TX Task: Automatic detection of focus organisms in biomedical publications

In biomedical information extraction (IE), a central problem is the disambiguation of ambiguous names for domain specific entities, such as proteins, genes, etc. One important dimension of ambiguity is the organism to which the entities belong: in order to disambiguate an ambiguous entity name (e.g. a protein), it is often necessary to identify the specific organism to which it refers. In this paper we present an approach to the detection and disambiguation of the focus organism(s), i.e. the organism(s) which are the subject of the research described in scientific papers, which can then be used for the disambiguation of other entities. The results are evaluated against a gold standard derived from IntAct annotations. The evaluation suggests that the results may already be useful within a curation environment and are certainly a baseline for more complex approaches

Writing clinical practice guidelines in controlled natural language

Clinicians could benefit from decision support systems incorporating the knowledge contained in clinical practice guidelines. However, the unstructured form of these guidelines makes them unsuitable for formal representation. To address this challenge we translated a complete set of pediatric guideline recommendations into Attempto Controlled English (ACE). One experienced pediatrician, one physician and a knowledge engineer assessed that a suitably extended version of ACE can accurately and naturally represent the clinical concepts and the proposed actions of the guidelines. Currently, we are developing a systematic and replicable approach to authoring guideline recommendations in ACE

OntoGene in BioCreative II

BACKGROUND: Research scientists and companies working in the domains of biomedicine and genomics are increasingly faced with the problem of efficiently locating, within the vast body of published scientific findings, the critical pieces of information that are needed to direct current and future research investment. RESULTS: In this report we describe approaches taken within the scope of the second BioCreative competition in order to solve two aspects of this problem: detection of novel protein interactions reported in scientific articles, and detection of the experimental method that was used to confirm the interaction. Our approach to the former problem is based on a high-recall protein annotation step, followed by two strict disambiguation steps. The remaining proteins are then combined according to a number of lexico-syntactic filters, which deliver high-precision results while maintaining reasonable recall. The detection of the experimental methods is tackled by a pattern matching approach, which has delivered the best results in the official BioCreative evaluation. CONCLUSION: Although the results of BioCreative clearly show that no tool is sufficiently reliable for fully automated annotations, a few of the proposed approaches (including our own) already perform at a competitive level. This makes them interesting either as standalone tools for preliminary document inspection, or as modules within an environment aimed at supporting the process of curation of biomedical literature

An environment for relation mining over richly annotated corpora: the case of GENIA

BACKGROUND: The biomedical domain is witnessing a rapid growth of the amount of published scientific results, which makes it increasingly difficult to filter the core information. There is a real need for support tools that 'digest' the published results and extract the most important information. RESULTS: We describe and evaluate an environment supporting the extraction of domain-specific relations, such as protein-protein interactions, from a richly-annotated corpus. We use full, deep-linguistic parsing and manually created, versatile patterns, expressing a large set of syntactic alternations, plus semantic ontology information. CONCLUSION: The experiments show that our approach described is capable of delivering high-precision results, while maintaining sufficient levels of recall. The high level of abstraction of the rules used by the system, which are considerably more powerful and versatile than finite-state approaches, allows speedy interactive development and validation

A model for verbalising relations with roles in multiple languages

Natural language renderings of ontologies facilitate communication with domain experts. While for ontologies with terms in English this is fairly straightforward, it is problematic for grammatically richer languages due to conjugation of verbs, an article that may be dependent on the preposition, or a preposition that modifies the noun. There is no systematic way to deal with such `complex' names of OWL object properties, or their verbalisation with existing language models for annotating ontologies. The modifications occur only when the object performs some {\em role} in a relation, so we propose a conceptual model that can handle this. This requires reconciling the standard view with relational expressions to a positionalist view, which is included in the model and in the formalisation of the mapping between the two. This eases verbalisation and it allows for a more precise representation of the knowledge, yet is still compatible with existing technologies. We have implemented it as a Prot\'eg\'e plugin and validated its adequacy with several languages that need it, such as German and isiZulu

Paraphrasing controlled English texts

We discuss paraphrasing controlled English texts, by defining two fragments of Attempto Controlled English (ACE): Core ACE and NP ACE. We show that these fragments have features that one would usually expect from paraphrases. We also describe a tool that paraphrases ACE sentences into these fragments

ACE View � an ontology and rule editor based on controlled English

We describe the architecture of a novel ontology and rule editor ACE View. The goal of ACE View is to simplify viewing and editing expressive and syntactically complex OWL/SWRL knowledge bases by making most of the interaction with the knowledge base happen via Attempto Controlled English (ACE). This makes ACE View radically different from current OWL/SWRL editors which are based on formal logic syntaxes and general purpose graphical user interface widgets. ACE View integrates two mappings, ACE →OWL/SWRL and OWLACE, and is implemented as a plug-in for Protégé 4