The Neuroscience Information Framework (NIF) hosts Webinar series on topics focused on collaborating with NIF, getting involved in building the NIF vocabulary, using NIF portal resources, as well as other appropriate NIF topics.

Our next NIF Webinar is scheduled for March 30th, 2010. Please join Dr. Amarnath Gupta  from the University of California, San Diego as he covers: NIF as a Multi-Model Semantic Information System–Part 1: Relational, XML, RDF and OWL models.  Below is information on how to join the online meeting and accompanying teleconference.

Date and Time: Tuesday, March 30, 2010 • 11:00-12:00 PST
Topic: NIF as a Multi-Model Semantic Information System–Part 1: Relational, XML, RDF and OWL models
Presenters: Amarnath Gupta
URL: http://connect.neuinfo.org/webinar
Dial-In (toll-free): 866-740-1260
Access Code: 8220739

An important goal of the Neuroscience Information Framework (NIF) is to develop a data infrastructure that can ingest structured, semi-structured and unstructured information and perform semantic search over them. This is the first presentation of a series that will cover the NIF data infrastructure. In this presentation. we lay out the foundation of the different forms of data models that NIF is equipped to handle at this point. We specifically describe the relational, object relational, XML, RDF and OWL models of data and knowledge, and touch upon some of their variants. For these models, we present a simplified overview of their semantics, capabilities, and limitations. We conclude the presentation with an outlook of the specialized data models that NIF expects to handle in the future.

We hope you can make it!

We are pleased to announce the new release of NIFSTD 1.7. Please visit http://purl.org/nif/ontology/nif.owl to access the owl file.

Major changes of this release include:

Feel free to take a look at the detailed NIFSTD 1.7 release notes and tell us what you think!

The Neuroscience Information Framework (NIF) hosts Webinar series on topics focused on collaborating with NIF, getting involved in building the NIF vocabulary, using NIF portal resources, as well as other appropriate NIF topics.

Our next NIF Webinar is scheduled for February 9th, 2010. Please join Dr. Maryann Martone, Principal Investigator of the NIF Project, and Fahim Imam, Ontology Engineer from UC San Diego,  for an informative session on the NIF Standard Ontology. Details follow.

Date and Time: Tuesday, February 9, 2010 • 11:00-12:00 PST
Topic: Defined versus Asserted Classes:  Working with the NIF OWL Ontologies
Presenters: Dr. Maryann Martone and Fahim Imam
URL: http://connect.neuinfo.org/webinar
Dial-In (toll-free): 866-740-1260
Access Code: 8220739

The NIF project has established a set of modular ontologies covering many of the major domains of relevance to neuroscience, the NIF Standard Ontology (NIFSTD).  This Webinar will focus on NIF’s approach to the asserted vs inferred hierarchy in the NIFSTD ontology and how NIF builds up more complicated relationships among NIF modules while keeping modularity intact.  When it comes to asserted hierarchy of classes, NIFSTD ontologies took the single inheritance principle which is also an important OBO foundry recommendation.  This principle allows us to have the classes that are univocal and unambiguous within the core NIFSTD modules. We believe that this principle is often misunderstood to mean that you can only have a single hierarchy in your ontology.  However, through the use of logical definitions with necessary and sufficient conditions, multiple parents can be inferred using automated reasoning.  This saves a great deal of manual labor and provides a logical reason as to how that class may exist in different hierarchies.  In this Webinar, we will provide examples including the NIF’s inferred hierarchy of neurons by neurotransmitter and by soma location.

We look forward to seeing you there.

NIF Version 2.1 has been released. This minor release includes the following improvements:

• Resolved issues of multiple scroll bars by using a new layout scheme for the results page
• Fixed the bug relating to mammals and primates in the selection of species from the gene preference section
• Removed thumbnail images from GENSAT to improve consistency
• Improved the handling of dots and slashes in indexes
• Implemented a grid view in the databases tab now to automatically resize and fill in the empty space with data
• Enabled the database tab to now show data from the first database in the list of results instead of a blank screen
• Changed the layout of two “clear” buttons, no longer placed next to each other to avoid confusion
• Fixed the paging issue with literature results

You informed us of the bugs. We fixed them.

