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An Object Model Based Repository for Biological Pathways Using XML Database Technology
[chapter]
2007
Lecture Notes in Computer Science
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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
2013
EMBnet journal
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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]
2016
bioRxiv
pre-print
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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]
2011
Biomedical Engineering - From Theory to Applications
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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
2018
JAMIA Journal of the American Medical Informatics Association
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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
2008
Genome Biology
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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
2013
Nucleic Acids Research
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, 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]
2017
arXiv
pre-print
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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)
2019
JMIR Medical Informatics
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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
2010
Bioinformatics
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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
2006
BMC Bioinformatics
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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)
2018
Proceedings of the 5th Spanish Conference on Information Retrieval - CERI '18
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Note that this fulltext copy is not of the "primary" version of this work. The version it corresponds to is:
2018 pre-print arXiv:1807.07937v1 fatcat:j2ok4l6otbgphgb24pcnft4nei
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
2008
Computer applications in the biosciences : CABIOS
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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
2014
Source Code for Biology and Medicine
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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
2006
International Journal of Web Services Research
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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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