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

BioSStore: A Client Interface for a Repository of Semantically Annotated Bioinformatics Web Services

Bioinformatics has shown itself to be a domain in which Web services are being used extensively. In this domain, simple but real services are being developed. Thus, there are huge repositories of real services available (for example BioMOBY main repository includes more than 1500 services). Besides, bioinformatics repositories usually have active communities using and working on improvements. However, these kinds of repositories do not exploit the full potential of Web services (and SOA, Service Oriented Applications, in general). On the other hand, sophisticated technologies have been proposed to improve SOA, including the annotation on Web services to explicitly describe them. However, these approaches are lacking in repositories with real services. In the work presented here, we address the drawbacks present in bioinformatics services and try to improve the current semantic model by introducing the use of the W3C standard Semantic Annotations for WSDL and XML Schema (SAWSDL) and related proposals (WSMO Lite). This paper focuses on a user interface that takes advantage of a repository of semantically annotated bioinformatics Web services. In this way, we exploit semantics for the discovery of Web services, showing how the use of semantics will improve the user searches. The BioSStore is available at http://biosstore.khaos.uma.es. This portal will contain also future developments of this proposal

D3.1. Architecture and design of the platform

This document aims to establish the requirements and the technological basis and design of the PANACEA platform. These are the main goals of the document: - Survey the different technological approaches that can be used in PANACEA. - Specify some guidelines for the metadata. - Establish the requirements for the platform. - Make a Common Interface proposal for the tools. - Propose a format for the data to be exchanged by the tools (Travelling Object). - Choose the technologies that will be used to develop the platform. - Propose a workplan

Collaborative Development and Evaluation of Text-processing Workflows in a UIMA-supported Web-based Workbench

Challenges in creating comprehensive text-processing worklows include a lack of the interoperability of individual components coming from different providers and/or a requirement imposed on the end users to know programming techniques to compose such workflows. In this paper we demonstrate Argo, a web-based system that addresses these issues in several ways. It supports the widely adopted Unstructured Information Management Architecture (UIMA), which handles the problem of interoperability; it provides a web browser-based interface for developing workflows by drawing diagrams composed of a selection of available processing components; and it provides novel user-interactive analytics such as the annotation editor which constitutes a bridge between automatic processing and manual correction. These features extend the target audience of Argo to users with a limited or no technical background. Here, we focus specifically on the construction of advanced workflows, involving multiple branching and merging points, to facilitate various comparative evalutions. Together with the use of user-collaboration capabilities supported in Argo, we demonstrate several use cases including visual inspections, comparisions of multiple processing segments or complete solutions against a reference standard, inter-annotator agreement, and shared task mass evaluations. Ultimetely, Argo emerges as a one-stop workbench for defining, processing, editing and evaluating text processing tasks

Functional units: Abstractions for Web service annotations

Computational and data-intensive science increasingly depends on a large Web Service infrastructure, as services that provide a broad array of functionality can be composed into workflows to address complex research questions. In this context, the goal of service registries is to offer accurate search and discovery functions to scientists. Their effectiveness, however, depends not only on the model chosen to annotate the services, but also on the level of abstraction chosen for the annotations. The work presented in this paper stems from the observation that current annotation models force users to think in terms of service interfaces, rather than of high-level functionality, thus reducing their effectiveness. To alleviate this problem, we introduce Functional Units (FU) as the elementary units of information used to describe a service. Using popular examples of services for the Life Sciences, we define FUs as configurations and compositions of underlying service operations, and show how functional-style service annotations can be easily realised using the OWL semantic Web language. Finally, we suggest techniques for automating the service annotations process, by analysing collections of workflows that use those services.</p

Third version (v4) of the integrated platform and documentation

The deliverable describes the third and final version of the PANACEA platform

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required. Results: EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers, application domains and data formats. EDAM supports semantic annotation of diverse entities such as Web services, databases, programmatic libraries, standalone tools, interactive applications, data schemas, datasets and publications within bioinformatics. EDAM applies to organizing and finding suitable tools and data and to automating their integration into complex applications or workflows. It includes over 2200 defined concepts and has successfully been used for annotations and implementations. Availability: The latest stable version of EDAM is available in OWL format from http://edamontology.org/EDAM.owl and in OBO format from http://edamontology.org/EDAM.obo. It can be viewed online at the NCBO BioPortal and the EBI Ontology Lookup Service. For documentation and license please refer to http://edamontology.org. This article describes version 1.2 available at http://edamontology.org/EDAM_1.2.owl.publishedVersio

Computational toxicology using the OpenTox application programming interface and Bioclipse

BACKGROUND: Toxicity is a complex phenomenon involving the potential adverse effect on a range of biological functions. Predicting toxicity involves using a combination of experimental data (endpoints) and computational methods to generate a set of predictive models. Such models rely strongly on being able to integrate information from many sources. The required integration of biological and chemical information sources requires, however, a common language to express our knowledge ontologically, and interoperating services to build reliable predictive toxicology applications. FINDINGS: This article describes progress in extending the integrative bio- and cheminformatics platform Bioclipse to interoperate with OpenTox, a semantic web framework which supports open data exchange and toxicology model building. The Bioclipse workbench environment enables functionality from OpenTox web services and easy access to OpenTox resources for evaluating toxicity properties of query molecules. Relevant cases and interfaces based on ten neurotoxins are described to demonstrate the capabilities provided to the user. The integration takes advantage of semantic web technologies, thereby providing an open and simplifying communication standard. Additionally, the use of ontologies ensures proper interoperation and reliable integration of toxicity information from both experimental and computational sources. CONCLUSIONS: A novel computational toxicity assessment platform was generated from integration of two open science platforms related to toxicology: Bioclipse, that combines a rich scriptable and graphical workbench environment for integration of diverse sets of information sources, and OpenTox, a platform for interoperable toxicology data and computational services. The combination provides improved reliability and operability for handling large data sets by the use of the Open Standards from the OpenTox Application Programming Interface. This enables simultaneous access to a variety of distributed predictive toxicology databases, and algorithm and model resources, taking advantage of the Bioclipse workbench handling the technical layers