Word Embeddings for Wine Recommender Systems Using Vocabularies of Experts and Consumers

This vision paper proposes an approach to use the most advanced word embeddings techniques to bridge the gap between the discourses of experts and non-experts and more specifically the terminologies used by the twocommunities. Word embeddings makes it possible to find equivalent terms between experts and non-experts, byapproach the similarity between words or by revealing hidden semantic relations. Thus, these controlledvocabularies with these new semantic enrichments are exploited in a hybrid recommendation system incorporating content-based ontology and keyword-based ontology to obtain relevant wines recommendations regardless of the level of expertise of the end user. The major aim is to find a non-expert vocabulary from semantic rules to enrich the knowledge of the ontology and improve the indexing of the items (i.e. wine) and the recommendation process

Towards interoperable discourse annotation: discourse features in the Ontologies of Linguistic Annotation

This paper describes the extension of the Ontologies of Linguistic Annotation (OLiA) with respect to discourse features. The OLiA ontologies provide a a terminology repository that can be employed to facilitate the conceptual (semantic) interoperability of annotations of discourse phenomena as found in the most important corpora available to the community, including OntoNotes, the RST Discourse Treebank and the Penn Discourse Treebank. Along with selected schemes for information structure and coreference, discourse relations are discussed with special emphasis on the Penn Discourse Treebank and the RST Discourse Treebank. For an example contained in the intersection of both corpora, I show how ontologies can be employed to generalize over divergent annotation schemes

An open annotation ontology for science on web 3.0

Background: There is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific researchers. The purpose of this paper is to provide an open, shareable structure for dynamic integration of biomedical domain ontologies with the scientific document, in the form of an Annotation Ontology (AO), thus closing this gap and enabling application of formal biomedical ontologies directly to the literature as it emerges. Methods: Initial requirements for AO were elicited by analysis of integration needs between biomedical web communities, and of needs for representing and integrating results of biomedical text mining. Analysis of strengths and weaknesses of previous efforts in this area was also performed. A series of increasingly refined annotation tools were then developed along with a metadata model in OWL, and deployed for feedback and additional requirements the ontology to users at a major pharmaceutical company and a major academic center. Further requirements and critiques of the model were also elicited through discussions with many colleagues and incorporated into the work. Results: This paper presents Annotation Ontology (AO), an open ontology in OWL-DL for annotating scientific documents on the web. AO supports both human and algorithmic content annotation. It enables "stand-off" or independent metadata anchored to specific positions in a web document by any one of several methods. In AO, the document may be annotated but is not required to be under update control of the annotator. AO contains a provenance model to support versioning, and a set model for specifying groups and containers of annotation. AO is freely available under open source license at http://purl.org/ao/, and extensive documentation including screencasts is available on AO's Google Code page: http://code.google.com/p/annotation-ontology/. Conclusions: The Annotation Ontology meets critical requirements for an open, freely shareable model in OWL, of annotation metadata created against scientific documents on the Web. We believe AO can become a very useful common model for annotation metadata on Web documents, and will enable biomedical domain ontologies to be used quite widely to annotate the scientific literature. Potential collaborators and those with new relevant use cases are invited to contact the authors

Conceptualization of Computational Modeling Approaches and Interpretation of the Role of Neuroimaging Indices in Pathomechanisms for Pre-Clinical Detection of Alzheimer Disease

With swift advancements in next-generation sequencing technologies alongside the voluminous growth of biological data, a diversity of various data resources such as databases and web services have been created to facilitate data management, accessibility, and analysis. However, the burden of interoperability between dynamically growing data resources is an increasingly rate-limiting step in biomedicine, specifically concerning neurodegeneration. Over the years, massive investments and technological advancements for dementia research have resulted in large proportions of unmined data. Accordingly, there is an essential need for intelligent as well as integrative approaches to mine available data and substantiate novel research outcomes. Semantic frameworks provide a unique possibility to integrate multiple heterogeneous, high-resolution data resources with semantic integrity using standardized ontologies and vocabularies for context- specific domains. In this current work, (i) the functionality of a semantically structured terminology for mining pathway relevant knowledge from the literature, called Pathway Terminology System, is demonstrated and (ii) a context-specific high granularity semantic framework for neurodegenerative diseases, known as NeuroRDF, is presented. Neurodegenerative disorders are especially complex as they are characterized by widespread manifestations and the potential for dramatic alterations in disease progression over time. Early detection and prediction strategies through clinical pointers can provide promising solutions for effective treatment of AD. In the current work, we have presented the importance of bridging the gap between clinical and molecular biomarkers to effectively contribute to dementia research. Moreover, we address the need for a formalized framework called NIFT to automatically mine relevant clinical knowledge from the literature for substantiating high-resolution cause-and-effect models

