AgreementMaker

Since different ontologies are mostly developed independently, establishing meaningful links between their entities, so-called ontology matching, is critical to ensure their communication. Due to the complexity of the ontology matching problem, Evolutionary Algorithm (EA) can present a good methodology for determining ontology alignments. However, since none of the similarity measure can distinguish all the identical ontology entities in any context, ontology alignments generated by the automatic matching tools should be validated by the users to ensure their qualities. To improve the quality of the ontology alignment, in this work, a similarity measure is first proposed to calculate the similarity value of two ontology entities; then, an optimal model for ontology matching problem is constructed; after that, an EA-based automatic matcher is presented to solve the ontology matching problem, which can also adaptively determine the timing of getting user involved; and finally, the ontology concept hierarchy graph based reasoning approaches are proposed to tradeoff the user's workload and his work's effect. The experiment is conducted on the Interactive track provided by the Ontology Alignment Evaluation Initiative (OAEI), and the comparisons with OAEI's participants show the effectiveness of our proposal.

To bridge the semantic gap between different offered ontologies, Ontology Engineers have proposed and implemented various matching techniques during the last decade. Still, these techniques require more efforts and investigations to achieve better precision and recall for the set of alignments. The ontology alignment process consists of mainly three different stages; namely, String based, Linguistic based and Structure based. This paper presents the evaluation and analysis of various linguistic based ontology alignment techniques and their performance during the overall alignment process. For this purpose, we have included those linguistic matching tools which are widely used in the alignment systems whose performance is relatively better in terms of precision and recall during the tests conducted for Ontology Alignment Evaluation Initiative (OAEI). The results presented in this paper were obtained using benchmark ontologies used in OAEI conference. The results and analysis shows the significance of linguistic tools in the overall alignment process. The analysis presented in this paper can also be used as future guidelines for the research community who utilizes the linguistic matchers for finding the semantically equal entities from different ontologies.

BackgroundOne of the longest running tracks in the Ontology Alignment Evaluation Initiative is the Anatomy track which focuses on aligning two anatomy ontologies. The Anatomy track was started in 2005. In 2005 and 2006 the task in this track was to align the Foundational Model of Anatomy and the OpenGalen Anatomy Model. Since 2007 the ontologies used in the track are the Adult Mouse Anatomy and a part of the NCI Thesaurus. Since 2015 the data in the Anatomy track is also used in the Interactive track of the Ontology Alignment Evaluation Initiative.ResultsIn this paper we focus on the Anatomy track in the years 2007–2016 and the Anatomy part of the Interactive track in 2015–2016. We describe the data set and the changes it went through during the years as well as the challenges it poses for ontology alignment systems. Further, we give an overview of all systems that participated in the track and the techniques they have used. We discuss the performance results of the systems and summarize the general trends.ConclusionsAbout 50 systems have participated in the Anatomy track. Many different techniques were used. The most popular matching techniques are string-based strategies and structure-based techniques. Many systems also use auxiliary information. The quality of the alignment has increased for the best performing systems since the beginning of the track and more and more systems check the coherence of the proposed alignment and implement a repair strategy. Further, interacting with an oracle is beneficial.

