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Supporting inter-topic entity search for biomedical Linked Data based on heterogeneous relationships

Nansu Zong, Sungin Lee, Jinhyun Ahn, Hong-Gee Kim
2017 Computers in Biology and Medicine  
Conclusion- The proposed method improved the keyword-based biomedical entity search by supporting the inter-topic search without affecting the intra-topic search based on the relations between different  ...  When given keywords and preferences are not related to the same biomedical topic, existing biomedical Linked Data search engines fail to deliver satisfactory results.  ...  Hyeoneui Kim and Victoria Ngo for their suggestions on improving the manuscript.  ... 
doi:10.1016/j.compbiomed.2017.05.026 pmid:28601712 pmcid:PMC5572073 fatcat:5sggqpufmfbctmmtltfyp6cgya

Combining OLAP and information networks for bibliographic data analysis: a survey

Sabine Loudcher, Wararat Jakawat, Edmundo Pavel Soriano Morales, Cécile Favre
2015 Scientometrics  
In Business Intelligence, OLAP is a technology supported by data warehousing systems. It provides tools for analyzing data according to multiple dimensions and multiple hierarchical levels.  ...  At the same time, several information networks (co-authors network, citations network, institutions network, etc.) can be built based on bibliographic databases.  ...  based on the relationships defined between entities.  ... 
doi:10.1007/s11192-015-1539-0 fatcat:unu6qfj4ebasnf3zq2vgesc63m

Life-iNet: A Structured Network-Based Knowledge Exploration and Analytics System for Life Sciences

Xiang Ren, Jiaming Shen, Meng Qu, Xuan Wang, Zeqiu Wu, Qi Zhu, Meng Jiang, Fangbo Tao, Saurabh Sinha, David Liem, Peipei Ping, Richard Weinshilboum (+1 others)
2017 Proceedings of ACL 2017, System Demonstrations  
It also provides functionalities for finding distinctive entities for given entity types, and generating hypothetical facts to assist literaturebased knowledge discovery (e.g., drug target prediction).  ...  Search engines running on scientific literature have been widely used by life scientists to find publications related to their research.  ...  W911NF-09-2-0053 (NSCTA), National Science Foundation IIS-1320617 and IIS 16-18481, and grant 1U54GM114838 awarded by NIGMS through funds provided by the trans-NIH Big Data to Knowledge (BD2K) initiative  ... 
doi:10.18653/v1/p17-4010 dblp:conf/acl/RenSQWWZJTSLPWH17 fatcat:l4imv6rw6zeqzaxsroze3i4g4u

Topic-based heterogeneous rank

Tehmina Amjad, Ying Ding, Ali Daud, Jian Xu, Vincent Malic
2015 Scientometrics  
This study proposes a new informative metric called Topic-based Heterogeneous Rank (TH Rank) which measures the impact of a scholarly entity with respect to a given topic in a heterogeneous scholarly network  ...  Topic-based Heterogeneous Rank (TH Rank) measures the prestige of academic entities in heterogeneous networks. Following assumptions have been followed in order to give weights to citations.  ...  techniques for topological predicates on complex spatial objects", "Picture query languages for pictorial data-base systems" and "Algorithms for nearest neighbor search on moving object trajectories" have  ... 
doi:10.1007/s11192-015-1601-y fatcat:32e2irzsbbfqpb726jsl4ohw2e

Social and Semantic Web Technologies for the Text-to-Knowledge Translation Process in Biomedicine [chapter]

Carlos Cano, Alberto Labarga, Armando Blanco, Leonid Peshki
2011 Biomedical Engineering, Trends, Research and Technologies  
Blanco are supported by the projects P08-TIC-4299 of J.  ...  ., Sevilla and TIN2009-13489 of DGICT, Madrid Manual curation is not sufficient for annotation of genomic databases, Bioinformatics References  ...  for data aggregation and search, easier reuse of data in unanticipated ways, and the application of logic to infer additional insights.  ... 
doi:10.5772/13560 fatcat:cmrfewlbhze3zmj55o3fbfozfi

