That’s an easy one, with all due respect to our former president.  As far as the NIF is concerned, “IS” is the inferior salivatory nucleus.  How do we know?

Perform a search in NIF and you will see various terms highlighted in the search results (the current highlighting color is brick red, but we are open to suggestions).   Hover over each of these highlighted terms and NIF will tell you what the term means to the NIF system.  If you hover over “IS,” NIF tells you it’s an anatomical structure. If you right click on it and ask to see “IS” in the Neurolex, it will tell you that IS is an abbreviation for the inferior salivitory nucleus.  This new feature is an example of what is often called “entity recognition.”

In the formal world of knowledge representation, an entity is that which is perceived, known, or inferred to have its own distinct existence.  For NIF, entities are those things like organisms, cells, molecules, and techniques that define our domain.  These entities are represented in the NIF ontologies.  Each entity has its own numerical identifier, sort of like a social security number, that uniquely identifies the entity.  This identifier is used to point to different ways of saying the same things to the same entity.  For example, NIF doesn’t care whether you call entity birnlex_2645, the IS, inferior salivary nucleus, or Freddy, for that matter.  They are all (and always) the same thing.

Unfortunately, the richness and complexity of our language makes recognizing entities a tricky thing, as everyone who uses a search engine knows.  Not only can we call the same entity many things, but we can call many entities the same thing.  Chances are that the IS highlighted by NIF in the search results actually is not the inferior salivatory nucleus but the third person form of the verb “to be,” or perhaps it is the initial segment of an axon or the Institute for Science.    Right now, NIF doesn’t really know.

In future releases of NIF, we will be working towards improving the accuracy of our entity recognition.  Why?  Because once we know that IS is a brain nucleus, we can find anything that is known about it:  its projections, its genes, the diseases in which it is affected.  A preview of what is coming can be seen in the NIF Cards.

Search for IS with NIF Card

NIF cards for each entity can be viewed by right clicking over the highlighted term and selecting “Show NIF card” from the menu. NIF cards currently are only implemented for anatomical structures and cells.

For now, however, we hope you will explore the new NIF and develop an appreciation for the difficulties of semantic search by seeing what NIF thinks the results mean.  You may be surprised!

NIF Version 2.5 is now released.  Please visit the list of top features.

Please provide your valuable feedback by sending an email to support@neuinfo.org.  Thank you.

The International Neuroinformatics Coordinating Facility (INCF) is an international organization devoted to advancing the field of neuroinformatics. The annual INCF Neuroinformatics Congress provides a meeting place for researchers in all fields related to neuroinformatics, including data- and knowledge-bases of the nervous system from molecular to behavioral levels; tools for the acquisition, analysis, and visualization of nervous system data; and theoretical, computational, and simulation environments for modeling the brain.

The very first Neuroinformatics Congress held in Stockholm, Sweden in 2008 attracted 260 attendees. The next year, there were 213 participants that came together for the 2009 Neuroinformatics Congress in Pilsen, Czech Republic. This year, Neuroinformatics 2010 will be held in Kobe, Japan from August 30th to September 1st.

This 3rd INCF Congress prepared with keynote lectures, workshops with speakers and panel discussions, and poster and demo sessions will be an exciting 3 days. The 2010 Congress will also feature a special session on Neuroinformatics in Japan and Asia. This session will constitute the last half day of the Congress and will be organized by the INCF Japan-Node.

View the Neuroinformatics 2010 Flyer!

The XNAT Workshop 2010 will be held from June 28 – 30.

It will provide an opportunity for XNAT site administrators and developers to deepen their understanding of the XNAT system. The Workshop will begin with sessions focused on successfully deploying XNAT in a range of research environments and will proceed to sessions focused on customizing and extending XNAT and on building client applicatins that interface with XNAT. The workshop will be divided into didactic presentation, breakout discussion, and practical working time.

It will be located at the Connor Auditorium, Farrell Learning and Teaching Center (map)
Washington University School of Medicine
St. Louis, MO

Topics to look forward to:

• Installation and basic setup
• Best practices for multi-site studies and institutional deployments
• Tuning, optimization, and monitoring
• Integrating with DICOM devices (modalities, PACS, workstations)
• Customizing XNAT
• Creating XNAT pipelines
• Building XNAT clients
• Building new XNAT features / open source development
• Interfacing with external applications
• Gripe session
• Ad hoc breakout discussions

A detailed agenda is coming soon.

Registration for the event is $100. Workshop materials and breakfast/lunch will be covered.
Please go here to register.

Hotel Options:
The Parkway Hotel: It’s a 5 minute walk to the meeting. When making reservations, ask for the XNAT Workshop rate ($119).
The Chase Park Plaza: A nicer hotel. It’s a 10 minute walk to the meeting.