Journal of biomedical discovery and collaboration最新文献

{"title":"Two Similarity Metrics for Medical Subject Headings (MeSH): An Aid to Biomedical Text Mining and Author Name Disambiguation.","authors":"Neil R Smalheiser,&nbsp;Gary Bonifield","doi":"10.5210/disco.v7i0.6654","DOIUrl":"https://doi.org/10.5210/disco.v7i0.6654","url":null,"abstract":"<p><p>In the present paper, we have created and characterized several similarity metrics for relating any two Medical Subject Headings (MeSH terms) to each other. The article-based metric measures the tendency of two MeSH terms to appear in the MEDLINE record of the same article. The author-based metric measures the tendency of two MeSH terms to appear in the body of articles written by the same individual (using the 2009 Author-ity author name disambiguation dataset as a gold standard). The two metrics are only modestly correlated with each other (r = 0.50), indicating that they capture different aspects of term usage. The article-based metric provides a measure of semantic relatedness, and MeSH term pairs that co-occur more often than expected by chance may reflect relations between the two terms. In contrast, the author metric is indicative of how individuals practice science, and may have value for author name disambiguation and studies of scientific discovery. We have calculated article metrics for all MeSH terms appearing in at least 25 articles in MEDLINE (as of 2014) and author metrics for MeSH terms published as of 2009. The dataset is freely available for download and can be queried at http://arrowsmith.psych.uic.edu/arrowsmith_uic/mesh_pair_metrics.html. Handling editor: Elizabeth Workman, MLIS, PhD. </p>","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":"7 ","pages":"e1"},"PeriodicalIF":0.0,"publicationDate":"2016-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.5210/disco.v7i0.6654","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34573326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The language of discovery.","authors":"Wiley Souba","doi":"10.5210/disco.v6i0.3634","DOIUrl":"10.5210/disco.v6i0.3634","url":null,"abstract":"<p><p>Discovery, as a public attribution, and discovering, the act of conducting research, are experiences that entail \"languaging\" the unknown. This distinguishing property of language - its ability to bring forth, out of the unspoken realm, new knowledge, original ideas, and novel thinking - is essential to the discovery process. In sharing their ideas and views, scientists create co-negotiated linguistic distinctions that prompt the revision of established mental maps and the adoption of new ones. While scientific mastery entails command of the conversational domain unique to a specific discipline, there is an emerging conversational domain that must be mastered that goes beyond the language unique to any particular specialty. Mastery of this new conversational domain gives researchers access to their hidden mental maps that limit their ways of thinking about and doing science. The most effective scientists use language to recontextualize their approach to problem-solving, which triggers new insights (previously unavailable) that result in new discoveries. While language is not a replacement for intuition and other means of knowing, when we try to understand what's outside of language we have to use language to do so.</p>","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":"6 ","pages":"53-69"},"PeriodicalIF":0.0,"publicationDate":"2011-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3139986/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30253163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bias associated with mining electronic health records.","authors":"George Hripcsak,&nbsp;Charles Knirsch,&nbsp;Li Zhou,&nbsp;Adam Wilcox,&nbsp;Genevieve Melton","doi":"10.5210/disco.v6i0.3581","DOIUrl":"https://doi.org/10.5210/disco.v6i0.3581","url":null,"abstract":"<p><p>Large-scale electronic health record research introduces biases compared to traditional manually curated retrospective research. We used data from a community-acquired pneumonia study for which we had a gold standard to illustrate such biases. The challenges include data inaccuracy, incompleteness, and complexity, and they can produce in distorted results. We found that a naïve approach approximated the gold standard, but errors on a minority of cases shifted mortality substantially. Manual review revealed errors in both selecting and characterizing the cohort, and narrowing the cohort improved the result. Nevertheless, a significantly narrowed cohort might contain its own biases that would be difficult to estimate.</p>","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":"6 ","pages":"48-52"},"PeriodicalIF":0.0,"publicationDate":"2011-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.5210/disco.v6i0.3581","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29918861","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Literature-based Resurrection of Neglected Medical Discoveries.","authors":"Don R Swanson","doi":"10.5210/disco.v6i0.3515","DOIUrl":"https://doi.org/10.5210/disco.v6i0.3515","url":null,"abstract":"<p><p>It is possible to find in the medical literature many articles that have been neglected or ignored, in some cases for many years, but which are worth bringing to light because they report unusual findings that may be of current scientific interest. Resurrecting previously published but neglected hypotheses that have merit might be overlooked because it would seem to lack the novelty of \"discovery\" -- but the potential value of so doing is hardly arguable. Finding neglected hypotheses may be not only of great practical value, but also affords the opportunity to study the structure of such hypotheses in the hope of illuminating the more general problem of hypothesis generation.