A single journal study : Malaysian Journal of Computer Science

Single journal studies are reviewed and measures used in the studies are highlighted. The following quantitative measures are used to study 272 articles published in Malaysian Journal of Computer Science, (1) the article productivity of the journal from 1985 to 2007, (2) the observed and expected authorship productivity tested using Lotka's Law of author productivity, identification and listing of core authors; (3) the authorship, co-authorship pattern by authors' country of origin and institutional affiliations; (4) the subject areas of research; (5) the citation analysis of resources referenced as well as the age and half-life of citations; the journals referenced and tested for zonal distribution using Bradford's law of journal scattering; the extent of web citations; and (6) the citations received by articles published in MJCS and impact factor of the journal based on information obtained from Google Scholar, the level of author and journal self-citation

Herb Target Prediction Based on Representation Learning of Symptom related Heterogeneous Network.

Traditional Chinese Medicine (TCM) has received increasing attention as a complementary approach or alternative to modern medicine. However, experimental methods for identifying novel targets of TCM herbs heavily relied on the current available herb-compound-target relationships. In this work, we present an Herb-Target Interaction Network (HTINet) approach, a novel network integration pipeline for herb-target prediction mainly relying on the symptom related associations. HTINet focuses on capturing the low-dimensional feature vectors for both herbs and proteins by network embedding, which incorporate the topological properties of nodes across multi-layered heterogeneous network, and then performs supervised learning based on these low-dimensional feature representations. HTINet obtains performance improvement over a well-established random walk based herb-target prediction method. Furthermore, we have manually validated several predicted herb-target interactions from independent literatures. These results indicate that HTINet can be used to integrate heterogeneous information to predict novel herb-target interactions

BICEPP: an example-based statistical text mining method for predicting the binary characteristics of drugs

<p>Abstract</p> <p>Background</p> <p>The identification of drug characteristics is a clinically important task, but it requires much expert knowledge and consumes substantial resources. We have developed a statistical text-mining approach (BInary Characteristics Extractor and biomedical Properties Predictor: BICEPP) to help experts screen drugs that may have important clinical characteristics of interest.</p> <p>Results</p> <p>BICEPP first retrieves MEDLINE abstracts containing drug names, then selects tokens that best predict the list of drugs which represents the characteristic of interest. Machine learning is then used to classify drugs using a document frequency-based measure. Evaluation experiments were performed to validate BICEPP's performance on 484 characteristics of 857 drugs, identified from the Australian Medicines Handbook (AMH) and the PharmacoKinetic Interaction Screening (PKIS) database. Stratified cross-validations revealed that BICEPP was able to classify drugs into all 20 major therapeutic classes (100%) and 157 (of 197) minor drug classes (80%) with areas under the receiver operating characteristic curve (AUC) > 0.80. Similarly, AUC > 0.80 could be obtained in the classification of 173 (of 238) adverse events (73%), up to 12 (of 15) groups of clinically significant cytochrome P450 enzyme (CYP) inducers or inhibitors (80%), and up to 11 (of 14) groups of narrow therapeutic index drugs (79%). Interestingly, it was observed that the keywords used to describe a drug characteristic were not necessarily the most predictive ones for the classification task.</p> <p>Conclusions</p> <p>BICEPP has sufficient classification power to automatically distinguish a wide range of clinical properties of drugs. This may be used in pharmacovigilance applications to assist with rapid screening of large drug databases to identify important characteristics for further evaluation.</p

Exploiting and integrating rich features for biological literature classification

<p>Abstract</p> <p>Background</p> <p>Efficient features play an important role in automated text classification, which definitely facilitates the access of large-scale data. In the bioscience field, biological structures and terminologies are described by a large number of features; domain dependent features would significantly improve the classification performance. How to effectively select and integrate different types of features to improve the biological literature classification performance is the major issue studied in this paper.</p> <p>Results</p> <p>To efficiently classify the biological literatures, we propose a novel feature value schema <it>TF</it>*<it>ML</it>, features covering from lower level domain independent “string feature” to higher level domain dependent “semantic template feature”, and proper integrations among the features. Compared to our previous approaches, the performance is improved in terms of <it>AUC</it> and <it>F-Score</it> by 11.5% and 8.8% respectively, and outperforms the best performance achieved in BioCreAtIvE 2006.</p> <p>Conclusions</p> <p>Different types of features possess different discriminative capabilities in literature classification; proper integration of domain independent and dependent features would significantly improve the performance and overcome the over-fitting on data distribution.</p

