The development of spatio–temporal geoscience information systems (TGSIS) as the next generation of geographic information systems (GIS) and geoscience information systems (GSIS) was investigated with respect to the following four aspects: concepts, data models, software, and applications. These systems are capable of capturing, storing, managing, and querying data of geo–objects subject to dynamic processes, thereby causing the evolution of their geometry, topology and geoscience properties. In this study, five data models were proposed. The first data model represents static geo–objects whose geometries are in the 3–dimensional space. The second and third data models represent geological surfaces evolving in a discrete and continuous manner, respectively. The fourth data model is a general model that represents geo–objects whose geometries are n–dimensional embedding in the m–dimensional space R^m, m >= 3. The topology and the properties of these geo–objects are also represented in the data model. In this model, time is represented as one dimension (valid time). Moreover, the valid time is an independent variable, whereas geometry, topology, and the properties are dependent (on time) variables. The fifth data model represents multiple indexed geoscience data in which time and other non–spatial dimensions are interpreted as larger spatial dimensions. To capture data in space and time, morphological interpolation methods were reviewed, and a new morphological interpolation method was proposed to model geological surfaces evolving continuously in a time interval. This algorithm is based on parameterisation techniques to locate the cross–reference and then compute the trajectories complying with geometrical constraints. In addition, the long transaction feature was studied, and the data schema, functions, triggers, and views were proposed to implement the long transaction feature and the database versioning in PostgreSQL. To implement database versioning tailored to geoscience applications, an algorithm comparing two triangulated meshes was also proposed. Therefore, TGSIS enable geologists to manage different versions of geoscience data for different geological paradigms, data, and authors. Finally, a prototype software system was built. This system uses the client/server architecture in which the server side uses the PostgreSQL database management system and the client side uses the gOcad geomodeling system. The system was also applied to certain sample applications.

Today, data is collected in ever increasing scale and variety, opening up enormous potential for new insights and data-centric products. However, in many cases the volume and heterogeneity of new data sources precludes up-front integration using traditional ETL processes and data warehouses. In some cases, it is even unclear if and in what context the collected data will be utilized. Therefore, there is a need for agile methods that defer the effort of integration until the usage context is established. This thesis introduces Query-Time Data Integration as an alternative concept to traditional up-front integration. It aims at enabling users to issue ad-hoc queries on their own data as if all potential other data sources were already integrated, without declaring specific sources and mappings to use. Automated data search and integration methods are then coupled directly with query processing on the available data. The ambiguity and uncertainty introduced through fully automated retrieval and mapping methods is compensated by answering those queries with ranked lists of alternative results. Each result is then based on different data sources or query interpretations, allowing users to pick the result most suitable to their information need. To this end, this thesis makes three main contributions. Firstly, we introduce a novel method for Top-k Entity Augmentation, which is able to construct a top-k list of consistent integration results from a large corpus of heterogeneous data sources. It improves on the state-of-the-art by producing a set of individually consistent, but mutually diverse, set of alternative solutions, while minimizing the number of data sources used. Secondly, based on this novel augmentation method, we introduce the DrillBeyond system, which is able to process Open World SQL queries, i.e., queries referencing arbitrary attributes not defined in the queried database. The original database is then augmented at query time with Web data sources providing those attributes. Its hybrid augmentation/relational query processing enables the use of ad-hoc data search and integration in data analysis queries, and improves both performance and quality when compared to using separate systems for the two tasks. Finally, we studied the management of large-scale dataset corpora such as data lakes or Open Data platforms, which are used as data sources for our augmentation methods. We introduce Publish-time Data Integration as a new technique for data curation systems managing such corpora, which aims at improving the individual reusability of datasets without requiring up-front global integration. This is achieved by automatically generating metadata and format recommendations, allowing publishers to enhance their datasets with minimal effort. Collectively, these three contributions are the foundation of a Query-time Data Integration architecture, that enables ad-hoc data search and integration queries over large heterogeneous dataset collections.

