SciCrunch is a collaboratively edited

knowledge base In computer science, a knowledge base (KB) is a set of sentences, each sentence given in a knowledge representation language, with interfaces to tell new sentences and to ask questions about what is known, where either of these interfaces migh ...

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. In some respect, it is for science and scholarly publishing, similar to what

Wikidata Wikidata is a collaboratively edited multilingual knowledge graph hosted by the Wikimedia Foundation. It is a common source of open data that Wikimedia projects such as Wikipedia, and anyone else, are able to use under the CC0 public domain ...

is for

Wikimedia Foundation The Wikimedia Foundation, Inc. (WMF) is an American 501(c)(3) nonprofit organization headquartered in San Francisco, California, and registered there as foundation (United States law), a charitable foundation. It is the host of Wikipedia, th ...

projects. Hosted by the

University of California, San Diego The University of California, San Diego (UC San Diego in communications material, formerly and colloquially UCSD) is a public university, public Land-grant university, land-grant research university in San Diego, California, United States. Es ...

, SciCrunch was also designed to help communities of researchers create their own portals to provide access to resources,

database In computing, a database is an organized collection of data or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and a ...

s and tools of relevance to their research areas

Research Resource Identifiers

Research Resource Identifiers (RRID) are globally unique and persistent. They were introduced and are promoted by the Resource Identification Initiative. Resources in this context are research resources like reagents, tools or materials. An example for such a resource would be a

cell line An immortalised cell line is a population of cells from a multicellular organism that would normally not proliferate indefinitely but, due to mutation, have evaded normal cellular senescence and instead can keep undergoing division. The cells ...

used in an experiment or

software tool A programming tool or software development tool is a computer program that is used to software development, develop another computer program, usually by helping the developer manage computer files. For example, a programmer may use a tool called ...

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. These identifiers should be fully searchable by

data mining Data mining is the process of extracting and finding patterns in massive data sets involving methods at the intersection of machine learning, statistics, and database systems. Data mining is an interdisciplinary subfield of computer science and ...

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: * Antibody: Millipore Cat# MAB377 (Lot) RRID:AB_2298772 * Model organism: NXR Cat# 1049, RRID:NXR_1049 * Cell line: Coriell Cat# GM03745, RRID:CVCL_1H60 * Plasmids: pMD2.G plasmid, RRID:Addgene_12259 * BioSamples: female without diabetes, HPAP, Cat# HPAP-066, RRID:SAMN19842595 * Tools: CellProfiler Image Analysis Software, (version or date) RRID:SCR_007358 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 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 The California Digital Library (CDL) was founded by the University of California in 1997. Under the leadership of then UC President Richard C. Atkinson, the CDL's original mission was to forge a better system for scholarly information management ...

can resolve any RRID using the following pattern https://n2t.net/ RIDexample https://n2t.net/RRID:NXR_1049 The Identifiers.org resolver can also resolve any RRID using the following pattern https://identifiers.org/RRID/ RIDexample https://identifiers.org/RRID/RRID:NXR_1049

Institutions and publishers recommending use of RRIDs

A number of publishing houses, initiatives, and

research institution A research institute, research centre, or research organization is an establishment founded for doing research. Research institutes may specialize in basic research or may be oriented to applied research. Although the term often implies natural ...

s encourage using SciCrunch‘s RRIDs: Common Citation Format Article in Nature,

Cell Press Cell Press is an all-science publisher of over 50 scientific journals across the life, physical, earth, and health sciences, both independently and in partnership with scientific societies. Cell Press was founded and is currently based in Cambri ...

eLife ''eLife'' is a not-for-profit, peer-reviewed, open access, scientific journal, science publisher for the Biomedicine, biomedical and life sciences. It was established at the end of 2012 by the Howard Hughes Medical Institute, Max Planck Society, ...

FORCE11 FORCE11 is an international coalition of researchers, librarians, publishers and research funders working to reform or enhance the research publishing and communication system. Initiated in 2011 as a community of interest on scholarly communicatio ...

Frontiers Media Frontiers Media SA is a publisher of peer-reviewed, open access, scientific journals currently active in science, technology, and medicine. It was founded in 2007 by Kamila and Henry Markram. Frontiers is based in Lausanne, Switzerland, with off ...

GigaScience ''GigaScience'' is a peer-reviewed scientific journal that was established in 2012. It covers research and large data-sets that result from work in the biomedical and life sciences. The editor-in-chief is Scott Edmunds. Originally, the journal was ...

, MIRIAM Registry, NIH, ''

PLOS Biology ''PLOS Biology'' is a monthly peer-reviewed scientific journal covering all aspects of biology. Publication began on October 13, 2003. It is the first journal published by the Public Library of Science. The editor-in-chief is Nonia Pariente. In ...

'' and '' PLOS Genetics''.

References

External links