An ontology to standardize research output of nutritional epidemiology : from paper-based standards to linked content

Background: The use of linked data in the Semantic Web is a promising approach to add value to nutrition research. An ontology, which defines the logical relationships between well-defined taxonomic terms, enables linking and harmonizing research output. To enable the description of domain-specific output in nutritional epidemiology, we propose the Ontology for Nutritional Epidemiology (ONE) according to authoritative guidance for nutritional epidemiology. Methods: Firstly, a scoping review was conducted to identify existing ontology terms for reuse in ONE. Secondly, existing data standards and reporting guidelines for nutritional epidemiology were converted into an ontology. The terms used in the standards were summarized and listed separately in a taxonomic hierarchy. Thirdly, the ontologies of the nutritional epidemiologic standards, reporting guidelines, and the core concepts were gathered in ONE. Three case studies were included to illustrate potential applications: (i) annotation of existing manuscripts and data, (ii) ontology-based inference, and (iii) estimation of reporting completeness in a sample of nine manuscripts. Results: Ontologies for food and nutrition (n = 37), disease and specific population (n = 100), data description (n = 21), research description (n = 35), and supplementary (meta) data description (n = 44) were reviewed and listed. ONE consists of 339 classes: 79 new classes to describe data and 24 new classes to describe the content of manuscripts. Conclusion: ONE is a resource to automate data integration, searching, and browsing, and can be used to assess reporting completeness in nutritional epidemiology

Improving the Representation and Conversion of Mathematical Formulae by Considering their Textual Context

Mathematical formulae represent complex semantic information in a concise form. Especially in Science, Technology, Engineering, and Mathematics, mathematical formulae are crucial to communicate information, e.g., in scientific papers, and to perform computations using computer algebra systems. Enabling computers to access the information encoded in mathematical formulae requires machine-readable formats that can represent both the presentation and content, i.e., the semantics, of formulae. Exchanging such information between systems additionally requires conversion methods for mathematical representation formats. We analyze how the semantic enrichment of formulae improves the format conversion process and show that considering the textual context of formulae reduces the error rate of such conversions. Our main contributions are: (1) providing an openly available benchmark dataset for the mathematical format conversion task consisting of a newly created test collection, an extensive, manually curated gold standard and task-specific evaluation metrics; (2) performing a quantitative evaluation of state-of-the-art tools for mathematical format conversions; (3) presenting a new approach that considers the textual context of formulae to reduce the error rate for mathematical format conversions. Our benchmark dataset facilitates future research on mathematical format conversions as well as research on many problems in mathematical information retrieval. Because we annotated and linked all components of formulae, e.g., identifiers, operators and other entities, to Wikidata entries, the gold standard can, for instance, be used to train methods for formula concept discovery and recognition. Such methods can then be applied to improve mathematical information retrieval systems, e.g., for semantic formula search, recommendation of mathematical content, or detection of mathematical plagiarism.Comment: 10 pages, 4 figure

A Semantic-Agent Framework for PaaS Interoperability

Suchismita Hoare, Na Helian, and Nathan Baddoo, 'A Semantic-Agent Framework for PaaS Interoperability', in Proceedings of the The IEEE International Conference on Cloud and Big Data Computing, Toulouse, France, 18-21, July 2016. DOI: 10.1109/UIC-ATC-ScalCom-CBDCom-IoP-SmartWorld.2016.0126 © 2017 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.Cloud Platform as a Service (PaaS) is poised for a wider adoption by its relevant stakeholders, especially Cloud application developers. Despite this, the service model is still plagued with several adoption inhibitors, one of which is lack of interoperability between proprietary application infrastructure services of public PaaS solutions. Although there is some progress in addressing the general PaaS interoperability issue through various devised solutions focused primarily on API compatibility and platform-agnostic application design models, interoperability specific to differentiated services provided by the existing public PaaS providers and the resultant disparity owing to the offered services’ semantics has not been addressed effectively, yet. The literature indicates that this dimension of PaaS interoperability is awaiting evolution in the state-of-the-art. This paper proposes the initial system design of a PaaS interoperability (IntPaaS) framework to be developed through the integration of semantic and agent technologies to enable transparent interoperability between incompatible PaaS services. This will involve uniform description through semantic annotation of PaaS provider services utilizing the OWL-S ontology, creating a knowledgebase that enables software agents to automatically search for suitable services to support Cloud-based Greenfield application development. The rest of the paper discusses the identified research problem along with the proposed solution to address the issue.Submitted Versio

Enriching ontological user profiles with tagging history for multi-domain recommendations