There is an ever-increasing amount and variety of open web data available that is insufficiently examined or not considered at all in decision making processes. This is because of the lack of end-user friendly tools that help to reuse this public data and to create knowledge out of it. Therefore, we propose a schema-optional data repository that provides the flexibility necessary to store and gradually integrate heterogeneous web data. Based on this repository, we propose a semi-automatic schema enrichment approach that efficiently augments the data in a “pay-as-you-go” fashion. Due to the inherently appearing ambiguities we further propose a crowd-based verification component that is able to resolve such conflicts in a scalable manner. / Die stetig wachsende Zahl offen verfügbarer Webdaten findet momentan viel zu wenig oder gar keine Berücksichtigung in Entscheidungsprozessen. Der Grund hierfür ist insbesondere in der mangelnden Unterstützung durch anwenderfreundliche Werkzeuge zu finden, die diese Daten nutzbar machen und Wissen daraus genieren können. Zu diesem Zweck schlagen wir ein schemaoptionales Datenrepositorium vor, welches ermöglicht, heterogene Webdaten zu speichern sowie kontinuierlich zu integrieren und mit Schemainformation anzureichern. Auf Grund der dabei inhärent auftretenden Mehrdeutigkeiten, soll dieser Prozess zusätzlich um eine Crowd-basierende Verifikationskomponente unterstützt werden.

Schema and ontology matching play an important part in the field of data integration and semantic web. Given two heterogeneous data sources, meta data matching usually constitutes the first step in the data integration workflow, which refers to the analysis and comparison of two input resources like schemas or ontologies. The result is a list of correspondences between the two schemas or ontologies, which is often called mapping or alignment. Many tools and research approaches have been proposed to automatically determine those correspondences. However, most match tools do not provide any information about the relation type that holds between matching concepts, for the simple but important reason that most common match strategies are too simple and heuristic to allow any sophisticated relation type determination. Knowing the specific type holding between two concepts, e.g., whether they are in an equality, subsumption (is-a) or part-of relation, is very important for advanced data integration tasks, such as ontology merging or ontology evolution. It is also very important for mappings in the biological or biomedical domain, where is-a and part-of relations may exceed the number of equality correspondences by far. Such more expressive mappings allow much better integration results and have scarcely been in the focus of research so far. In this doctoral thesis, the determination of the correspondence types in a given mapping is the focus of interest, which is referred to as semantic mapping enrichment. We introduce and present the mapping enrichment tool STROMA, which obtains a pre-calculated schema or ontology mapping and for each correspondence determines a semantic relation type. In contrast to previous approaches, we will strongly focus on linguistic laws and linguistic insights. By and large, linguistics is the key for precise matching and for the determination of relation types. We will introduce various strategies that make use of these linguistic laws and are able to calculate the semantic type between two matching concepts. The observations and insights gained from this research go far beyond the field of mapping enrichment and can be also applied to schema and ontology matching in general. Since generic strategies have certain limits and may not be able to determine the relation type between more complex concepts, like a laptop and a personal computer, background knowledge plays an important role in this research as well. For example, a thesaurus can help to recognize that these two concepts are in an is-a relation. We will show how background knowledge can be effectively used in this instance, how it is possible to draw conclusions even if a concept is not contained in it, how the relation types in complex paths can be resolved and how time complexity can be reduced by a so-called bidirectional search. The developed techniques go far beyond the background knowledge exploitation of previous approaches, and are now part of the semantic repository SemRep, a flexible and extendable system that combines different lexicographic resources. Further on, we will show how additional lexicographic resources can be developed automatically by parsing Wikipedia articles. The proposed Wikipedia relation extraction approach yields some millions of additional relations, which constitute significant additional knowledge for mapping enrichment. The extracted relations were also added to SemRep, which thus became a comprehensive background knowledge resource. To augment the quality of the repository, different techniques were used to discover and delete irrelevant semantic relations. We could show in several experiments that STROMA obtains very good results w.r.t. relation type detection. In a comparative evaluation, it was able to achieve considerably better results than related applications. This corroborates the overall usefulness and strengths of the implemented strategies, which were developed with particular emphasis on the principles and laws of linguistics.