• “When I right click on a Neurolex term in the expand box, it gives me the “show in NCBI” option but  link doesn’t work”
• “On the NIF Literature’s tab, the  ‘More information’ link along the top is broken”
• “Genes get duplicate synonyms”
• “Genes should not allow expansion (Genes should not have a folder or allow expansion in the term tree)”
• “Boolean conditions are getting mixed up in the Gene Query”
• “For some queries e.g. Hippocampus the web results show the first page as blank although there is data on that page. The web result is blank, but moved to page 2 and page 2 displays results”
• “Database results ’sort’ function not working (aside from the capitalization, numerical value issues)

Feel free to take a look at the NIF Version 2.1 Release Notes. NIF continues to improve to better fit your neuroscience needs. Visit NIF now and tell us what you think!

The Neuroscience Information Framework (NIF) hosts Webinar series on topics focused on collaborating with NIF, getting involved in building the NIF vocabulary, using NIF portal resources, as well as other appropriate NIF topics.

Our next NIF Webinar is scheduled for January 19th, 2010. Please join Dr. Trish Whetzel from the Stanford Center for Biomedical Informatics Research (BMIR) for an informative session about the Annotator Tool done by the National Center for Biomedical Ontology (NCBO). Details follow.

Date and Time: Tuesday, January 19, 2010 • 11:00-12:00 PST
Topic: NCBO Annotator
Presenters: Dr. Trish Whetzel
URL: http://connect.neuinfo.org/webinar
Dial-In (toll-free): 866-740-1260
Access Code: 8220739

This Webinar will provide a demonstration of the NCBO Annotator, an ontology-based Web service used for annotation of textual metadata from public datasets with biomedical ontology concepts, thus facilitating data integration and translational discoveries. Through annotation or tagging of datasets with ontology concepts, unstructured free-text data becomes structured and standardized. Despite these benefits, wide-scale semantic annotation is not common due to the need for trained curators and lack of an ontology repository. We will go through the NCBO Annotator web service workflow and show how it provides an alternative to manual annotation through use of a fast and accurate concept recognition tool and access to almost two hundred ontologies from BioPortal and UMLS.

We really hope you can make it.

Thanks!

On December 15, NIF conducted a Webinar featuring the MIREOT tool.  For those of you who missed the Webinar, we have an archive of all our past Webinars available at http://www.neuinfo.org/webinars/archive.shtm.   It’s almost as good as being there!

We look forward to seeing you at the next NIF Webinar.  Until then, enjoy all of the NIF Webinar archives.

Happy Holidays.

The Neuroscience Information Framework (NIF) hosts a biweekly Webinar series on
topics focused on collaborating with NIF, getting involved in building
the NIF vocabulary, using NIF portal resources, as well as other
appropriate NIF topics.

Our next Webinar is scheduled for Tuesday, December 15, 2009 and will
focus on the MIREOT Tool (Minimum Information to Reference External Ontology Terms).

Date and Time: Tuesday, December 15, 2009 • 11:00-12:00 PST
Topic: MIREOT Tool
Presenters: Alan Ruttenberg and Melanie Courtot
URL: http://connect.neuinfo.org/webinar
Dial-In (toll-free): 866-740-1260
Access Code: 8220739

This Webinar will provide a demonstration of the MIREOT Tool and the
rationale for using tools such as MIREOT to synchronize ontology
development.  MIREOT is a mechanism and a minimal information standard
used for importing required terms into an ontology.  The focus of the
demonstration will be on the simple workflow of allowing selective use
of classes from external ontologies.  We will provide suggestions on
implementation for this mechanism and how it can be extended over time.

We hope you can make it.

Thanks!

It has been a month since the release of NIF 2.0, but we want to know — What do you think of NIF 2.0? Do you know of the changes made?

We created a short presentation of the improvements incorporated in NIF 2.0 (in case you missed them).
Do check it out and tell us what you think!

We look forward to hearing from you.

Hello everybody! The next NIF Webinar is scheduled for November 17, 2009. Please join Sridevi Polavaram from George Mason University for an informative and interactive session about Cell Ontology. Details follow.

Date: November 17, 2009 / 11:00 – 12:00 noon PDT
Topic: Cell Ontology
Presenter: Sridevi Polavaram
URL: http://connect.neuinfo.org/webinar
Dial-In (toll free): 866-740-1260
Access Code: 8220739

Description: This Webinar provides an explanation of how NIF is building on its cell ontology. We will discuss standard naming conventions and set properties that have been made to ensure proper granularity. We will highlight tools such as the Neurolex Wiki to show how the population of the ontology has been realized. Most of this demonstration will involve the user’s perspective.

As this Webinar will mainly be from the user’s perspective, we strongly encourage you to join us! We look forward to seeing you there.