</p>","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":"6 ","pages":"34-47"},"PeriodicalIF":0.0,"publicationDate":"2011-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.5210/disco.v6i0.3515","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29830973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A cognitive task analysis of a visual analytic workflow: Exploring molecular interaction networks in systems biology.","authors":"Barbara Mirel, Felix Eichinger, Benjamin J Keller, Matthias Kretzler","doi":"10.5210/disco.v6i0.3410","DOIUrl":"10.5210/disco.v6i0.3410","url":null,"abstract":"<p><strong>Background: </strong>Bioinformatics visualization tools are often not robust enough to support biomedical specialists’ complex exploratory analyses. Tools need to accommodate the workflows that scientists actually perform for specific translational research questions. To understand and model one of these workflows, we conducted a case-based, cognitive task analysis of a biomedical specialist’s exploratory workflow for the question: What functional interactions among gene products of high throughput expression data suggest previously unknown mechanisms of a disease?</p><p><strong>Results: </strong>From our cognitive task analysis four complementary representations of the targeted workflow were developed. They include: usage scenarios, flow diagrams, a cognitive task taxonomy, and a mapping between cognitive tasks and user-centered visualization requirements. The representations capture the flows of cognitive tasks that led a biomedical specialist to inferences critical to hypothesizing. We created representations at levels of detail that could strategically guide visualization development, and we confirmed this by making a trial prototype based on user requirements for a small portion of the workflow.</p><p><strong>Conclusions: </strong>Our results imply that visualizations should make available to scientific users “bundles of features” consonant with the compositional cognitive tasks purposefully enacted at specific points in the workflow. We also highlight certain aspects of visualizations that: (a) need more built-in flexibility; (b) are critical for negotiating meaning; and (c) are necessary for essential metacognitive support.</p>","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":"6 ","pages":"1-33"},"PeriodicalIF":0.0,"publicationDate":"2011-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3090070/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29785942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"NEMO: Extraction and normalization of organization names from PubMed affiliations.","authors":"Siddhartha Reddy Jonnalagadda, Philip Topham","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Background: </strong>Today, there are more than 18 million articles related to biomedical research indexed in MEDLINE, and information derived from them could be used effectively to save the great amount of time and resources spent by government agencies in understanding the scientific landscape, including key opinion leaders and centers of excellence. Associating biomedical articles with organization names could significantly benefit the pharmaceutical marketing industry, health care funding agencies and public health officials and be useful for other scientists in normalizing author names, automatically creating citations, indexing articles and identifying potential resources or collaborators. Large amount of extracted information helps in disambiguating organization names using machine-learning algorithms.</p><p><strong>Results: </strong>We propose NEMO, a system for extracting organization names in the affiliation and normalizing them to a canonical organization name. Our parsing process involves multi-layered rule matching with multiple dictionaries. The system achieves more than 98% f-score in extracting organization names. Our process of normalization that involves clustering based on local sequence alignment metrics and local learning based on finding connected components. A high precision was also observed in normalization.</p><p><strong>Conclusion: </strong>NEMO is the missing link in associating each biomedical paper and its authors to an organization name in its canonical form and the Geopolitical location of the organization. This research could potentially help in analyzing large social networks of organizations for landscaping a particular topic, improving performance of author disambiguation, adding weak links in the co-author network of authors, augmenting NLM's MARS system for correcting errors in OCR output of affiliation field, and automatically indexing the PubMed citations with the normalized organization name and country. Our system is available as a graphical user interface available for download along with this paper.</p>","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":"5 ","pages":"50-75"},"PeriodicalIF":0.0,"publicationDate":"2010-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990275/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29331539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"EpiphaNet: An Interactive Tool to Support Biomedical Discoveries.","authors":"Trevor Cohen,&nbsp;G Kerr Whitfield,&nbsp;Roger W Schvaneveldt,&nbsp;Kavitha Mukund,&nbsp;Thomas Rindflesch","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Unlabelled: </strong>Background. EpiphaNet is an interactive knowledge discovery system which enables researchers to explore visually sets of relations extracted from MEDLINE using a combination of language processing techniques. In this paper, we discuss the theoretical and methodological foundations of the system, and evaluate the utility of the models that underlie it for literature-based discovery. In addition, we present a summary of results drawn from a qualitative analysis of over six hours of interaction with the system by basic medical scientists.</p><p><strong>Results: </strong>The system is able to simulate open and closed discovery, and is shown to generate associations that are both surprising and interesting within the area of expertise of the researchers concerned.</p><p><strong>Conclusions: </strong>EpiphaNet provides an interactive visual representation of associations between concepts, which is derived from distributional statistics drawn from across the spectrum of biomedical citations in MEDLINE. This tool is available online, providing biomedical scientists with the opportunity to identify and explore associations of interest to them.