A review of drug knowledge discovery using BioNLP and tensor or matrix decomposition

Mina Gachloo, Yuxing Wang, Jingbo Xia
2019 Genomics & Informatics  
Prediction of the relations among drug and other molecular or social entities is the main knowledge discovery pattern for the purpose of drug-related knowledge discovery.  ...  Computational approaches have combined the information from different sources and levels for drug-related knowledge discovery, which provides a sophisticated comprehension of the relationship among drugs  ...  Kevin Bretonnel Cohen for many interesting discussions and nice suggestions about the paper, as well as Dr. Jin-Dong Kim for many illuminative discussions during the BLAH5 workshop.  ... 
doi:10.5808/gi.2019.17.2.e18 pmid:31307133 pmcid:PMC6808632 fatcat:w65sf7kkevflneg4marbtnmw6m

Open Biomedical Ontology-based Medline exploration

Weijian Xuan, Manhong Dai, Barbara Mirel, Jean Song, Brian Athey, Stanley J Watson, Fan Meng
2009 BMC Bioinformatics  
The PubOnto program is a rich internet application based on the FLEX platform.  ...  While existing solutions enhance Medline exploration through different approaches such as document clustering, network presentations of underlying conceptual relationships and the mapping of search results  ...  for topics of great interest for many biomedical research and they are almost orthogonal to each other conceptually.  ... 
doi:10.1186/1471-2105-10-s5-s6 pmid:19426463 pmcid:PMC2679406 fatcat:6tlpqsg34zaqbophjqaurnudey

Biological Systems as Heterogeneous Information Networks: A Mini-review and Perspectives [article]

Koki Tsuyuzaki, Itoshi Nikaido
2017 arXiv   pre-print
In the real world, most objects and data have multiple types of attributes and inter-connections.  ...  In this work, we review various applications of HIN methods to biological and chemical data, discuss some advanced topics, and describe some future research directions.  ...  complicated and inter-connected data.  ... 
arXiv:1712.08865v1 fatcat:ariridu3tfardbxyd7khftlqwq

Research information management: the CERIF approach

Keith Jeffery, Nikos Houssos, Brigitte Jörg, Anne Asserson
2014 International Journal of Metadata, Semantics and Ontologies  
research information; (b) separates base entities from link entities thus providing flexibility in expressing role based temporal relationships; (c) defines a distinct semantic layer so that relationship  ...  roles in link entities and controlled value lists in base entities are separately managed and multiple vocabularies can be used and related to each other; (d) can generate the common metadata formats  ...  The key features are the separation of base and link entities providing integrity and flexibility and the use of a semantic layer so that terminology can be maintained with integrity and flexibility.  ... 
doi:10.1504/ijmso.2014.059142 fatcat:rvlxqbm7xfd4fohmh2vw4boi64

Survey: When semantics meet crowdsourcing to enhance big data variety

Houssein Dhayne, Rima Kilany Chamoun, Maria Sokhn
2018 2018 IEEE Middle East and North Africa Communications Conference (MENACOMM)  
Semantic technologies, as a means of integration and coordination of heterogeneous systems, may help big data to manage terminology and relationships to link various data from different data sources.  ...  Crowdsourcing platforms have the potential to integrate (entity matching, entity resolution) and analyze (sentiment analysis, image recognition) heterogeneous data sources when in some cases these integration  ...  In short, semantic and crowdsourcing analysis are applied to the heterogeneous data at the entry of the workflow and the resulting extracted entities are stored in a knowledge base, inter-linked with linked  ... 
doi:10.1109/menacomm.2018.8371011 dblp:conf/menacomm/DhayneCS18 fatcat:gntbt5gv2zg63ppzldatfur5tq

