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An Object Model Based Repository for Biological Pathways Using XML Database Technology [chapter]

Keyuan Jiang
2007 Lecture Notes in Computer Science  
With the availability of a growing collection of biological pathway datasets, there is an increasing need for an efficient repository with the powerful search capability to facility large scaled analyses  ...  of biological pathway.  ...  The author wishes to thank Microsoft Research for its support to this project, Christopher Nash and Qian Wu for their efforts in implementing the system, and reviewers for their constructive comments.  ... 
doi:10.1007/978-3-540-72586-2_56 fatcat:zgcqrvrzind2lk6sreokcm337i

Extracting more value from data silos: using the semantic web to link chemistry and biology for innovation

Tim P Eyres
2013 EMBnet journal  
Data type Source Provider Integration technique Compound identifiers and activity Syngenta chemistry repository (internal) Syngenta D2RQ federation Document metadata Syngenta document repository  ...  The integrated use of biological data can help eliminate false positive molecular candidates and improve the chances of finding the correct candidates for development.Information about the biological activity  ...  Complicated search formulation for the x-ray related competency questions made the solution difficult to use with ad hoc queries.  ... 
doi:10.14806/ej.19.b.725 fatcat:qw24hcs2lzalhnvxfjg4v7iop4

Omics Discovery Index - Discovering and Linking Public Omics Datasets [article]

Yasset Perez-Riverol, Mingze Bai, Felipe Leprevost, Silvano Squizzato, Young Mi Park, Ove Kenneth Haug, Adam J. Carroll, Dylan Spalding, Justin Paschall, Mingxun Wang, Noemi del-Toro, Tobias Ternent (+14 others)
2016 bioRxiv   pre-print
For example the research community must now find more efficient ways for storing, organizing and providing access to biomedical data across platforms.  ...  Therefore, there is a great need for development of new platforms and applications to make possible to search datasets across different omics fields, making such information accessible to the end-user.  ...  Acknowledgements This work has been supported by the US NIH BD2K grant U54 GM114833, the National Natural Science Foundation of China grant [61501071], AIN is supported by  ... 
doi:10.1101/049205 fatcat:2aj2k6of3rde5aumoqjgiv53lm

Biomedical Web, Collections and Meta-Analysis Literature Applications [chapter]

Layla Michan, Israel Munoz-Velasco, Eduardo Alvarez, Lyssania Macias
2011 Biomedical Engineering - From Theory to Applications  
Using multiple and varied fields of search. Disadvantages Few or no options for meta-analysis. Ambiguity in the identification of authors and documents.  ...  Abstract Yes Interface language English URL http://www.ncbi.nlm.nih.gov/pubmed Related document Yes Web 2.0 apps RSS, bookmarks, alerts, saved search results by e-mail.  ...  Twease Twease is a web-based tool to search in the abstracts for Medline. Index the words of Medline and provides features to expand a query and thereby find what you are looking for.  ... 
doi:10.5772/18133 fatcat:cjogvh6gindgbabo3aqh6qetyu

DataMed – an open source discovery index for finding biomedical datasets

Xiaoling Chen, Anupama E Gururaj, Burak Ozyurt, Ruiling Liu, Ergin Soysal, Trevor Cohen, Firat Tiryaki, Yueling Li, Nansu Zong, Min Jiang, Deevakar Rogith, Mandana Salimi (+12 others)
2018 JAMIA Journal of the American Medical Informatics Association  
Materials and Methods: DataMed, which can efficiently index and search diverse types of biomedical datasets across repositories, is developed through the National Institutes of Health-funded biomedical  ...  In addition to describing its architecture and techniques, we evaluated individual components within DataMed, including the accuracy of the ingestion pipeline, the prevalence of the DATS model across repositories  ...  DataMed uses a modular architecture and supports use cases from the general, biological, and translational communities with a number of common needs for metadata searches.  ... 
doi:10.1093/jamia/ocx121 pmid:29346583 fatcat:skzpza7qgvew3nexxdlkl74kfi

