Search Tutorial

To find information and images about any neuroscience relevant topic just search for a keyword in the NIF:

This query term will be translated by the NIF systems in several ways:

If the NIF system recognizes the term then several interesting things occur:

Looking at the search options box, we find that there are various related concepts to Alzheimer’s disease, including the disease class and related disorders.
Each folder can be opened and it can be checked.  If you open the folders or right click on the terms you can find out more information about the terms.  Clicking on the gray squares includes the term in the search. 

The View / Edit Query box expands all synonyms and acronyms known to the NIF.  This box is a free text editor so highlighting terms and hitting the delete button can remove them.  Clicking on the search box will search the newly edited list.

NOTE:  Acronyms always give many more non-specific results, so deleting these will bring back a much more targeted results set.  For example, AD is a brain region abbreviation, and the AD brain region is not related to Alzheimers disease. 

The default view of the NIF is the Data Federation, which is a group of databases that are queried with each search.  There are human readable categories for each database and the search brings up a list of database records that have something to do with your search term.  For example, the category mice shown below, contains a database called the international mouse resource (IMSR) and the data here represent transgenic mice that can be purchased.

Other categories are broken down into Data Types and Nervous System Levels, but a single database can appear in more than one category. 

The second tab is called the NIF Registry, which is a set of human curated records labeled with categories such as: Database, Software, and Tissue Bank.
These data are searched at the same time as the databases.  In this example 144 registry items are somehow related to Alzheimer’s disease.

The registry can also be browsed as well as being searched.  For the 144 results, 9 of these are labeled with funding opportunities.  If you click on the Category that you would like to view, like funding opportunities then only those 9 records will be shown on the right. 

Note that the blue highlighting represents resources funded by the blueprint for neuroscience.

The NIF Web tab is the result of a targeted search of the web based on the NIF registry.  These results are not human curated.

The literature tab shows the result of searches of both PubMed and the NIF literature corpus, using all of the vocabulary expansion of NIF.

The NIF literature corpus ranks literature results by relevance not year, sometimes bringing back papers that would be buried in PubMed, but are quite relevant to the search.

The grants tab has funded grant data from NIH, NSF and many private foundations.  Although not as up to date as CRISP, the data are much richer.

Using the NIF vocabularies to search.

In this interface, there is an autocomplete feature that can be used to find out what NIF knows about.  For example, NIF cell and NIF brain region have a large amount of data associated with each.  Below, we are searching for gaba-ergic cells. 

In this case, there are no synonyms to this term, but there are many things found in the search options box including a large list of gabaergic neurons.

Any term in the search options box can be right clicked and information can be found on this term from various sources.  Below, we click on GABA and we will click on the Show in Neurolex option.

The Neurolex is a vocabulary (ontology) wiki that allows any user to add synonyms, definitions and anything else he or she deems reasonable. 

To edit any entry and add a synonym all that one has to do is to hit the edit button and fill in the synonym into the synonyms box, then hit save.  There are tutorials available in the Neurolex for more complicated things. 

The content is curated before it is incorporated into the NIF systems.

MyNIF functionality:

You can search for genes using NIF by typing in gene:grm1.  The NCBI database of genes and synonyms is searched when this type of search is created.  However, there are different synonyms for genes depending on the species and to chose your favorite species, you can do the following:

Log into NIF by using your Google or Yahoo account.

Chose your preferences for species sets.

Then search for gene synonyms:

Gene:grm1 is being searched below and synonyms are found in plants and phages.