An unsupervised data-driven method to discover equivalent relations in large linked datasets

This article addresses a number of limitations of state-of-the-art methods of Ontology Alignment: 1) they primarily address concepts and entities while relations are less well-studied; 2) many build on the assumption of the ‘well-formedness’ of ontologies which is unnecessarily true in the domain of Linked Open Data; 3) few have looked at schema heterogeneity from a single source, which is also a common issue particularly in very large Linked Dataset created automatically from heterogeneous resources, or integrated from multiple datasets. We propose a domain- and language-independent and completely unsupervised method to align equivalent relations across schemata based on their shared instances. We introduce a novel similarity measure able to cope with unbalanced population of schema elements, an unsupervised technique to automatically decide similarity threshold to assert equivalence for a pair of relations, and an unsupervised clustering process to discover groups of equivalent relations across different schemata. Although the method is designed for aligning relations within a single dataset, it can also be adapted for cross-dataset alignment where sameAs links between datasets have been established. Using three gold standards created based on DBpedia, we obtain encouraging results from a thorough evaluation involving four baseline similarity measures and over 15 comparative models based on variants of the proposed method. The proposed method makes significant improvement over baseline models in terms of F1 measure (mostly between 7% and 40%), and it always scores the highest precision and is also among the top performers in terms of recall. We also make public the datasets used in this work, which we believe make the largest collection of gold standards for evaluating relation alignment in the LOD context

Computational functional annotation of crop genomics using hierarchical orthologous groups

Improving agronomically important traits, such as yield, is important in order to meet the ever growing demands of increased crop production. Knowledge of the genes that have an effect on a given trait can be used to enhance genomic selection by prediction of biologically interesting loci. Candidate genes that are strongly linked to a desired trait can then be targeted by transformation or genome editing. This application of prioritisation of genetic material can accelerate crop improvement. However, the application of this is currently limited due to the lack of accurate annotations and methods to integrate experimental data with evolutionary relationships. Hierarchical orthologous groups (HOGs) provide nested groups of genes that enable the comparison of highly diverged and similar species in a consistent manner. Over 2,250 species are included in the OMA project, resulting in over 600,000 HOGs. This thesis provides the required methodology and a tool to exploit this rich source of information, in the HOGPROP algorithm. The potential of this is then demonstrated in mining crop genome data, from metabolic QTL studies and utilising Gene Ontology (GO) annotations as well as ChEBI terms (Chemical Entities of Biological Interest) in order to prioritise candidate causal genes. Gauging the performance of the tool is also important. When considering GO annotations, the CAFA series of community experiments has provided the most extensive benchmarking to-date. However, this has not fully taken into account the incomplete knowledge of protein function – the open world assumption (OWA). This will require extra negative annotations, for which one such source has been identified based on expertly curated gene phylogenies. These negative annotations are then utilised in the proposed, OWA-compliant, improved framework for benchmarking. The results show that current benchmarks tend to focus on the general terms, which means that conclusions are not merely uninformative, but misleading

Semantic Web for Everyone: Exploring Semantic Web Knowledge Bases via Contextual Tag Clouds and Linguistic Interpretations

The amount of Semantic Web data is huge and still keeps growing rapidly today. However most users are still not able to use a Semantic Web Knowledge Base (KB) effectively as desired to due to the lack of various background knowledge. Furthermore, the data is usually heterogeneous, incomplete, and even contains errors, which further impairs understanding the dataset. How to quickly familiarize users with the ontology and data in a KB is an important research challenge to the Semantic Web community.The core part of our proposed resolution to the problem is the contextual tag cloud system: a novel application that helps users explore a large scale RDF(Resource Description Framework) dataset. The tags in our system are ontological terms (classes and properties), and a user can construct a context with a set of tags that defines a subset of instances. Then in the contextual tag cloud, the font size of each tag depends on the number of instances that are associated with that tag and all tags in the context. Each contextual tag cloud serves as a summary of the distribution of relevant data, and by changing the context, the user can quickly gain an understanding of patterns in the data. Furthermore, the user can choose to include different RDFS entailment regimes in the calculations of tag sizes, thereby understanding the impact of semantics on the data. To resolve the key challenge of scalability, we combine a scalable preprocessing approach with a specially-constructed inverted index and co-occurrence matrix, use three approaches to prune unnecessary counts for faster online computations, and design a paging and streaming interface. Via experimentation, we show how much our design choices benefit the responsiveness of our system. We conducted a preliminary user study on this system, and find novice participants felt the system provided a good means to investigate the data and were able to complete assigned tasks more easily than using a baseline interface.We then extend the definition of tags to more general categories, particularly including property values, chaining property values, or functions on these values. With a totally different scenario and more general tags, we find the system can be used to discover interesting value space patterns. To adapt the different dataset, we modify the infrastructure with new indexing data structure, and propose two strategies for online queries, which will be chosen based on different requests, in order to maintain responsiveness of the system.In addition, we consider other approaches to help users locate classes by natural language inputs. Using an external lexicon, Word Sense Disambiguation (WSD) on the label words of classes is one way to understand these classes. We propose our novel WSD approach with our probability model, derive the problem formula into small computable pieces, and propose ways to estimate the values of these pieces. For the other approach, instead of relying on external sources, we investigate how to retrieve query-relevant classes by using the annotations of instances associated with classes in the knowledge base. We propose a general framework of this approach, which consists of two phases: the keyword query is first used to locate relevant instances; then we induce the classes given this list of weighted matched instances.Following the description of the accomplished work, I propose some important future work for extending the current system, and finally conclude the dissertation

