It is not easy to apply XML in e-commerce development for achieving interoperability in heterogeneous environments. One of the reasons is a multitude of XML-based Frameworks for Internet Commerce (XFIC), or industrial standards. This thesis surveys 15 frameworks, i.e., ebXML, eCo Framework, UDDI, SOAP, BizTalk, cXML, ICE, Open Applications Group, RosettaNet, Wf-XML, OFX, VoiceXML, RDF, WSDL and xCBL. This thesis provides three models to systematically understand how the 15 frameworks meet the requirements of e-commerce. A hierarchical model is presented to show the purpose and focus of various XFIC initiatives. A relationship model is given to show the cooperative and competitive relationships between XFIC. A chronological model is provided to look at the development of XFIC. In addition, the thesis offers guidelines for how to apply XFIC in an e-commerce development. We have also implemented a B2B e-procurement system. That not only demonstrates the feasibility of opensource or freeware, but also validates the complementary roles of XML and Java: XML is for describing contents and Java is for automating XML documents (session handling). Auction-based dynamic pricing is also realized as a feature of interest. Moreover, the implementation shows the suitability of e-procurement for educational purposes in e-commerce development. / <p>Report code: LiU-Tek-Lic-2001:19.</p>

Duplex stainless steels (DSSs) are important engineering materials due to their combination of good mechanical properties and corrosion resistance. However, as a consequence of their ferrite content, DSSs are sensitive to the so-called ‘475°C embrittlement’, which is induced by phase separation, namely, the ferrite decomposed into Fe-rich ferrite (α) and Cr-rich ferrite (α'), respectively. The phase separation is accompanied with a severe loss of toughness. Thus, the ‘475°C embrittlement’ phenomenon limits DSSs’ upper service temperature to around 250°C. In the present work, Fe-Cr binary model alloys and commercial DSSs from weldments were investigated for the study of phase separation in ferrite. Different techniques were employed to study the phase separation in model alloys and commercial DSSs, including atom probe tomography, transmission electron microscopy and micro-hardness test. Three different model alloys, Fe-25Cr, Fe-30Cr and Fe-35Cr (wt. %) were analyzed by atom probe tomography after different aging times. A new method based on radial distribution function was developed to evaluate the wavelength and amplitude of phase separation in these Fe-Cr binary alloys. The results were compared with the wavelengths obtained from 1D auto-correlation function and amplitudes from Langer-Bar-On-Miller method. It was found that the wavelengths from 1D auto-correlation function cannot reflect the 3D nano-scaled structures as accurate as those obtained by radial distribution function. Furthermore, the Langer-Bar-On-Miller method underestimates the amplitudes of phase separation. Commercial DSSs of SAF2205, 2304, 2507 and 25.10.4L were employed to investigate the connections between phase separation and mechanical properties from different microstructures (base metal, heat-affected-zone and welding bead) in welding. Moreover, the effect of external tensile stress during aging on phase separation of ferrite was also investigated. It was found that atom probe tomography is very useful for the analysis of phase separation in ferrite and the radial distribution function (RDF) is an effective method to compare the extent of phase separation at the very early stages. RDF is even more sensitive than frequency diagrams. In addition, the results indicate that the mechanical properties are highly connected with the phase separation in ferrite and other phenomena, such as Ni-Mn-Si-Cu clusters, that can also deteriorate the mechanical properties. / <p>QC 20130308</p>

Federated RDF querying systems provide an interface to multiple autonomous RDF data sources, allowing a user to execute a SPARQL query on multiple data sources at once and get one unified result. When these autonomous data sources use different vocabularies, the SPARQL query must be rewritten to the vocabulary of the data source in order to get the desired results. This thesis describes how vocabulary mappings can be used to rewrite SPARQL queries for federated RDF query processing. In this thesis, different types of vocabulary mappings are explored to find a suitable vocabulary mapping representation to use in formulating an approach for query rewriting. The approach describes how the SPARQL subqueries and solution mappings can be rewritten in order to handle heterogeneous vocabularies. The thesis then presents how the query federation engine HeFQUIN is extended to rewrite the federated queries and their results. A final evaluation of the implementation shows how implementing a query rewriting approach can improve the federated query engine’s execution times.

