Jouni Tuominen

Building a national semantic web ontology and ontology service infrastructure the FinnONTO approach

This paper presents the vision and results of creating a national level cross-domain ontology and ontology service infrastructure in Finland. The novelty of the infrastructure is based on two ideas. First, a system of open source core ontologies is being developed by transforming thesauri into mutually aligned lightweight ontologies, including a large top ontology that is extended by various domain specific ontologies. Second, the ONKI Ontology Server framework for publishing ontologies as ready to use services has been designed and implemented. ONKI provides legacy and other applications with ready to use functionalities for using ontologies on the HTML level by Ajax and semantic widgets. The idea is to use ONKI for creating mash-up applications in a way analogous to using Google or Yahoo Maps, but in our case external applications are mashed-up with ontology support.

ONKI SKOS Server for Publishing and Utilizing SKOS Vocabularies and Ontologies as Services

Vocabularies are the building blocks of the Semantic Web providing shared terminological resources for content indexing, information retrieval, data exchange, and content integration. Most semantic web applications in practical use are based on lightweight ontologies and, more recently, on the Simple Knowledge Organization System (SKOS) data model being standardized by W3C. Easy and cost-efficient publication, integration, and utilization methods of vocabulary services are therefore highly important for the proliferation of the Semantic Web. This paper presents the ONKI SKOS Server for these tasks. Using ONKI SKOS, a SKOS vocabulary or a lightweight ontology can be published on the web as ready-to-use services in a matter of minutes. The services include not only a browser for human usage, but also Web Service and AJAX interfaces for concept finding, selecting and transporting resources from the ONKI SKOS Server to connected systems. Code generation services for AJAX and Web Service APIs are provided automatically, too. ONKI SKOS services are also used for semantic query expansion in information retrieval tasks. The idea of publishing ontologies as services is analogous to Google Maps. In our case, however, vocabulary services are provided and mashed-up in applications. ONKI SKOS was published in the beginning of 2008 and is to our knowledge the first generic SKOS server of its kind. The system has been used to publish and utilize some 60 vocabularies and ontologies in the National Finnish Ontology Service ONKI www.yso.fi.

Ontology Libraries for Production Use: The Finnish Ontology Library Service ONKI

This paper discusses problems of creating and using ontology library services in production use. One approach to a solution is presented with an online implementation--the Finnish Ontology Library Service ONKI-- that is in pilot use on a national level in Finland. ONKI contributes to previous research on ontology libraries in many ways: First, mashup and web service support with various tools is provided for cost-efficient utilization of ontologies in indexing and search applications. Second, services covering the different phases of the ontology life cycle are provided. Third, the services are provided and used in real world applications on a national scale. Fourth, the ontology framework is being developed by a collaborative effort by organizations representing different application domains, such as health, culture, and business.

CultureSampo: A National Publication System of Cultural Heritage on the Semantic Web 2.0

CultureSampo is an application demonstration of a national level publication system of cultural heritage contents on the Web, based on ideas and technologies of the Semantic (Web and) Web 2.0. On the semantic side, the system presents new solutions to interoperability problems of dealing with multiple ontologies of different domains, and to problems of integrating multiple metadata schemas and cross-domain content into a homogeneous semantic portal. A novelty of the system is to use semantic models based on events and narrative process descriptions for modeling and visualizing cultural phenomena, and for semantic recommendations. On the Web 2.0 side, CultureSampo proposes and demonstrates a content creation process for collaborative, distributed ontology and content development including different memory organizations and citizens. The system provides the cultural heritage contents to end-users in a new way through multiple (nine) thematic perspectives, based on semantic visualizations. Furthermore, CultureSampo services are available for external web-applications to use through semantic AJAX widgets.

Biological names and taxonomies on the semantic web: managing the change in scientific conception

Biodiversity management requires the usage of heterogeneous biological information from multiple sources. Indexing, aggregating, and finding such information is based on names and taxonomic knowledge of organisms. However, taxonomies change in time due to new scientific findings, opinions of authorities, and changes in our conception about life forms. Furthermore, organism names and their meaning change in time, different authorities use different scientific names for the same taxon in different times, and various vernacular names are in use in different languages. This makes data integration and information retrieval difficult without detailed biological information. This paper introduces a meta-ontology for managing the names and taxonomies of organisms, and presents three applications for it: 1) publishing biological species lists as ontology services (ca. 20 taxonomies including more than 80,000 names), 2) collaborative management of the vernacular names of vascular plants (ca. 26,000 taxa), and 3) management of individual scientific name changes based on research results, covering a group of beetles. The applications are based on the databases of the Finnish Museum of Natural History and are used in a living lab environment on the web.

