SciCrunch
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.{{Cite journal |last=Bandrowski |first=Anita |date=2022 |title=A decade of GigaScience: What can be learned from half a million RRIDs in the scientific literature? |url=https://doi.org/10.1093/gigascience/giac058 |journal=GigaScience |volume=11 |doi=10.1093/gigascience/giac058 |issn=2047-217X |pmc=9197678 |pmid=35701373}} 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 {{cite journal|last1=Jeffrey|first1=Grethe|last2=Anita|first2=Bandrowski|last3=Davis|first3=Banks|last4=Christopher|first4=Condit|last5=Amarnath|first5=Gupta|last6=Stephen|first6=Larson|last7=Yueling|first7=Li|last8=Ibrahim|first8=Ozyurt|last9=Andrea|first9=Stagg|last10=Patricia|first10=Whetzel|last11=Luis|first11=Marenco|last12=Perry|first12=Miller|last13=Rixin|first13=Wang|last14=Gordon|first14=Shepherd|last15=Maryann|first15=Martone|title=SciCrunch: A cooperative and collaborative data and resource discovery platform for scientific communities|journal=Frontiers in Neuroinformatics|date=2014|volume=8|doi=10.3389/conf.fninf.2014.18.00069|doi-access=free}}
{{anchor|Research Resource Identifier}}Research Resource Identifiers
Research Resource Identifiers (RRID) are globally unique and persistent.
{{cite journal
| last1 = Bandrowski
| first1 = Anita
| last2 = Brush
| first2 = Matthew
| last3 = Grethe
| first3 = Jeffery S.
| last4 = Haendel
| first4 = Melissa A.
| last5 = Kennedy
| first5 = David N.
| last6 = Hill
| first6 = Sean
| last7 = Hof
| first7 = Patrick R.
| last8 = Martone
| first8 = Maryann E.
| last9 = Pols
| first9 = Maaike
| last10 = Tan
| first10 = Serena
| last11 = Washington
| first11 = Nicole
| last12 = Zudilova-Seinstra
| first12 = Elena
| last13 = Vasilevsky
| first13 = Nicole
| date = 19 November 2015
| version = 2
| title = The Resource Identification Initiative: A cultural shift in publishing
| journal = F1000Research
| volume = 4
| issue = 134
| pages = 134
| pmc = 4648211
| pmid=26594330
| doi = 10.12688/f1000research.6555.2
| doi-access = free
}}
{{anchor|Resource Identification Initiative}}They were introduced and are promoted by the Resource Identification Initiative.
Resources in this context are research resources like reagents, tools or materials.
{{cite web
|url= https://scicrunch.org/resources/about/resource
|title= What is a Resource?
|website= scicrunch.org
|publisher= SciCrunch
|access-date= 11 April 2023
}}
An example for such a resource would be a cell line used in an experiment or software tool used in a computational analysis.
{{anchor|Resource Identification Portal}}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.
{{cite web
|url= https://scicrunch.org/resources
|title= Resource Identification Portal
|website= scicrunch.org
|publisher= SciCrunch
|access-date= 11 April 2023
}}
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:
- 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 {{cite journal |last1=Ozyurt | journal = PLoS One |doi=10.1371/journal.pone.0146300 |title=Resource Disambiguator for the Web: Extracting Biomedical Resources and Their Citations from the Scientific Literature |date=2016 | volume = 11 | issue = 1 | pages = e0146300 | pmid = 26730820 | pmc = 5156472 | bibcode = 2016PLoSO..1146300O | doi-access = free }} 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 =
{{Prose|date=March 2021}}
A number of publishing houses, initiatives, and research institutions encourage using SciCrunch‘s RRIDs:
Common Citation Format Article in Nature,{{cite journal |last1=Singh Chawla |first1=Dalmeet |title=Researchers argue for standard format to cite lab resources |journal=Nature |date=29 May 2015 |doi=10.1038/nature.2015.17652 |s2cid=211730637 }} Cell Press, eLife, FORCE11, Frontiers Media,{{cite web|title=Frontiers Author Guidelines|url=http://home.frontiersin.org/about/author-guidelines#MaterialsandDataPolicies|website=Frontiers|accessdate=19 April 2016}}
GigaScience,{{Cite web|url=https://academic.oup.com/gigascience/pages/technical_note#Preparing%20main%20manuscript%20text|title=Technical Note {{!}} GigaScience {{!}} Oxford Academic|website=academic.oup.com|language=en|access-date=2019-07-15}}
MIRIAM Registry,{{cite web|title=identifiers.org|url=http://identifiers.org/rrid/|website=Data collection: RRID|accessdate=18 April 2016}}
NIH,{{cite web|title=NIDA supports SciCrunch and RRIDs in making research resources visible in science|url=https://www.force11.org/blog/nida-supports-scicrunch-and-rrids-making-research-resources-visible-science|website=FORCE11|accessdate=18 April 2016|date=2016-03-07}}
PLOS Biology and PLOS Genetics.{{cite news |title=Introducing the Research Resource Identification Initiative at PLOS Biology & PLOS Genetics |url=https://biologue.plos.org/2015/01/29/introducing-the-research-resource-identification-initiative-at-plos-biology-plos-genetics/ |work=PLOS Biologue |date=29 January 2015 }}
See also
References
External links
- {{Official website}}
- [https://www.rrids.org/journals full list of institutes and publishers]
- [https://scicrunch.org/resolver RRID Resolver]
- [https://www.enago.com/academy/know-more-about-scicrunch-and-rrids-an-interview-with-dr-anita-bandrowski/ Know More About SciCrunch and RRIDs: An Interview with Dr. Anita Bandrowski]
{{Semantic Web}}