information storage and retrieval

Summary

Summary: Organized activities related to the storage, location, search, and retrieval of information.

Top Publications

  1. Ohmann C, Kuchinke W, Canham S, Lauritsen J, Salas N, Schade Brittinger C, et al. Standard requirements for GCP-compliant data management in multinational clinical trials. Trials. 2011;12:85 pubmed publisher
    ..It is the intention that ECRIN will use these requirements as the basis for the certification of ECRIN data centres. ..
  2. Chen Y, Lu J, Jan J. A secure EHR system based on hybrid clouds. J Med Syst. 2012;36:3375-84 pubmed publisher
    ..In this paper, we propose an EHR sharing and integration system in healthcare clouds and analyze the arising security and privacy issues in access and management of EHRs. ..
  3. Ohno Machado L, Bafna V, Boxwala A, Chapman B, Chapman W, Chaudhuri K, et al. iDASH: integrating data for analysis, anonymization, and sharing. J Am Med Inform Assoc. 2012;19:196-201 pubmed publisher
  4. Veseli H, Kopanitsa G, Demski H. Standardized EHR interoperability - preliminary results of a German pilot project using the archetype methodology. Stud Health Technol Inform. 2012;180:646-50 pubmed
    ..Furthermore, the server provides rich visualization capabilities (e.g. language-switch, custom charts etc.) which are useful for those EHR systems that don't provide these features. ..
  5. Mate S, Bürkle T, Köpcke F, Breil B, Wullich B, Dugas M, et al. Populating the i2b2 database with heterogeneous EMR data: a semantic network approach. Stud Health Technol Inform. 2011;169:502-6 pubmed
    ..By using Semantic Web standards, it is the authors' goal to reuse the laboriously compiled "mapping knowledge" in future projects, such as a comprehensive cancer ontology or even a hospital-wide clinical ontology. ..
  6. Zheluk A, Gillespie J, Quinn C. Searching for truth: internet search patterns as a method of investigating online responses to a Russian illicit drug policy debate. J Med Internet Res. 2012;14:e165 pubmed publisher
  7. Lokker C, Haynes R, Wilczynski N, McKibbon K, Walter S. Retrieval of diagnostic and treatment studies for clinical use through PubMed and PubMed's Clinical Queries filters. J Am Med Inform Assoc. 2011;18:652-9 pubmed publisher
    ..Retrieving clinically important research studies from Medline is a challenging task for physicians. Methodological search filters can improve search retrieval. ..
  8. Avillach P, Dufour J, Diallo G, Salvo F, Joubert M, Thiessard F, et al. Design and validation of an automated method to detect known adverse drug reactions in MEDLINE: a contribution from the EU-ADR project. J Am Med Inform Assoc. 2013;20:446-52 pubmed publisher
  9. Sansone S, Rocca Serra P, Field D, Maguire E, Taylor C, Hofmann O, et al. Toward interoperable bioscience data. Nat Genet. 2012;44:121-6 pubmed publisher
    ..Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision. ..
  10. Zhang Y, Yu P, Shen J. The benefits of introducing electronic health records in residential aged care facilities: a multiple case study. Int J Med Inform. 2012;81:690-704 pubmed publisher
    ..The benefits were derived from the nature of the aged care EHR systems, staff members' continuous use of the systems, and one benefit led to the other. ..

Detail Information

Publications62

  1. Ohmann C, Kuchinke W, Canham S, Lauritsen J, Salas N, Schade Brittinger C, et al. Standard requirements for GCP-compliant data management in multinational clinical trials. Trials. 2011;12:85 pubmed publisher
    ..It is the intention that ECRIN will use these requirements as the basis for the certification of ECRIN data centres. ..
  2. Chen Y, Lu J, Jan J. A secure EHR system based on hybrid clouds. J Med Syst. 2012;36:3375-84 pubmed publisher
    ..In this paper, we propose an EHR sharing and integration system in healthcare clouds and analyze the arising security and privacy issues in access and management of EHRs. ..
