News

The 1st International Workshop on Semantic Repositories for the Web (SERES 2010) will be held at the 9th International Semantic Web Conference in Shanghai, China on November 7, 2010.

Ontologies and Linked Data vocabularies are being actively developed and used by numerous applications. Several domains are making their vocabularies available for others to reuse. In addition, good practices when developing ontologies are often followed, particularly for producing reusable modules. The Semantic Web is a modular and highly federated environment of reusable knowledge sources; these provide the meaning so that SW applications change our experience of the web. Within this context, the need for repositories delivering the added value that makes the SW a concrete step beyond our current experience of the web is palpable. SERES addresses issues around semantic repositories within the context of the SW.  

The National Center for Biomedical Ontology is pleased to announce the release of BioPortal 2.5, a Web-based platform for browsing, visualizing, mapping, and commenting on biomedical ontologies and terminologies.  Our new release of BioPortal includes many new features, Web services, and bug fixes. 

BioPortal (http://bioportal.bioontology.org) is a comprehensive repository of biomedical ontologies that enables users to access and share ontologies that are actively used in biomedical communities. Users can publish their ontologies in BioPortal, link ontologies to each other, review ontologies and comment on specific terms, list projects that use ontologies, annotate textual metadata with ontologies, and use Web services to incorporate ontologies or their components into their software applications.

Major new features in this release include the following:

-       Support for structured notes and term requests: Users can now use BioPortal to request that content developers add new terms.  BioPortal provides a structured template for making such requests, allowing users to suggest preferred names, synonyms, and definitions for the requested terms. BioPortal stores the requests as structured notes that are attached to the ontology and that other ontology tools, such as Protégé, will be able to use.

-       Support for email notifications to interested parties whenever a BioPortal user creates new notes for an ontology of interest. (If you would like to subscribe to notifications about a particular ontology, please send email to support@bioontology.org.  We will have an interactive form to sign-up for notifications shortly.)

-       A set of prototype Web services to generate RDF representation for terms in ontologies in BioPortal (see documentation [1] for details).

-       A prototype end-point for SPARQL access to all ontologies in BioPortal: http://sparql.bioontology.org  

-       A set of Web services for retrieving instance information for OWL ontologies [1]. We are planning to release a user interface for viewing instances shortly.

-       New ontology widgets that developers can embed on their Web sites, including an ontology tree widget that allows Web-site authors to present a display of an ontology or an ontology subtree for any BioPortal ontology in any Web page.

-       A preview release of Bio-Mixer, a mashup tool that provides extremely flexible browsing and exploration of ontologies and their mappings

 [1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services

collocated with the 19th Int. World Wide Web Conference (WWW2010) April 27th, Raleigh Convention Center, Raleigh, North Carolina
-- workshop program now available at http://msw.deri.ie --

The idea of a prize in ontology has become necessary at a time when philosophy is moving out of the confines of academia and making contributions to the better understanding and management of the wider world in fields such as social ontology, bioinformatics, intelligence analysis, and many more. The prize, which was designed especially by the artist Ugo Nespolo, is being awarded for the first time to Barry Smith, SUNY Distinguished Professor in the University at Buffalo and founder of IFOMIS, the Institute for Formal Ontology and Medical Information Science in Saarbrücken, Germany, which was the first to initiate a large-scale ontological research initiative in the biomedical sciences.

Smith has made groundbreaking contributions in practically all important areas of ontology. He is Director of the US National Center for Ontological Research, a founder of the Open Biomedical Ontologies (OBO) Foundry, and a lead scientist in the Ontology for General Medical Science (OGMS), Protein Ontology (PRO) and Infectious Disease Ontology (IDO) initiatives. He also works with the US Army Net-Centric Data Strategy Center of Excellence on ontology-based data integration and reasoning and with Hernando de Soto of the Institute for Liberty and Democracy in Lima, Peru on the role of documentation in social and economic development.

The award ceremony will be held on Thursday, April 15, 2010 at 4p.m. in the Aula of the Faculty of Humanities of the University of Turin. It will be followed by a lecture given by Barry Smith and a laudatio by Professor Maurizio Ferraris.

The Award was conceived by Maurizio Ferraris, who has made decisive contributions to social ontology through the foundation of LabOnt (the Laboratory of Ontology) in the University of Turin, and in particular through his development of the theme of "documentality", a theory of how social reality is intimately related to the systems of documents which underlie it. The title of Smith's lecture, "How to Do Things with Documents," fits exactly with this scheme.

Why dedicate the award to Paolo Bozzi? Paolo Bozzi (1930-2003) was professor of psychology at the University of Trieste. He was a proponent of radical ontological realism, who became the standard bearer of a philosophy that does not see the real world as dissolving into words, but actually gives it weight, autonomy and dignity, and thereby frees it from the stench and fluidity of postmodernism. Bozzi's life work demonstrates the need for an ontological reconstruction of philosophy exactly as manifested in initiatives such as IFOMIS and LabOnt.

NCBO will present a panel on "Using Ontologies to Drive Biomedical Research" at the 2010 AMIA Summit on Translational Bioinformatics. Participants include Drs. Mark Musen and David Paik from Stanford University, Ida Sim from UCSF, Simon Twigger from the Medical College of Wisconsin, and Rai Winslow from Johns Hopkins University.

