Resource Identification Initiative

RII

Looking to get RRIDs for your paper (scicrunch.org/resources)

The Resource Identification Initiative is underway and shows no sign of stopping. We invite publishers, editors, authors, biocurators, librarians, resource provides, and vendors to participate.

Authors can participate by adding RRIDs to their papers, go to scicrunch.org/resources

The Resource Identifiers (RRIDs) are in the published literature; publications currently reporting RRIDs can be found in Google Scholar or PubMed

The Resource Identification Initiative (#RII) is designed to help researchers sufficiently cite the key resources used to produce the scientific findings reported in the biomedical literature. A diverse group of collaborators are leading the project, including the Neuroscience Information Framework and the Oregon Health & Science University Library, with the support of the National Institutes of Health and the International Neuroinformatics Coordinating Facility.

Resources (e.g. antibodies, model organisms, and software projects) reported in the biomedical literature often lack sufficient detail to enable reproducibility or reuse. For example, catalog numbers for antibody reagents are infrequently reported, and the version numbers for software programs used for data analysis are often omitted. This has been called out as a serious enough problem by the NIH to introduce new guidelines for Rigor and Transparency for almost all awards in starting in May of 2016. 

These guidelines argue for authentication of key research resources, and transparency of how they are reported.

RII

The Resource Identification Initiative aims to enable resource transparency within the biomedical literature through promoting the use of unique Research Resource Identifiers (RRIDs). In addition to being unique, RRID’s meet three key criteria, they are:

  1. Machine readable.
  2. Free to generate and access.
  3. Consistent across publishers and journals.

The first step in this project was to test the feasibility of the system for a limited set of resources: antibodies, model organisms (mice, zebrafish, flies) and tools (i.e. software and databases) in the biomedical literature. Authors publishing in participating journals were asked to provide RRID's for their resources. RRID's will be drawn from:

To make it easy for authors to find the appropriate RRID's and to format their citations, we have created the Resource Identification Portal, where authors can search across all of sources from a single location.

In addition to facilitating reproducibility and reuse, the inclusion of RRID citations in the literature allows resource providers, funders and others to better track usage and impact. Ultimately, we believe that the outcome of the pilot phase showed:

  • The need for better reporting of materials and methods to promote reproducible science.  Proper resource identification is a step towards this goal.
  • The need for a cultural shift in the way we write and structure papers. We must recognize the increasing dominant model of interacting with the literature through automated agents; therefore, the conventions we adopt should be tailored towards greater machine-processability.
  • The need for a cultural shift in the way we view the literature. The literature is not only a source of papers for people to read, but a connected set of data: observations and claims in biomedicine that span journals, publishers, and formats. The synthesis of information from the literature and other sources requires universal machine access to key entities.

The pilot project was an outcome of a meeting held at the NIH on Jun 26th, 2013.  A draft report from the meeting is available. We are working with commercial partners, tools builders and others in the FORCE11 community to provide a set of interfaces that will allow authors to access the data set acquired in various ways that will demonstrate the power of this approach.  We hope the Resource Identification Initiative will be a small step towards improving scholarly communication and scientific reproducibility.

Please see this guide if you are interested in participating.  For an overview of the project visit the FAQ.


ENDORSE THIS PROJECT

Relevant publications

Bandrowski et al. (2015) The Resource Identification Initiative: A cultural shift in publishing.

   Co-Published: Journal of Comparative Neurology [10.1002/cne.23913], Brain and Behavior [10.1002/brb3.417], F1000 Research [10.12688/f1000research.6555.2], and Neuroinformatics [10.1007/s12021-015-9284-3].

 

Vasilevsky et al.  (2013) On the reproducibility of science: unique identification of research resources in the biomedical literature  Peer J.

Another reason why we are doing this:  Faulty Antibodies Continue to Enter US and European Markets, Warns Top Clinical Chemistry Researcher

Helsby et al (2013) Reporting research antibody use: how to increase experimental reproducibility. F1000 Research

Biocompare:  Taking Steps Towards Scientific Reproducibility

Group Events
Working Group Participation

Comments

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...

 

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...

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...

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!*

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

Great quote from a blog post by Joseph Esposito that describes our aim in the RRID project and why we're seeing such growth:

 

"What we need are not new systems but new services. Services are not top-down comprehensive solutions to all the problems (and some of the merits) of scholarly communications but activities that address specific needs...

"What all of these things have in common is that they did not set out to change the entire world but to improve one piece of it."

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.

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