Dataset Information

Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer.

ABSTRACT: To understand the molecular mechanisms involved in cancer development, significant efforts are being invested in cancer research. This has resulted in millions of scientific articles. An efficient and thorough review of the existing literature is crucially important to drive new research. This time-demanding task can be supported by emerging computational approaches based on text mining which offer a great opportunity to organize and retrieve the desired information efficiently from sizable databases. One way to organize existing knowledge on cancer is to utilize the widely accepted framework of the Hallmarks of Cancer. These hallmarks refer to the alterations in cell behaviour that characterize the cancer cell.We created an extensive Hallmarks of Cancer taxonomy and developed automatic text mining methodology and a tool (CHAT) capable of retrieving and organizing millions of cancer-related references from PubMed into the taxonomy. The efficiency and accuracy of the tool was evaluated intrinsically as well as extrinsically by case studies. The correlations identified by the tool show that it offers a great potential to organize and correctly classify cancer-related literature. Furthermore, the tool can be useful, for example, in identifying hallmarks associated with extrinsic factors, biomarkers and therapeutics targets.CHAT can be accessed at: http://chat.lionproject.net. The corpus of hallmark-annotated PubMed abstracts and the software are available at: http://chat.lionproject.net/about.simon.baker@cl.cam.ac.uk.Supplementary data are available at Bioinformatics online.

SUBMITTER: Baker S

PROVIDER: S-EPMC5860084 | biostudies-other | 2017 Dec

REPOSITORIES: biostudies-other

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Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer.

Baker Simon S Ali Imran I Silins Ilona I Pyysalo Sampo S Guo Yufan Y Högberg Johan J Stenius Ulla U Korhonen Anna A

Bioinformatics (Oxford, England) 20171201 24

<h4>Motivation</h4>To understand the molecular mechanisms involved in cancer development, significant efforts are being invested in cancer research. This has resulted in millions of scientific articles. An efficient and thorough review of the existing literature is crucially important to drive new research. This time-demanding task can be supported by emerging computational approaches based on text mining which offer a great opportunity to organize and retrieve the desired information efficientl ...[more]

PMID: 29036271

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Project description:BackgroundWorldwide, veterinary practitioners and students are reported to be at higher risk of suicide, burnout, and depression compared to other occupational groups. The aim of the current study was to apply text mining and topic modelling analysis on scientific literature regarding suicide, burnout, and depression among veterinary practitioners and students to extract meaningful and synthetic information. These statistical approaches can be used to comprehend more in deep the phenomena involving veterinarians and veterinary students and to suggest the potential changes needed in admission to veterinary school, veterinary curricula, and post-graduation initiatives as preventive actions.ResultsA systematic search protocol was set up to identify scientific literature that published on the topic from 1985 to 2019. Two-hundred-eleven records were selected with abstracts/texts submitted to text mining and topic modelling analysis. Student, stress, work, anim*, and euthanasia resulted the most frequent terms. Topics modelling allowed to differentiate groups of words and papers in 3 areas of interest: 1) students' difficulties encountered during their studies that increase stress and anxiety impairing their psychological health; 2) exposure to death and euthanasia as risk factor for mental health; and 3) need of support among those providing medical and health care, and of supportive group work to cope with such profession.ConclusionBased on the most frequent words included in the clouds and on the contents of the papers clusterised in them, some suggestions are interfered. It is emphasized that the veterinary curricula should include courses that prepare them early to deal with animal death and post-death grief of pet owners, to handle ethical dilemmas and moral stressors, to communicate with clients and staff members, to work in team, to balance work-family life and to promote individual and team resources. Specific courses for veterinary practitioners could keep them updated on their new roles and ways to handle them among functioning as potential feedbacks to monitor their psychological wellbeing.

Project description:Systematically evaluating scientific literature is a time consuming endeavor that requires hours of coding and rating. Here, we describe a method to distribute these tasks across a large group through online crowdsourcing. Using Amazon's Mechanical Turk, crowdsourced workers (microworkers) completed four groups of tasks to evaluate the question, "Do nutrition-obesity studies with conclusions concordant with popular opinion receive more attention in the scientific community than do those that are discordant?" 1) Microworkers who passed a qualification test (19% passed) evaluated abstracts to determine if they were about human studies investigating nutrition and obesity. Agreement between the first two raters' conclusions was moderate (??=?0.586), with consensus being reached in 96% of abstracts. 2) Microworkers iteratively synthesized free-text answers describing the studied foods into one coherent term. Approximately 84% of foods were agreed upon, with only 4 and 8% of ratings failing manual review in different steps. 3) Microworkers were asked to rate the perceived obesogenicity of the synthesized food terms. Over 99% of responses were complete and usable, and opinions of the microworkers qualitatively matched the authors' expert expectations (e.g., sugar-sweetened beverages were thought to cause obesity and fruits and vegetables were thought to prevent obesity). 4) Microworkers extracted citation counts for each paper through Google Scholar. Microworkers reached consensus or unanimous agreement for all successful searches. To answer the example question, data were aggregated and analyzed, and showed no significant association between popular opinion and attention the paper received as measured by Scimago Journal Rank and citation counts. Direct microworker costs totaled $221.75, (estimated cost at minimum wage: $312.61). We discuss important points to consider to ensure good quality control and appropriate pay for microworkers. With good reliability and low cost, crowdsourcing has potential to evaluate published literature in a cost-effective, quick, and reliable manner using existing, easily accessible resources.

Dataset Information

Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer.

Publications

Cancer Hallmarks Analytics Tool (CHAT): a text mining approach to organize and evaluate scientific literature on cancer.

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