SciCrunch

Key takeaways

SciCrunch belongs to science; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect SciCrunch to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of SciCrunch from memory before moving on to harder problems.

Reference excerpt

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. 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

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 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. 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 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, Cell Press, eLife, FORCE11, Frontiers Media, GigaScience, MIRIAM Registry, NIH, PLOS Biology and PLOS Genetics.

See also LSID Resource Description Framework Tag (metadata)

References

External links

Official website full list of institutes and publishers RRID Resolver Know More About SciCrunch and RRIDs: An Interview with Dr. Anita Bandrowski

Worked examples

Example 1 — a first encounter with SciCrunch

Start with the simplest possible case. Write down what SciCrunch claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In science, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to SciCrunch before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about SciCrunch ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of SciCrunch

In research: SciCrunch appears in science research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses SciCrunch in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: SciCrunch is common in secondary-school and first-year university syllabi. It links to neighbouring topics Bioinformatics, Identifiers, Index (publishing), so understanding it makes those chapters shorter.
In everyday life: Look for SciCrunch outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

How to study SciCrunch in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what SciCrunch means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain SciCrunch out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is SciCrunch in simple terms?

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.

Why does SciCrunch matter?

Because it connects several science ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study SciCrunch?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on SciCrunch.