  3. Ohno Machado L, Bafna V, Boxwala A, Chapman B, Chapman W, Chaudhuri K, et al. iDASH: integrating data for analysis, anonymization, and sharing. J Am Med Inform Assoc. 2012;19:196-201 pubmed publisher
  4. Veseli H, Kopanitsa G, Demski H. Standardized EHR interoperability - preliminary results of a German pilot project using the archetype methodology. Stud Health Technol Inform. 2012;180:646-50 pubmed
    ..Furthermore, the server provides rich visualization capabilities (e.g. language-switch, custom charts etc.) which are useful for those EHR systems that don't provide these features. ..
  5. Mate S, Bürkle T, Köpcke F, Breil B, Wullich B, Dugas M, et al. Populating the i2b2 database with heterogeneous EMR data: a semantic network approach. Stud Health Technol Inform. 2011;169:502-6 pubmed
    ..By using Semantic Web standards, it is the authors' goal to reuse the laboriously compiled "mapping knowledge" in future projects, such as a comprehensive cancer ontology or even a hospital-wide clinical ontology. ..
  6. Zheluk A, Gillespie J, Quinn C. Searching for truth: internet search patterns as a method of investigating online responses to a Russian illicit drug policy debate. J Med Internet Res. 2012;14:e165 pubmed publisher
  7. Lokker C, Haynes R, Wilczynski N, McKibbon K, Walter S. Retrieval of diagnostic and treatment studies for clinical use through PubMed and PubMed's Clinical Queries filters. J Am Med Inform Assoc. 2011;18:652-9 pubmed publisher
    ..Retrieving clinically important research studies from Medline is a challenging task for physicians. Methodological search filters can improve search retrieval. ..
  8. Avillach P, Dufour J, Diallo G, Salvo F, Joubert M, Thiessard F, et al. Design and validation of an automated method to detect known adverse drug reactions in MEDLINE: a contribution from the EU-ADR project. J Am Med Inform Assoc. 2013;20:446-52 pubmed publisher
  9. Sansone S, Rocca Serra P, Field D, Maguire E, Taylor C, Hofmann O, et al. Toward interoperable bioscience data. Nat Genet. 2012;44:121-6 pubmed publisher
    ..Here we describe the prerequisites for data commoning and present an established and growing ecosystem of solutions using the shared 'Investigation-Study-Assay' framework to support that vision. ..
  10. Zhang Y, Yu P, Shen J. The benefits of introducing electronic health records in residential aged care facilities: a multiple case study. Int J Med Inform. 2012;81:690-704 pubmed publisher
    ..The benefits were derived from the nature of the aged care EHR systems, staff members' continuous use of the systems, and one benefit led to the other. ..
  11. Schulz M, Krause F, Le Novère N, Klipp E, Liebermeister W. Retrieval, alignment, and clustering of computational models based on semantic annotations. Mol Syst Biol. 2011;7:512 pubmed publisher
    ..Beyond similarity searches, the representation of models by semantic feature vectors may pave the way for visualisation, exploration, and statistical analysis of large collections of models and corresponding data. ..
  12. El Emam K, Paton D, Dankar F, Koru G. De-identifying a public use microdata file from the Canadian national discharge abstract database. BMC Med Inform Decis Mak. 2011;11:53 pubmed publisher
    ..However, to create a more detailed file with less information loss suitable for more complex health services research, the risk would need to be mitigated by requiring the data recipient to commit to a data sharing agreement. ..
  13. Peissig P, Rasmussen L, Berg R, Linneman J, McCarty C, Waudby C, et al. Importance of multi-modal approaches to effectively identify cataract cases from electronic health records. J Am Med Inform Assoc. 2012;19:225-34 pubmed publisher
    ..These algorithms provide a high level of accuracy even when implemented across multiple EHRs and institutional boundaries. ..