Linking genes to literature: text mining, information extraction, and retrieval applications for biology

Martin Krallinger, Alfonso Valencia, Lynette Hirschman
2008 Genome Biology  
The biological literature also constitutes the main information source for manual literature curation used by expert-curated databases.  ...  Efficient access to information contained in online scientific literature collections is essential for life science research, playing a crucial role from the initial stage of experiment planning to the  ...  Thanks to Carlos Rodriguez Penagos and Florian Leitner for useful discussions and feedback. The participation of LH was supported under National Science Foundation Grant II-0640153.  ... 
doi:10.1186/gb-2008-9-s2-s8 pmid:18834499 pmcid:PMC2559992 fatcat:oeqr7ctzgjeo5nnw53fimelwxa

The Global Genome Biodiversity Network (GGBN) Data Portal

Gabriele Droege, Katharine Barker, Jonas J. Astrin, Paul Bartels, Carol Butler, David Cantrill, Jonathan Coddington, Félix Forest, Birgit Gemeinholzer, Donald Hobern, Jacqueline Mackenzie-Dodds, Éamonn Ó Tuama (+4 others)
2013 Nucleic Acids Research  
, discoverable for research through a networked community of biodiversity repositories.  ...  This is linked not only to accelerating biodiversity loss and demands to improve conservation efforts but also to a lack of standardized methods for providing access to genomic samples.  ...  ACKNOWLEDGEMENTS The authors thank all reviewers for comments that improved the article.  ... 
doi:10.1093/nar/gkt928 pmid:24137012 pmcid:PMC3965106 fatcat:dr6fltjpx5crbjwzufdfi6rmm4

Aztec: A Platform to Render Biomedical Software Findable, Accessible, Interoperable, and Reusable [article]

Wei Wang, Brian Bleakley, Chelsea Ju, Vincent Kyi, Patrick Tan, Howard Choi, Xinxin Huang, Yichao Zhou, Justin Wood, Ding Wang, Alex Bui, Peipei Ping
2017 arXiv   pre-print
Precision medicine and health requires the characterization and phenotyping of biological systems and patient datasets using a variety of data formats.  ...  This scenario mandates the centralization of various tools and resources in a unified platform to render them Findable, Accessible, Interoperable, and Reusable (FAIR Principles).  ...  Acknowledgements This work was supported in part by NIH Awards U54GM114833 to WW and PP, as well as R35HL135772 to PP; and the UCLA Laubisch endowment, to PP.  ... 
arXiv:1706.06087v1 fatcat:w4p5gihw3jfijezlskmhx3uhze

On Cohort Retrieval System from Clinical Data Repositories using OMOP Common Data Model: A Proof-of-Concept Implementation (Preprint)

Sijia Liu, Yanshan Wang, Andrew Wen, Liwei Wang, Na Hong, Feichen Shen, Steven Bedrick, William Hersh, Hongfang Liu
2019 JMIR Medical Informatics  
We designed a hierarchical index to support the common data model concept search utilizing information retrieval techniques and frameworks.  ...  Widespread adoption of electronic health records has enabled the secondary use of electronic health record data for clinical research and health care delivery.  ...  Warehouse, proposed by Garcelon et al [25] , is a free-text search engine using Oracle Text to index its documents.  ... 
doi:10.2196/17376 pmid:33021486 fatcat:jnr452ywrzbuhajeamukcb4aqi

