Semantic information systems engineering: A query-based approach for semi-automatic annotation of web services

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.There has been an increasing interest in Semantic Web services (SWS) as a proposed solution to facilitate automatic discovery, composition and deployment of existing syntactic Web services. Successful implementation and wider adoption of SWS by research and industry are, however, profoundly based on the existence of effective and easy to use methods for service semantic description. Unfortunately, Web service semantic annotation is currently performed by manual means. Manual annotation is a difficult, error-prone and time-consuming task and few approaches exist aiming to semi-automate that task. Existing approaches are difficult to use since they require ontology building. Moreover, these approaches employ ineffective matching methods and suffer from the Low Percentage Problem. The latter problem happens when a small number of service elements - in comparison to the total number of elements – are annotated in a given service. This research addresses the Web services annotation problem by developing a semi-automatic annotation approach that allows SWS developers to effectively and easily annotate their syntactic services. The proposed approach does not require application ontologies to model service semantics. Instead, a standard query template is used: This template is filled with data and semantics extracted from WSDL files in order to produce query instances. The input of the annotation approach is the WSDL file of a candidate service and a set of ontologies. The output is an annotated WSDL file. The proposed approach is composed of five phases: (1) Concept extraction; (2) concept filtering and query filling; (3) query execution; (4) results assessment; and (5) SAWSDL annotation. The query execution engine makes use of name-based and structural matching techniques. The name-based matching is carried out by CN-Match which is a novel matching method and tool that is developed and evaluated in this research. The proposed annotation approach is evaluated using a set of existing Web services and ontologies. Precision (P), Recall (R), F-Measure (F) and Percentage of annotated elements are used as evaluation metrics. The evaluation reveals that the proposed approach is effective since - in relation to manual results - accurate and almost complete annotation results are obtained. In addition, high percentage of annotated elements is achieved using the proposed approach because it makes use of effective ontology extension mechanisms

Ontology Enrichment from Free-text Clinical Documents: A Comparison of Alternative Approaches

While the biomedical informatics community widely acknowledges the utility of domain ontologies, there remain many barriers to their effective use. One important requirement of domain ontologies is that they achieve a high degree of coverage of the domain concepts and concept relationships. However, the development of these ontologies is typically a manual, time-consuming, and often error-prone process. Limited resources result in missing concepts and relationships, as well as difficulty in updating the ontology as domain knowledge changes. Methodologies developed in the fields of Natural Language Processing (NLP), Information Extraction (IE), Information Retrieval (IR), and Machine Learning (ML) provide techniques for automating the enrichment of ontology from free-text documents. In this dissertation, I extended these methodologies into biomedical ontology development. First, I reviewed existing methodologies and systems developed in the fields of NLP, IR, and IE, and discussed how existing methods can benefit the development of biomedical ontologies. This previously unconducted review was published in the Journal of Biomedical Informatics. Second, I compared the effectiveness of three methods from two different approaches, the symbolic (the Hearst method) and the statistical (the Church and Lin methods), using clinical free-text documents. Third, I developed a methodological framework for Ontology Learning (OL) evaluation and comparison. This framework permits evaluation of the two types of OL approaches that include three OL methods. The significance of this work is as follows: 1) The results from the comparative study showed the potential of these methods for biomedical ontology enrichment. For the two targeted domains (NCIT and RadLex), the Hearst method revealed an average of 21% and 11% new concept acceptance rates, respectively. The Lin method produced a 74% acceptance rate for NCIT; the Church method, 53%. As a result of this study (published in the Journal of Methods of Information in Medicine), many suggested candidates have been incorporated into the NCIT; 2) The evaluation framework is flexible and general enough that it can analyze the performance of ontology enrichment methods for many domains, thus expediting the process of automation and minimizing the likelihood that key concepts and relationships would be missed as domain knowledge evolves

Melis: an incremental method for the lexical annotation of domain ontologies

In this paper, we present MELIS (Meaning Elicitation and Lexical Integration System), a method and a software tool for enabling an incremental process of automatic annotation of local schemas (e.g. relational database schemas, directory trees) with lexical information. The distinguishing and original feature of MELIS is the incremental process: the higher the number of schemas which are processed, the more background/domain knowledge is cumulated in the system (a portion of domain ontology is learned at every step), the better the performance of the systems on annotating new schemas.MELIS has been tested as component of MOMIS-Ontology Builder, a framework able to create a domain ontology representing a set of selected data sources, described with a standard W3C language wherein concepts and attributes are annotated according to the lexical reference database.We describe the MELIS component within the MOMIS-Ontology Builder framework and provide some experimental results of ME LIS as a standalone tool and as a component integrated in MOMIS

D3.8 Lexical-semantic analytics for NLP

UIDB/03213/2020 UIDP/03213/2020The present document illustrates the work carried out in task 3.3 (work package 3) of ELEXIS project focused on lexical-semantic analytics for Natural Language Processing (NLP). This task aims at computing analytics for lexical-semantic information such as words, senses and domains in the available resources, investigating their role in NLP applications. Specifically, this task concentrates on three research directions, namely i) sense clustering, in which grouping senses based on their semantic similarity improves the performance of NLP tasks such as Word Sense Disambiguation (WSD), ii) domain labeling of text, in which the lexicographic resources made available by the ELEXIS project for research purposes allow better performances to be achieved, and finally iii) analysing the diachronic distribution of senses, for which a software package is made available.publishersversionpublishe