Today, data is collected in ever increasing scale and variety, opening up enormous potential for new insights and data-centric products. However, in many cases the volume and heterogeneity of new data sources precludes up-front integration using traditional ETL processes and data warehouses. In some cases, it is even unclear if and in what context the collected data will be utilized. Therefore, there is a need for agile methods that defer the effort of integration until the usage context is established. This thesis introduces Query-Time Data Integration as an alternative concept to traditional up-front integration. It aims at enabling users to issue ad-hoc queries on their own data as if all potential other data sources were already integrated, without declaring specific sources and mappings to use. Automated data search and integration methods are then coupled directly with query processing on the available data. The ambiguity and uncertainty introduced through fully automated retrieval and mapping methods is compensated by answering those queries with ranked lists of alternative results. Each result is then based on different data sources or query interpretations, allowing users to pick the result most suitable to their information need. To this end, this thesis makes three main contributions. Firstly, we introduce a novel method for Top-k Entity Augmentation, which is able to construct a top-k list of consistent integration results from a large corpus of heterogeneous data sources. It improves on the state-of-the-art by producing a set of individually consistent, but mutually diverse, set of alternative solutions, while minimizing the number of data sources used. Secondly, based on this novel augmentation method, we introduce the DrillBeyond system, which is able to process Open World SQL queries, i.e., queries referencing arbitrary attributes not defined in the queried database. The original database is then augmented at query time with Web data sources providing those attributes. Its hybrid augmentation/relational query processing enables the use of ad-hoc data search and integration in data analysis queries, and improves both performance and quality when compared to using separate systems for the two tasks. Finally, we studied the management of large-scale dataset corpora such as data lakes or Open Data platforms, which are used as data sources for our augmentation methods. We introduce Publish-time Data Integration as a new technique for data curation systems managing such corpora, which aims at improving the individual reusability of datasets without requiring up-front global integration. This is achieved by automatically generating metadata and format recommendations, allowing publishers to enhance their datasets with minimal effort. Collectively, these three contributions are the foundation of a Query-time Data Integration architecture, that enables ad-hoc data search and integration queries over large heterogeneous dataset collections.

Web data is characterized by a great structural diversity as well as frequent changes, which poses a great challenge for web applications based on that data. We want to address this problem by developing a schema-optional and flexible data model that supports the integration of heterogenous and volatile web data. Therefore, we want to rely on graph-based models that allow to incrementally extend the schema by various information and constraints. Inspired by the on-going web 2.0 trend, we want users to participate in the design and management of the schema. By incrementally adding structural information, users can enhance the schema to meet their very specific requirements.

Storing and processing data at different locations using a heterogeneous set of formats and data managements systems is state-of-the-art in many organizations. However, data analyses can often provide better insight when data from several sources is integrated into a combined perspective. In this paper we present an overview of our data integration system DataCalc. DataCalc is an extensible integration platform that executes adhoc analytical queries on a set of heterogeneous data processors. Our novel platform uses an expressive function shipping interface that promotes local computation and reduces data movement between processors. In this paper, we provide a discussion of the overall architecture and the main components of DataCalc. Moreover, we discuss the cost of integrating additional processors and evaluate the overall performance of the platform.

Many organizations store and process data at different locations using a heterogeneous set of formats and data management systems. However, data analyses can often provide better insight when data from several sources is integrated into a combined perspective. DataCalc is an extensible data integration platform that executes ad-hoc analytical queries on a set of heterogeneous data processors. The platform uses an expressive function shipping interface that promotes local computation and reduces data movement between processors. In this paper, we provide a detailed discussion of the architecture and implementation of DataCalc. We introduce data processors for plain files, JDBC, the MongoDB document store, and a custom in memory system. Finally, we discuss the cost of integrating additional processors and evaluate the overall performance of the platform. Our main contribution is the specification and evaluation of the DataCalc code delegation interface.