Adaptive Semantic Annotation of Entity and Concept Mentions in Text

The recent years have seen an increase in interest for knowledge repositories that are useful across applications, in contrast to the creation of ad hoc or application-specific databases. These knowledge repositories figure as a central provider of unambiguous identifiers and semantic relationships between entities. As such, these shared entity descriptions serve as a common vocabulary to exchange and organize information in different formats and for different purposes. Therefore, there has been remarkable interest in systems that are able to automatically tag textual documents with identifiers from shared knowledge repositories so that the content in those documents is described in a vocabulary that is unambiguously understood across applications. Tagging textual documents according to these knowledge bases is a challenging task. It involves recognizing the entities and concepts that have been mentioned in a particular passage and attempting to resolve eventual ambiguity of language in order to choose one of many possible meanings for a phrase. There has been substantial work on recognizing and disambiguating entities for specialized applications, or constrained to limited entity types and particular types of text. In the context of shared knowledge bases, since each application has potentially very different needs, systems must have unprecedented breadth and flexibility to ensure their usefulness across applications. Documents may exhibit different language and discourse characteristics, discuss very diverse topics, or require the focus on parts of the knowledge repository that are inherently harder to disambiguate. In practice, for developers looking for a system to support their use case, is often unclear if an existing solution is applicable, leading those developers to trial-and-error and ad hoc usage of multiple systems in an attempt to achieve their objective. In this dissertation, I propose a conceptual model that unifies related techniques in this space under a common multi-dimensional framework that enables the elucidation of strengths and limitations of each technique, supporting developers in their search for a suitable tool for their needs. Moreover, the model serves as the basis for the development of flexible systems that have the ability of supporting document tagging for different use cases. I describe such an implementation, DBpedia Spotlight, along with extensions that we performed to the knowledge base DBpedia to support this implementation. I report evaluations of this tool on several well known data sets, and demonstrate applications to diverse use cases for further validation

Information-based methods for predicting gene function from systematic gene knock-downs

<p>Abstract</p> <p>Background</p> <p>The rapid annotation of genes on a genome-wide scale is now possible for several organisms using high-throughput RNA interference assays to knock down the expression of a specific gene. To date, dozens of RNA interference phenotypes have been recorded for the nematode <it>Caenorhabditis elegans</it>. Although previous studies have demonstrated the merit of using knock-down phenotypes to predict gene function, it is unclear how the data can be used most effectively. An open question is how to optimally make use of phenotypic observations, possibly in combination with other functional genomics datasets, to identify genes that share a common role.</p> <p>Results</p> <p>We compared several methods for detecting gene-gene functional similarity from phenotypic knock-down profiles. We found that information-based measures, which explicitly incorporate a phenotype's genomic frequency when calculating gene-gene similarity, outperform non-information-based methods. We report the presence of newly predicted modules identified from an integrated functional network containing phenotypic congruency links derived from an information-based measure. One such module is a set of genes predicted to play a role in regulating body morphology based on their multiply-supported interactions with members of the TGF-<it>β </it>signaling pathway.</p> <p>Conclusion</p> <p>Information-based metrics significantly improve the comparison of phenotypic knock-down profiles, based upon their ability to enhance gene function prediction and identify novel functional modules.</p

Proceedings of The Tenth International Workshop on Ontology Matching (OM-2015)

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A semantic framework for textual data enrichment

In this work we present a semantic framework suitable of being used as support tool for recommender systems. Our purpose is to use the semantic information provided by a set of integrated resources to enrich texts by conducting different NLP tasks: WSD, domain classification, semantic similarities and sentiment analysis. After obtaining the textual semantic enrichment we would be able to recommend similar content or even to rate texts according to different dimensions. First of all, we describe the main characteristics of the semantic integrated resources with an exhaustive evaluation. Next, we demonstrate the usefulness of our resource in different NLP tasks and campaigns. Moreover, we present a combination of different NLP approaches that provide enough knowledge for being used as support tool for recommender systems. Finally, we illustrate a case of study with information related to movies and TV series to demonstrate that our framework works properly.This research work has been partially funded by the University of Alicante, Generalitat Valenciana, Spanish Government and the European Commission through the Projects, TIN2015-65136-C2-2- R, TIN2015-65100-R, SAM (FP7-611312), and PROMETEOII/2014/001