Many advanced recommendation frameworks employ ontologies of various complexities to model individuals and items, providing a mechanism for the expression of user interests and the representation of item attributes. As a result, complex matching techniques can be applied to support individuals in the discovery of items according to explicit and implicit user preferences. Recently, the rapid adoption of Web2.0, and the proliferation of social networking sites, has resulted in more and more users providing an increasing amount of information about themselves that could be exploited for recommendation purposes. However, the unification of personal information with ontologies using the contemporary knowledge representation methods often associated with Web2.0 applications, such as community tagging, is a non-trivial task. In this paper, we propose a method for the unification of tags with ontologies by grounding tags to a shared representation in the form of Wordnet and Wikipedia. We incorporate individuals' tagging history into their ontological profiles by matching tags with ontology concepts. This approach is preliminary evaluated by extending an existing news recommendation system with user tagging histories harvested from popular social networking sites

Integration of Biological Sources: Exploring the Case of Protein Homology

Data integration is a key issue in the domain of bioin- formatics, which deals with huge amounts of heteroge- neous biological data that grows and changes rapidly. This paper serves as an introduction in the field of bioinformatics and the biological concepts it deals with, and an exploration of the integration problems a bioinformatics scientist faces. We examine ProGMap, an integrated protein homology system used by bioin- formatics scientists at Wageningen University, and several use cases related to protein homology. A key issue we identify is the huge manual effort required to unify source databases into a single resource. Un- certain databases are able to contain several possi- ble worlds, and it has been proposed that they can be used to significantly reduce initial integration efforts. We propose several directions for future work where uncertain databases can be applied to bioinformatics, with the goal of furthering the cause of bioinformatics integration

From XML to XML: The why and how of making the biodiversity literature accessible to researchers

We present the ABLE document collection, which consists of a set of annotated volumes of the Bulletin of the British Museum (Natural History). These follow our work on automating the markup of scanned copies of the biodiversity literature, for the purpose of supporting working taxonomists. We consider an enhanced TEI XML markup language, which is used as an intermediate stage in translating from the initial XML obtained from Optical Character Recognition to the target taXMLit. The intermediate representation allows additional information from external sources such as a taxonomic thesaurus to be incorporated before the final translation into taXMLit

Applications of Natural Language Processing in Biodiversity Science

Centuries of biological knowledge are contained in the massive body of scientific literature, written for human-readability but too big for any one person to consume. Large-scale mining of information from the literature is necessary if biology is to transform into a data-driven science. A computer can handle the volume but cannot make sense of the language. This paper reviews and discusses the use of natural language processing (NLP) and machine-learning algorithms to extract information from systematic literature. NLP algorithms have been used for decades, but require special development for application in the biological realm due to the special nature of the language. Many tools exist for biological information extraction (cellular processes, taxonomic names, and morphological characters), but none have been applied life wide and most still require testing and development. Progress has been made in developing algorithms for automated annotation of taxonomic text, identification of taxonomic names in text, and extraction of morphological character information from taxonomic descriptions. This manuscript will briefly discuss the key steps in applying information extraction tools to enhance biodiversity science

Advanced Knowledge Technologies at the Midterm: Tools and Methods for the Semantic Web

