biology

Neuroscience Information Framework

Neuroscience Information Framework is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Neuroscience Information Framework rather than just read about it. In short: The Neuroscience Information Framework is a repository of global neuroscience web resources, including experimental, clinical, and translational neuroscience databases, knowledge bases, atlases, and genetic/genomic resources and provides many authoritative links throughout the neuroscience portal of Wikipedia. Description The Neuroscience Information Framework (NIF) is an initiative of the NIH Blueprint for Neurosci…

Key takeaways

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

Reference excerpt

The Neuroscience Information Framework is a repository of global neuroscience web resources, including experimental, clinical, and translational neuroscience databases, knowledge bases, atlases, and genetic/genomic resources and provides many authoritative links throughout the neuroscience portal of Wikipedia.

Description The Neuroscience Information Framework (NIF) is an initiative of the NIH Blueprint for Neuroscience Research, which was established in 2004 by the National Institutes of Health. Development of the NIF started in 2008, when the UC San Diego School of Medicine obtained an NIH contract to create and maintain "a dynamic inventory of web-based neurosciences data, resources, and tools that scientists and students can access via any computer connected to the Internet". The project is headed by Maryann Martone, co-director of the National Center for Microscopy and Imaging Research (NCMIR), part of the multi-disciplinary Center for Research in Biological Systems (CRBS), headquartered at University of California, San Diego. Together with co-principal investigators Jeffrey S. Grethe and Amarnath Gupta, Martone leads a national collaboration that includes researchers at Yale University, the California Institute of Technology, George Mason University, Harvard University, and Washington University in St. Louis.

Goals Unlike general search engines, NIF provides much deeper access to a focused set of resources that are relevant to neuroscience, search strategies tailored to neuroscience, and access to content that is traditionally “hidden” from web search engines. The NIF is a dynamic inventory of neuroscience databases, annotated and integrated with a unified system of biomedical terminology (i.e. NeuroLex). NIF supports concept-based queries across multiple scales of biological structure and multiple levels of biological function, making it easier to search for and understand the results. NIF will also provide a registry through which resources providers can disclose availability of resources relevant to neuroscience research. NIF is not intended to be a warehouse or repository itself, but a means for disclosing and locating resources elsewhere available via the web. The NIFSTD, or NIF Standard Ontology contains many of the terms, synonyms and abbreviations useful for neuroscience, as well as dynamic categories such as defined cell classes based on various properties like neuron by neurotransmitter or by circuit role or drugs of abuse according to the National Institutes on Drug Abuse. Any term (with associated synonyms) or dynamic category (all terms with their synonyms) can be used to simultaneously query all of the data that NIF currently indexes, please find several examples below:

available data about the hippocampus including synonyms data about parkinson's disease including archaic synonyms like paralysis agitans neocortical neuron a dynamic category includes all neurons that have cell soma in any part of the neocortex

Content NIF content can be thought of as a Catalog (NIF Registry) and deep database search (NIF Data Federation)

The NIF Catalog has the largest listing of NIH-funded, neuroscience-relevant resources, including scientific databases, software tools, experimental reagents and tools, knowledge bases and portals, and other entities identified by the neuroscience research community. A listing of current resources can be found at www.neuinfo.org/registry

The NIF Data Federation searches deep database content of over 150 databases including: various NCBI databases (PubMed, Gensat, Entrez Gene, Homologene, GEO) as well as many large and small databases that have something to do with neuroscience including Gemma (microarray data from the nervous system), CCDB & CIL (images of neurons and astrocytes, mainly), GeneNetwork, AgingGenesDB, XNAT, 1000 Functional Connectomes. The 'complete' list (as of April 2013) can be found in the table below. An updated list can be found on the Data Federation page. In addition many databases that have very similar types of data have been integrated into 'virtual databases', which combine many databases into one table. For example, the AntibodyRegistry combines data from 200+ vendors, the NIF Integrated BrainGeneExpression combines gene expression data from Gensat, Alan Brain, and Mouse Genome Informatics, the Connectivity view combines six databases that have statements about nervous system connectivity, the Integrated Animal view combines data about experimental animal catalogs available to researchers from transgenic or inbred worms, zebrafish, mice and rats. We add more of these as data are registered, so check back to this page to see the current contents. For an exhaustive and up to date list of Databases and Datasets registered to NIF please check this page www.neurolex.org. The table below was updated April 9, 2013.

Data Via Web Services The idea of NIF is that while scientific databases do have a plethora of interfaces, some quite complex, there should be a uniform way of looking at them and searching though them. This uniform search idea has been extended to services so that developers can take advantage of the work done at NIF to enhance their own applications by gaining access to all of the data available through the NIF interface. When data is made public via NIF, it also becomes immediately available via web services. These RESTful web services can be thought of as programming functions that can be built into other applications. Currently, the data can be queried and pulled as an XML feed and several other sites are now pulling NIF data via services, including DOMEO and Eagle i. Developers can learn how to access data by viewing the WADL file available at http://neuinfo.org/developers Below are some public RESTful services that can be accessed by students or used in building applications:

Annotate any text by using this url: * http://nif-services.neuinfo.org/servicesv1/v1/annotate?content=The%20cerebellum%20is%20a%20wonderful%20thing&longestOnly=true

… excerpt ends here. Continue reading the full article.

Illustrations

Worked examples

Example 1 — a first encounter with Neuroscience Information Framework

Start with the simplest possible case. Write down what Neuroscience Information Framework claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, 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 Neuroscience Information Framework 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 Neuroscience Information Framework 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 Neuroscience Information Framework

In research: Neuroscience Information Framework appears in biology 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 Neuroscience Information Framework 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: Neuroscience Information Framework is common in secondary-school and first-year university syllabi. It links to neighbouring topics Anatomy websites, Biological databases, Internet search engines, so understanding it makes those chapters shorter.
In everyday life: Look for Neuroscience Information Framework 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.

Affiliate

Preply — study more efficiently by working with a personal tutor. 50% off.

How to study Neuroscience Information Framework in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Neuroscience Information Framework 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 Neuroscience Information Framework out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Neuroscience Information Framework in simple terms?

Why does Neuroscience Information Framework matter?

Because it connects several biology 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 Neuroscience Information Framework?

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 Neuroscience Information Framework.