Novel metrics for evaluating the functional coherence of protein groups via protein semantic network

Metrics are presented for assessing overall functional coherence of a group of proteins based on the associated biomedical literature

Bibliometric studies on single journals: a review

This paper covers a total of 82 bibliometric studies on single journals (62 studies cover unique titles) published between 1998 and 2008 grouped into the following fields; Arts, Humanities and Social Sciences (12 items); Medical and Health Sciences (19 items); Sciences and Technology (30 items) and Library and Information Sciences (21 items). Under each field the studies are described in accordance to their geographical location in the following order, United Kingdom, United States and Americana, Europe, Asia (India, Africa and Malaysia). For each study, elements described are (a) the journal’s publication characteristics and indexation information; (b) the objectives; (c) the sampling and bibliometric measures used; and (d) the results observed. A list of journal titles studied is appended. The results show that (a)bibliometric studies cover journals in various fields; (b) there are several revisits of some journals which are considered important; (c) Asian and African contributions is high (41.4 of total studies; 43.5 covering unique titles), United States (30.4 of total; 31.0 on unique titles), Europe (18.2 of total and 14.5 on unique titles) and the United Kingdom (10 of total and 11 on unique titles); (d) a high number of bibliometrists are Indians and as such coverage of Indian journals is high (28 of total studies; 30.6 of unique titles); and (e) the quality of the journals and their importance either nationally or internationally are inferred from their indexation status

Literature Mapping with PubAtlas — extending PubMed with a ‘BLASTing interface’ *

PubAtlas (www.pubatlas.org) is a web service and standalone program providing literature maps for the biomedical research literature. It accepts user-defined sets of terms (PubMed queries) as input, and permits ‘BLASTing’ of one set against another: for all terms x and y in these sets, deriving the results of the pairwise intersections x AND y. This all vs. all capability extends PubMed with a literature analysis interface. Correspondingly, the basic form of literature map that PubAtlas provides for exploring associations among sets of terms is an interactive tabular display, in heatmap/microarray format

What can management theories offer evidence-based practice? A comparative analysis of measurement tools for organisational context

Background: Given the current emphasis on networks as vehicles for innovation and change in health service delivery, the ability to conceptualise and measure organisational enablers for the social construction of knowledge merits attention. This study aimed to develop a composite tool to measure the organisational context for evidence-based practice (EBP) in healthcare. Methods: A structured search of the major healthcare and management databases for measurement tools from four domains: research utilisation (RU), research activity (RA), knowledge management (KM), and organisational learning (OL). Included studies were reports of the development or use of measurement tools that included organisational factors. Tools were appraised for face and content validity, plus development and testing methods. Measurement tool items were extracted, merged across the four domains, and categorised within a constructed framework describing the absorptive and receptive capacities of organisations. Results: Thirty measurement tools were identified and appraised. Eighteen tools from the four domains were selected for item extraction and analysis. The constructed framework consists of seven categories relating to three core organisational attributes of vision, leadership, and a learning culture, and four stages of knowledge need, acquisition of new knowledge, knowledge sharing, and knowledge use. Measurement tools from RA or RU domains had more items relating to the categories of leadership, and acquisition of new knowledge; while tools from KM or learning organisation domains had more items relating to vision, learning culture, knowledge need, and knowledge sharing. There was equal emphasis on knowledge use in the different domains. Conclusion: If the translation of evidence into knowledge is viewed as socially mediated, tools to measure the organisational context of EBP in healthcare could be enhanced by consideration of related concepts from the organisational and management sciences. Comparison of measurement tools across domains suggests that there is scope within EBP for supplementing the current emphasis on human and technical resources to support information uptake and use by individuals. Consideration of measurement tools from the fields of KM and OL shows more content related to social mechanisms to facilitate knowledge recognition, translation, and transfer between individuals and groups

Advancing the Study of Violence Against Women: Evolving Research Agendas Into Science

Decades of research produced by multiple disciplines has documented withering rates of violence against women in the United States and around the globe. To further an understanding of gendered violence, a field of research has developed, but recent critiques have highlighted weaknesses that inhibit a full scientific exploration of these crimes and their impacts. This review extends beyond prior reviews to explore the field’s unique challenges, its community of scientists, and the state of its written knowledge. The review argues for moving beyond “research agendas” and proposes creation of a transdisciplinary science for the field of study of violence against women