Business process modelling is an important part of system design. When designing or redesigning a business process, stakeholders specify, negotiate, and agree on business requirements to be satisfied, including non-functional requirements that concern the quality of the business process. This thesis addresses the question of how to specify and compute the quality of a business process, given the model that stakeholders use. The motivation for this thesis is the increasing importance of the quality of business processes. Knowing the quality of specific business processes enables stakeholders to judge if these processes need improvement. Knowing the quality of the constructs of those processes (viz., events, inputs, activities, and outputs) and the way they are structured enables a more detailed analysis of their shortcomings and provides a basis for the design of improvements. The research challenge of this thesis is grounded in the assumption that: “Organisations need an appropriate means to effectively compute achievement of their goals and objectives by their business processes.” Given this challenge, the main research question on which this thesis focuses is: “Can the quality of a business process be computed quantitatively at different levels of granularity?” The research objective is: “To develop frameworks, factors, and metrics for computing non-functional requirements (quality) of business processes quantitatively at different levels of granularity.” The outcomes of this thesis are: 1) BPIMM, a language-independent business process integrating meta-model, based on the concepts of seven mainstream business process modelling languages: BPMN, EPC, RAD, UML AD, SADT, IDEF0, and IDEF3. 2) BPC-QC (Business Process Concept - Quality Computation), an approach to quality computation at the lowest level of granularity of a business process. The approach consists of: i. BPC-QEF (Business Process Concept - Quality Evaluation Framework), a language-independent generic framework and algorithm to compute the quality of the constructs of a business process: event, input, activity, and output. ii. A set of business process quality dimensions and factors. The following quality dimensions are distinguished: performance, efficiency, reliability, recoverability, permissibility, and availability. Each dimension categorises different quality aspects in terms of factors. A non-exhaustive set of sixteen quantitative factors is provided. iii. Quality metrics for each of the quality factors, to facilitate a quantitative computation of the quality of a specific construct of a business process. 3) BP-QC (Business Process - Quality Computation), an approach to compute the quality at the highest level of granularity of a business process. The approach consists of: i. BP-CQCF (Business Process - Compositional Quality Computation Framework), a language-independent generic framework and algorithm to compute the quality of a business process as a whole, given the quality of its constructs. ii. A set of generic business process modelling patterns to decompose a business process into more succinct parts, namely: sequential, parallel with synchronisation, exclusive, inclusive, simple loop, and complex loop. iii. A set of over one hundred computational formulae. For each combination of modelling pattern and a quality factor, there is a formula to compute the quality. 4) AAV (Approach to Application and Validation), an evaluation plan to evaluate BPIMM, BPC-QC and BP-QC in practice, together with expert stakeholders. The plan consists of the units of measure, a measurement model, and a case study procedure. To evaluate the applicability of the contributions of this thesis to real world business needs, four case studies have been conducted in different environments: a Dutch educational institution, a global financial institution, an international financial service provider, and a Dutch research project on crisis management. Each of these case studies concerns a different, single business process. This thesis shows that: 1) A quality computation approach can be adopted independent of a business process modelling language. 2) Quantitative quality factors can be introduced specifically for the constructs of a business process. 3) Quantitative metrics and computational formulae can be developed for specific quality factors, allowing the computation of different aspects of the quality of a business process quantitatively at different levels of granularity. 4) An evaluation plan can be developed to evaluate the applicability of the contributions of this thesis (viz., BPIMM, BPC-QC, and BP-QC). The contributions of this thesis are designed to be beneficial to the areas of business and management, requirements engineering, software engineering, and business process modelling. In the areas of requirements engineering and software engineering, these contributions are intended to help practitioners to consider non-functional requirements at the earliest stage. In the area of business process modelling, information systems, service computing, and cloud computing, the contributions can be used for quality-driven modelling, design, and redesign. To conclude, knowing the quality value of a business process at different levels of granularity provides a basis for its improvement.

Nowadays, most real-world decision problems consist of two or more incommensurable or conflicting objectives to be optimized simultaneously, so-called multiobjective optimization problems (MOPs). Usually, a decision maker (DM) prefers only a single optimum solution in the Pareto front (PF), and the PF’s knee solution is logically the one if there are no user-specific or problem-specific preferences. In this context, the biomedical ontology matching problem in the Semantic Web (SW) domain is investigated, which can be of help to integrate the biomedical knowledge and facilitate the translational discoveries. Since biomedical ontologies often own large-scale concepts with rich semantic meanings, it is difficult to find a perfect alignment that could meet all DM’s requirements, and usually, the matching process needs to trade-off two conflict objectives, i.e., the alignment’s recall and precision. To this end, in this work, the biomedical ontology matching problem is first defined as a MOP, and then a compact multiobjective particle swarm optimization algorithm driven by knee solution (CMPSO-K) is proposed to address it. In particular, a compact evolutionary mechanism is proposed to efficiently optimize the alignment’s quality, and a max-min approach is used to determine the PF’s knee solution. In the experiment, three biomedical tracks provided by Ontology Alignment Evaluation Initiative (OAEI) are used to test CMPSO-K’s performance. The comparisons with OAEI’s participants and PSO-based matching technique show that CMPSO-K is both effective and efficient.

The Ontology Alignment Evaluation Initiative (OAEI) is an annual evaluation of ontology matching tools. In 2018, we have started the Knowledge Graph track, whose goal is to evaluate the simultaneous matching of entities and schemas of large-scale knowledge graphs. In this paper, we discuss the design of the track and two different strategies of gold standard creation. We analyze results and experiences obtained in first editions of the track, and, by revealing a hidden task, we show that all tools submitted to the track (and probably also to other tracks) suffer from a bias which we name the golden hammer bias.

