DataCite Metadata Schema 4.6 includes RRIDs!

The DataCite Metadata Working Group. (2024) just released the new version of the DataCite Metadata and one of the things that it includes is RRIDs.

DataCite Metadata Schema Documentation for the Publication and Citation of Research Data and Other Research Outputs. Version 4.6. DataCite e.V. https://doi.org/10.14454/mzv1-5b55

Why should someone include an RRID in their DataCite record?

Even though data is fast becoming a first class citizen in research, academic databases are not yet on par with journals when it comes to data citations. The RRID relatedIdentifier element will give databases, which have an RRID, a metadata element that will enable them to assert who they are when releasing a DOI for a dataset.

Do DOIs not have a place to store the Database, already?

Yes and no, some databases like SPARC or Dryad, have a name that is unique to these projects and their datasets are findable by searching for this name, but other databases like the ODC-Sci and ODC-TBI (open data commons for spinal cord injury and traumatic brain injury) are simply listed as being from UC San Diego along with about 50 of their friends from earth sciences to biomedicine, which is true but not very specific.

The RRID project has been tracking databases, like SPARC and ODC-Sci, for over a decade but did not track the datasets associated with these databases, so the update to the DataCite metadata schema is a first in a set of steps to better bring these bits of information together enabling the database and the data set to both be first class citizens among research products.

Understanding RRID and ROR for Facilities

This blog is cross posted on RRIDs.org and ROR blog

Authors: Anita Bandrowski (RRID) and Amanda French (ROR)

In the rapidly evolving landscape of academic research, clear identification of entities such as research outputs, people, organizations, and resources is crucial. What about cases where it isn't clear which persistent identifier to use for a given entity? This blog post explores the difference between "core facilities" in RRID and "facilities" in ROR and provides guidance for those who run facilities on how to effectively use these identifiers.

What is RRID and what is its scope? 

RRIDs help identify a wide variety of resources which are inputs to experiments, especially biomedical experiments. Examples of resources identified by RRID:

  • Antibodies 

  • BioSamples

  • Cell lines 

  • Core facilities

  • Databases

  • Instruments (capital equipment)

  • Organisms 

  • Plasmids 

  • Reagents

  • Software


RRIDs started in 2014 as an agreement between 25 journal editors to improve how research resources, especially antibodies, are cited in the scientific literature. The infrastructure has been supported in the FAIR Data Informatics Lab at the University of California at San Diego and SciCrunch Inc, a company devoted to improving scientific literature. RRIDs.org has recently become a stand-alone not-for-profit entity, enabling sustainability. The RRID registry at scicrunch.org currently includes nearly 25,000 records, including around 3,000 facilities.

What is ROR and what is its scope? 

ROR IDs help identify research organizations, defined as "any organization that is involved in research," including organizations that produce, fund, facilitate, manage, and publish research as well as organizations that educate or employ researchers. Examples of research organizations identified by ROR: 


  • Archives

  • Colleges and universities

  • Companies that fund or conduct research

  • Government agencies and units that fund or conduct research

  • Hospitals and healthcare centers

  • Laboratories

  • Nonprofits and non-governmental organizations that fund or conduct research

  • Private foundations that fund research

  • Research facilities

  • Research institutes

  • Research libraries

  • Scholarly publishers

  • Zoos


ROR is an initiative jointly supported and managed by Crossref, DataCite, and the California Digital Library that makes it easy to disambiguate institution names and connect research organizations to researchers and research outputs. ROR was launched in 2019 after three years of consultations with working groups and stakeholders, developed to solve the problem of identifying organizations in an open and community-driven way. The ROR registry currently includes nearly 110,000 active records and is currently widely adopted by many essential scholarly systems. 

Definitions of Facilities for both RRID and ROR 

 

As you can see above, RRID includes a resource type for "core facilities," and ROR includes an organization type "facility." Despite this apparent similarity, the definitions for "core facilities" in RRID and "facilities" in ROR differ quite a bit, and indeed there is very little overlap between  core facilities in RRID and facilities in ROR. Let’s look now at how RRID and ROR define "core facility" and “facility” and at some examples of each.

What are “core facilities” in RRID?

Core facilities are centralized resources within universities that offer access to instruments, technologies, and expert services. These semi-autonomous units are essential for scientific and clinical investigators, enabling them to conduct cutting-edge research without the need for individual investment in expensive equipment or staff. 

Core facilities have joined forces and created a society called the Association of Biomolecular Resource Facilities (ABRF), which began as a society for US biomedical facilities but now encompasses international facilities from many disciplines. The ABRF Core Marketplace is the listing of member Core Facilities that is primarily used to advertise Core services. One issue that has come up for Cores is the lack of proper citation of the facilities and the tremendous waste of time that searching the literature takes from each Core. 

