There will be a discussion period involving the Shared Names Project and the NCBO BioPortal.

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 April 6th, 2010. Please join Dr. Anita Bandrowski for an informational session on the new features offered in NIF 2.5.  Below is information on how to join the online meeting and accompanying teleconference.

Date and Time: Tuesday, April 6, 2010 • 11:00-12:00 PST
Topic: Preview of NIF 2.5 Release
Presenters: Dr. Anita Bandrowski
URL: http://connect.neuinfo.org/webinar
Dial-In (toll-free): 866-740-1260
Access Code: 8220739

NIF 2.5 will include new services, incorporate new features to the search interface, and solve known issues/bugs. Through this informational session, find out more about NIF cards, NIFSTD entity recognition, new literature, and improvements on search.  Learn more about the services such as the Ontology Access Service, SOLR Service, and  the varying API interfaces. New features to look forward to are Concept-based search through autoexpansion, MyNIF capabilities to save searches, highlighted search results according to a semantic category in the NIF ontologies, and many more. Known issues regarding the scroll bar, browser compatibility, and search box behavior have been resolved and we have even improved on performance and stability of NIF Literature and Pubmed Results.

We hope you can make it to this exciting session!

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!

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 23rd, 2010. Please join Dr. Rebecca Crowley, MD, MSIS, from the University of Pittsburgh School of Medicine and she covers the progress of the ODIE Toolkit. Below is information on how to join the online meeting and accompanying teleconference. For a schedule of the 2010 presentations or for more information about the NCBO Seminar series, see: http://www.bioontology.org/seminar-series.

Date and Time: Tuesday, March 23, 2010 • 11:00-12:00 PST
Topic: Progress on the ODIE Toolkit
Presenters: Dr. Rebecca Crowley, MD, MSIS
URL: http://connect.neuinfo.org/webinar
Dial-In (toll-free): 866-740-1260
Access Code: 8220739

A few months ago, ODIE 1.0 was quietly released on the NCBO GForge site. ODIE is an application that lets researchers (1) analyze text corpora using BioPortal ontologies to map text to BioPortal concepts, and (2) identify candidate concepts within text corpora that could be considered for addition to an existing ontology. The ODIE project has made some significant advances this year – including (1) complete redesign to use the UIMA platform, (2) integration of Mayo cTAKES pipeline into ODIE, (3) addition of a simple co-reference resolution algorithm as UIMA resource, and (4) addition of statistical as well as linguistic methods for discovering candidate concepts. In addition to the software, we’ve been working on developing co-reference corpora, and testing a variety of existing methods for ontology enrichment using domain experts and ontology developers as judges. This talk will demonstrate the latest release and will sample some of the year’s research project findings. Dr. Rebecca Crowley from the University of Pittsburgh School of Medicine, will preview the upcoming release of ODIE 1.1 which includes improved installation, visualization, placement of candidate concepts and export of proposals as OWL files.

We look forward to seeing you there.

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.

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!

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!

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.

Date: October 27, 2009 / 11:00 – 12:00 noon PDT
Topic: Brede Tools
Presenter: Dr. Finn Aarup Nielsen
URL: http://connect.neuinfo.org/webinar
Dial-In (toll free): 866-740-1260
Access Code: 8220739

Description: This Webinar provides an introduction to the Brede tools. The tools consist of the Brede Toolbox, Brede Database, and Brede Wiki. The database and the wiki are collections of neuroimaging studies and their brain activations as well as taxonomies/ontologies. The toolbox is able to process and perform a range of meta-analyses with the data and present the results on the Web. This Webinar will demonstrate the database and the search facility as it appears on the Web.

Check out Nielsen’s journal article on Visualizing data mining results with the Brede tools!

We look forward to seeing you there.