The University of Edinburgh and research sponsors are authorised to reproduce and distribute reprints and on-line copies for their purposes notwithstanding any copyright annotation hereon. The views and conclusions contained herein are the author’s and shouldn’t be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of other parties.In a celebrated essay on the new electronic media, Marshall McLuhan wrote in 1962:Our private senses are not closed systems but are endlessly translated into each other in that experience which we call consciousness. Our extended senses, tools, technologies, through the ages, have been closed systems incapable of interplay or collective awareness. Now, in the electric age, the very instantaneous nature of co-existence among our technological instruments has created a crisis quite new in human history. Our extended faculties and senses now constitute a single field of experience which demands that they become collectively conscious. Our technologies, like our private senses, now demand an interplay and ratio that makes rational co-existence possible. As long as our technologies were as slow as the wheel or the alphabet or money, the fact that they were separate, closed systems was socially and psychically supportable. This is not true now when sight and sound and movement are simultaneous and global in extent. (McLuhan 1962, p.5, emphasis in original)Over forty years later, the seamless interplay that McLuhan demanded between our technologies is still barely visible. McLuhan’s predictions of the spread, and increased importance, of electronic media have of course been borne out, and the worlds of business, science and knowledge storage and transfer have been revolutionised. Yet the integration of electronic systems as open systems remains in its infancy.Advanced Knowledge Technologies (AKT) aims to address this problem, to create a view of knowledge and its management across its lifecycle, to research and create the services and technologies that such unification will require. Half way through its sixyear span, the results are beginning to come through, and this paper will explore some of the services, technologies and methodologies that have been developed. We hope to give a sense in this paper of the potential for the next three years, to discuss the insights and lessons learnt in the first phase of the project, to articulate the challenges and issues that remain.The WWW provided the original context that made the AKT approach to knowledge management (KM) possible. AKT was initially proposed in 1999, it brought together an interdisciplinary consortium with the technological breadth and complementarity to create the conditions for a unified approach to knowledge across its lifecycle. The combination of this expertise, and the time and space afforded the consortium by the IRC structure, suggested the opportunity for a concerted effort to develop an approach to advanced knowledge technologies, based on the WWW as a basic infrastructure.The technological context of AKT altered for the better in the short period between the development of the proposal and the beginning of the project itself with the development of the semantic web (SW), which foresaw much more intelligent manipulation and querying of knowledge. The opportunities that the SW provided for e.g., more intelligent retrieval, put AKT in the centre of information technology innovation and knowledge management services; the AKT skill set would clearly be central for the exploitation of those opportunities.The SW, as an extension of the WWW, provides an interesting set of constraints to the knowledge management services AKT tries to provide. As a medium for the semantically-informed coordination of information, it has suggested a number of ways in which the objectives of AKT can be achieved, most obviously through the provision of knowledge management services delivered over the web as opposed to the creation and provision of technologies to manage knowledge.AKT is working on the assumption that many web services will be developed and provided for users. The KM problem in the near future will be one of deciding which services are needed and of coordinating them. Many of these services will be largely or entirely legacies of the WWW, and so the capabilities of the services will vary. As well as providing useful KM services in their own right, AKT will be aiming to exploit this opportunity, by reasoning over services, brokering between them, and providing essential meta-services for SW knowledge service management.Ontologies will be a crucial tool for the SW. The AKT consortium brings a lot of expertise on ontologies together, and ontologies were always going to be a key part of the strategy. All kinds of knowledge sharing and transfer activities will be mediated by ontologies, and ontology management will be an important enabling task. Different applications will need to cope with inconsistent ontologies, or with the problems that will follow the automatic creation of ontologies (e.g. merging of pre-existing ontologies to create a third). Ontology mapping, and the elimination of conflicts of reference, will be important tasks. All of these issues are discussed along with our proposed technologies.Similarly, specifications of tasks will be used for the deployment of knowledge services over the SW, but in general it cannot be expected that in the medium term there will be standards for task (or service) specifications. The brokering metaservices that are envisaged will have to deal with this heterogeneity.The emerging picture of the SW is one of great opportunity but it will not be a wellordered, certain or consistent environment. It will comprise many repositories of legacy data, outdated and inconsistent stores, and requirements for common understandings across divergent formalisms. There is clearly a role for standards to play to bring much of this context together; AKT is playing a significant role in these efforts. But standards take time to emerge, they take political power to enforce, and they have been known to stifle innovation (in the short term). AKT is keen to understand the balance between principled inference and statistical processing of web content. Logical inference on the Web is tough. Complex queries using traditional AI inference methods bring most distributed computer systems to their knees. Do we set up semantically well-behaved areas of the Web? Is any part of the Web in which semantic hygiene prevails interesting enough to reason in? These and many other questions need to be addressed if we are to provide effective knowledge technologies for our content on the web

Enriched biodiversity data as a resource and service

Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source “data enrichment” workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in which software developers and taxonomists came together to address the challenges and highlight the opportunities in the enrichment of such biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon. Results: The hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries: Belgium, Bulgaria, Canada, Finland, Germany, Italy, the Netherlands, New Zealand, the UK, and the US. The participants brought expertise in processing structured data, text mining, development of ontologies, digital identification keys, geographic information systems, niche modeling, natural language processing, provenance annotation, semantic integration, taxonomic name resolution, web service interfaces, workflow tools and visualisation. Most use cases and exemplar data were provided by taxonomists. One goal of the meeting was to facilitate re-use and enhancement of biodiversity knowledge by a broad range of stakeholders, such as taxonomists, systematists, ecologists, niche modelers, informaticians and ontologists. The suggested use cases resulted in nine breakout groups addressing three main themes: i) mobilising heritage biodiversity knowledge; ii) formalising and linking concepts; and iii) addressing interoperability between service platforms. Another goal was to further foster a community of experts in biodiversity informatics and to build human links between research projects and institutions, in response to recent calls to further such integration in this research domain. Conclusions: Beyond deriving prototype solutions for each use case, areas of inadequacy were discussed and are being pursued further. It was striking how many possible applications for biodiversity data there were and how quickly solutions could be put together when the normal constraints to collaboration were broken down for a week. Conversely, mobilising biodiversity knowledge from their silos in heritage literature and natural history collections will continue to require formalisation of the concepts (and the links between them) that define the research domain, as well as increased interoperability between the software platforms that operate on these concepts