As a key representation model of knowledge, ontology has been widely used in a lot of NLP related tasks, such as semantic parsing, information extraction and text mining etc. In this paper, we study the task of ontology matching, which concentrates on finding semantically related entities between different ontologies that describe the same domain, to solve the semantic heterogeneity problem. Previous works exploit different kinds of descriptions of an entity in ontology directly and separately to find the correspondences without considering the higher level correlations between the descriptions. Besides, the structural information of ontology haven’t been utilized adequately for ontology matching. We propose in this paper an ontology matching approach, named ERSOM, which mainly includes an unsupervised representation learning method based on the deep neural networks to learn the general representation of the entities and an iterative similarity propagation method that takes advantage of more abundant structure information of the ontology to discover more mappings. The experimental results on the datasets from Ontology Alignment Evaluation Initiative (OAEI1) show that ERSOM achieves a competitive performance compared to the state-of-the-art ontology matching systems. The OAEI is an international initiative organizing annual campaigns for evaluating ontology matching systems. All of the ontologies provided by OAEI are described in OWL-DL language, and like most of the other participates our ERSOM also manages the OWL ontology in its current version. OAEI: http://oaei.ontologymatching.org/

Ontology matching is usually performed to find semantic correspondences between the entity elements of different ontologies to enable interoperability. Current research on ontology matching has largely focused on representation learning. However, there still exist two limitations. Firstly, they are only used in the element level matching phase, ignoring relations of the entity. Secondly, the final alignment threshold is usually determined manually within these methods. It is difficult for an expert to adjust the threshold value and even more for non-expert user. To address these issues, we propose an alternative ontology matching framework, which models the matching process by embedding techniques with jointly encoding ontology terminological description and network structure. We further improve our iterative final alignment method by introducing an automatic adjustment of threshold method. Finally, we perform an experimental evaluation and compare it with state-of-the-art ontology matching systems on four Ontology Alignment Evaluation Initiative (OAEI) datasets. Our approach performs better than most of the systems and achieves a competitive performance. Moreover, we obtained F-measure values of 93.8% and 90.8% on the OAEI Large Biomedical Ontologies FMA-NCI and FMA-SNOMED subtasks.

Ontology matching is an effective technique to solve the ontology heterogeneous problem in Semantic Web. Since different ontology matchers do not necessarily find the same correct correspondences, usually several competing matchers are applied to the same pair of entities in order to increase evidence towards a potential match or mismatch. How to select, combine and tune various ontology matchers to obtain the high quality ontology alignment is one of the main challenges in ontology matching domain. Recently, Evolutionary Algorithms (EA) has become the most suitable methodology to face this challenge, however, the huge memory consumption, slow convergence and premature convergence limit its application and reduce the solution’s quality. To this end, in this paper, we propose a Hybrid Population-based Incremental Learning algorithm (HPBIL) to automatically select, combine and tune different ontology matchers, which can overcome three drawbacks of EA based ontology matching techniques and improve the ontology alignment’s quality. In one hand, HPBIL makes use of a probabilistic representation of the population to perform the optimization process, which can significantly reduce EA’s the memory consumption and the possibility of the premature convergence. In the other, we introduce the local search strategy into PBIL’s evolving process to trade off its exploration and exploitation, and this marriage between global search and local search is helpful to reduce the runtime. In the experiment, we utilize different scale testing cases provided by the Ontology Alignment Evaluation Initiative (OAEI 2016) to test HPBIL’s performance, and the experimental results show that HPBIL’s results significantly outperform other EA based ontology matching techniques and top-performers of the OAEI competitions.

With the explosive growth in generating data in the hydrographical domain, many hydrography ontologies have been developed and maintained to describe hydrographical features and the relationships between them. However, the existing hydrography ontologies are developed with varying project perspectives and objectives, which inevitably results in the differences in terms of knowledge representation. Determining various relationships between two entities in different ontologies offers the opportunity to link hydrographical data for multiple purposes, though the research on this topic is in its infancy. Different from the traditional ontology alignment whose cardinality is 1:1, i.e. one source ontology entity is mapping with one target ontology entity and vice versa, and the relationship is the equivalence, matching hydrography ontologies is a more complex task, whose cardinality could be 1:1, 1:n or m:n and the relationships could be equivalence or subsumption. To efficiently optimize the ontology alignment, in this paper, a discrete optimal model is first constructed for the ontology matching problem, and then a Compact Particle Swarm Optimization algorithm (CPSO) based matching technique is proposed to efficiently solve it. CPSO utilizes the compact real-value encoding and decoding mechanism and the objective-decomposing strategy to approximate the PSO’s evolving process, which can dramatically reduce PSO’s memory consumption and runtime while at the same time ensure the solution’s quality. The experiment exploits the Hydrography dataset in Complex track provided by the Ontology Alignment Evaluation Initiative (OAEI) to test our proposal’s performance. The experimental results show that CPSO-based approach can effectively reduce PSO’s runtime and memory consumption, and determine high-quality hydrography ontology alignments.

