The role of ontologies in biological and biomedical research: a functional perspective.

Ontologies are widely used in biological and biomedical research. Their success lies in their combination of four main features present in almost all ontologies: provision of standard identifiers for classes and relations that represent the phenomena within a domain; provision of a vocabulary for a domain; provision of metadata that describes the intended meaning of the classes and relations in ontologies; and the provision of machine-readable axioms and definitions that enable computational access to some aspects of the meaning of classes and relations. While each of these features enables applications that facilitate data integration, data access and analysis, a great potential lies in the possibility of combining these four features to support integrative analysis and interpretation of multimodal data. Here, we provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research. We also outline perspectives for using ontologies in data-driven science, in particular their application in structured data mining and machine learning applications.This is the final version of the article. It first appeared from Oxford University Press via http://dx.doi.org/10.1093/bib/bbv01

Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting

Over the 14 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 selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data from wikis, innovative methods of annotating and mining electronic health records, advances in annotating web documents and biomedical literature, quality control of ontology alignments, and the ontology support for predictive models about toxicity and open access to the toxicity data

Ontology of core data mining entities

In this article, we present OntoDM-core, an ontology of core data mining entities. OntoDM-core defines themost essential datamining entities in a three-layered ontological structure comprising of a specification, an implementation and an application layer. It provides a representational framework for the description of mining structured data, and in addition provides taxonomies of datasets, data mining tasks, generalizations, data mining algorithms and constraints, based on the type of data. OntoDM-core is designed to support a wide range of applications/use cases, such as semantic annotation of data mining algorithms, datasets and results; annotation of QSAR studies in the context of drug discovery investigations; and disambiguation of terms in text mining. The ontology has been thoroughly assessed following the practices in ontology engineering, is fully interoperable with many domain resources and is easy to extend

Semantic process mining tools: core building blocks

Process mining aims at discovering new knowledge based on information hidden in event logs. Two important enablers for such analysis are powerful process mining techniques and the omnipresence of event logs in today's information systems. Most information systems supporting (structured) business processes (e.g. ERP, CRM, and workflow systems) record events in some form (e.g. transaction logs, audit trails, and database tables). Process mining techniques use event logs for all kinds of analysis, e.g., auditing, performance analysis, process discovery, etc. Although current process mining techniques/tools are quite mature, the analysis they support is somewhat limited because it is purely based on labels in logs. This means that these techniques cannot benefit from the actual semantics behind these labels which could cater for more accurate and robust analysis techniques. Existing analysis techniques are purely syntax oriented, i.e., much time is spent on filtering, translating, interpreting, and modifying event logs given a particular question. This paper presents the core building blocks necessary to enable semantic process mining techniques/tools. Although the approach is highly generic, we focus on a particular process mining technique and show how this technique can be extended and implemented in the ProM framework tool

Towards an ontology for process monitoring and mining

Business Process Analysis (BPA) aims at monitoring, diagnosing, simulating and mining enacted processes in order to support the analysis and enhancement of process models. An effective BPA solution must provide the means for analysing existing e-businesses at three levels of abstraction: the Business Level, the Process Level and the IT Level. BPA requires semantic information that spans these layers of abstraction and which should be easily retrieved from audit trails. To cater for this, we describe the Process Mining Ontology and the Events Ontology which aim to support the analysis of enacted processes at different levels of abstraction spanning from fine grain technical details to coarse grain aspects at the Business Level

Ontology-based knowledge representation of experiment metadata in biological data mining

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes

Ontology Enrichment by Discovering Multi-Relational Association Rules from Ontological Knowledge Bases

International audienceIn the Semantic Web context, OWL ontologies represent the con-ceptualization of domains of interest while the corresponding as-sertional knowledge is given by the heterogeneous Web resources referring to them. Being strongly decoupled, ontologies and assertion can be out-of-sync. An ontology can be incomplete, noisy and sometimes inconsistent with regard to the actual usage of its conceptual vocabulary in the assertions. Data mining can support the discovery of hidden knowledge patterns in the data, to enrich the ontologies. We present a method for discovering multi-relational association rules, coded in SWRL, from ontological knowledge bases. Unlike state-of-the-art approaches, the method is able to take the intensional knowledge into account. Furthermore, since discovered rules are represented in SWRL, they can be straightforwardly integrated within the ontology, thus (i) enriching its expressive power and (ii) augmenting the assertional knowledge that can be derived. Discovered rules may also suggest new axioms to be added to the ontology. We performed experiments on publicly available ontologies validating the performances of our approach

Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain

Using Neural Networks for Relation Extraction from Biomedical Literature

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely, using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1