  14. Hu Q, Huang J, Miao J. A robust approach to optimizing multi-source information for enhancing genomics retrieval performance. BMC Bioinformatics. 2011;12 Suppl 5:S6 pubmed publisher
    ..Meanwhile, under the same combination, the better the baseline performance is, the more contribution the baseline provides. These conclusions are very useful to direct the fusion work in the field of biomedical information retrieval. ..
  15. Salgado D, Krallinger M, Depaule M, Drula E, Tendulkar A, Leitner F, et al. MyMiner: a web application for computer-assisted biocuration and text annotation. Bioinformatics. 2012;28:2285-7 pubmed
    ..The usefulness and efficiency of this application have been tested for a range of real-life annotation scenarios of various research topics. http://myminer.armi.monash.edu.au. ..
  16. Hausner E, Waffenschmidt S, Kaiser T, Simon M. Routine development of objectively derived search strategies. Syst Rev. 2012;1:19 pubmed publisher
    ..Besides creating high-quality strategies, the widespread application of this approach will result in a substantial increase in the transparency of the development process of search strategies. ..
  17. Danecek P, Auton A, Abecasis G, Albers C, Banks E, DePristo M, et al. The variant call format and VCFtools. Bioinformatics. 2011;27:2156-8 pubmed publisher
    ..VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API. http://vcftools.sourceforge.net ..
  18. Church G, Gao Y, Kosuri S. Next-generation digital information storage in DNA. Science. 2012;337:1628 pubmed
    ..We developed a strategy to encode arbitrary digital information in DNA, wrote a 5.27-megabit book using DNA microchips, and read the book by using next-generation DNA sequencing. ..
  19. Chen T, Liu C, Chen T, Chen C, Bau J, Lin T. Secure Dynamic access control scheme of PHR in cloud computing. J Med Syst. 2012;36:4005-20 pubmed publisher
  20. Silva L, Costa C, Oliveira J. A PACS archive architecture supported on cloud services. Int J Comput Assist Radiol Surg. 2012;7:349-58 pubmed publisher
    ..The presented architecture uses the cloud to setup medical data repositories and can have a significant impact on healthcare institutions by reducing IT infrastructures. ..
  21. Dräger A, Rodriguez N, Dumousseau M, Dorr A, Wrzodek C, Le Novère N, et al. JSBML: a flexible Java library for working with SBML. Bioinformatics. 2011;27:2167-8 pubmed publisher
    ..Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML. ..
  22. Ruau D, Mbagwu M, Dudley J, Krishnan V, Butte A. Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets. J Biomed Inform. 2011;44 Suppl 1:S39-43 pubmed publisher
  23. Bonnet J, Subsoontorn P, Endy D. Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc Natl Acad Sci U S A. 2012;109:8884-9 pubmed publisher
    ..The serine recombinase functions used here do not require cell-specific cofactors and should be useful in extending computing and control methods to the study and engineering of many biological systems. ..
  24. Workman T, Stoddart J. Rethinking information delivery: using a natural language processing application for point-of-care data discovery. J Med Libr Assoc. 2012;100:113-20 pubmed publisher
    ..57. This new approach to point-of-care information delivery holds promise as a decision support tool for clinicians. Health sciences libraries could implement such technologies to deliver tailored information to their users. ..
  25. Jones R, Goldsmith L, Williams C, Kamel Boulos M. Accuracy of geographically targeted internet advertisements on Google AdWords for recruitment in a randomized trial. J Med Internet Res. 2012;14:e84 pubmed publisher
    ..Clinicaltrials.gov NCT01469689; http://clinicaltrials.gov/ct2/show/NCT01469689 (Archived by WebCite at http://www.webcitation.org/681iro5OU). ..
  26. Bauer M, Berleant D. Usability survey of biomedical question answering systems. Hum Genomics. 2012;6:17 pubmed publisher
    ..We present a review and comparison of three biomedical question answering systems: askHERMES (http://www.askhermes.org/), EAGLi (http://eagl.unige.ch/EAGLi/), and HONQA (http://services.hon.ch/cgi-bin/QA10/qa.pl). ..
