BackgroundThis article provides an overview of the first BioASQ challenge, a competition on large-scale biomedical semantic indexing and question answering (QA), which took place between March and September 2013. BioASQ assesses the ability of systems to semantically index very large numbers of biomedical scientific articles, and to return concise and user-understandable answers to given natural language questions by combining information from biomedical articles and ontologies.ResultsThe 2013 BioASQ competition comprised two tasks, Task 1a and Task 1b. In Task 1a participants were asked to automatically annotate new PubMed documents with MeSH headings. Twelve teams participated in Task 1a, with a total of 46 system runs submitted, and one of the teams performing consistently better than the MTI indexer used by NLM to suggest MeSH headings to curators. Task 1b used benchmark datasets containing 29 development and 282 test English questions, along with gold standard (reference) answers, prepared by a team of biomedical experts from around Europe and participants had to automatically produce answers. Three teams participated in Task 1b, with 11 system runs. The BioASQ infrastructure, including benchmark datasets, evaluation mechanisms, and the results of the participants and baseline methods, is publicly available.ConclusionsA publicly available evaluation infrastructure for biomedical semantic indexing and QA has been developed, which includes benchmark datasets, and can be used to evaluate systems that: assign MeSH headings to published articles or to English questions; retrieve relevant RDF triples from ontologies, relevant articles and snippets from PubMed Central; produce “exact” and paragraph-sized “ideal” answers (summaries). The results of the systems that participated in the 2013 BioASQ competition are promising. In Task 1a one of the systems performed consistently better from the NLM’s MTI indexer. In Task 1b the systems received high scores in the manual evaluation of the “ideal” answers; hence, they produced high quality summaries as answers. Overall, BioASQ helped obtain a unified view of how techniques from text classification, semantic indexing, document and passage retrieval, question answering, and text summarization can be combined to allow biomedical experts to obtain concise, user-understandable answers to questions reflecting their real information needs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-015-0564-6) contains supplementary material, which is available to authorized users.

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BackgroundMass spectrometric-based measurements of the steroid metabolome have been introduced to diagnose disorders featuring abnormal steroidogenesis. Defined reference intervals are important for interpreting such data.MethodsLiquid chromatography–tandem mass spectrometry was used to establish reference intervals for 16 steroids (pregnenolone, progesterone, 11-deoxycorticosterone, corticosterone, aldosterone, 18-oxocortisol, 18-hydroxycortisol, 17-hydroxyprogesterone, 21-deoxycortisol, 11-deoxycortisol, cortisol, cortisone, dehydroepiandrosterone, dehydroepiandrosterone-sulfate, androstenedione, testosterone) measured in plasma from 525 volunteers with (n = 227) and without (n = 298) hypertension, including 68 women on oral contraceptives.ResultsWomen showed variable plasma concentrations of several steroids associated with menstrual cycle phase, menopause and oral contraceptive use. Progesterone was higher in females than males, but most other steroids were higher in males than females and almost all declined with advancing age. Using models that corrected for age and gender, body mass index showed weak negative relationships with corticosterone, 21-deoxycortisol, cortisol, cortisone, testosterone, progesterone, 17-hydroxyprogesterone and 11-deoxycorticosterone, but a positive relationship with 18-hydroxycortisol. Hypertensives and normotensives showed negligible differences in plasma concentrations of steroids.ConclusionAge and gender are the most important variables for plasma steroid reference intervals, which have been established here according to those variables for a panel of 16 steroids primarily useful for diagnosis and subtyping of patients with endocrine hypertension.

The computation of relatedness between two fragments of text in an automated manner requires taking into account a wide range of factors pertaining to the meaning the two fragments convey, and the pairwise relations between their words. Without doubt, a measure of relatedness between text segments must take into account both the lexical and the semantic relatedness between words. Such a measure that captures well both aspects of text relatedness may help in many tasks, such as text retrieval, classification and clustering. In this paper we present a new approach for measuring the semantic relatedness between words based on their implicit semantic links. The approach exploits only a word thesaurus in order to devise implicit semantic links between words. Based on this approach, we introduce Omiotis, a new measure of semantic relatedness between texts which capitalizes on the word-to-word semantic relatedness measure (SR) and extends it to measure the relatedness between texts. We gradually validate our method: we first evaluate the performance of the semantic relatedness measure between individual words, covering word-to-word similarity and relatedness, synonym identification and word analogy; then, we proceed with evaluating the performance of our method in measuring text-to-text semantic relatedness in two tasks, namely sentence-to-sentence similarity and paraphrase recognition. Experimental evaluation shows that the proposed method outperforms every lexicon-based method of semantic relatedness in the selected tasks and the used data sets, and competes well against corpus-based and hybrid approaches.

Abstract. The introduction of hierarchical thesauri (HT) that contain significant semantic information, has led researchers to investigate their potential for improving performance of the text classification task, extending the traditional "bag of words" representation, incorporating syntactic and semantic relationships among words. In this paper we address this problem by proposing a Word Sense Disambiguation (WSD) approach based on the intuition that word proximity in the document implies proximity also in the HT graph. We argue that the high precision exhibited by our WSD algorithm in various humanly-disambiguated benchmark datasets, is appropriate for the classification task. Moreover, we define a semantic kernel, based on the general concept of GVSM kernels, that captures the semantic relations contained in the hierarchical thesaurus. Finally, we conduct experiments using various corpora achieving a systematic improvement in classification accuracy using the SVM algorithm, especially when the training set is small.

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