SEARCH TIPS | WHAT IS THIS? (example searches: cerebellum, "pulvinar nucleus", gene:grm1)
NIF 3.0 Search Tutorial
View our NIF 3.0 Search Tutorial Video on Sci Vee.
To find information and images about any neuroscience relevant topic just search for a keyword in the NIF, such as dorsal striatum, or browse by category using the NIF Navigator on the right. The NIF Navigator displays the current holdings of the NIF, including database content organized by category.
New Search Functionality: Going to the NeuroLex from main NIF page
If the input is a single recognized term (note, the term can be multiple words), then the user will be taken to the corresponding wiki page where users can view and contribute to the general information about the term specified. In this case, we find that our original term “dorsal striatum” was translated to the Caudoputamen. This translation of anatomical terms within the NIF system is based on a consensus terminology for the nervous system arrived at by the Program on Ontologies of the Neural Structures (the International Neuroinformatics Coordinating Facility taskforce).
On the right NIF Navigator panel, you may explore NIF search results by category. Displayed are results from the federated databases that match this particular term, grouped by nervous system level and data type. The above example shows that there are 618 gene results for the Caudoputamen. Below that are your search results within the NIF Registry and Literature.
Clicking on a selection within the Navigator will take you to the advanced search interface where the search term can be explored. This query term will be translated by the NIF systems in several ways:
Any time the NIF system recognizes the term then several interesting things occur:
The View / Edit Query box expands all synonyms and acronyms known to NIF. This box is a free text editor so highlighting terms and hitting the delete button can remove them. Clicking on the search button 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, when searching for Alzheimer’s disease AD is the acronym, but AD is also a brain region abbreviation, which has no relationship to Alzheimers disease.
Looking at the search options box, we find that there are various related terms, including the various parts of the basal ganglia.
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.
Data Federation, the Default View
The default view of the NIF is the Data Federation, which is a group of databases that are queried with each search.
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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. Other categories are broken down into Data Types and Nervous System Levels, but a single database can appear in more than one category.
NIF Registry
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, as well as all the other data, are searched at the same time as the databases. In this example 6 registry items are somehow related to the caudoputamen; not surprisingly half are atlases. Clicking on the Category ‘Atlas’ in the left panel, displays only those results that are Atlases and match the current query.
To see all Registry’s 3000+ results, clear the search terms.
Literature
The literature tab displays the search results of the simultaneously searched multiple literature indices - Pub Med, Open Access and neuroscience-centered literature databases (Neuronal Morphology and a neuroscience literature corpus) , using all of the vocabulary expansion of NIF.
NIF Cards
Find more information on cells and brain regions using NIF cards. In any results tab, right clicking on an underlined term (example: interneuron) will bring up options that may include the NIF card. NIF cards, shown above, are mini information cards that display basic information about the highlighted entity and contain links to other data. The user can also choose to add the term to the query or replace query terms.
Grants
The grants tab contains a database of funded grant data from NIH, NSF and many private foundations; however, these data are not as up to date as the NIH RePORTER database, which can be found under the Data Federation tab, in the grants category.
Using the NIF vocabularies to search
In the advanced search interface, there is an auto-complete 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, the NIF uses the term expansion feature to pull a list of all neurons that have the property of releasing GABA. The NIF then searches across all of the publications and database records that match any GABAergic neuron.
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 wiki translated from the NIFSTD ontology that allows any user to add synonyms, definitions and anything else he or she deems reasonable. To edit any entry, such as adding a synonym, all that one has to do is to hit the [Edit draft] tab, insert the synonym into the synonyms box, and then hit save. There are tutorials available in the Neurolex for more complicated wiki editing.
The content is curated before it is incorporated into the NIF search systems.
My NIF functionality / Searching for genes
You can search for genes in NIF by typing in “gene:” and then the gene; e.g., gene:grm1. The NCBI database of genes and synonyms is searched when this type of search is created.
As there are different synonyms for genes depending on the species, you may select your species of choice, by doing the following:
Log into NIF by using your Google or Yahoo account.
Choose your preferences for species sets.
Then perform your search, e.g., gene: grm1. The only synonyms searched for are specific to the organisms chosen.
View Images using Pivot
The Data Federation uses Pivot to view images in a dynamic way. To use the image viewer, select the option, ‘View in Pivot’.
The tool allows the user to sort or search in a variety of ways, including viewing results as a grid or graph, by species, age, gender, etc.
NIF Navigator