Session number and title: S13 (Panel): Using Ontologies to Drive Biomedical Research
Presentation type: Podium, 90 Minutes (15-20 minutes per presenter plus Q&A)
Date and Time: Thursday, March 11, 1:30 pm - 3:00 pm

Abstract: Biomedical research has become increasingly data intensive, making it difficult to effectively and efficiently utilize and integrate the vast amount and diversity of data. Computers can aid in the process of data analysis, however knowledge about the data and points of integration are needed. Ontologies provide this domain knowledge to drive data annotation, data integration, information retrieval, natural language processing, and decision support. This panel will demonstrate the use of biomedical ontologies to annotate electrocardiogram data, facilitating the use of machine learning algorithms to discover features to support diagnosis of heart disease and predict risk for Sudden Cardiac death; to automatically tag free text descriptions of microarray expression data with ontology terms, facilitating information retrieval; to describe the complex, multi-factorial components of nanoparticles facilitating decision support in the design of nanoparticles; and to provide structured knowledge representation to provide cognitive support to integrate complex data. Each panelist has participated as a Driving Biological Project of the National Center for Biomedical Ontology (NCBO) providing a feedback mechanism between the biomedical research objectives and development of NCBO technology.

Please check 2010 AMIA Summit for Translational Bioinformatics for further details.

The 3rd International Provenance and Annotation Workshop (IPAW'2010)
Troy NY, USA, June 15-16, 2010
http://tw.rpi.edu/ipaw2010

Interest in and needs for provenance are growing as data proliferates. Data is increasing in a wide array of application areas, including scientific workflow systems, logical reasoning systems, text extraction, social media, and linked data. As data increases and as applications become more hybrid and distributed in nature, there is increasing interest in where data came from and how it was produced in order to understand when and how to rely on it.

Provenance, or the origin or source of something, can capture a wide range of information. This includes, for example, who or what generated the data, history of data stewardship, manner of manufacture, place and time of manufacture, and so on. Annotation is tightly connected with provenance since data is often commented on, described, and referred to. These descriptions or annotations are often critical to the understandability, reusability, and reproducibility of data and thus are often critical components of today’s data and knowledge systems.

Provenance has been recognized to be important in a wide range of areas including databases, workflows, knowledge representation and reasoning, and digital libraries. Thus, many disciplines have proposed a wide range of provenance models, techniques, and infrastructure for encoding and using provenance. One timely challenge for the broader community is to understand the range of strengths and weaknesses of different approaches sufficiently to find and use the best models for any given situation. This also comes at a time when a new incubator group has been formed at the World Wide Web Consortium (W3C) to provide a state of the art understanding and develop a roadmap in the area of provenance for Semantic Web technologies, development, and possible standardization.

== Topics ==

This workshop builds on a successful line of provenance and annotation workshops (http://www.ipaw.info/). It aims to bring together a broad range of provenance researchers and users in order to discuss progress in and open research problems related to provenance and annotation. Topics of interest include but are not limited to:

* Provenance models
* Architectures and data management techniques for provenance data
* Provenance requirements and use cases
* Provenance-aware reasoning
* Provenance-aware Semantic Web applications and technologies
* Presentation techniques and tools for provenance data
* Security and privacy issues for provenance data
* Provenance integration and interoperability
* Provenance for social media
* Provenance for linked data
* Query languages and query processing techniques for provenance data
* Storage and query interfaces for workflow provenance
* Provenance analysis, mining and visualization
* Provenance systems, functionality, protocols, implementation
* Provenance, business processes and compliance
* Provenance prototypes and commercial solutions
* Provenance in scientific publications
* Provenance and its relationship to annotation and metadata
* Provenance for digital libraries

== Submission ==

Authors are invited to submit original, unpublished research papers that are not under review for publication elsewhere. Papers may be up to 12 pages in length, including reference and appendix. Detailed submission instructions will be available on the Submission page http://www.easychair.org/conferences/?conf=ipaw2010. Submitted research papers will also be automatically considered for the poster-only option. Proceedings will be published after the workshop by Springer.

IPAW 2010 is also soliciting shorter submissions of ongoing work in the form of proposals for demonstrations, posters, or statements of interest. Short papers may be up to 4 pages in length. Demonstration proposals should describe the context and highlights of the proposed demonstration and include a brief description of the demonstration scenario.

== Important Dates ==

* Abstract deadline: March 8, 2010
* Submission deadline (papers, demos & posters): March 15, 2010
* Notification to authors: April 22, 2010
* Camera-ready deadline: June 1, 2010
* Presentation deadline: June 13, 2010
* Workshop: June 15-16, 2010

== Collocated Events ==

Provenance Hackathon (June 14, 2010) The day before the workshop. There will be a one day hackathon with a prize awarded during the conference.

Provenance Challenge Planning day (June 17, 2010) The day after the workshop. There will be a one day planning meeting for the next provenance challenge.
 

The goal of the OBO Foundry initiative is to create an evolving group of biological and biomedical ontologies which will have the potential to cover a wide range of life science phenomena in a modular fashion. To realize this goal, we have subjected a number of candidate ontologies to a process of review, the first phase of which has now been completed. The following ontologies

CHEBI: Chemical Entities of Biological Interest
GO: Gene Ontology
PATO: Phenotypic Quality Ontology
PRO: Protein Ontology
XAO: Xenopus Anatomy Ontology
ZFA: Zebrafish Anatomy Ontology

have satisfied the OBO Foundry principles and are recommended as preferred targets for community convergence. More details concerning these recommendations, and also concerning the next steps in the OBO Foundry review process, have been published at:
http://www.obofoundry.org/wiki/index.php/Announcement_of_First_Set_of_OBO_Foundry_Ontologies.

Check out FriendFeed from CSHALS at: http://friendfeed.com/cshals-2010.

For more information on the conference see: http://www.iscb.org/cshals2010-home.