SEARCH TIPS | WHAT IS THIS? (example searches: cerebellum, "pulvinar nucleus", gene:grm1)
Advanced Search Tutorial
New Search Functionality: Going to the NeuroLex from main NIF page:
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.
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 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 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).
Information about the brain region is contained on this page and the right hand ‘view data by category navigator’ brings back results from the federated data that match this particular term. The above example shows that there are 1800 gene results, from the caudoputamen.
Clicking on the Navigator leads to the advanced search interface where data matching 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 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, 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.
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. 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 6 registry items are somehow related to the caudoputamen, not surprisingly half are atlases. Clicking on the label Atlas on the left displays only those results that are Atlases and match the current query. To see all registry 3000+ results, we recommend clearing the search terms.
The literature tab shows the result of searches of PubMed and various other literature databases, using all of the vocabulary expansion of NIF. 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 chose to add the term to the query or replace query terms.
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 in the Data Federation tab, under grants.
Using the NIF vocabularies to search
In the advanced search 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, 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.
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 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 wiki editing.
The content is curated before it is incorporated into the NIF search 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.
NIF Navigator
