The devices, experimental scaffolds, and biomaterials ontology (DEB): a tool for mapping, annotation, and analysis of biomaterials' data

The size and complexity of the biomaterials literature makes systematic data analysis an excruciating manual task. A practical solution is creating databases and information resources. Implant design and biomaterials research can greatly benefit from an open database for systematic data retrieval. Ontologies are pivotal to knowledge base creation, serving to represent and organize domain knowledge. To name but two examples, GO, the gene ontology, and CheBI, Chemical Entities of Biological Interest ontology and their associated databases are central resources to their respective research communities. The creation of the devices, experimental scaffolds, and biomaterials ontology (DEB), an open resource for organizing information about biomaterials, their design, manufacture, and biological testing, is described. It is developed using text analysis for identifying ontology terms from a biomaterials gold standard corpus, systematically curated to represent the domain's lexicon. Topics covered are validated by members of the biomaterials research community. The ontology may be used for searching terms, performing annotations for machine learning applications, standardized meta-data indexing, and other cross-disciplinary data exploitation. The input of the biomaterials community to this effort to create data-driven open-access research tools is encouraged and welcomed.Preprin

empathi: An ontology for Emergency Managing and Planning about Hazard Crisis

In the domain of emergency management during hazard crises, having sufficient situational awareness information is critical. It requires capturing and integrating information from sources such as satellite images, local sensors and social media content generated by local people. A bold obstacle to capturing, representing and integrating such heterogeneous and diverse information is lack of a proper ontology which properly conceptualizes this domain, aggregates and unifies datasets. Thus, in this paper, we introduce empathi ontology which conceptualizes the core concepts concerning with the domain of emergency managing and planning of hazard crises. Although empathi has a coarse-grained view, it considers the necessary concepts and relations being essential in this domain. This ontology is available at https://w3id.org/empathi/

A lightweight web video model with content and context descriptions for integration with linked data

The rapid increase of video data on the Web has warranted an urgent need for effective representation, management and retrieval of web videos. Recently, many studies have been carried out for ontological representation of videos, either using domain dependent or generic schemas such as MPEG-7, MPEG-4, and COMM. In spite of their extensive coverage and sound theoretical grounding, they are yet to be widely used by users. Two main possible reasons are the complexities involved and a lack of tool support. We propose a lightweight video content model for content-context description and integration. The uniqueness of the model is that it tries to model the emerging social context to describe and interpret the video. Our approach is grounded on exploiting easily extractable evolving contextual metadata and on the availability of existing data on the Web. This enables representational homogeneity and a firm basis for information integration among semantically-enabled data sources. The model uses many existing schemas to describe various ontology classes and shows the scope of interlinking with the Linked Data cloud

Selected papers from the 15th Annual Bio-Ontologies special interest group meeting

© 2013 Soldatova et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Over the 15 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The seven papers and the commentary selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data, annotating patent records, NCBO Web services, ontology developments for probabilistic reasoning and for physiological processes, and analysis of the progress of annotation and structural GO changes