Biomedical literature, bio-databases and bio-ontologies all play an important role in supporting the work of biological researchers. Much of the biological knowledge in our community is held in electronic form as natural language text. However, not all experimental data is appropriate to include in such research publications, and so is instead stored in more structured bio-databases. Bio-ontologies provide a common conceptual framework for structuring and annotating this data to enable it to be pooled across databases. These three resources contain overlapping information in different forms, and the inter-dependencies between them are complex.
Text mining of biomedical literature is one way to ensure that the large quantity of information in text is better reflected within ontologies and databases. It can be used, for example, to add ontology based annotation to bio-database entries. By exposing the vocabulary and relationships within the literature, it can also assist in the construction, refinement and validation of the ontologies themselves. Even when used in isolation, the meaning of concepts within an ontology must be interpreted by humans as well as computer systems. Natural language, therefore, plays a vital role in ontology design.
Ontologies in turn can support text mining by for example: (i) providing a framework for structuring terminologies and for clustering synonyms; and (ii) defining the types of entities and relations that text mining aims to discover during the process of analysing text.
Therefore text mining and ontologies have a lot in common and can be mutually beneficial. However, bio-ontologies are frequently built without explicitly taking into account the needs of the language processing community. As a consequence language processing researchers either ignore these valuable resources or are forced to adapt them with difficulty. Furthermore, ontology builders are frequently unaware of language processing tools, methodologies and applications and how they might assist in the construction and evaluation of ontologies.
The goal of this workshop is to bring together researchers from the bio-ontology community with those from the biomedical text processing community with a view to furthering their understanding each other's needs and capabilities. Previous workshops in the area have tended focus more either on bio-ontologies or on bio-text processing. While some research has attempted to bridge this gap the aim of current workshop is to focus explicitly on the relationship between bio-ontologies and bio-text processing.
To that end we solicit papers that address any aspect of the relationship between bio-ontologies and biomedical text processing. Possible topics include, but are not limited to:
The workshop will include paper presentations and discussion. The papers should describe recent and previously unpublished work and may be preliminary in nature. The programme committee will arrange the presentations and discussion based on the quality of submissions and may invite other presentations as well. See http://www.nlp.shef.ac.uk/eccb05-ont+text for further details. Abstracts of the workshop papers will be published in the main ECCB05 conference proceedings and the papers themselves will be published in a separate workshop proceedings. Negotiations are underway for a journal special issue in which the best papers from the workshop will be published.