</p>","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":" ","pages":"21-49"},"PeriodicalIF":0.0,"publicationDate":"2010-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990276/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40085089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recall and bias of retrieving gene expression microarray datasets through PubMed identifiers.","authors":"Heather Piwowar,&nbsp;Wendy Chapman","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Background: </strong>The ability to locate publicly available gene expression microarray datasets effectively and efficiently facilitates the reuse of these potentially valuable resources. Centralized biomedical databases allow users to query dataset metadata descriptions, but these annotations are often too sparse and diverse to allow complex and accurate queries. In this study we examined the ability of PubMed article identifiers to locate publicly available gene expression microarray datasets, and investigated whether the retrieved datasets were representative of publicly available datasets found through statements of data sharing in the associated research articles.</p><p><strong>Results: </strong>In a recent article, Ochsner and colleagues identified 397 studies that had generated gene expression microarray data. Their search of the full text of each publication for statements of data sharing revealed 203 publicly available datasets, including 179 in the Gene Expression Omnibus (GEO) or ArrayExpress databases. Our scripted search of GEO and ArrayExpress for PubMed identifiers of the same 397 studies returned 160 datasets, including six not found by the original search for data sharing statements. As a proportion of datasets found by either method, the search for data sharing statements identified 91.4% of the 209 publicly available datasets, compared to only 76.6% found by our search carried out using PubMed identifiers. Searching GEO or ArrayExpress alone retrieved 63.2% and 46.9% of all available datasets, respectively. There was no difference in the type of datasets found by PubMed identifier searches in terms of research theme or the technology used. However, the studies identified were more likely to have larger sample sizes, were more frequently cited, and published in higher impact journals.</p><p><strong>Conclusions: </strong>Searching database entries using PubMed identifiers can identify the majority of publicly available datasets, but caution is required when this method is used to collect data for policy evaluation since studies in low impact journals are disproportionately excluded. We urge authors of all datasets to complete the citation fields for their dataset submissions once publication details are known, thereby ensuring their work has maximum visibility and can contribute to subsequent studies.</p>","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":"5 ","pages":"7-20"},"PeriodicalIF":0.0,"publicationDate":"2010-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990274/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28885476","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MLTrends: Graphing MEDLINE term usage over time.","authors":"Gareth A Palidwor,&nbsp;Miguel A Andrade-Navarro","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The MEDLINE database of medical literature is routinely used by researchers and doctors to find articles pertaining to their area of interest. Insight into historical changes in research areas may be gained by chronological analysis of the 18 million records currently in the database, however such analysis is generally complex and time consuming. The authors' MLTrends web application graphs term usage in MEDLINE over time, allowing the determination of emergence dates for biomedical terms and historical variations in term usage intensity. MLTrends may be used at: http://www.ogic.ca/mltrends.</p>","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":"5 ","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2010-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28870764","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MLTrends: Graphing MEDLINE term usage over time","authors":"Gareth A. Palidwor, Miguel Andrade","doi":"10.5210/DISCO.V5I0.2680","DOIUrl":"https://doi.org/10.5210/DISCO.V5I0.2680","url":null,"abstract":"The MEDLINE database of medical literature is routinely used by researchers and doctors to find articles pertaining to their area of interest. Insight into historical changes in research areas and use of scientific language may be gained by chronological analysis of the 18 million records currently in the database, however such analysis is generally complex and time consuming. The authors’ MLTrends web application graphs term usage in MEDLINE over time, allowing the determination of emergence dates for biomedical terms and historical variations in term usage intensity. Terms considered are individual words or quoted phrases which may be combined using Boolean operators. MLTrends can plot the number of records in MEDLINE per year whose titles or abstracts match each queried term for multiple terms simultaneously. The MEDLINE database is stored and indexed on the MLTrends server allowing queries to be completed and graphs generated in less than one second. Queries may be performed on all titles and/or abstracts in MEDLINE and can include stop words. The resulting graphs may be normalized by total publications or words per year to facilitate term usage comparison between years.This makes MLTrends a powerful tool for rapid evaluation of the evolution of biomedical research and language in a graphical way. MLTrends may be used at: http://www.ogic.ca/mltrends","PeriodicalId":87404,"journal":{"name":"Journal of biomedical discovery and collaboration","volume":"5 1","pages":"1 - 6"},"PeriodicalIF":0.0,"publicationDate":"2010-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70826947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}