  27. Pruski C, Wisniewski F. Efficient medical information retrieval in encrypted Electronic Health Records. Stud Health Technol Inform. 2012;180:225-9 pubmed
    ..Furthermore, we provide an overview of the approach together with illustrating examples and a discussion on the advantages and limitations of the provided framework. ..
  28. Lapsia V, Lamb K, Yasnoff W. Where should electronic records for patients be stored?. Int J Med Inform. 2012;81:821-7 pubmed publisher
    ..Choice of architecture may have implications on the efficiency, usability, and effectiveness of the NHII at the point of care. ..
  29. Fernández Cardeñosa G, de la Torre Díez I, López Coronado M, Rodrigues J. Analysis of cloud-based solutions on EHRs systems in different scenarios. J Med Syst. 2012;36:3777-82 pubmed publisher
    ..Finally it's considered the fact of deploying a hybrid solution: in which EHRs with images will be hosted in the Hospital or Primary Care Centers and the rest of them will be migrated to the Cloud. ..
  30. Grosjean J, Merabti T, Dahamna B, Kergourlay I, Thirion B, Soualmia L, et al. Health multi-terminology portal: a semantic added-value for patient safety. Stud Health Technol Inform. 2011;166:129-38 pubmed
    ..It can also be very useful for teaching or performing audits in terminology management. ..
  31. Zhang L, Gu S, Liu Y, Wang B, Azuaje F. Gene set analysis in the cloud. Bioinformatics. 2012;28:294-5 pubmed publisher
    ..YunBe is open-source and freely accessible within the Amazon Elastic MapReduce service at s3n://lrcv-crp-sante/app/yunbe.jar. Source code and user's guidelines can be downloaded from http://tinyurl.com/yunbedownload. ..
  32. Schweitzer E. Reconciliation of the cloud computing model with US federal electronic health record regulations. J Am Med Inform Assoc. 2012;19:161-5 pubmed publisher
    ..EHRs built with the cloud computing model can achieve acceptable privacy and security through business associate contracts with cloud providers that specify compliance requirements, performance metrics and liability sharing. ..
  33. Young S, Duffull S. A learning-based approach for performing an in-depth literature search using MEDLINE. J Clin Pharm Ther. 2011;36:504-12 pubmed publisher
    ..The introduction of automatic, learning tools for searching is desirable and we present a possible approach. ..
  34. Masseroli M, Ghisalberti G, Ceri S. Bio-Search Computing: integration and global ranking of bioinformatics search results. J Integr Bioinform. 2011;8:166 pubmed publisher
    ..This current prototype application, the available services that it uses, the queries that are supported, the kind of interaction that is therefore made available to the users, and the future scenarios are here described and discussed. ..
  35. Schütze B. [Use of medical treatment data outside of the patient supply: best way pseudonymisation]. Dtsch Med Wochenschr. 2012;137:844-50 pubmed publisher
  36. Huebner Bloder G, Duftschmid G, Kohler M, Rinner C, Saboor S, Ammenwerth E. An EHR prototype using structured ISO/EN 13606 documents to respond to identified clinical information needs of diabetes specialists: a controlled study on feasibility and impact. AMIA Annu Symp Proc. 2012;2012:380-9 pubmed
    ..The participants also appreciated the extended query options. ..
  37. Li Q, Zhai H, Deleger L, Lingren T, Kaiser M, Stoutenborough L, et al. A sequence labeling approach to link medications and their attributes in clinical notes and clinical trial announcements for information extraction. J Am Med Inform Assoc. 2013;20:915-21 pubmed publisher
    ..Using parsimonious feature sets both the SVM-based binary classification and CRF-based MLSL methods achieved high performance in detecting medication name and attribute linkages in CTA and CN. ..
