Ontology-Based MEDLINE Document Classification

An increasing and overwhelming amount of biomedical information is available in the research literature mainly in the form of free-text. Biologists need tools that automate their information search and deal with the high volume and ambiguity of free-text. Ontologies can help automatic information processing by providing standard concepts and information about the relationships between concepts. The Medical Subject Headings (MeSH) ontology is already available and used by MEDLINE indexers to annotate the conceptual content of biomedical articles. This paper presents a domain-independent method that uses the MeSH ontology inter-concept relationships to extend the existing MeSH-based representation of MEDLINE documents. The extension method is evaluated within a document triage task organized by the Genomics track of the 2005 Text REtrieval Conference (TREC). Our method for extending the representation of documents leads to an improvement of 17% over a non-extended baseline in terms of normalized utility, the metric defined for the task. The SVMlight software is used to classify documents

Automatically linking MEDLINE abstracts to the Gene Ontology

Much has been written recently about the need for effective tools and methods for mining the wealth of information present in biomedical literature (Mack and Hehenberger, 2002; Blagosklonny and Pardee, 2001; Rindflesch et al., 2002)—the activity of conceptual biology. Keyword search engines operating over large electronic document stores (such as PubMed and the PNAS) offer some help, but there are fundamental obstacles that limit their effectiveness. In the first instance, there is no general consensus among scientists about the vernacular to be used when describing research about genes, proteins, drugs, diseases, tissues and therapies, making it very difficult to formulate a search query that retrieves the right documents. Secondly, finding relevant articles is just one aspect of the investigative process. A more fundamental goal is to establish links and relationships between facts existing in published literature in order to “validate current hypotheses or to generate new ones” (Barnes and Robertson, 2002)—something keyword search engines do little to support

Formulating MEDLINE queries for article retrieval based on PubMed exemplars

Bibliographic search engines allow endless possibilities for building queries based on specific words or phrases in article titles and abstracts, indexing terms, and other attributes. Unfortunately, deciding which attributes to use in a methodologically sound query is a non-trivial process. In this paper, we describe a system to help with this task, given an example set of PubMed articles to retrieve and a corresponding set of articles to exclude. The system provides the users with unigram and bigram features from the title, abstract, MeSH terms, and MeSH qualifier terms in decreasing order of precision, given a recall threshold. From this information and their knowledge of the domain, users can formulate a query and evaluate its performance. We apply the system to the task of distinguishing original research articles of functional magnetic resonance imaging (fMRI) of sensorimotor function from fMRI studies of higher cognitive functions

Chi-square-based scoring function for categorization of MEDLINE citations

Objectives: Text categorization has been used in biomedical informatics for identifying documents containing relevant topics of interest. We developed a simple method that uses a chi-square-based scoring function to determine the likelihood of MEDLINE citations containing genetic relevant topic. Methods: Our procedure requires construction of a genetic and a nongenetic domain document corpus. We used MeSH descriptors assigned to MEDLINE citations for this categorization task. We compared frequencies of MeSH descriptors between two corpora applying chi-square test. A MeSH descriptor was considered to be a positive indicator if its relative observed frequency in the genetic domain corpus was greater than its relative observed frequency in the nongenetic domain corpus. The output of the proposed method is a list of scores for all the citations, with the highest score given to those citations containing MeSH descriptors typical for the genetic domain. Results: Validation was done on a set of 734 manually annotated MEDLINE citations. It achieved predictive accuracy of 0.87 with 0.69 recall and 0.64 precision. We evaluated the method by comparing it to three machine learning algorithms (support vector machines, decision trees, na\"ive Bayes). Although the differences were not statistically significantly different, results showed that our chi-square scoring performs as good as compared machine learning algorithms. Conclusions: We suggest that the chi-square scoring is an effective solution to help categorize MEDLINE citations. The algorithm is implemented in the BITOLA literature-based discovery support system as a preprocessor for gene symbol disambiguation process.Comment: 34 pages, 2 figure

