The NIF Forums provides a good place for users to discuss scientific topics and to post any questions or concerns that they may have. Here, NIF curators and colleagues can provide suggestions on how to help.
You can increase the viewing area by moving the area between the query and the results to change the size of the components.
The NIF search interface provides several options for managing table views in the NIF data federation. You can resize columns, sort results alphabetically within a column or turn columns off and on. You can change the number of results displayed within a page. You can also export the results to a spreadsheet. To resize columns, place your mouse at the border between two columns until the resize icon appears. Then left click and drag the column to the desired size. To sort data within a column, mouse over the column header until a down arrow appears to the right of the column header. Click on the arrow and select "Sort ascending" or "Sort descending." To turn off individual columns, perform the same procedure but navigate to the "Columns" menu below the sort options.
In a future version, MyNIF will allow you to save these preferences. To change the number of results within a page, select a value from the list on the upper right corner of the NIF search results window. To export results, click on the "Export" link at the upper right corner of the search results window. For more help in using these features, see the NIF Search and Display Interface Tutorial.
Currently, NIF exposes content from three grant databases which are queried each time a search is conducted:
Results from your search can be viewed from the Grants tab and the Data Federation tab, under the Category, Grants. The Grants tab only exposes results from the Grants.gov database while the Data Federation exposes results from all of the databases.
You may also find results in the NIF Registry. Look for search results that are categorized as a Funding Opportunity (left panel).
NIF continues to seek out and register relevant, non-profit organizations that provide grants to neuroscientists. If you know of any additional resources, please recommend the resource for inclusion in the NIF.
Each time a search is conducted NIF's Antibody Registry and Antibody Table are queried. Relevant results can be retrieved under the Data Federation tab, by clicking on the tabs under the Antibodies category (left panel). Product information is organized according to genes, species, and reagent types (antibodies, recombinant proteins, ELISA, siRNA, cDNA clones).
The Antibody Registry serves the scientific community by providing a list of antibodies (>890,000) as well as a set of unique identifiers for commercial and non-commercial antibody reagents enhancing scientist’s ability to keep track of data generated using a specific antibody.
Additional search results for antibodies may also be found under the NIF Registry tab.
NIF is working to increase the number of antibody resources and we invite you to recommend a resource. Additionally, the Antibody Registry allows any user to submit a new antibody or a set of antibodies via web form or spreadsheet upload.
For more information on the Antibody Registry, please refer to the Antibody Registry tutorial.
NIF provide a search of the full text of the paper at the Neuroscience Literature tab and the Open Access tab but does not provide a way to view the full text in NIF (but stay tuned, we are working on it). You may, however, view the full text by using the links to PubMedCentral, or PubMed may have a link to the full text, which you can view if you have an institutional or personal subscription.
The registered resource will be immediately available through the NeuroLex. It will be available in the NIF Registry after it is curated and indexed by NIF. Curation is completed within 7 days and the NIF system is indexed over the weekend.
For an up-to-date number of resources (make sure the search field is cleared), refer to the number displayed on the NIF Registry tab. There are currently over 3,500 resources that have been reviewed by a human curator, but the number changes weekly as new resources are continually added. With only a few exceptions, commercial sites are not listed. We anticipate that this may change in the future. Increase the count by registering your favorite resource.
NIF generally lists only non-profit entities in the NIF Registry; however, there have been a few exceptions. Our policies on including commercial sites are still under development, so this situation may change.
Your search parameters may not yield a result or the entry you are searching for may not exist. NIF offers several search options, and it may be that by expanding or refining a search, the resource you are looking for will be returned. If you still can't find what you are searching for, ask the NIF curators through the NIF Forum. You can also ask that your favorite resource be included by recommending a resource online.
If you would like to see a resource added to the NIF Registry, register a resource online.
The NIF Registry is a catalog of neuroscience relevant resources that has been manually annotated using a set of descriptors to characterize the type of resource (e.g., reagent provider, software resource, database, etc.) and its biological scope (e.g., neurophysiology, Parkinson's disease, neurodevelopment, etc.). Additional information like short name and parent organization has also been provided. In general, the detailed content within the resource is not characterized. For example, if a site has MRI data on many different neurodegenerative diseases, the site will be classified under “MRI” and "neurodegenerative disease" and not all the specific types of neurodegenerative diseases it contains. Content presented on dynamically generated pages, i.e., contained in a database, will not have been indexed in the Registry and therefore is inaccessible to NIF Registry queries. The NIF provides access to this deep hidden content through the Data Federation. Once a resource is registered to the Data Federation, direct queries can be made against the database or dataset through the NIF interface.
To register a database to be included in the Data Federation, begin by registering your resource. Once curated, create a resource description (sitemap); then set up a consultation with the NIF interoperability team. For more information, please see related section on the NIF interoperation page.
A concept-based search is a search based on the meaning of a term rather than the literal string. NIF includes all synonyms of a term with each search. For example, Parkinson's Disease has an archaic synonym, Paralysis Agitans, and a common synonym used in medical literature, Idiopathic PD. A search for Parkinson's Disease will return all these terms. A concept-based query allows a user to search for GABAergic neuron, returning a list of all neurons that are GABAergic, such as purkinje cell, rather than searching just for the term GABAergic. Terms such as GABAergic neuron or drug of abuse are bolded in the search field autocomplete drop-down list to indicate that they are concept terms and thus will return a concept-based search.
Although NIF offers a concept-based search (using the formal semantics of the NIFSTD ontology), the NIF also uses a string based search in order to maximize the possibility of locating relevant resources. As mentioned above, because the concept-based search currently relies on human annotation, and because resources and vocabularies are constantly evolving, only a subset of the registered resources in the NIF have access to the concept-based query. The annotation process is also not completely straightforward, as many resource descriptions require capturing complex inter-related semantic facets, a process that is difficult to automate. For this reason, we have also implemented a standard, term-based search common in Web search engines. Though the results of such term or string-based searches cannot provide the advantages offered by concept-based searches, they do comprehensively cover the NIF’s registered resource pool. In the course of ongoing NIF development, these two forms of search will be synergistically combined to gradually increase both the conceptual accuracy and comprehensive coverage of the NIF resource repository searching.
The NeuroLex Wiki provides a way for the community to contribute, edit, or comment on the NIF vocabularies. Please refer to the How to Contribute link for specific details or you may provide feedback directly to the NIF team. If you have a terminology that covers a domain not currently represented in NIF, please consider working with the NIF to make your vocabulary available.
The Professor Icon indicates a tutorial is available for the database or tool retrieved through a NIF search. The tutorials show how users access a particular resource through the NIF and what functions and information are available from that resource.
NIF Version: 5.0
Ontology Version: 2.5
Level 2.5/3.0 Resources: 889
Registry Entries: 6,339
Total Records: 356,197,652