The ABRF Core Marketplace joined the RRID initiative as a partner and now lists RRIDs on each active Core listing, gathering data about Core usage from the RRID efforts, search of the PubMedCentral database as well as the Core directors. “RRIDs allow our cores to be uniquely identified and many of our members push their users to use RRIDs to cite / acknowledge their facilities” explains Nate Herzog, the Core Marketplace director. As of this writing, the ABRF Core Marketplace maintains 1597 active facility profiles, 576 of which have been cited by RRID. 

Some active core facilities with RRIDs include the following: 

  • New York University School of Medicine Langone Health Microscopy Laboratory Core Facility (RRID:SCR_017934)

  • Salk Institute Razavi Newman Integrative Genomics and Bioinformatics Core Facility (IGC) (RRID:SCR_014842)

  • Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility (RRID:SCR_017801)

These core facilities with RRIDs do not have corresponding ROR IDs, but the parent organizations do: 

What are “facilities” in ROR?

ROR’s list of organization types includes a value for “facility,” defined as “A specialized facility where research takes place, such as a laboratory or telescope or dedicated research area.” There are currently over 11,000 organizations of the type “facility” in ROR. 

Facilities in ROR include the following: 

These facilities in ROR do not have corresponding RRIDs, reflecting the broader nature of the definition of “facility” in ROR as well as ROR’s history of comprehensive coverage of non-US and non-biomedical organizations. Facilities in ROR are usually organizations like national laboratories that may be loosely associated with a university but are not dependent on it.


What are the main differences between "core facilities" in RRID and "facilities" in ROR? 


RRID identifies core facilities because they can be considered as "inputs to experiments," especially when the main contribution of the core facility is to provide researchers with access to particular instruments. University-based core facilities are typically funded by individual grants, and in many cases those are instrument-related grants intended to bring a capability to a certain university. These are typically large instruments that are made available to multiple individual laboratories in the department or university. The success of the core facility depends on the usage of the core resources, the publication of scientific work based on the data produced at the core facility, and on the successful interactions between core facility staff and local investigators. Because these facilities are grant-driven, an accounting of impact typically centers on counting papers that core facilities / instruments have been acknowledged in. RRIDs help core facilities better identify the manuscripts that need to be accounted for as they measure their impact.


In the majority of cases, these core facilities are not in scope for ROR because they are subsections or service offerings at a university instead of being functionally separate organizations in the way that hospitals, national laboratories, or large research institutes are. Core facilities offer researchers access to resources such as large instruments, and the researchers who use the core facility often acknowledge this contribution in their published research outputs, as explained above, but the researchers do not give the core facility as an affiliation when they publish datasets and/or journal articles. One of the primary uses of ROR is to help organizations track research outputs by contributor affiliation. 


This difference can be seen by looking at a sample article [published in 2022 in the journal Leukemia by Baeten et al.](https://doi.org/10.1038/s41375-021-01491-z) The authors are affiliated with research organizations that can be identified by ROR IDs, including The University of Chicago Medicine Comprehensive Cancer Center (https://ror.org/042wftp98).  

Author affiliations of researchers for the article https://doi.org/10.1038/s41375-021-01491-z, best tracked with ROR 

In the same paper, the authors also acknowledge support from the DNA Sequencing and Genotyping Facility Core, also known as the University of Chicago Functional Genomics Core Facility, identified by RRID:SCR_019196. 

Acknowledgements of support from core facilities in the article https://doi.org/10.1038/s41375-021-01491-z, best tracked with RRID


In short, then, RRIDs help track core facility acknowledgements while ROR IDs help track contributor affiliations. 

Let's look now at how to use RRID and ROR. 

How to use RRID and ROR

How to use RRIDs

RRIDs are usually added to the main text of the manuscript; they are present in materials or resource tables (STAR Table example), in the methods section text (see example), or in the acknowledgement section (many core facilities are cited this way). This enables the core owner, and any robot (or undergraduate student) to easily extract the fact that this manuscript is associated with this resource or core facility. Being part of the JATS standard means that publishers will pull these identifiers into article metadata for you, at some point, but we are not holding our breath until that happens. Based on the hard work of robots and undergraduate students, RRID pages on both the RRID and Core Marketplace sides list the papers associated with each Core Facility, owners of facilities can also help to fill out this data, for example https://n2t.net/RRID:SCR_019195

Using RRIDs to track papers associated with the University of Alberta Faculty of Medicine and Dentistry Flow Cytometry Core Facility (RRID:SCR_019195)

ORCID records also accept RRIDs, enabling data to be harvested from or sent to an individual researcher’s ORCID profile, which means that analysts can examine ORCID data for RRIDs. RRIDs are proposed for inclusion in the next DataCite metadata schema, which means that one day analysts will also be able to look for RRIDs in DataCite data. 