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Tesis por compendio / [ES] La mejora genética vegetal tiene como objetivo la obtención de plantas con rasgos mejorados o características novedosas que podrían ayudar a superar los objetivos de sostenibilidad. Para este fin, la biotecnología vegetal necesita incorporar nuevas herramientas de ingeniería genética que combinen una mayor precisión con una mayor capacidad de mejora. Las herramientas de edición genética recientemente descubiertas basadas en la tecnología CRISPR/Cas9 han abierto el camino para modificar los genomas de las plantas con una precisión sin precedentes. Por otro lado, los nuevos enfoques de biología sintética basados en la modularidad y la estandarización de los elementos genéticos han permitido la construcción de dispositivos genéticos cada vez más complejos y refinados aplicados a la mejora genética vegetal. Con el objetivo final de expandir la caja de herramientas biotecnológicas para la mejora vegetal, esta tesis describe el desarrollo y la adaptación de dos nuevas herramientas: una nueva endonucleasa específica de sitio (SSN) y un interruptor genético modular para la regulación de la expresión transgénica. En una primera parte, esta tesis describe la adaptación de CRISPR/Cas12a para la expresión en plantas y compara la eficiencia de las variantes de Acidaminococcus (As) y Lachnospiraceae (Lb) Cas12a con Streptococcus pyogens Cas9 (SpCas9) descritos anteriormente en ocho loci de Nicotiana benthamiana usando expresión transitoria. LbCas12a mostró la actividad de mutagénesis promedio más alta en los loci analizados. Esta actividad también se confirmó en experimentos de transformación estable realizados en tres plantas modelo diferentes, a saber, N. benthamiana, Solanum lycopersicum y Arabidopsis thaliana. Para este último, los efectos mutagénicos colaterales fueron analizados en líneas segregantes sin la endonucleasa Cas12a, mediante secuenciación del genoma descartándose efectos indiscriminados. En conjunto, los resultados muestran que LbCas12a es una alternativa viable a SpCas9 para la edición genética en plantas. En una segunda parte, este trabajo describe un interruptor genético reversible destinado a controlar la expresión génica en plantas con mayor precisión que los sistemas inducibles tradicionales. Este interruptor, basado en el sistema de recombinación del fago PhiC31, fue construido como un dispositivo modular hecho de partes de ADN estándar y diseñado para controlar el estado transcripcional (encendido o apagado) de dos genes de interés mediante la inversión alternativa de un elemento regulador central de ADN. El estado del interruptor puede ser operado externa y reversiblemente por la acción de los actuadores de recombinación y su cinética, memoria y reversibilidad fueron ampliamente caracterizados en experimentos de transformación transitoria y estable en N. benthamiana. En conjunto, esta tesis muestra el diseño y la caracterización funcional de herramientas para la ingeniería del genómica y biología sintética de plantas que ahora ha sido completada con el sistema de edición genética CRISPR/Cas12a y un interruptor genético reversible y biestable basado en el sistema de recombinación del fago PhiC31. / [CA] La millora genètica vegetal té com a objectiu l'obtenció de plantes amb trets millorats o característiques noves que podrien ajudar a superar els objectius de sostenibilitat. Amb aquesta finalitat, la biotecnologia vegetal necessita incorporar noves eines d'enginyeria genètica que combinen una major precisió amb una major capacitat de millora. Les eines d'edició genètica recentment descobertes basades en la tecnologia CRISPR/Cas9 han obert el camí per modificar els genomes de les plantes amb una precisió sense precedents. D'altra banda, els nous enfocaments de biologia sintètica basats en la modularitat i l'estandardització dels elements genètics han permès la construcció de dispositius genètics cada vegada més complexos i sofisticats aplicats a la millora genètica vegetal. Amb l'objectiu final d'expandir la caixa d'eines biotecnològiques per a la millora vegetal, aquesta tesi descriu el desenvolupament i l'adaptació de dues noves eines: una nova endonucleasa específica de lloc (SSN) i un interruptor genètic modular per a la regulació de l'expressió transgènica . En una primera part, aquesta tesi descriu l'adaptació de CRISPR/Cas12a per a l'expressió en plantes i compara l'eficiència de les variants de Acidaminococcus (As) i Lachnospiraceae (Lb) Cas12a amb la ben establida Streptococcus pyogens Cas9 (SpCas9), en vuit loci de Nicotiana benthamiana usant expressió transitòria. LbCas12a va mostrar l'activitat de mutagènesi mitjana més alta en els loci analitzats. Aquesta activitat també es va confirmar en experiments de transformació estable realitzats en tres plantes model diferents, a saber, N. benthamiana, Solanum lycopersicum i Arabidopsis thaliana. Per a aquest últim, els efectes mutagènics col·laterals van ser analitzats en línies segregants sense l'endonucleasa Cas12a, mitjançant seqüenciació completa del genoma i descartant efectes indiscriminats. En conjunt, els resultats mostren que LbCas12a és una alternativa viable a SpCas9 per a l'edició genètica en plantes. En una segona part, aquest treball descriu un interruptor genètic reversible destinat a controlar l'expressió gènica en plantes amb major precisió que els sistemes induïbles tradicionals. Aquest interruptor, basat en el sistema de recombinació del bacteriòfag PhiC31, va ser construït com un dispositiu modular fet de parts d'ADN estàndard i dissenyat per controlar l'estat transcripcional (encès o apagat) de dos gens d'interès mitjançant la inversió alternativa d'un element regulador central d'ADN. L'estat de l'interruptor pot ser operat externa i reversiblement per acció dels actuadors de recombinació i la seva cinètica, memòria i reversibilitat van ser àmpliament caracteritzats en experiments de transformació transitòria i estable en N. benthamiana. En conjunt, aquesta tesi mostra el disseny i la caracterització funcional d'eines per a l'enginyeria del genòmica i biologia sintètica de plantes que ara ha sigut completat amb el sistema d'edició genètica CRISPR/Cas12a i un interruptor genètic biestable i reversible basat en el sistema de recombinació del bacteriòfag PhiC31. / [EN] Plant breeding aims to provide plants with improved traits or novel features that could help to overcome sustainability goals. To this end, plant biotechnology needs to incorporate new genetic engineering tools that combine increased precision with higher breeding power. The recently discovered genome editing tools based on CRISPR/Cas9 technology have opened the way to modify plant¿s genomes with unprecedented precision. On the other hand, new synthetic biology approaches based on modularity and standardization of genetic elements have enabled the construction of increasingly complex and refined genetic devices applied to plant breeding. With the ultimate goal of expanding the toolbox of plant breeding techniques, this thesis describes the development and adaptation to plant systems of two new breeding tools: a site-specific nuclease (SSNs), and a modular gene switch for the regulation of transgene expression. In a first part, this thesis describes the adoption of the SSN CRISPR/Cas12a for plant expression and compares the efficiency of Acidaminococcus (As) and Lachnospiraceae (Lb) Cas12a variants with the previously described Streptococcus pyogens Cas9 (SpCas9) in eight Nicotiana benthamiana loci using transient expression experiments. LbCas12a showed highest average mutagenesis activity in the loci assayed. This activity was also confirmed in stable genome editing experiments performed in three different model plants, namely N. benthamiana, Solanum lycopersicum and Arabidopsis thaliana. For the latter, off-target effects in Cas12a-free segregating lines were discarded at genomic level by deep sequencing. Collectively, the results show that LbCas12a is a viable alternative to SpCas9 for plant genome engineering. In a second part, this work describes the engineering of a new reversible genetic switch aimed at controlling gene expression in plants with higher precision than traditional inducible systems. This switch, based on the bacteriophage PhiC31 recombination system, was built as a modular device made of standard DNA parts and designed to control the transcriptional state (on or off) of two genes of interest by alternative inversion of a central DNA regulatory element. The state of the switch can be externally and reversibly operated by the action of the recombination actuators and its kinetics, memory, and reversibility were extensively characterized in N. benthamiana using both transient expression and stable transgenics. Altogether, this thesis shows the design and functional characterization of refined tools for genome engineering and synthetic biology in plants that now has been expanded with the CRISPR/Cas12a gene editing system and the phage PhiC31-based toggle switch. / Bernabé Orts, JM. (2019). Development and characterization of two new tools for plant genetic engineering: A CRISPR/Cas12a-based mutagenesis system and a PhiC31-based gene switch [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/133055 / Compendio