Comparing knowledge sources for nominal anaphora resolution

We compare two ways of obtaining lexical knowledge for antecedent selection in other-anaphora and definite noun phrase coreference. Specifically, we compare an algorithm that relies on links encoded in the manually created lexical hierarchy WordNet and an algorithm that mines corpora by means of shallow lexico-semantic patterns. As corpora we use the British National Corpus (BNC), as well as the Web, which has not been previously used for this task. Our results show that (a) the knowledge encoded in WordNet is often insufficient, especially for anaphor-antecedent relations that exploit subjective or context-dependent knowledge; (b) for other-anaphora, the Web-based method outperforms the WordNet-based method; (c) for definite NP coreference, the Web-based method yields results comparable to those obtained using WordNet over the whole dataset and outperforms the WordNet-based method on subsets of the dataset; (d) in both case studies, the BNC-based method is worse than the other methods because of data sparseness. Thus, in our studies, the Web-based method alleviated the lexical knowledge gap often encountered in anaphora resolution, and handled examples with context-dependent relations between anaphor and antecedent. Because it is inexpensive and needs no hand-modelling of lexical knowledge, it is a promising knowledge source to integrate in anaphora resolution systems

An incremental method for meaning elicitation of a domain ontology

Internet has opened the access to an overwhelming amount of data, requiring the development of new applications to automatically recognize, process and manage informationavailable in web sites or web-based applications. The standardSemantic Web architecture exploits ontologies to give a shared(and known) meaning to each web source elements.In this context, we developed MELIS (Meaning Elicitation and Lexical Integration System). MELIS couples the lexical annotation module of the MOMIS system with some components from CTXMATCH2.0, a tool for eliciting meaning from severaltypes of schemas and match them. MELIS uses the MOMIS WNEditor and CTXMATCH2.0 to support two main tasks in theMOMIS ontology generation methodology: the source annotationprocess, i.e. the operation of associating an element of a lexicaldatabase to each source element, and the extraction of lexicalrelationships among elements of different data sources

Exploiting extensible background knowledge for clustering-based automatic keyphrase extraction

Keyphrases are single- or multi-word phrases that are used to describe the essential content of a document. Utilizing an external knowledge source such as WordNet is often used in keyphrase extraction methods to obtain relation information about terms and thus improves the result, but the drawback is that a sole knowledge source is often limited. This problem is identified as the coverage limitation problem. In this paper, we introduce SemCluster, a clustering-based unsupervised keyphrase extraction method that addresses the coverage limitation problem by using an extensible approach that integrates an internal ontology (i.e., WordNet) with other knowledge sources to gain a wider background knowledge. SemCluster is evaluated against three unsupervised methods, TextRank, ExpandRank, and KeyCluster, and under the F1-measure metric. The evaluation results demonstrate that SemCluster has better accuracy and computational efficiency and is more robust when dealing with documents from different domains

Semantic information systems engineering : a query-based approach for semi-automatic annotation of web services

There has been an increasing interest in Semantic Web services (SWS) as a proposed solution to facilitate automatic discovery, composition and deployment of existing syntactic Web services. Successful implementation and wider adoption of SWS by research and industry are, however, profoundly based on the existence of effective and easy to use methods for service semantic description. Unfortunately, Web service semantic annotation is currently performed by manual means. Manual annotation is a difficult, error-prone and time-consuming task and few approaches exist aiming to semi-automate that task. Existing approaches are difficult to use since they require ontology building. Moreover, these approaches employ ineffective matching methods and suffer from the Low Percentage Problem. The latter problem happens when a small number of service elements - in comparison to the total number of elements – are annotated in a given service. This research addresses the Web services annotation problem by developing a semi-automatic annotation approach that allows SWS developers to effectively and easily annotate their syntactic services. The proposed approach does not require application ontologies to model service semantics. Instead, a standard query template is used: This template is filled with data and semantics extracted from WSDL files in order to produce query instances. The input of the annotation approach is the WSDL file of a candidate service and a set of ontologies. The output is an annotated WSDL file. The proposed approach is composed of five phases: (1) Concept extraction; (2) concept filtering and query filling; (3) query execution; (4) results assessment; and (5) SAWSDL annotation. The query execution engine makes use of name-based and structural matching techniques. The name-based matching is carried out by CN-Match which is a novel matching method and tool that is developed and evaluated in this research. The proposed annotation approach is evaluated using a set of existing Web services and ontologies. Precision (P), Recall (R), F-Measure (F) and Percentage of annotated elements are used as evaluation metrics. The evaluation reveals that the proposed approach is effective since - in relation to manual results - accurate and almost complete annotation results are obtained. In addition, high percentage of annotated elements is achieved using the proposed approach because it makes use of effective ontology extension mechanisms.EThOS - Electronic Theses Online ServiceGBUnited Kingdo