How to use ROR

ROR is “infrastructure for infrastructure,” meaning that ROR is meant to be directly incorporated into software applications or added to scholarly metadata by information professionals rather than being used by individual researchers or by facility administrators. ROR offers both a REST API and a downloadable dataset for use by developers in their applications, and those who register DOIs with Crossref or DataCite can also include ROR IDs in DOI metadata. Typically, a ROR-enabled system will build a ROR-powered lookup into forms so that a user can simply search for the name of their organization and select it without ever seeing or using the ROR ID. Research outputs such as journal articles and datasets can then be tracked by all kinds of different ROR-enabled systems, including OpenAlex, the Web of Science, Crossref, and DataCite Commons. 

DataCite Commons uses the ROR ID to enable tracking of datasets associated with the National High Magnetic Field Laboratory (https://ror.org/03s53g630).

ROR is the preferred organization identifier for contributor affiliations in ORCID, DataCite, and Crossref and is used in DOI metadata for many item types, including journal articles, datasets, projects, instruments, software, data management plans, and grants.

Recommendations for Facilities

If you are managing a facility, it’s important to adopt a strategy that incorporates either a ROR ID, an RRID, or both. Here are our recommendations. 

  1. University-based core facilities: Obtain an RRID. RRIDs will enhance the visibility of your research and allow for proper attribution in research outputs. To request an RRID simply go to the RRID website and fill out a form (3 fields are required for the initial step). You will direct the curator to look at your core facility webpages and we will in turn ask you to also register with CoreMarketplace (one click option is coming soon!). Curation will provide a set of instructions for how to use your RRID and we will start tracking papers citing your core as soon as the record is approved. 

  2. Other facilities: Obtain a ROR ID. If your facility has multiple parent organizations or is frequently used as an affiliation to identify research outputs (e.g., in contributor affiliations or dataset attributions) without reference to its parent organizations, first check to see if your facility is already in ROR, and if not, request a ROR ID. A ROR ID enables disambiguation from your parent organization(s) while preserving the connection, allowing for proper attribution and impact tracking.

  3. Educate researchers about RRID: Inform researchers about the importance of using RRIDs and encourage them to include RRIDs in their publications for accurate representation of the resources used. Your acceptance letter will include the pointers from a survey from cores that implemented RRIDs successfully. 

  4. Choose systems that use ROR: Check to see if the tools and platforms used within your facility to manage and track your activities use ROR, and if not, ask the provider to integrate ROR (see more in the FAIR Facilities Report). 

Conclusion

The use of persistent identifier systems like RRID and ROR is essential for the effective management and recognition of research facilities. Implementing these identifiers will not only streamline operations but also foster collaboration and transparency in research. Using these identifiers can help facilities of various kinds enhance their visibility, track their impact more effectively, and contribute to the larger academic community.

Perhaps they don't hear this a lot, but thank you, Internal Revenue Service!

RRIDs have been recognized as a proper 501(s)(3) organization this week.

What is the 501(c)(3)?

According to the IRS, organizations described in section 501(c)(3) are commonly referred to as charitable organizations. Organizations described in section 501(c)(3), other than testing for public safety organizations, are eligible to receive tax-deductible contributions in accordance with Code section 170.

What does it mean for RRIDs?
While RRIDs have been incorporated into many guidelines, instructions to authors, and other policy documents, they have been held back from being fully accepted at least by some boards by the lack of legal clarity around them.

RRIDs may now also begin to solicit grants or tax deductible donations as an entity separate from UCSD, or Force11, if the board decides that this is desirable. This non-for-profit organization now owns RRIDs.

Does this mean you will now need to buy a cookie to get your RRIDs?
No, the organization holds RRIDs in trust so that they can be freely and openly available for reuse by the community.

Retraction watch - Misspelled Cell lines and how to prevent them

Thanks to Jennifer Byrne and Retraction Watch for highlighting a very important topic of reproducibility, misspelling of reagent and resource names. As Dr. Byrnes points out, these ghost cell lines take a life of their own, most likely, as they are shared between labs. This makes it impossible to check for authenticity of the cell line and is associated with significant mistakes in the literature.

To combat this, Byrnes suggests that all papers using cell lines, check the cell line names with the authority, Cellosaurus, and add the RRID to each cell line used, that way the information about the cell line is accurate.