This thesis is a compendium of scientific works and engineering specifications that have been contributed to a large community of stakeholders to be copied, adapted, mixed, built upon and exploited in any way possible to achieve a common goal: Integrating Natural Language Processing (NLP) and Language Resources Using Linked Data The explosion of information technology in the last two decades has led to a substantial growth in quantity, diversity and complexity of web-accessible linguistic data. These resources become even more useful when linked with each other and the last few years have seen the emergence of numerous approaches in various disciplines concerned with linguistic resources and NLP tools. It is the challenge of our time to store, interlink and exploit this wealth of data accumulated in more than half a century of computational linguistics, of empirical, corpus-based study of language, and of computational lexicography in all its heterogeneity. The vision of the Giant Global Graph (GGG) was conceived by Tim Berners-Lee aiming at connecting all data on the Web and allowing to discover new relations between this openly-accessible data. This vision has been pursued by the Linked Open Data (LOD) community, where the cloud of published datasets comprises 295 data repositories and more than 30 billion RDF triples (as of September 2011). RDF is based on globally unique and accessible URIs and it was specifically designed to establish links between such URIs (or resources). This is captured in the Linked Data paradigm that postulates four rules: (1) Referred entities should be designated by URIs, (2) these URIs should be resolvable over HTTP, (3) data should be represented by means of standards such as RDF, (4) and a resource should include links to other resources. Although it is difficult to precisely identify the reasons for the success of the LOD effort, advocates generally argue that open licenses as well as open access are key enablers for the growth of such a network as they provide a strong incentive for collaboration and contribution by third parties. In his keynote at BNCOD 2011, Chris Bizer argued that with RDF the overall data integration effort can be “split between data publishers, third parties, and the data consumer”, a claim that can be substantiated by observing the evolution of many large data sets constituting the LOD cloud. As written in the acknowledgement section, parts of this thesis has received numerous feedback from other scientists, practitioners and industry in many different ways. The main contributions of this thesis are summarized here: Part I – Introduction and Background. During his keynote at the Language Resource and Evaluation Conference in 2012, Sören Auer stressed the decentralized, collaborative, interlinked and interoperable nature of the Web of Data. The keynote provides strong evidence that Semantic Web technologies such as Linked Data are on its way to become main stream for the representation of language resources. The jointly written companion publication for the keynote was later extended as a book chapter in The People’s Web Meets NLP and serves as the basis for “Introduction” and “Background”, outlining some stages of the Linked Data publication and refinement chain. Both chapters stress the importance of open licenses and open access as an enabler for collaboration, the ability to interlink data on the Web as a key feature of RDF as well as provide a discussion about scalability issues and decentralization. Furthermore, we elaborate on how conceptual interoperability can be achieved by (1) re-using vocabularies, (2) agile ontology development, (3) meetings to refine and adapt ontologies and (4) tool support to enrich ontologies and match schemata. Part II - Language Resources as Linked Data. “Linked Data in Linguistics” and “NLP & DBpedia, an Upward Knowledge Acquisition Spiral” summarize the results of the Linked Data in Linguistics (LDL) Workshop in 2012 and the NLP & DBpedia Workshop in 2013 and give a preview of the MLOD special issue. In total, five proceedings – three published at CEUR (OKCon 2011, WoLE 2012, NLP & DBpedia 2013), one Springer book (Linked Data in Linguistics, LDL 2012) and one journal special issue (Multilingual Linked Open Data, MLOD to appear) – have been (co-)edited to create incentives for scientists to convert and publish Linked Data and thus to contribute open and/or linguistic data to the LOD cloud. Based on the disseminated call for papers, 152 authors contributed one or more accepted submissions to our venues and 120 reviewers were involved in peer-reviewing. “DBpedia as a Multilingual Language Resource” and “Leveraging the Crowdsourcing of Lexical Resources for Bootstrapping a Linguistic Linked Data Cloud” contain this thesis’ contribution to the DBpedia Project in order to further increase the size and inter-linkage of the LOD Cloud with lexical-semantic resources. Our contribution comprises extracted data from Wiktionary (an online, collaborative dictionary similar to Wikipedia) in more than four languages (now six) as well as language-specific versions of DBpedia, including a quality assessment of inter-language links between Wikipedia editions and internationalized content negotiation rules for Linked Data. In particular the work described in created the foundation for a DBpedia Internationalisation Committee with members from over 15 different languages with the common goal to push DBpedia as a free and open multilingual language resource. Part III - The NLP Interchange Format (NIF). “NIF 2.0 Core Specification”, “NIF 2.0 Resources and Architecture” and “Evaluation and Related Work” constitute one of the main contribution of this thesis. The NLP Interchange Format (NIF) is an RDF/OWL-based format that aims to achieve interoperability between Natural Language Processing (NLP) tools, language resources and annotations. The core specification is included in and describes which URI schemes and RDF vocabularies must be used for (parts of) natural language texts and annotations in order to create an RDF/OWL-based interoperability layer with NIF built upon