PathText: a text mining integrator for biological pathway visualizations

B. Kemper, T. Matsuzaki, Y. Matsuoka, Y. Tsuruoka, H. Kitano, S. Ananiadou, J. Tsujii
2010 Bioinformatics  
is being used by groups of biologists from these locations.  ...  The system, PathText, is developed by Systems Biology Institute, Okinawa Institute of Science and Technology, National Centre for Text Mining (University of Manchester) and the University of Tokyo, and  ...  ACKNOWLEDGEMENTS We wish to thank Kanae Oda from Tokyo Medical and Dental University for the development of pathway models and testing of PathText, Chikashi Nobata at the National Centre for Text Mining  ... 
doi:10.1093/bioinformatics/btq221 pmid:20529930 pmcid:PMC2881405 fatcat:yjvz2wmtcfc5lmg3ef44udgw3q

Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice

Feng Li, Maoyu Li, Zhiqiang Xiao, Pengfei Zhang, Jianling Li, Zhuchu Chen
2006 BMC Bioinformatics  
Our 2D/MS repository can be used to share the raw NPC proteomics data that are generated from gel-based proteomics experiments.  ...  The database, as well as the PHP source codes for constructing users' own proteome repository, can be accessed at http://www.xyproteomics.org/.  ...  Database indexes are a powerful technology to improve the efficiency of database querying.  ... 
doi:10.1186/1471-2105-7-13 pmid:16403238 pmcid:PMC1351203 fatcat:hjvhppsrgnbz5n5qoojym2m3a4

About BIRDS project (Bioinformatics and Information Retrieval Data Structures Analysis and Design)

Guillermo de Bernardo, Susana Ladra
2018 Proceedings of the 5th Spanish Conference on Information Retrieval - CERI '18  
The research will address challenges in storing, processing, indexing, searching and navigating genome-scale data by designing new algorithms and data structures for sequence analysis, networks representation  ...  The overall goal of BIRDS is to establish a long term international network involving leading researchers in the development of efficient data structures in the fields of Bioinformatics and Information  ...  We expect to develop tools that help navigate and analyze biological trees or graphs using compact space, being time-efficient.  ... 
doi:10.1145/3230599.3230602 dblp:conf/ceri/BernardoL18 fatcat:q3svde6gizeefjofdz7s7ftd6m

Better bioinformatics through usability analysis

Davide Bolchini, Anthony Finkelstein, Vito Perrone, Sylvia Nagl
2008 Computer applications in the biosciences : CABIOS  
These specifically concern the design of the navigation and search mechanisms available to the user.  ...  In addition to characterizing these issues, specific recommendations for improvements are proposed leveraging proven practices from web and usability engineering.  ...  David Jones for their feedback and support to the work.  ... 
doi:10.1093/bioinformatics/btn633 pmid:19073592 fatcat:mavgsirad5hwnp2dxftye3a34a

A dedicated database system for handling multi-level data in systems biology

Natapol Pornputtapong, Kwanjeera Wanichthanarak, Avlant Nilsson, Intawat Nookaew, Jens Nielsen
2014 Source Code for Biology and Medicine  
Results and conclusion: In this study we present the design of database system which offers an extensible environment to efficiently capture the majority of biological entities and relations encountered  ...  Critical functions and control processes were designed and implemented to ensure consistent, efficient, secure and reliable transactions.  ...  These relation objects were used in the cases below to search and explore relationship between one biological object to another.  ... 
doi:10.1186/1751-0473-9-17 pmid:25053973 pmcid:PMC4106218 fatcat:h2eb3suv7bchtioo4h6tbozoga

Metadata, Ontologies, and Information Models for Grid PSE Toolkits Based on Web Services

Carmela Comito, Carlo Mastoroianni, Domenico Talia
2006 International Journal of Web Services Research  
These two components contribute to define a general model of metadata management for supporting the design and implementation of problem solving environments on Grids.  ...  The effective use of a PSE toolkit requires the management of the heterogeneity of the involved resources that can include computers, data, network facilities, sensors, and software tools provided by different  ...  Metadata Repository and WSRF Web Services The metadata repository stores the metadata documents related to the components/services provided by the PSE toolkit.  ... 
doi:10.4018/jwsr.2006100103 fatcat:qz4n36tfpzfwndxujv2uvavslu
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