Ontology alignment is the task of identifying semantically equivalent entities from two given ontologies. Different ontologies have different representations of the same entity, resulting in a need to de-duplicate entities when merging ontologies. We propose a method for enriching entities in an ontology with external definition and context information, and use this additional information for ontology alignment. We develop a neural architecture capable of encoding the additional information when available, and show that the addition of external data results in an F1-score of 0.69 on the Ontology Alignment Evaluation Initiative (OAEI) largebio SNOMED-NCI subtask, comparable with the entity-level matchers in a SOTA system.

Over the recent years, ontologies are widely used in the biomedical domains. However, biomedical ontology heterogeneity problem hamper the cooperation between intelligent applications based on biomedical ontologies. It is crucial to establish correspondences between the heterogeneous biomedical concepts in different ontologies, which is so-called biomedical ontology matching. Approaches based on Multi-Objective Evolutionary Algorithm (MOEA), such as NSGA-II, are emerging as a new methodology to solve the ontology matching problem. In this paper, to further improve the quality of biomedical ontology alignments, a hybrid NSGA-II is proposed, which modifies the knee solutions in the Pareto front by using a local search method. Experiment utilizes two biomedical ontology matching tracks provided by Ontology Alignment Evaluation Initiative (OAEI 2017). The experimental results show that our approach outperforms the participants of OAEI 2017 and NSGA-II based ontology matching technique.

The exploding number of computational models produced by Systems Biologists over the last years is an invitation to structure and exploit this new wealth of information. Researchers would like to trace models relevant to specific scientific questions, to explore their biological content, to align and combine them, and to match them with experimental data. To automate these processes, it is essential to consider semantic annotations, which describe their biological meaning. As a prerequisite for a wide range of computational methods, we propose general and flexible similarity measures for Systems Biology models computed from semantic annotations. By using these measures and a large extensible ontology, we implement a platform that can retrieve, cluster, and align Systems Biology models and experimental data sets. At present, its major application is the search for relevant models in the BioModels Database, starting from initial models, data sets, or lists of biological concepts. Beyond similarity searches, the representation of models by semantic feature vectors may pave the way for visualisation, exploration, and statistical analysis of large collections of models and corresponding data.

In traditional formal concept analysis, the attributes in the formal context are considered fixed. However, in the real world data set, attributes always have different levels of granularity, correspondingly, the derived concept lattice may reveal different information and patterns. Therefore, the capability to change the level of granularity of an attribute in formal concept analysis to capture relevant patterns in data is a natural requirement. In this paper, a theoretical study has been undertaken in multi-scale formal contexts, where attributes with different levels of granularity possess different attribute values. Two types of formal concepts, i.e., object-oriented and property-oriented multi-scale concepts, are introduced and studied in detail. The collection of object-oriented concept lattices and property-oriented concept lattices can be obtained at different granularity levels of attributes. It has been shown that the set of extents in the derived concept lattices increases when we choose to use a finer level of granularity. Moreover, a corresponding bidirectional approach to concept construction(i.e., from coarser to finer and from finer to coarser, respectively) is exhibited, and some characterization theorems have been obtained.

This paper presents a novel background knowledge approach which selects and combines existing mappings from a given biomedical ontology repository to improve ontology alignment. Current background knowledge approaches usually select either manually or automatically a limited number of different ontologies and use them as a whole for background knowledge. Whereas in our approach, we propose to pick up only relevant concepts and relevant existing mappings linking these concepts all together in a specific and customized background knowledge graph. Paths within this graph will help to discover new mappings. We have implemented and evaluated our approach using the content of the NCBO BioPortal repository and the Anatomy benchmark from the Ontology Alignment Evaluation Initiative. We used the mapping gain measure to assess how much our final background knowledge graph improves results of state-of-the-art alignment systems. Furthermore, the evaluation shows that our approach produces a high quality alignment and discovers mappings that have not been found by state-of-the-art systems.