We could not agree more, thank you for highlighting how RRIDs can help clean up the scientific literature.

https://retractionwatch.com/2024/03/11/misspelled-cell-lines-take-on-new-lives-and-why-thats-bad-for-the-scientific-literature/

SciScore and the Karger Vesalius innovation award

Vesalius Innovation Award

by Karger Publishers

"From the third time on, it's tradition!"- True to this principle, Karger Publishers is pleased to invite innovative companies with a focus on Open Science and Health Sciences to participate in the 3rd Vesalius Innovation Award in 2022 once again.

Eponym Surgeon Andreas Vesalius not only revolutionized anatomy when he published De Humanis Corporis Fabrica in 1543. His work also took typography and illustration to a new level, laying the foundation for an entirely new view of the human body for many generations to come.

Fast forward to 2022, Health Sciences publishing is ready for a new revolution. The movement towards Open Research and the increased use of digital technologies in healthcare fundamentally change the way researchers, doctors, and patients create and consume knowledge.

For the further development of the award, this year the focus for participating startups will be expanded to include "Open Science", which further reflects the innovative spirit of Andreas Vesalius.

Our Finalists

The last weeks were very exciting for the Vesalius Innovation Award team as well as for the members of the Jury, since the five finalists who will now be benefitting from the mentoring program had to be chosen.

All participants were amazed by the high quality of the applications, which made the selection process pleasantly difficult, but led to very fruitful discussions within the decision-making committee.

We are delighted that we can now present the five finalists.

alviss.ai develops AI software to assist scientists and publishers in the scientific article reviewing process. Our software provides a toolkit for users to optimize any article and streamline the publication process.

ImageTwin is the solution to detect manipulations and duplications in figures of scientific articles. By comparing the figures with a database of existing literature, problematic images will be identified within seconds for all relevant image types, including blots, microscopy images, and light photography.

Prophy believes that fair, transparent and efficient peer-review lies at the foundation of all good scientific research. As an organisation founded by scientists for science, they use Artificial Intelligence to power automated expert finder, delivering independent reviewers who can review any manuscript from any discipline, ensuring you can trust in the science you read.

SciScore is a scientific content checker / validation tool that verifies common rigor criteria (NIH, MDAR, ARRIVE) and research resources (antibodies, cell lines, organisms). SciScore uses text mining techniques to perform this critical validation in minutes, providing a report to the editors, reviewers, or authors about criteria that have and have not been addressed.

scientifyRESEARCH is an open access, curated and structured research funding database to connect researchers with research funding information. Our database covers global funding across all disciplines and all career stages.

https://www.karger.com/company/innovation/vesalius-innovation-award

FASEB Journals Now Provide Researchers with SciScore Tool to Improve Rigor and Reproducibility

FASEB has a new tool available for researchers to improve the rigor and reproducibility of science submitted to FASEB journals. An automated tool, SciScore, is now integrated into the journals’ submission system, and provides key recommendations and practical steps researchers can take to improve the rigor and reproducibility of their reported science.

“As part of our mission to advance health and well-being by promoting research and education in biological and biomedical sciences, FASEB has long demonstrated a commitment to scientific integrity,” says Darla Henderson, PhD, Director of FASEB Open Science and Research Integrity. “Rigor and reproducibility are a core component of scientific integrity and integrating the SciScore tool into our submission and peer review system provides instant feedback directly to the researcher outlining practical steps they can take to improve reporting.”

SciScore is an automated text-mining tool that evaluates the methods section of scientific articles and checks compliance against recommendations, requirements, and best practices for rigor and reproducibility. The tool generates for researchers both an overall score and a detailed report that provides guidance on potential improvements. FASEB has included the tool in their submission and peer review process as a support tool for authors, available for use at submission and again prior to publication.

“We are very excited to be able to collaborate with our FASEB colleagues and really hope that we can be of service to the authors.” says Anita Bandrowski, CEO of SciCrunch, the company that built SciScore. “At the end of the day, checking and verifying little things like whether an antibody includes enough information to find the reagent is fairly tedious and authors can miss something. However, that missing bit of information can really scuttle another researcher's project, so we hope that these little reminders to make the manuscript better at publication will improve the overall quality of the FASEB journals.” 

