Ontologies tend to be found everywhere. They are viewed as the silver bullet for many applications, such as database integration, peer-to-peer systems, e-commerce, semantic web services, or social networks. However, in open or evolving systems, such as the semantic web, different parties would, in general, adopt different ontologies. Thus, merely using ontologies, like using XML, does not reduce heterogeneity: it just raises heterogeneity problems to a higher level. Euzenat and Shvaikos book is devoted to ontology matching as a solution to the semantic heterogeneity problem faced by computer systems. Ontology matching aims at finding correspondences between semantically related entities of different ontologies. These correspondences may stand for equivalence as well as other relations, such as consequence, subsumption, or disjointness, between ontology entities. Many different matching solutions have been proposed so far from various viewpoints, e.g., databases, information systems, and artificial intelligence. The second edition of Ontology Matching has been thoroughly revised and updated to reflect the most recent advances in this quickly developing area, which resulted in more than 150 pages of new content. In particular, the book includes a new chapter dedicated to the methodology for performing ontology matching. It also covers emerging topics, such as data interlinking, ontology partitioning and pruning, context-based matching, matcher tuning, alignment debugging, and user involvement in matching, to mention a few. More than 100 state-of-the-art matching systems and frameworks were reviewed. With Ontology Matching, researchers and practitioners will find a reference book that presents currently available work in a uniform framework. In particular, the work and the techniques presented in this book can be equally applied to database schema matching, catalog integration, XML schema matching and other related problems. The objectives of the book include presenting (i) the state of the art and (ii) the latest research results in ontology matching by providing a systematic and detailed account of matching techniques and matching systems from theoretical, practical and application perspectives.

Ontology Matching

The Gene Ontology (GO; http://wwwgeneontologyorg) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology

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Gene Ontology Consortium: going forward

The Gene Ontology resource (GO; http://geneontology.org) provides structured, computable knowledge regarding the functions of genes and gene products. Founded in 1998, GO has become widely adopted in the life sciences, and its contents are under continual improvement, both in quantity and in quality. Here, we report the major developments of the GO resource during the past two years. Each monthly release of the GO resource is now packaged and given a unique identifier (DOI), enabling GO-based analyses on a specific release to be reproduced in the future. The molecular function ontology has been refactored to better represent the overall activities of gene products, with a focus on transcription regulator activities. Quality assurance efforts have been ramped up to address potentially out-of-date or inaccurate annotations. New evidence codes for high-throughput experiments now enable users to filter out annotations obtained from these sources. GO-CAM, a new framework for representing gene function that is more expressive than standard GO annotations, has been released, and users can now explore the growing repository of these models. We also provide the ‘GO ribbon’ widget for visualizing GO annotations to a gene; the widget can be easily embedded in any web page.

The Gene Ontology Resource: 20 years and still GOing strong

Regulated transcription controls the diversity, developmental pathways and spatial organization of the hundreds of cell types that make up a mammal Using single-molecule cDNA sequencing, we mapped transcription start sites (TSSs) and their usage in human and mouse primary cells, cell lines and tissues to produce a comprehensive overview of mammalian gene expression across the human body We find that few genes are truly 'housekeeping', whereas many mammalian promoters are composite entities composed of several closely separated TSSs, with independent cell-type-specific expression profiles TSSs specific to different cell types evolve at different rates, whereas promoters of broadly expressed genes are the most conserved Promoter-based expression analysis reveals key transcription factors defining cell states and links them to binding-site motifs The functions of identified novel transcripts can be predicted by coexpression and sample ontology enrichment analyses The functional annotation of the mammalian genome 5 (FANTOM5) project provides comprehensive expression profiles and functional annotation of mammalian cell-type-specific transcriptomes with wide applications in biomedical research

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A promoter-level mammalian expression atlas

Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity.

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A communal catalogue reveals Earth’s multiscale microbial diversity

Effective usage of multimedia digital libraries has to deal with the problem of building efficient content annotation and retrieval tools. MOM (Multimedia Ontology Manager) is a complete system that allows the creation of multimedia ontologies, supports automatic annotation and creation of extended text (and audio) commentaries of video sequences, and permits complex queries by reasoning on the ontology.

Automatic annotation and semantic retrieval of video sequences using multimedia ontologies

In this paper, we present the dynamic pictorial ontology paradigm for video annotation. Ontologies are often used to describe a given domain for different goals, including description of multimedia data. In the case of video annotation, the visual knowledge cannot be described using only abstract concepts but is more effectively represented in a visual form. To this aim, we introduce visual concepts, elicited from the data set as the most representative prototypes that specialize abstract concepts. The ontology created is intrinsically dynamic since it must embrace the perceptual and visual experience during annotation. Thus visual concepts can change, adapting to the multimedia content analyzed. Motivation for this new ontology paradigm are discussed together with a proposal of a framework for ontology creation, maintenance, and automatic annotation of video. The creation and usage of dynamic pictorial ontologies have been tested for soccer domain exploiting low level perceptual features and higher level domain features.

Dynamic pictorial ontologies for video digital libraries annotation

Recent research in Technology-Enhanced Learning (TEL) demonstrated several important benefits that semantic technologies can bring to the TEL domain. An underlying assumption for most of these research efforts is the existence of a domain ontology. The second unspoken assumption follows that educators will build domain ontologies for their courses. However, ontologies are hard to build, especially for not-tech-savvy users. Tools for ontology extraction from text aim to overcome this problem. We have conducted an empirical study with educators, both from Information Technology (IT) and non-IT domains, where they used current ontology extraction tools to build domain ontologies for their courses from their existing course material. Based on the obtained study results we have drawn conclusions about the existing ontology extraction tools and provided recommendations for their future development so that they can be beneficial for the TEL domain.

Ontology Extraction Tools: An Empirical Study with Educators

A method for deriving data provenance information corresponding to a workflow process having lower-level workflow processes includes deriving internal provenance information for data pertaining to at least one of the lower-level workflow processes, identifying data objects that are shared between at least a pair of lower-level workflow processes to derive external provenance information for the identified data objects, in response to a user-submitted query, using the internal and external provenance information to retrieve the data provenance information for the workflow process, and outputting the derived data provenance to a user.

System and method for data provenance management

We present Uberon, an integrated cross-species ontology consisting of over 6,500 classes representing a variety of anatomical entities, organized according to traditional anatomical classification criteria. The ontology represents structures in a species-neutral way and includes extensive associations to existing species-centric anatomical ontologies, allowing integration of model organism and human data. Uberon provides a necessary bridge between anatomical structures in different taxa for cross-species inference. It uses novel methods for representing taxonomic variation, and has proved to be essential for translational phenotype analyses. Uberon is available at http://uberon.org

https://link.springer.com/content/pdf/10.1186/gb-2012-13-1-r5.pdf

Carlo Torniai

Papers

Automatic annotation and semantic retrieval of video sequences using multimedia ontologies

Dynamic pictorial ontologies for video digital libraries annotation

Ontology Extraction Tools: An Empirical Study with Educators

System and method for data provenance management

Uberon, an integrative multi-species anatomy