  38. Zhang H, Fiszman M, Shin D, Miller C, Rosemblat G, Rindflesch T. Degree centrality for semantic abstraction summarization of therapeutic studies. J Biomed Inform. 2011;44:830-8 pubmed publisher
    ..The results showed that recall for system results was 72%, precision was 73%, and F-score was 0.72. The system F-score was considerably higher than that for the baseline (0.47). ..
  39. Davis P. The effect of public deposit of scientific articles on readership. Physiologist. 2012;55:161, 163-5 pubmed
  40. van de Glind E, van Munster B, Spijker R, Scholten R, Hooft L. Search filters to identify geriatric medicine in Medline. J Am Med Inform Assoc. 2012;19:468-72 pubmed publisher
    ..The filters are useful to both the clinician who wants to find a quick answer to a clinical question and the researcher who wants to find as many relevant articles as possible without retrieving too many irrelevant articles. ..
  41. Tang X, Krzeminski C, Lecavelier des Etangs Levallois A, Chen Z, Dubois E, Kasper E, et al. Energy-band engineering for improved charge retention in fully self-aligned double floating-gate single-electron memories. Nano Lett. 2011;11:4520-6 pubmed publisher
    ..The dimensions and position of each floating gate are well-defined and controlled. The devices exhibit a long retention time and single-electron injection at room temperature. ..
  42. Wilczynski N, McKibbon K, Haynes R. Search filter precision can be improved by NOTing out irrelevant content. AMIA Annu Symp Proc. 2011;2011:1506-13 pubmed
    ..Search filter precision can be improved by NOTing out irrelevant content. ..
  43. Rocktäschel T, Weidlich M, Leser U. ChemSpot: a hybrid system for chemical named entity recognition. Bioinformatics. 2012;28:1633-40 pubmed publisher
    ..1% on the SCAI corpus, outperforming the only other freely available chemical NER tool, OSCAR4, by 10.8 percentage points. ChemSpot is freely available at: http://www.informatik.hu-berlin.de/wbi/resources. ..
  44. Fusaro V, Patil P, Gafni E, Wall D, Tonellato P. Biomedical cloud computing with Amazon Web Services. PLoS Comput Biol. 2011;7:e1002147 pubmed publisher
    ..amazon.com/importexport/). More information about cloud computing, detailed cost analysis, and security can be found in references. ..
  45. Agoritsas T, Merglen A, Courvoisier D, Combescure C, Garin N, Perrier A, et al. Sensitivity and predictive value of 15 PubMed search strategies to answer clinical questions rated against full systematic reviews. J Med Internet Res. 2012;14:e85 pubmed publisher
    ..These results can help clinicians apply effective strategies to answer their questions at the point of care. ..
  46. Davis P. Open access, readership, citations: a randomized controlled trial of scientific journal publishing. FASEB J. 2011;25:2129-34 pubmed publisher
    ..The real beneficiaries of open access publishing may not be the research community but communities of practice that consume, but rarely contribute to, the corpus of literature. ..
  47. Homorodean C, Olinic M, Olinic D. Development of a methodology for structured reporting of information in echocardiography. Med Ultrason. 2012;14:29-33 pubmed
    ..In the future, our template-based reporting methodology might be extended to other imaging modalities. ..
  48. Morgan J, Lichtman J. Digital tissue and what it may reveal about the brain. BMC Biol. 2017;15:101 pubmed publisher
    ..One field where this transformation is occurring is connectomics: the mapping of neural connections in large volumes of digitized brain tissue. ..
  49. Ayorinde A, Wilde K, Lemon J, Campbell D, Bhattacharya S. Data Resource Profile: The Aberdeen Maternity and Neonatal Databank (AMND). Int J Epidemiol. 2016;45:389-94 pubmed publisher
  50. Kowal B, Schreier T, Dauer J, Helikar T. Programmatic access to logical models in the Cell Collective modeling environment via a REST API. Biosystems. 2016;139:12-6 pubmed publisher
    ..org). thelikar2@unl.edu. Technical user documentation: https://goo.gl/U52GWo. ..
