Linking genes to literature: text mining, information extraction, and retrieval applications for biology

Efficient access to information contained in online scientific literature collections is essential for life science research, playing a crucial role from the initial stage of experiment planning to the final interpretation and communication of the results. The biological literature also constitutes the main information source for manual literature curation used by expert-curated databases. Following the increasing popularity of web-based applications for analyzing biological data, new text-mining and information extraction strategies are being implemented. These systems exploit existing regularities in natural language to extract biologically relevant information from electronic texts automatically. The aim of the BioCreative challenge is to promote the development of such tools and to provide insight into their performance. This review presents a general introduction to the main characteristics and applications of currently available text-mining systems for life sciences in terms of the following: the type of biological information demands being addressed; the level of information granularity of both user queries and results; and the features and methods commonly exploited by these applications. The current trend in biomedical text mining points toward an increasing diversification in terms of application types and techniques, together with integration of domain-specific resources such as ontologies. Additional descriptions of some of the systems discussed here are available on the internet

Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction

<p>Abstract</p> <p>Background</p> <p>This paper describes and evaluates a sentence selection engine that extracts a GeneRiF (Gene Reference into Functions) as defined in ENTREZ-Gene based on a MEDLINE record. Inputs for this task include both a gene and a pointer to a MEDLINE reference. In the suggested approach we merge two independent sentence extraction strategies. The first proposed strategy (LASt) uses argumentative features, inspired by discourse-analysis models. The second extraction scheme (GOEx) uses an automatic text categorizer to estimate the density of Gene Ontology categories in every sentence; thus providing a full ranking of all possible candidate GeneRiFs. A combination of the two approaches is proposed, which also aims at reducing the size of the selected segment by filtering out non-content bearing rhetorical phrases.</p> <p>Results</p> <p>Based on the TREC-2003 Genomics collection for GeneRiF identification, the LASt extraction strategy is already competitive (52.78%). When used in a combined approach, the extraction task clearly shows improvement, achieving a Dice score of over 57% (+10%).</p> <p>Conclusions</p> <p>Argumentative representation levels and conceptual density estimation using Gene Ontology contents appear complementary for functional annotation in proteomics.</p

Answering clinical questions with knowledge-based and statistical techniques

The combination of recent developments in question-answering research and the availability of unparalleled resources developed specifically for automatic semantic processing of text in the medical domain provides a unique opportunity to explore complex question answering in the domain of clinical medicine. This article presents a system designed to satisfy the information needs of physicians practicing evidence-based medicine. We have developed a series of knowledge extractors, which employ a combination of knowledge-based and statistical techniques, for automatically identifying clinically relevant aspects of MEDLINE abstracts. These extracted elements serve as the input to an algorithm that scores the relevance of citations with respect to structured representations of information needs, in accordance with the principles of evidencebased medicine. Starting with an initial list of citations retrieved by PubMed, our system can bring relevant abstracts into higher ranking positions, and from these abstracts generate responses that directly answer physicians ’ questions. We describe three separate evaluations: one focused on the accuracy of the knowledge extractors, one conceptualized as a document reranking task, and finally, an evaluation of answers by two physicians. Experiments on a collection of real-world clinical questions show that our approach significantly outperforms the already competitive PubMed baseline. 1

Semantic metadata annotation. Tagging Medline abstracts for enhanced information access.

International audiencePurpose - The object of this study is to develop methods for automatically annotating the argumentative role of sentences in scientific abstracts. Working from Medline abstracts, sentences were classified into four major argumentative roles: objective, method, result, and conclusion. The idea is that, if the role of each sentence can be marked up, then these metadata can be used during information retrieval to seek particular types of information such as novelty, conclusions, methodologies, aims/goals of a scientific piece of work. Design/methodology/approach - Two approaches were tested: linguistic cues and positional heuristics. Linguistic cues are lexico-syntactic patterns modelled as regular expressions implemented in a linguistic parser. Positional heuristics make use of the relative position of a sentence in the abstract to deduce its argumentative class. Findings - The experiments showed that positional heuristics attained a much higher degree of accuracy on Medline abstracts with an F-score of 64 per cent, whereas the linguistic cues only attained an F-score of 12 per cent. This is mostly because sentences from different argumentative roles are not always announced by surface linguistic cues. Research limitations/implications - A limitation to the study was the inability to test other methods to perform this task such as machine learning techniques which have been reported to perform better on Medline abstracts. Also, to compare the results of the study with earlier studies using Medline abstracts, the different argumentative roles present in Medline had to be mapped on to four major argumentative roles. This may have favourably biased the performance of the sentence classification by positional heuristics. Originality/value - To the best of one's knowledge, this study presents the first instance of evaluating linguistic cues and positional heuristics on the same corpus

Is searching full text more effective than searching abstracts?