Esta tesis se enmarca en los procesos de recuperación de información en la Web, mediante la aplicación de tesauros y orientada hacia las propuestas de representación de información en la Web Semántica. Se plantea la creación de un modelo conceptual para desarrollar aplicaciones web para la gestión colaborativa de tesauros basados en SKOS y su aplicación en la indización de recursos de información, agrupados en repositorios y descritos mediante metadatos. Se han estudiado modelos de recuperación de información aplicados a la Web, junto con el significado, estructura, tecnologías y evolución de la Web Semántica, así como la representación de tesauros en este ámbito a partir de iniciativas basadas en RDF, analizando detalladamente SKOS. Se ha llevado a cabo una descripción funcional de las principales características de una aplicación de este tipo. La formalización de la propuesta se ha realizado con diagramas UML de casos de uso y de clases. / The field of this thesis is the web information retrieval process applying thesauri and its orientation is the representation of information in the Semantic Web. It raises the creation of a conceptual model in order to develop web applications for the collaborative management of SKOS based thesauri and the information resorces indexing, group by repositories and using metadata to describe it. Web information retrieval models has been analized, likewise meaning, structure, technologies and evolution of the Semantic Web and the representation of thesauri in this enviroment using RDF specifications, specially SKOS. Main characteristics of this type of applications have been studied. The author use case of use and class UML diagrams to formalize the proposal.

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.

Ontologies are foundational to, and upper ontologies provide semantic integration across, the Semantic Web. Multilingualism has been shown to be a key challenge to the development of the Semantic Web, and is a particular challenge to the universality requirement of upper ontologies. Universality implies a qualitative mapping from lexical ontologies, like WordNet, to an upper ontology, such as SUMO. Are a given natural language family's core concepts currently included in an existing, accepted upper ontology? Does SUMO preserve an ontological non-bias with respect to the multilingual challenge, particularly in the context of the African languages? The approach to developing WordNets mapped to shared core concepts in the non-Indo-European language families has highlighted these challenges and this is examined in a unique new context: the Southern African languages. This is achieved through a new mapping from African language core concepts to SUMO. It is shown that SUMO has no signi ficant natural language ontology bias. / Computing / M. Sc. (Computer Science)