  51. Kholghi M, Sitbon L, Zuccon G, Nguyen A. Active learning: a step towards automating medical concept extraction. J Am Med Inform Assoc. 2016;23:289-96 pubmed publisher
    ..Incremental active learning is a promising approach for building effective and robust medical concept extraction models while significantly reducing the burden of manual annotation. ..
  52. Powell C, Ginier E. Lessons learned: year-by-year improvement of a required information competency course. Med Ref Serv Q. 2013;32:290-313 pubmed publisher
    ..The course teaches students to access, organize, read, and analyze the biomedical research literature. ..
  53. Zhu D, Li D, Carterette B, Liu H. Integrating information retrieval with distant supervision for gene ontology annotation. Database (Oxford). 2014;2014: pubmed publisher
    ..075 based on exact match and 0.301 considering hierarchical matches. Our search-based systems for subtask B significantly outperformed the similarity-based system. https://github.com/noname2020/Bioc. ..
  54. Ainsworth J, Buchan I. Combining Health Data Uses to Ignite Health System Learning. Methods Inf Med. 2015;54:479-87 pubmed publisher
  55. Hsieh J, Li A, Yang C. Mobile, cloud, and big data computing: contributions, challenges, and new directions in telecardiology. Int J Environ Res Public Health. 2013;10:6131-53 pubmed publisher
    ..Most importantly, these services will increase global collaboration and advance clinical practice, education, and scientific research in cardiology. ..
  56. Arnold C, Oh A, Chen S, Speier W. Evaluating topic model interpretability from a primary care physician perspective. Comput Methods Programs Biomed. 2016;124:67-75 pubmed publisher
    ..Our results indicate that PCPs find discovered topics more coherent and representative of clinical reports relative to students, warranting further research into their use for automatic summarization. ..
  57. Park H, Shin Y, Choi S, Kim Y. Symbolic and graphical representation scheme for sensors deployed in large-scale structures. Sensors (Basel). 2013;13:9774-89 pubmed publisher
    ..The results also demonstrate the superiority of the SGRS over conventional expression methods in which a box diagram or tree diagram representing the ID of sensors and data loggers is used. ..
  58. Gindre D, Iliopoulos K, Krupka O, Evrard M, Champigny E, Sallé M. Coumarin-Containing Polymers for High Density Non-Linear Optical Data Storage. Molecules. 2016;21:147 pubmed publisher
    ..Second harmonic generation microscopy was used to read the stored information. ..
  59. Howard B, Phillips J, Miller K, Tandon A, Mav D, Shah M, et al. SWIFT-Review: a text-mining workbench for systematic review. Syst Rev. 2016;5:87 pubmed publisher
    ..Text-mining and machine learning software such as SWIFT-Review can be valuable tools to reduce the human screening burden and assist in problem formulation. ..
  60. Lelong R, Soualmia L, Dahamna B, Griffon N, Darmoni S. Querying EHRs with a Semantic and Entity-Oriented Query Language. Stud Health Technol Inform. 2017;235:121-125 pubmed
    ..Several types of queries on a test database containing 2,000 anonymized patients EHRs (i.e. approximately 200,000 records) were tested. These queries were able to accurately treat symbolic, textual, numerical and chronological data. ..
  61. Febres G, Jaffe K. Music viewed by its entropy content: A novel window for comparative analysis. PLoS ONE. 2017;12:e0185757 pubmed publisher
    ..These classification techniques promise to be useful in other disciplines for pattern recognition and machine learning...
  62. Sheets L, Liu F, Sarmiento R, Gavino A, Fontelo P. Optimizing the txt2MEDLINE search portal for low-resource clinical decision support. AMIA Annu Symp Proc. 2013;2013:1277-81 pubmed
    ..This reached our predefined criterion for clinical significance, a difference of 0.5 standard deviations. Improving this technology could improve clinical information resources in the world's most medically underserved communities. ..