Constructive Ontology Engineering

The proliferation of the Semantic Web depends on ontologies for knowledge sharing, semantic annotation, data fusion, and descriptions of data for machine interpretation. However, ontologies are difficult to create and maintain. In addition, their structure and content may vary depending on the application and domain. Several methods described in literature have been used in creating ontologies from various data sources such as structured data in databases or unstructured text found in text documents or HTML documents. Various data mining techniques, natural language processing methods, syntactical analysis, machine learning methods, and other techniques have been used in building ontologies with automated and semi-automated processes. Due to the vast amount of unstructured text and its continued proliferation, the problem of constructing ontologies from text has attracted considerable attention for research. However, the constructed ontologies may be noisy, with missing and incorrect knowledge. Thus ontology construction continues to be a challenging research problem. The goal of this research is to investigate a new method for guiding a process of extracting and assembling candidate terms into domain specific concepts and relationships. The process is part of an overall semi automated system for creating ontologies from unstructured text sources and is driven by the user’s goals in an incremental process. The system applies natural language processing techniques and uses a series of syntactical analysis tools for extracting grammatical relations from a list of text terms representing the parts of speech of a sentence. The extraction process focuses on evaluating the subject predicate-object sequences of the text for potential concept-relation-concept triples to be built into an ontology. Users can guide the system by selecting seedling concept-relation-concept triples to assist building concepts from the extracted domain specific terms. As a result, the ontology building process develops into an incremental one that allows the user to interact with the system, to guide the development of an ontology, and to tailor the ontology for the user’s application needs. The main contribution of this work is the implementation and evaluation of a new semi- automated methodology for constructing domain specific ontologies from unstructured text corpus

Molecular Interactions. On the Ambiguity of Ordinary Statements in Biomedical Literature

Statements about the behavior of biochemical entities (e.g., about the interaction between two proteins) abound in the literature on molecular biology and are increasingly becoming the targets of information extraction and text mining techniques. We show that an accurate analysis of the semantics of such statements reveals a number of ambiguities that have to be taken into account in the practice of biomedical ontology engineering: Such statements can not only be understood as event reporting statements, but also as ascriptions of dispositions or tendencies that may or may not refer to collectives of interacting molecules or even to collectives of interaction events

Automatic annotation of bioinformatics workflows with biomedical ontologies

Legacy scientific workflows, and the services within them, often present scarce and unstructured (i.e. textual) descriptions. This makes it difficult to find, share and reuse them, thus dramatically reducing their value to the community. This paper presents an approach to annotating workflows and their subcomponents with ontology terms, in an attempt to describe these artifacts in a structured way. Despite a dearth of even textual descriptions, we automatically annotated 530 myExperiment bioinformatics-related workflows, including more than 2600 workflow-associated services, with relevant ontological terms. Quantitative evaluation of the Information Content of these terms suggests that, in cases where annotation was possible at all, the annotation quality was comparable to manually curated bioinformatics resources.Comment: 6th International Symposium on Leveraging Applications (ISoLA 2014 conference), 15 pages, 4 figure