Unicode Code Points in Normal Form C. In , classes and properties of the NIF Core Ontology are described to formally define the relations between text, substrings and their URI schemes. contains the evaluation of NIF. In a questionnaire, we asked questions to 13 developers using NIF. UIMA, GATE and Stanbol are extensible NLP frameworks and NIF was not yet able to provide off-the-shelf NLP domain ontologies for all possible domains, but only for the plugins used in this study. After inspecting the software, the developers agreed however that NIF is adequate enough to provide a generic RDF output based on NIF using literal objects for annotations. All developers were able to map the internal data structure to NIF URIs to serialize RDF output (Adequacy). The development effort in hours (ranging between 3 and 40 hours) as well as the number of code lines (ranging between 110 and 445) suggest, that the implementation of NIF wrappers is easy and fast for an average developer. Furthermore the evaluation contains a comparison to other formats and an evaluation of the available URI schemes for web annotation. In order to collect input from the wide group of stakeholders, a total of 16 presentations were given with extensive discussions and feedback, which has lead to a constant improvement of NIF from 2010 until 2013. After the release of NIF (Version 1.0) in November 2011, a total of 32 vocabulary employments and implementations for different NLP tools and converters were reported (8 by the (co-)authors, including Wiki-link corpus, 13 by people participating in our survey and 11 more, of which we have heard). Several roll-out meetings and tutorials were held (e.g. in Leipzig and Prague in 2013) and are planned (e.g. at LREC 2014). Part IV - The NLP Interchange Format in Use. “Use Cases and Applications for NIF” and “Publication of Corpora using NIF” describe 8 concrete instances where NIF has been successfully used. One major contribution in is the usage of NIF as the recommended RDF mapping in the Internationalization Tag Set (ITS) 2.0 W3C standard and the conversion algorithms from ITS to NIF and back. One outcome of the discussions in the standardization meetings and telephone conferences for ITS 2.0 resulted in the conclusion there was no alternative RDF format or vocabulary other than NIF with the required features to fulfill the working group charter. Five further uses of NIF are described for the Ontology of Linguistic Annotations (OLiA), the RDFaCE tool, the Tiger Corpus Navigator, the OntosFeeder and visualisations of NIF using the RelFinder tool. These 8 instances provide an implemented proof-of-concept of the features of NIF. starts with describing the conversion and hosting of the huge Google Wikilinks corpus with 40 million annotations for 3 million web sites. The resulting RDF dump contains 477 million triples in a 5.6 GB compressed dump file in turtle syntax. describes how NIF can be used to publish extracted facts from news feeds in the RDFLiveNews tool as Linked Data. Part V - Conclusions. provides lessons learned for NIF, conclusions and an outlook on future work. Most of the contributions are already summarized above. One particular aspect worth mentioning is the increasing number of NIF-formated corpora for Named Entity Recognition (NER) that have come into existence after the publication of the main NIF paper Integrating NLP using Linked Data at ISWC 2013. These include the corpora converted by Steinmetz, Knuth and Sack for the NLP & DBpedia workshop and an OpenNLP-based CoNLL converter by Brümmer. Furthermore, we are aware of three LREC 2014 submissions that leverage NIF: NIF4OGGD - NLP Interchange Format for Open German Governmental Data, N^3 – A Collection of Datasets for Named Entity Recognition and Disambiguation in the NLP Interchange Format and Global Intelligent Content: Active Curation of Language Resources using Linked Data as well as an early implementation of a GATE-based NER/NEL evaluation framework by Dojchinovski and Kliegr. Further funding for the maintenance, interlinking and publication of Linguistic Linked Data as well as support and improvements of NIF is available via the expiring LOD2 EU project, as well as the CSA EU project called LIDER, which started in November 2013. Based on the evidence of successful adoption presented in this thesis, we can expect a decent to high chance of reaching critical mass of Linked Data technology as well as the NIF standard in the field of Natural Language Processing and Language Resources.

Motivation: Although various high-throughput technologies provide a lot of valuable information, each of them is giving an insight into different aspects of cellular activity and each has its own limitations. Thus, a complete and systematic understanding of the cellular machinery can be achieved only by a combined analysis of results coming from different approaches. However, methods and tools for integration and analysis of heterogenous biological data still have to be developed. Results: This work presents systemic analysis of basic cellular processes, i.e. cell viability and cell cycle, as well as embryonic stem cell pluripotency and differentiation. These phenomena were studied using several high-throughput technologies, whose combined results were analysed with existing and novel clustering and hit selection algorithms. This thesis also introduces two novel data management and data analysis tools. The first, called DSViewer, is a database application designed for integrating and querying results coming from various genome-wide experiments. The second, named PhenoFam, is an application performing gene set enrichment analysis by employing structural and functional information on families of protein domains as annotation terms. Both programs are accessible through a web interface. Conclusions: Eventually, investigations presented in this work provide the research community with novel and markedly improved repertoire of computational tools and methods that facilitate the systematic analysis of accumulated information obtained from high-throughput studies into novel biological insights.