Visual Exploration across Biomedical Databases

M D Lieberman, S Taheri, Huimin Guo, F Mirrashed, I Yahav, A Aris, B Shneiderman
2011 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
A new approach is offered for visualizing and exploring a query-based subset of multiple heterogeneous biomedical databases.  ...  Though biomedical research often draws on knowledge from a wide variety of fields, few visualization methods for biomedical data incorporate meaningful cross-database exploration.  ...  Bruce Bray, Marcelo Fiszman, Dina Demner-Fushman, Michael Galperin, Adam Lee, Jimmy Lin, Adam Phillippy, Louiqa Raschid, Tom Rindflesch, Charles Sneiderman, George Thoma, and the anonymous reviewers for  ... 
doi:10.1109/tcbb.2010.1 pmid:21233530 fatcat:iuozdgjukrbsxaz422xbxxa2mm

Knowledge Representation and Ontologies [chapter]

Kin Wah Fung, Olivier Bodenreider
2012 Health Informatics Series  
Originally created for editing frame-based ontologies, Protégé now supports OWL and other Semantic Web languages.  ...  ., for visualization, reasoning services, support for specific data formats) and the recently-developed web version of Protégé supports the collaborative development of ontologies.  ...  Acknowledgments This research was supported in part by the Intramural Research Program of the National Institutes of Health (NIH), National Library of Medicine (NLM).  ... 
doi:10.1007/978-1-84882-448-5_14 fatcat:r7e2fbulcrcddpxh7jo6lu77wa

Biomedical text mining and its applications in cancer research

Fei Zhu, Preecha Patumcharoenpol, Cheng Zhang, Yang Yang, Jonathan Chan, Asawin Meechai, Wanwipa Vongsangnak, Bairong Shen
2013 Journal of Biomedical Informatics  
There have been an enormous number of publications on cancer research. This integrated but unstructured biomedical text is of great value for cancer diagnostics, treatment, and prevention.  ...  Biomedical text mining on cancer research is computationally automatic and high-throughput in nature. However, it is error-prone due to the complexity of natural language processing.  ...  In addition, researchers are focusing on the relationship between genes and other biomedical entities, as well as the relationship between proteins and other biomedical entities, such as gene-disease relationships  ... 
doi:10.1016/j.jbi.2012.10.007 pmid:23159498 fatcat:xd7j77sbwfhklkat6tael64lbq

Automatic Entity Recognition and Typing in Massive Text Corpora

Xiang Ren, Ahmed El-Kishky, Chi Wang, Jiawei Han
2016 Proceedings of the 25th International Conference Companion on World Wide Web - WWW '16 Companion  
To turn such massive unstructured text data into actionable knowledge, one of the grand challenges is to gain an understanding of entities and the relationships between them.  ...  In today's computerized and information-based society, we are soaked with vast amounts of natural language text data, ranging from news articles, product reviews, advertisements, to a wide range of user-generated  ...  to Knowledge (BD2K) initiative (www.bd2k.nih.gov), and MIAS, a DHS-IDS Center for Multimodal Information Access and Synthesis at UIUC.  ... 
doi:10.1145/2872518.2891065 dblp:conf/www/RenEWH16 fatcat:nhwxdfwwpbdgpm2mhuitgnmtkm

Entity Set Search of Scientific Literature: An Unsupervised Ranking Approach [article]

Jiaming Shen, Jinfeng Xiao, Xinwei He, Jingbo Shang, Saurabh Sinha, Jiawei Han
2018 arXiv   pre-print
Entity-set queries reflect user's need for finding documents that contain multiple entities and reveal inter-entity relationships and thus pose non-trivial challenges to existing search algorithms that  ...  Literature search is critical for any scientific research.  ...  For example, given the input document title "Training linear SVMs in linear time", this tool will link the entity mention "SVMs"' to the entity "Support Vector Machine" with Freebase id '/m/0hc2f'.  ... 
arXiv:1804.10877v1 fatcat:5yqwge7kq5ah3niqnvy5h7ulm4
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