Death, dying and informatics: misrepresenting religion on MedLine

BACKGROUND: The globalization of medical science carries for doctors worldwide a correlative duty to deepen their understanding of patients' cultural contexts and religious backgrounds, in order to satisfy each as a unique individual. To become better informed, practitioners may turn to MedLine, but it is unclear whether the information found there is an accurate representation of culture and religion. To test MedLine's representation of this field, we chose the topic of death and dying in the three major monotheistic religions. METHODS: We searched MedLine using PubMed in order to retrieve and thematically analyze full-length scholarly journal papers or case reports dealing with religious traditions and end-of-life care. Our search consisted of a string of words that included the most common denominations of the three religions, the standard heading terms used by the National Reference Center for Bioethics Literature (NRCBL), and the Medical Subject Headings (MeSH) used by the National Library of Medicine. Eligible articles were limited to English-language papers with an abstract. RESULTS: We found that while a bibliographic search in MedLine on this topic produced instant results and some valuable literature, the aggregate reflected a selection bias. American writers were over-represented given the global prevalence of these religious traditions. Denominationally affiliated authors predominated in representing the Christian traditions. The Islamic tradition was under-represented. CONCLUSION: MedLine's capability to identify the most current, reliable and accurate information about purely scientific topics should not be assumed to be the same case when considering the interface of religion, culture and end-of-life care

Informetrics on accidents and trauma

MEDLINE database has been analysed for 1995-97 on index Accidents and Trauma. Publications output has been classified year-wise country-wise, journal-wise and other fine structure characteristics have been found. High frequency keywords have been identified. Other valuable data have been compiled. The value of informater for decision-making is brought out by this study and the comprehensive data compilation by MEDLINE is established

Affective modulation of cognitive control is determined by performance-contingency and mediated by ventromedial prefrontal and cingulate cortex

Cognitive control requires a fine balance between stability, the protection of an on-going task-set, and flexibility, the ability to update a task-set in line with changing contingencies. It is thought that emotional processing modulates this balance, but results have been equivocal regarding the direction of this modulation. Here, we tested the hypothesis that a crucial determinant of this modulation is whether affective stimuli represent performance-contingent or task-irrelevant signals. Combining functional magnetic resonance imaging with a conflict task-switching paradigm, we contrasted the effects of presenting negative- and positive-valence pictures on the stability/flexibility trade-off in humans, depending on whether picture presentation was contingent on behavioral performance. Both the behavioral and neural expressions of cognitive control were modulated by stimulus valence and performance contingency: in the performance-contingent condition, cognitive flexibility was enhanced following positive pictures, whereas in the nonperformance-contingent condition, positive stimuli promoted cognitive stability. The imaging data showed that, as anticipated, the stability/flexibility trade-off per se was reflected in differential recruitment of dorsolateral frontoparietal and striatal regions. In contrast, the affective modulation of stability/flexibility shifts was mirrored, unexpectedly, by neural responses in ventromedial prefrontal and posterior cingulate cortices, core nodes of the “default mode” network. Our results demonstrate that the affective modulation of cognitive control depends on the performance contingency of the affect-inducing stimuli, and they document medial default mode regions to mediate the flexibility-promoting effects of performance-contingent positive affect, thus extending recent work that recasts these regions as serving a key role in on-task control processes

Reporting methodological search filter performance comparisons : a literature review

© 2014 The authors. Health Information and Libraries Journal © 2014 Health Libraries Journal.Peer reviewedPostprin

Searching a biomedical database from Bulgaria : the ABS database

The University of Sofia, Bulgaria, disseminates local biomedical literature (1994 to present) through a free online database, ABS. We systematically searched ABS to identify citations to controlled trials and find what proportion of these studies are to be found on MEDLINE. We searched using Bulgarian and English phrases; manually selected citations of controlled trials and sought these citations on MEDLINE. Using the two languages we found a total of 628 unique citations, of which 47 of which seem to be relevant controlled trials (precision 7.48%, 13% of ABS citations were found on MEDLINE). The trials in ABS commonly focused on evaluation of care for people with cardiovascular or urological problems