Elements of a National SemanticWeb Infrastructure--Case Study Finland on the Semantic Web

This article presents the vision and results of creating the basis for a national semantic Web content infrastructure in Finland in 2003-2007. The main elements of the infrastructure are shared and open metadata schemas, core ontologies, and public ontology services. Several practical applications testing and demonstrating the usefulness of the infrastructure are overviewed in the fields of eculture, ehealth, egovernment, elearning, and ecommerce.

Linked Data Finland: A 7-star Model and Platform for Publishing and Re-using Linked Datasets

The idea of Linked Data is to aggregate, harmonize, integrate, enrich, and publish data for re-use on the Web in a cost-efficient way using Semantic Web technologies. We concern two major hindrances for re-using Linked Data: It is often difficult for a re-user to (1) understand the characteristics of the dataset and (2) evaluate the quality the data for the intended purpose. This paper introduces the “Linked Data Finland” platform LDF.fi addressing these issues. We extend the famous 5-star model of Tim Berners-Lee, with the sixth star for providing the dataset with a schema that explains the dataset, and the seventh star for validating the data against the schema. LDF.fi also automates data publishing and provides data curation tools. The first prototype of the platform is available on the web as a service, hosting tens of datasets and supporting several applications.

Representing and Utilizing Changing Historical Places as an Ontology Time Series

Place names and their geographical coverage change in time. This causes problems when retrieving information content related to different times. Geo-content is usually indexed using place names of the time of indexing (e.g. a photo of the 1968 upraise of Czechoslovakia indexed then) or of the time that the content has been used or created (e.g. a spear used in the Punic Wars in 146 b.c. in Carthago but indexed at a later time using place names of that time). Finally, end-users may query content in terms of contemporary place names (e.g. Check Republic or Slovakia) or overlapping historic names of different times (e.g. Roman Empire). This chapter presents an ontology-based approach to this problem. The idea is to represent and maintain a time series of spatial ontologies in terms of easily manageable local spatio-temporal changes from which the actual time series ontology can be generated automatically with semantic enrichment. This ontology can then be used for indexing and for mapping spatio-temporal regions and their names onto each other. As a proof-of-concept, the system has been applied to modeling the history municipalities of Finland in 1865–2010. We present the model, a tool for maintaining the change history in a user-friendly way, transformation of the place change history into an ontology time series with semantic enrichment, and publication of the ontology as a ready to use ontology services on the web with AJAX, Web Service, and REST interfaces. The system has been applied in the semantic cultural heritage portal CultureSampo for semantic search and recommendation, as well as an external service for indexing cultural heritage content, and for query expansion search in a legacy cultural heritage database system.

Making species checklists understandable to machines - a shift from relational databases to ontologies.

BackgroundThe scientific names of plants and animals play a major role in Life Sciences as information is indexed, integrated, and searched using scientific names. The main problem with names is their ambiguous nature, because more than one name may point to the same taxon and multiple taxa may share the same name. In addition, scientific names change over time, which makes them open to various interpretations. Applying machine-understandable semantics to these names enables efficient processing of biological content in information systems. The first step is to use unique persistent identifiers instead of name strings when referring to taxa. The most commonly used identifiers are Life Science Identifiers (LSID), which are traditionally used in relational databases, and more recently HTTP URIs, which are applied on the Semantic Web by Linked Data applications.ResultsWe introduce two models for expressing taxonomic information in the form of species checklists. First, we show how species checklists are presented in a relational database system using LSIDs. Then, in order to gain a more detailed representation of taxonomic information, we introduce meta-ontology TaxMeOn to model the same content as Semantic Web ontologies where taxa are identified using HTTP URIs. We also explore how changes in scientific names can be managed over time.ConclusionsThe use of HTTP URIs is preferable for presenting the taxonomic information of species checklists. An HTTP URI identifies a taxon and operates as a web address from which additional information about the taxon can be located, unlike LSID. This enables the integration of biological data from different sources on the web using Linked Data principles and prevents the formation of information silos. The Linked Data approach allows a user to assemble information and evaluate the complexity of taxonomical data based on conflicting views of taxonomic classifications. Using HTTP URIs and Semantic Web technologies also facilitate the representation of the semantics of biological data, and in this way, the creation of more “intelligent” biological applications and services.

The Birds of the World Ontology AVIO

We present an ontology for managing the scientific and common names of birds. The ontology is based on the TaxMeOn meta-ontology model for biological names. The ontology is in use as an ontology service and it has been applied in a bird watching system.