Henderson adds “Research integrity and quality are at the center of everything we do. By taking a slightly different approach, giving researchers direct access to the tool, the report, and the score at both initial submission and again pre-publication, we are empowering the community with resources to better understand rigor and reproducibility issues and to enact their own change, much in the same way we give researchers resources to improve data sharing and reuse through our recently launched DataWorks! initiative. FASEB will also be able to review aggregated scores over time and assess how our community is improving in this key metric for research integrity, helping us identify and solve additional researcher needs as we move together towards an open science world.”

https://stagingfaseb.citrodigital.biz/journals-and-news/latest-news/faseb-journals-provide-researchers-with-sciscore-tool-to-improve-rigor-and-reproducibility

OpenBehavior adopts RRIDs

The RRID Initiative by OpenBehavior and SciCrunch

The OpenBehavior project received support from the National Science Foundation in January 2021. There are three main goals for the initial funding period: (1) create a database of open-source tools used in behavioral neuroscience research and issue Research Resource IDentification (RRID) for all projects featured on the OpenBehavior website, (2) initiate a repository of video recordings for common neuroscience tasks and community conversations on video analysis, and (3) host training sessions on the use of open-source hardware and software at conferences such as the annual Society for Neuroscience meeting.

The first goal of the project has been achieved this summer due to hard work of Marty Isaacson, a senior majoring in Neuroscience at American University and working in the Laubach Lab, and Anita Bandrowski and Edyta Vieth from SciCrunch.

Full article: https://edspace.american.edu/openbehavior/2021/08/05/rrid-initiative/

Research Square Launches Beta Testing for SciScore Automated Assessment Tool

The SciScore tool is now being offered to Research Square preprint authors. The tool detects RRIDs, it verifies them, it also detects sentences where RRIDs should be and attempts to suggest RRIDs if it can find a catalog number. Please see the press release.

https://www.sspnet.org/community/news/research-square-launches-beta-testing-for-sciscore-automated-assessment-tool/

RRIDs are now part of the MDAR Checklist

The MDAR checklist has been announced:

https://www.cos.io/blog/minimal-reporting-standards

The checklist includes RRIDs for antibodies, cell lines, and organisms. https://osf.io/bj3mu/

This checklist is well accepted by authors:

http://crosstalk.cell.com/blog/testing-the-materials-design-analysis-reporting-mdar-checklist

The checklist is now required by Science publications:

https://blogs.sciencemag.org/sciencehound/2018/11/09/towards-minimal-reporting-standards-for-life-sciences/

https://science.sciencemag.org/content/367/6473/5.full

MedTech News: SciScore’s Innovative Solution Supports Pre-clinical Research Reproducibility

Boston’s MedTech news finds the story about the RRID compliance tool, SciScore intriguing:

https://massachusettsnewswire.com/medtech-news-sciscores-innovative-solution-supports-pre-clinical-research-reproducibility-44125/

SAN DIEGO, Calif., Nov 22, 2019 (SEND2PRESS NEWSWIRE) — SciScore announces the release of its innovative solution, the first and only working application of its kind, in support of the pre-clinical scientific research community’s pursuit of reproducibility and transparency.

“Finding the cure for any medical ailment facing our society, costs money. And, rightly so, the public has great expectation that the money spent on research will advance healthcare,” says Anita Bandrowski, a neuroscience researcher at the University of California, San Diego and CEO of SciScore. “This tool makes it easier for researchers to focus on the work-at-hand by indicating when, or if, something was overlooked or omitted in the process of reporting the research in a manuscript.”

In January 2016, the National Institute of Health (NIH) introduced new grant review guidelines that focused on four key areas of reproducibility and transparency. This move changed the way in which grants are awarded today. “It remains to be seen in time but it’s possible that NIH changed the business of pre-clinical medical research for the better, and for good,” Bandrowski said.

In conjunction with NIH, many journals have revised author guidelines to direct researchers to include and emphasize elements required for reproducibility and transparency: PLoS, JBC, eLife, AACR, MBoC, and GSA. SciScore is being piloted by the following publishers: Wiley & Sons, NatureResearch, and eLife.

SciScore provides a score and supporting report that is used by the agency, publisher, or individual author to identify if key areas of reproducibility and transparency are addressed in the manuscript. It uses AI and deep learning technology to calculate a score by looking for evidence of randomization, blinded conduct of experiment, sample size estimation, whether sex is included as a biological characteristic, and cell line authentication or contamination. It also detects any resource ambiguity, like a mislabeled or unidentified cell line.

An author may improve a score by adding information that may be missing or correcting information that is obscure. The manuscript submitted for analysis is removed from the cloud server almost immediately after scoring, keeping information secure and private.

For more information, visit http://sciscore.com/.

About SciScore:

SciScore (SciScore.com) is an application developed by SciCrunch Inc. (scicrunch.com) supported by the Small Business Innovation Research (SBIR) program grants R43OD024432 and R44MH119094.