Literature DB >> 26589523

The Resource Identification Initiative: A Cultural Shift in Publishing.

Anita Bandrowski1, Matthew Brush2, Jeffery S Grethe3, Melissa A Haendel2, David N Kennedy4, Sean Hill5, Patrick R Hof6, Maryann E Martone3, Maaike Pols7, Serena S Tan8, Nicole Washington9, Elena Zudilova-Seinstra10, Nicole Vasilevsky2.   

Abstract

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to identify the exact resources that are reported or to answer basic questions such as "How did other studies use resource X?" To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and scientific reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (i.e., software and databases). RRIDs are assigned by an authoritative database, for example a model organism database, for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal ( http://scicrunch.org/resources ). RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40 with RRIDs appearing in 62 different journals to date. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are able to identify resources and are supportive of the goals of the project. Identifiability of the resources post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on identifiability of research resources.

Entities:  

Keywords:  Informatics; RRID:nif-0000-25673; RRID:nlx_153866; Reproducibility

Mesh:

Year:  2016        PMID: 26589523      PMCID: PMC5072392          DOI: 10.1007/s12021-015-9284-3

Source DB:  PubMed          Journal:  Neuroinformatics        ISSN: 1539-2791


  14 in total

Review 1.  Power failure: why small sample size undermines the reliability of neuroscience.

Authors:  Katherine S Button; John P A Ioannidis; Claire Mokrysz; Brian A Nosek; Jonathan Flint; Emma S J Robinson; Marcus R Munafò
Journal:  Nat Rev Neurosci       Date:  2013-04-10       Impact factor: 34.870

2.  Cell line cross-contamination: WSU-CLL is a known derivative of REH and is unsuitable as a model for chronic lymphocytic leukaemia.

Authors: 
Journal:  Leuk Res       Date:  2014-05-23       Impact factor: 3.156

3.  Promoting research resource identification at JCN.

Authors:  Anita Bandrowski; Serena Tan; Patrick R Hof
Journal:  J Comp Neurol       Date:  2014-06-01       Impact factor: 3.215

4.  Treatment needs and diagnosis awareness in primary care patients with chronic kidney disease.

Authors:  Natasha J McIntyre; Richard Fluck; Chris McIntyre; Maarten Taal
Journal:  Br J Gen Pract       Date:  2012-04       Impact factor: 5.386

5.  Minimal NF-κB activity in neurons.

Authors:  Samuel J Listwak; Priyanka Rathore; Miles Herkenham
Journal:  Neuroscience       Date:  2013-07-17       Impact factor: 3.590

6.  Enhanced consumption of salient solutions following pedunculopontine tegmental lesions.

Authors:  D A A MacLaren; T Markovic; D Daniels; S D Clark
Journal:  Neuroscience       Date:  2014-10-08       Impact factor: 3.590

7.  The effects of FreeSurfer version, workstation type, and Macintosh operating system version on anatomical volume and cortical thickness measurements.

Authors:  Ed H B M Gronenschild; Petra Habets; Heidi I L Jacobs; Ron Mengelers; Nico Rozendaal; Jim van Os; Machteld Marcelis
Journal:  PLoS One       Date:  2012-06-01       Impact factor: 3.240

8.  Statistical inferences under the Null hypothesis: common mistakes and pitfalls in neuroimaging studies.

Authors:  Jean-Michel Hupé
Journal:  Front Neurosci       Date:  2015-02-19       Impact factor: 4.677

9.  On the reproducibility of science: unique identification of research resources in the biomedical literature.

Authors:  Nicole A Vasilevsky; Matthew H Brush; Holly Paddock; Laura Ponting; Shreejoy J Tripathy; Gregory M Larocca; Melissa A Haendel
Journal:  PeerJ       Date:  2013-09-05       Impact factor: 2.984

10.  Extending the NIF DISCO framework to automate complex workflow: coordinating the harvest and integration of data from diverse neuroscience information resources.

Authors:  Luis N Marenco; Rixin Wang; Anita E Bandrowski; Jeffrey S Grethe; Gordon M Shepherd; Perry L Miller
Journal:  Front Neuroinform       Date:  2014-05-28       Impact factor: 4.081

View more
  18 in total

1.  The Information Sharing Statement Grows Some Teeth.

Authors:  David N Kennedy
Journal:  Neuroinformatics       Date:  2017-04

2.  A proposal for validation of antibodies.

Authors:  Mathias Uhlen; Anita Bandrowski; Steven Carr; Aled Edwards; Jan Ellenberg; Emma Lundberg; David L Rimm; Henry Rodriguez; Tara Hiltke; Michael Snyder; Tadashi Yamamoto
Journal:  Nat Methods       Date:  2016-09-05       Impact factor: 28.547

3.  Contextual fear retrieval-induced Fos expression across early development in the rat: An analysis using established nervous system nomenclature ontology.

Authors:  Anthony J Santarelli; Arshad M Khan; Andrew M Poulos
Journal:  Neurobiol Learn Mem       Date:  2018-05-25       Impact factor: 2.877

4.  The Integrated Islet Distribution Program answers the call for improved human islet phenotyping and reporting of human islet characteristics in research articles.

Authors:  Marcela Brissova; Joyce C Niland; James Cravens; Barbara Olack; Janice Sowinski; Carmella Evans-Molina
Journal:  Diabetologia       Date:  2019-05-15       Impact factor: 10.122

5.  Detection of cell markers from single cell RNA-seq with sc2marker.

Authors:  Ronghui Li; Bella Banjanin; Rebekka K Schneider; Ivan G Costa
Journal:  BMC Bioinformatics       Date:  2022-07-12       Impact factor: 3.307

Review 6.  What's wrong with my experiment?: The impact of hidden variables on neuropsychopharmacology research.

Authors:  Hanna M Butler-Struben; Amanda C Kentner; Brian C Trainor
Journal:  Neuropsychopharmacology       Date:  2022-03-25       Impact factor: 8.294

7.  Integrative biological simulation praxis: Considerations from physics, philosophy, and data/model curation practices.

Authors:  Gopal P Sarma; Victor Faundez
Journal:  Cell Logist       Date:  2017-11-29

8.  A snapshot of 3649 Web-based services published between 1994 and 2017 shows a decrease in availability after 2 years.

Authors:  Ágnes Ősz; Lőrinc Sándor Pongor; Danuta Szirmai; Balázs Győrffy
Journal:  Brief Bioinform       Date:  2019-05-21       Impact factor: 11.622

9.  Antibody Watch: Text mining antibody specificity from the literature.

Authors:  Chun-Nan Hsu; Chia-Hui Chang; Thamolwan Poopradubsil; Amanda Lo; Karen A William; Ko-Wei Lin; Anita Bandrowski; Ibrahim Burak Ozyurt; Jeffrey S Grethe; Maryann E Martone
Journal:  PLoS Comput Biol       Date:  2021-05-27       Impact factor: 4.475

10.  Data Citation in Neuroimaging: Proposed Best Practices for Data Identification and Attribution.

Authors:  Leah B Honor; Christian Haselgrove; Jean A Frazier; David N Kennedy
Journal:  Front Neuroinform       Date:  2016-08-12       Impact factor: 4.081

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.