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Release Notes for NIF 4.5

Improvements:

Release Date: August 8, 2012

NIF 4.5 features the following:

 

Search within a section of publications

The NIF search box now can be used to search not just the full text of papers but also to restrict search to  individual sections, e.g., methods, discussion, acknowledgements.  For example, users looking for papers that used antibodies to a particular protein or resource providers who want to see who is using their database or tool can restrict search to just the methods section (see Figures 1 and 2 below). We encourage users to play with this feature. Be mindful that this is a filter, so turning it off before moving onto a new search may be required to get the expected result set. Refreshing the entire page will also turn off the filter.

fig 1

Figure 1

fig 2

Figure 2

LinkOut for papers

The job of NIF is to connect researchers to resources.  Over the past few years, NIF has been providing Pub Med with a list of link outs from individual papers to data, materials and tools using their Link Out feature.  Now, these link outs can be viewed directly within NIF literature.  For example, this paper dealing with pigeon calcium binding proteins, lists 3 antibodies as LinkOuts (Figure 3). These exact antibodies were used in the paper.

fig 3

Figure 3

Annotate papers

A preview of the new NIF annotation function for the literature is now available.  Using this feature, NIF users will be able to create and store annotations on top of the open access papers using the DOMEO tool (documentation available here http://annotationframework.org/).  These annotations will be used to make it easier for users within MyNIF to keep track of their papers, but more importantly, will help make the NIF better by allowing us to link these annotations to additional information like resources.  We will be hosting several in depth tutorials on NIF annotation at the upcoming Society for Neuroscience meeting in October.  In the meanwhile, feel free to play with the tool.  Here is a brief tutorial:

Clicking the annotate button will open the DOMEO tool in a default NIFuser that makes all of the annotations public (Figure 4).

DOMEO annotations are viewable by clicking on the right hand side yellow tab, and they can be made by selecting text and clicking on either the text mine button or the annotate button. Text mining will give a suggestion for the section text mined (Figure 5 shows the results for chemokine receptor that can now be given a thumbs up or down).

Annotations can be thought of as notes. These annotations will be made available to anyone viewing this paper in DOMEO and in a few weeks also through the NIF interface and PubMed as LinkOuts.

fig 4

Figure 4

fig 5

Figure 5



Release Notes for NIF 4.1

Improvements:

Release Date: March 21, 2012

  • Release Date: March 21, 2012

    • Multiple word autocomplete (more information)
    • NeuroLex - bug reporting (more information)
    • NeuroLex skinned for mobile devices
    • beta version of NIF Digest - literature delivered to your mailbox to sign up (this is currently a limited release) please go to http://neuinfo.org/mynif/login.php
    • weighting scheme updated for literature results without abstracts
    • NOT feature in the view/edit query box (more information)

Release Notes for NIF 4.0

Improvements:

  • Filter within results sets: ability to filter results per column (video tutorial)
  • Significant changes to Literature search results: (video tutorial)
    • Collapsed PubMed and PubMed Central tabs into a single index
    • Checkbox option to choose to include full text in your search
    • Faceting by Year, by Author, by Journal
    • Snippets from the full text of the paper are included in search results where search term was found
  • Advanced Search Features: "Load in a New Window," "Pivot," and "Export" (video tutorial)

 

Release Notes for NIF 3.6

Improvements:

  • Add a "strict search" option
  • Mailing list accessible from NIF home page

 

Release Notes for NIF 3.5

Improvements:

  • Toxin:Tetrodo - this query syntax will now bring back a list of toxins.
  • Autocomplete options can now be alphabetized
  • "All" functionality added to literature results
  • Registry search service added to REST suite
  • Registry can now be sorted by date
  • Button added to search bar - can now choose NIF or NeuroLex for search results.
  • Default weighting support for columns added - data fields such as Gene or Protein are now weighted higher than comment, whcih should help rank appropriate results higher
  • Asterisk (*) can now be used to retrieve "all" results; "nifall" support has been deprecated

 

Release Notes for NIF 3.1

Improvements:

  • Search terms and its synonyms now appear bold in database and literature search results
  • NIF navigator is available as downloadable software link
  • NIF Disease, has been aligned to the disease ontology and disease terms are now available from NIFSTD
  • NIF Cards now pull information directly from the NIFSTD ontology via Ontoquest
  • Central Nervous System connectivity data from 5 databases is now available in RDF link
  • Link-out broker has been extended and all Link-out data updated link
  • NIF has further integrated a distributed index infrastructure (using RMI)
  • NIF indices have been updated to to accept ids in more formats (from more databases)

 

Release Notes for NIF 3.0.1

Improvements:

  • Bold inferred classes (try autocomplete for "Gabaergic neuron")

Release Notes for NIF 3.0

Improvements:

  • Improved design of the website brings a new look and feel with significant improvements in usability and integration with the complete set of NIF tools.
  • The new website is more community and social networking enabled.
  • Simple search is tied to the Neurolex wiki: if a search term is contained in the neurolex, users are provided with the basic information about that concept.
  • Community Forum - To discuss hot topics in the neurosciences community.
  • New look and user friendly design on the Neurolex Wiki for exploring, editing and creating new concepts.
  • Improved resource  registration user interface, including tools to link your resource to NIF and also to PubMed via the NIF LinkOut Broker.
  • NIF Registry Catalog is now served through Neurolex Wiki.
  • Several additional datasets now available in RDF format.

New Products

  • NIF Navigator - An information panel that provides the ability to dynamically link to NIF search results based on the NIF categories:
  • Literature (Pubmed, Open Access)
  • Data Type (Animals, Antibodies, Brain Activation Foci, Clinical Trials, Connectivity, Dataset, Disease, Drugs, Grants, Images, Microarray, Models, Pathways, People, Plasmids, Software)
  • Nervous System Levels (Brain Regions, Cellular Level, Genes, Modular Level, Multi-level, Nervous System Function)
  • NIF Registry
  • For each category, the number of results is displayed.
  • This information panel can also be incorporated into your site or application and customized to link your resource into NIF’s collection of resources and data.
  • A global registry of more than 800,000 antibodies that provides an authoritative reference to disambiguateantibody products. http://antibody registry.org.
  • Additional services and enhancements to currently available services:
    • Access to NIF Federated Database Indices.
    • Access to NIF Registry Catalog Indices.
  • New look and feel for NIF Cards, info boxes that can be added to your application or website through simple web links, with additional modules including:
    • NIF Antibody
    • NIF Disease
  • FIN - An entity highlighting service that provides dynamic links from neuroscience terms in your documents, website, or application to the rich resources within NIF.

NIF Statistics



NIF Version: 5.0

Ontology Version: 2.5

Level 2.5/3.0 Resources: 889

Registry Entries: 6,339

Total Records: 356,197,652





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