DutchHatTrick: semantic query modeling, ConText, section detection, and match score maximization

This report discusses the collaborative work of the ErasmusMC, University of Twente, and the University of Amsterdam on the TREC 2011 Medical track. Here, the task is to retrieve patient visits from the University of Pittsburgh NLP Repository for 35 topics. The repository consists of 101,711 patient reports, and a patient visit was recorded in one or more reports

Mapping queries to the Linking Open Data cloud: A case study using DBpedia.

a b s t r a c t We introduce the task of mapping search engine queries to DBpedia, a major linking hub in the Linking Open Data cloud. We propose and compare various methods for addressing this task, using a mixture of information retrieval and machine learning techniques. Specifically, we present a supervised machine learning-based method to determine which concepts are intended by a user issuing a query. The concepts are obtained from an ontology and may be used to provide contextual information, related concepts, or navigational suggestions to the user submitting the query. Our approach first ranks candidate concepts using a language modeling for information retrieval framework. We then extract query, concept, and search-history feature vectors for these concepts. Using manual annotations we inform a machine learning algorithm that learns how to select concepts from the candidates given an input query. Simply performing a lexical match between the queries and concepts is found to perform poorly and so does using retrieval alone, i.e., omitting the concept selection stage. Our proposed method significantly improves upon these baselines and we find that support vector machines are able to achieve the best performance out of the machine learning algorithms evaluated

Structuring and extracting knowledge for the support of hypothesis generation in molecular biology

Background: Hypothesis generation in molecular and cellular biology is an empirical process in which knowledge derived from prior experiments is distilled into a comprehensible model. The requirement of automated support is exemplified by the difficulty of considering all relevant facts that are contained in the millions of documents available from PubMed. Semantic Web provides tools for sharing prior knowledge, while information retrieval and information extraction techniques enable its extraction from literature. Their combination makes prior knowledge available for computational analysis and inference. While some tools provide complete solutions that limit the control over the modeling and extraction processes, we seek a methodology that supports control by the experimenter over these critical processes. Results: We describe progress towards automated support for the generation of biomolecular hypotheses. Semantic Web technologies are used to structure and store knowledge, while a workflow extracts knowledge from text. We designed minimal proto-ontologies in OWL for capturing different aspects of a text mining experiment: the biological hypothesis, text and documents, text mining, and workflow provenance. The models fit a methodology that allows focus on the requirements of a single experiment while supporting reuse and posterior analysis of extracted knowledge from multiple experiments. Our workflow is composed of services from the 'Adaptive Information Disclosure Application' (AIDA) toolkit as well as a few others. The output is a semantic model with putative biological relations, with each relation linked to the corresponding evidence. Conclusion: We demonstrated a 'do-it-yourself' approach for structuring and extracting knowledge in the context of experimental research on biomolecular mechanisms. The methodology can be used to bootstrap the construction of semantically rich biological models using the results of knowledge extraction processes. Models specific to particular experiments can be constructed that, in turn, link with other semantic models, creating a web of knowledge that spans experiments. Mapping mechanisms can link to other knowledge resources such as OBO ontologies or SKOS vocabularies. AIDA Web Services can be used to design personalized knowledge extraction procedures. In our example experiment, we found three proteins (NF-Kappa B, p21, and Bax) potentially playing a role in the interplay between nutrients and epigenetic gene regulation