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

Ontology-Based Recommendation of Editorial Products

Major academic publishers need to be able to analyse their vast catalogue of products and select the best items to be marketed in scientific venues. This is a complex exercise that requires characterising with a high precision the topics of thousands of books and matching them with the interests of the relevant communities. In Springer Nature, this task has been traditionally handled manually by publishing editors. However, the rapid growth in the number of scientific publications and the dynamic nature of the Computer Science landscape has made this solution increasingly inefficient. We have addressed this issue by creating Smart Book Recommender (SBR), an ontology-based recommender system developed by The Open University (OU) in collaboration with Springer Nature, which supports their Computer Science editorial team in selecting the products to market at specific venues. SBR recommends books, journals, and conference proceedings relevant to a conference by taking advantage of a semantically enhanced representation of about 27K editorial products. This is based on the Computer Science Ontology, a very large-scale, automatically generated taxonomy of research areas. SBR also allows users to investigate why a certain publication was suggested by the system. It does so by means of an interactive graph view that displays the topic taxonomy of the recommended editorial product and compares it with the topic-centric characterization of the input conference. An evaluation carried out with seven Springer Nature editors and seven OU researchers has confirmed the effectiveness of the solution

Semantic web service automation with lightweight annotations

Web services, both RESTful and WSDL-based, are an increasingly important part of the Web. With the application of semantic technologies, we can achieve automation of the use of those services. In this paper, we present WSMO-Lite and MicroWSMO, two related lightweight approaches to semantic Web service description, evolved from the WSMO framework. WSMO-Lite uses SAWSDL to annotate WSDL-based services, whereas MicroWSMO uses the hRESTS microformat to annotate RESTful APIs and services. Both frameworks share an ontology for service semantics together with most of automation algorithms

A pattern-based approach to a cell tracking ontology

Time-lapse microscopy has thoroughly transformed our understanding of biological motion and developmental dynamics from single cells to entire organisms. The increasing amount of cell tracking data demands the creation of tools to make extracted data searchable and interoperable between experiment and data types. In order to address that problem, the current paper reports on the progress in building the Cell Tracking Ontology (CTO): An ontology framework for describing, querying and integrating data from complementary experimental techniques in the domain of cell tracking experiments. CTO is based on a basic knowledge structure: the cellular genealogy serving as a backbone model to integrate specific biological ontologies into tracking data. As a first step we integrate the Phenotype and Trait Ontology (PATO) as one of the most relevant ontologies to annotate cell tracking experiments. The CTO requires both the integration of data on various levels of generality as well as the proper structuring of collected information. Therefore, in order to provide a sound foundation of the ontology, we have built on the rich body of work on top-level ontologies and established three generic ontology design patterns addressing three modeling challenges for properly representing cellular genealogies, i.e. representing entities existing in time, undergoing changes over time and their organization into more complex structures such as situations

The Materials Science Procedural Text Corpus: Annotating Materials Synthesis Procedures with Shallow Semantic Structures

Materials science literature contains millions of materials synthesis procedures described in unstructured natural language text. Large-scale analysis of these synthesis procedures would facilitate deeper scientific understanding of materials synthesis and enable automated synthesis planning. Such analysis requires extracting structured representations of synthesis procedures from the raw text as a first step. To facilitate the training and evaluation of synthesis extraction models, we introduce a dataset of 230 synthesis procedures annotated by domain experts with labeled graphs that express the semantics of the synthesis sentences. The nodes in this graph are synthesis operations and their typed arguments, and labeled edges specify relations between the nodes. We describe this new resource in detail and highlight some specific challenges to annotating scientific text with shallow semantic structure. We make the corpus available to the community to promote further research and development of scientific information extraction systems.Comment: Accepted as a long paper at the Linguistic Annotation Workshop (LAW) at ACL 201