Neuroscience Information Framework

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About

The Neuroscience Information Framework (NIF) is a gigantic and dynamic collection of web-based neuroscience resources - it is an interactive website which allows you to do advanced queries across multiple databases, materials, tools and ontologies. Neuroscience data is spread vastly across the web, with much of it private (not searchable via google), most of it difficult to machine read of it private and almost none of it adhering to any standards. NIF tries to make all this information easier to find by mapping these resources into a single framework. NIF has a full time curator to do this (plus many part time) and currently indexes over 1500 separate databases/resources and counting.

Structure

NIF is funded by an NIH Blueprint and housed under NCMIR at the University of California, San Diego and the PI is Maryann Martone. To learn more about what NIF is and its goals I highly recommend you watch this youtube video of a seminar presented by Maryann Martone.


Tools / Features

A more official explanation of NIF is available at the NIF website at: www.neuinfo.org. In the list below I only mention the tools of NIF which I am familiar with:


NIF Search Portal

The NIF 3.0 Search Portal is an advanced web search portal which ties together all of NIF's many resources (databases, literature mining, shared vocabularies etc). Although the interface looks quite complex, it's very logically laid out, very powerful and worth learning how to use - they have some documentation for that here and a great youtube video introduction to using the site. My favourite feature here is the auto-complete feature: allowing you to type in the name of an antibody, subcellar compartment, animal etc, and it will show a dropdown of terms in the database. Once you hit search it generates an advanced semantic query and you're able to see any matching entries in literature and many sources of image data, including several brain atlases and image databases such as NIF's own Cell Centered Database:


Cell Centered Database (CCDB)

The Cell Centred Database (CCDB) is a web accessible database for high resolution 2D, 3D and 4D data from light and electron microscopy. The goal of CCDB is to encourage cell biologists all over the world to easily store, openly share and (ultimately) determine the huge dataset they acquire. I recommend any cell biologist with any data get in contact with CCDB if they'd like to show off their data and make sure it's used to its greatest potential. An especially cool way to browse some of this data is using their new interactive "Pivot" interface.


NeuroLex

NeuroLex is a wiki where you can search through and add to a large collection of cellular and subcellular compartments. This is where it gets a bit tricky because you have to know what an "onotology" is. Think of an ontology as a way a computer represents relationships between objects, such as: "Mitochondrion is an Membrane Bound Organelle" and "Membrane Bound Organelle is part of Cell" - which (together) tells the computer that even mitochondrion must be part of a cell. These ontologies also represent a "shared vocabulary" (proper names with any synonyms attached) and every object is given a uniqueID which makes it unique. I'm a fan of Neurolex because (a) it combines/maps together multiple ontologies at different resolutions/scale, with the most famous being geneontology.org, and if an entry doesn't exist it's not too hard to add it yourself - and eventually it will be curated (someone checks it to verify the name is real, doesn't already exist under a different name, and has been entered correctly).




Links