The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside

Background: Translational medicine requires the integration of knowledge using heterogeneous data from health care to the life sciences. Here, we describe a collaborative effort to produce a prototype Translational Medicine Knowledge Base (TMKB) capable of answering questions relating to clinical practice and pharmaceutical drug discovery. Results: We developed the Translational Medicine Ontology (TMO) as a unifying ontology to integrate chemical, genomic and proteomic data with disease, treatment, and electronic health records. We demonstrate the use of Semantic Web technologies in the integration of patient and biomedical data, and reveal how such a knowledge base can aid physicians in providing tailored patient care and facilitate the recruitment of patients into active clinical trials. Thus, patients, physicians and researchers may explore the knowledge base to better understand therapeutic options, efficacy, and mechanisms of action. Conclusions: This work takes an important step in using Semantic Web technologies to facilitate integration of relevant, distributed, external sources and progress towards a computational platform to support personalized medicine. Availability: TMO can be downloaded from http://code.google.com/p/translationalmedicineontology and TMKB can be accessed at http://tm.semanticscience.org/sparql

Supporting interoperability and context-awareness in e-learning through situation-driven learning processes

Current E-Learning technologies primarily follow a data and metadata-centric paradigm by providing the learner with composite content containing the learning resources and the learning process description, usually based on specific metadata standards such as ADL SCORM or IMS Learning Design. Due to the design-time binding of learning resources, the actual learning context cannot be considered appropriately at runtime, what limits the reusability and interoperability of learning resources. This paper proposes Situation-driven Learning Processes (SDLP) which describe learning processes semantically from two perspectives: the user perspective considers a learning process as a course of learning goals which lead from an initial situation to a desired situation, whereas the system perspective utilizes Semantic Web Services (SWS) technology to semantically describe necessary resources for each learning goal within a specific learning situation. Consequently, a learning process is composed dynamically and accomplished in terms of SWS goal achievements by automatically allocating learning resources at runtime. Moreover, metadata standard independent SDLP are mapped to established standards such as ADL SCORM and IMS LD. As a result, dynamic adaptation to specific learning contexts as well as interoperability across different metadata standards and application environments is achieved. To prove the feasibility, a prototypical application is described finally

DAFOE: A Platform for Building Ontologies from Texts

International audienceAlthough text-based ontology engineering gained much popularity in the last 10 years, very few ontology engineering platforms exploit the full potential of the connection between texts and ontologies. We propose DAFOE, a new platform for building ontologies with a terminological component using diff erent types of linguistic entries (text corpora, results of natural language processing tools, terminologies or thesauri). DAFOE supports knowledge structuring and conceptual modelling from these linguistic entries as well as ontology formalization. DAFOE outputs models with two main original features: an ontology articulated with a lexical component and a connection with the text or linguistic entry that motivated their defi nition

SEBIO: A Semantic BioInformatics Platform for the New E-Science

Knowledge integration and exchange of data within and among organizations is a universally recognized need in bioinformatics and genomics research through the e-science field. The main problem looming over the lack of integration is the fact that the current Web is an environment primarily developed for human users and micro-array data resources lack widely accepted standards; this leads to a tremendous data heterogeneity. Using semantic technologies as a key technology for interoperation of various datasets enables knowledge integration of the vast amount of biological and biomedical data. In this paper, we aim at providing a semantically-enhanced bioinformatics platform (SEBIO), which handles these issues effectively. We will describe the problems arisen and the solutions applied so far. For that, the SEBIO approach is unfolded and its main components explained, to see in more detail how perfectly it copes with the aforementioned difficulties