SciCrunch

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SciCrunch is a collaboratively edited knowledge base about scientific resources. It is a community portal for researchers and a content management system for data and databases. It is intended to provide a common source of data to the research community and the data about Research Resource Identifiers (RRIDs), which can be used in scientific publications. After starting as a pilot of two journals in 2014, by 2022 over 1,000 journals have been using them and over half a million RRIDs have been quoted in the scientific literature. [1] In some respect, it is for science and scholarly publishing, similar to what Wikidata is for Wikimedia Foundation projects. Hosted by the University of California, San Diego, SciCrunch was also designed to help communities of researchers create their own portals to provide access to resources, databases and tools of relevance to their research areas [2]

Contents

Research Resource Identifiers

Research Resource Identifiers (RRID) are globally unique and persistent. [3] They were introduced and are promoted by the Resource Identification Initiative. [3] Resources in this context are research resources like reagents, tools or materials. [3] [4] An example for such a resource would be a cell line used in an experiment or software tool used in a computational analysis. The Resource Identification Portal (https://scicrunch.org/resources) was created in support of this initiative and is a central service where these identifiers can be searched and created. [3] [5] These identifiers should be fully searchable by data mining unlike supplementary files, and can be updated to new versions as basic methodology changes over time.

Format for RRID citations

The recommendation for citing research resources is shown below for key biological resources:

The Resource Identification Portal lists existing RRIDs and instructions for creating a new one if an RRID matching the resource does not already exist.

Features of RRIDs

Description: Each RRID contains an ID, a type, a URL, and a name. There are hundreds of other attributes but most are specific to the type, for example antibody type RRIDs include an attribute called clonality, denoting whether the reagent is monoclonal or polyclonal, while cell lines have an attribute of "parental cell line" denoting the origin of the cell line being described.

RRID Citations: RRIDs denote those research resources that have been used in the conduct of a study. They are not intended to be casual citations. RRIDs that have been used in scientific papers have been mined from the literature using both automated tools [6] and semi-automated tools thanks to a partnership with Hypothes.is. The data that defines which paper cites a particular RRID is usually available on the resolver page for that RRID, for example: https://scicrunch.org/resolver/CVCL_0038 shows the list of 44 papers (as of April 11, 2023) that have used this cell line in research. Each reference will show how authors have used the RRID by including a short snippet of the sentence in which the resource is defined by authors.

External Resolver Services for RRIDs: Name to thing resolver from the California Digital Library can resolve any RRID using the following pattern https://n2t.net/[RRID] example https://n2t.net/RRID:NXR_1049

The Identifiers.org resolver can also resolve any RRID using the following pattern https://identifiers.org/RRID/[RRID] example https://identifiers.org/RRID/RRID:NXR_1049

Institutions and publishers recommending use of RRIDs

A number of publishing houses, initiatives, and research institutions encourage using SciCrunch‘s RRIDs: Common Citation Format Article in Nature, [7] Cell Press, eLife, FORCE11, Frontiers Media, [8] GigaScience, [9] MIRIAM Registry, [10] NIH, [11] PLOS Biology and PLOS Genetics . [12]

See also

Related Research Articles

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A Uniform Resource Identifier (URI) is a unique sequence of characters that identifies a logical or physical resource used by web technologies. URIs may be used to identify anything, including real-world objects, such as people and places, concepts, or information resources such as web pages and books. Some URIs provide a means of locating and retrieving information resources on a network ; these are Uniform Resource Locators (URLs). A URL provides the location of the resource. A URI identifies the resource by name at the specified location or URL. Other URIs provide only a unique name, without a means of locating or retrieving the resource or information about it; these are Uniform Resource Names (URNs). The web technologies that use URIs are not limited to web browsers. URIs are used to identify anything described using the Resource Description Framework (RDF), for example, concepts that are part of an ontology defined using the Web Ontology Language (OWL), and people who are described using the Friend of a Friend vocabulary would each have an individual URI.

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<span class="mw-page-title-main">Digital object identifier</span> ISO standard unique string identifier for a digital object

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<span class="mw-page-title-main">MIRIAM Registry</span>

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<span class="mw-page-title-main">FORCE11</span> Non-profit organisation to enhance research publishing and communication

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References

  1. ↑ Bandrowski, Anita (2022). "A decade of GigaScience: What can be learned from half a million RRIDs in the scientific literature?". GigaScience. 11. doi:10.1093/gigascience/giac058. ISSN   2047-217X. PMC   9197678 . PMID   35701373.
  2. ↑ Jeffrey, Grethe; Anita, Bandrowski; Davis, Banks; Christopher, Condit; Amarnath, Gupta; Stephen, Larson; Yueling, Li; Ibrahim, Ozyurt; Andrea, Stagg; Patricia, Whetzel; Luis, Marenco; Perry, Miller; Rixin, Wang; Gordon, Shepherd; Maryann, Martone (2014). "SciCrunch: A cooperative and collaborative data and resource discovery platform for scientific communities". Frontiers in Neuroinformatics. 8. doi: 10.3389/conf.fninf.2014.18.00069 .
  3. 1 2 3 4 Bandrowski, Anita; Brush, Matthew; Grethe, Jeffery S.; Haendel, Melissa A.; Kennedy, David N.; Hill, Sean; Hof, Patrick R.; Martone, Maryann E.; Pols, Maaike; Tan, Serena; Washington, Nicole; Zudilova-Seinstra, Elena; Vasilevsky, Nicole (19 November 2015). "The Resource Identification Initiative: A cultural shift in publishing". F1000Research . 2. 4 (134): 134. doi: 10.12688/f1000research.6555.2 . PMC   4648211 . PMID   26594330.
  4. ↑ "What is a Resource?". scicrunch.org. SciCrunch. Retrieved 11 April 2023.
  5. ↑ "Resource Identification Portal". scicrunch.org. SciCrunch. Retrieved 11 April 2023.
  6. ↑ Ozyurt (2016). "Resource Disambiguator for the Web: Extracting Biomedical Resources and Their Citations from the Scientific Literature". PLoS One . 11 (1): e0146300. Bibcode:2016PLoSO..1146300O. doi: 10.1371/journal.pone.0146300 . PMC   5156472 . PMID   26730820.
  7. ↑ Singh Chawla, Dalmeet (29 May 2015). "Researchers argue for standard format to cite lab resources". Nature. doi:10.1038/nature.2015.17652. S2CID   211730637.
  8. ↑ "Frontiers Author Guidelines". Frontiers. Retrieved 19 April 2016.
  9. ↑ "Technical Note | GigaScience | Oxford Academic". academic.oup.com. Retrieved 2019-07-15.
  10. ↑ "identifiers.org". Data collection: RRID. Retrieved 18 April 2016.
  11. ↑ "NIDA supports SciCrunch and RRIDs in making research resources visible in science". FORCE11. 2016-03-07. Retrieved 18 April 2016.
  12. ↑ "Introducing the Research Resource Identification Initiative at PLOS Biology & PLOS Genetics". PLOS Biologue. 29 January 2015.
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