<p>Abstract</p> <p>Background</p> <p>With the growing availability of full-text articles online, scientists and other consumers of the life sciences literature now have the ability to go beyond searching bibliographic records (title, abstract, metadata) to directly access full-text content. Motivated by this emerging trend, I posed the following question: is searching full text more effective than searching abstracts? This question is answered by comparing text retrieval algorithms on MEDLINE^®abstracts, full-text articles, and spans (paragraphs) within full-text articles using data from the TREC 2007 genomics track evaluation. Two retrieval models are examined: <it>bm25 </it>and the ranking algorithm implemented in the open-source Lucene search engine.</p> <p>Results</p> <p>Experiments show that treating an entire article as an indexing unit does not consistently yield higher effectiveness compared to abstract-only search. However, retrieval based on spans, or paragraphs-sized segments of full-text articles, consistently outperforms abstract-only search. Results suggest that highest overall effectiveness may be achieved by combining evidence from spans and full articles.</p> <p>Conclusion</p> <p>Users searching full text are more likely to find relevant articles than searching only abstracts. This finding affirms the value of full text collections for text retrieval and provides a starting point for future work in exploring algorithms that take advantage of rapidly-growing digital archives. Experimental results also highlight the need to develop distributed text retrieval algorithms, since full-text articles are significantly longer than abstracts and may require the computational resources of multiple machines in a cluster. The MapReduce programming model provides a convenient framework for organizing such computations.</p

Complex Network Analysis for Scientific Collaboration Prediction and Biological Hypothesis Generation

With the rapid development of digitalized literature, more and more knowledge has been discovered by computational approaches. This thesis addresses the problem of link prediction in co-authorship networks and protein--protein interaction networks derived from the literature. These networks (and most other types of networks) are growing over time and we assume that a machine can learn from past link creations by examining the network status at the time of their creation. Our goal is to create a computationally efficient approach to recommend new links for a node in a network (e.g., new collaborations in co-authorship networks and new interactions in protein--protein interaction networks). We consider edges in a network that satisfies certain criteria as training instances for the machine learning algorithms. We analyze the neighborhood structure of each node and derive the topological features. Furthermore, each node has rich semantic information when linked to the literature and can be used to derive semantic features. Using both types of features, we train machine learning models to predict the probability of connection for the new node pairs. We apply our idea of link prediction to two distinct networks: a co-authorship network and a protein--protein interaction network. We demonstrate that the novel features we derive from both the network topology and literature content help improve link prediction accuracy. We also analyze the factors involved in establishing a new link and recurrent connections

Bridging formalisation and expert judgement in searches for studies for systematic reviews

Systematic reviews aim to use pre-specified and explicitly described methods. This entails an element of formalisation in which methods are described according to a fixed structure. However, qualitative studies show that too much emphasis on formalisation can obscure how expert judgement is required even after clearly defined methods are established. Thus, there is a gap between how systematic review methods are formalised in guidance and reported in systematic reviews, and how they are carried out in practice using undisclosed expert judgement. The aim of this thesis is to describe and bridge the gap between formalisation and expert judgement with respect to searching for studies for systematic reviews, with a particular focus on forward citation searching and web searching. Forward citation searching and web searching are useful search methods to consider due to observed variability in both if and how they are used in systematic reviews, in contrast to searches of bibliographic databases which are routine in almost all systematic reviews. To this end, the thesis seeks to fulfil three objectives: first, to formalise the conduct and reporting of forward citation searching and web searching in systematic reviews; secondly, to describe and evaluate the conduct and reporting of forward citation searching and web searching in systematic reviews; thirdly, to explore the role of expert judgement when using forward citation searching and web searching. Both aggregative and configurative review types are considered throughout. The findings show that formalised approaches to searching are apparent in guidance to different degrees. However, systematic reviews do not always reflect formalised guidance. Qualitative investigation describes hitherto hidden practical knowledge which underpins searching decisions. The thesis draws these findings together and proposes that guidance on searching for studies should be framed in terms of the practical understanding which informs how searching is undertaken rather than limited to describing recommended processes

www.litbaskets.io, an IT Artifact Supporting Exploratory Literature Searches for Information Systems Research

Information Systems (IS) researchers currently lack an obvious place to start their literature searches. Existing tools suffer from being either too narrow in their coverage of existing research, leading to an insufficiency effect (low recall); or they are too encompassing, leading to an impracticality effect (low precision). From 11 listings of IS-related journals, we identify a set of 1,042 journals receptive to IS research. We introduce a web interface that allows searching for literature across most of these journals. The search tool enables researchers to narrow or widen the focus of searches, thus allowing researchers to optimise the precision-recall trade-off of their literature searches. We provide an evaluation of our artifact and discuss the relevance of our artifact for exploratory literature searches. Our artifact seeks to facilitate knowledge claims in IS research based on a shared body of knowledge beyond the AIS basket of eight journals