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A framework for information extraction from tables in biomedical literature

Nikola Milosevic, Cassie Gregson, Robert Hernandez, Goran Nenadic
2019 International Journal on Document Analysis and Recognition  
We present a requirement analysis template and an integral methodology for information extraction from tables in clinical domain that contains 7 steps: (1) table detection, (2) functional processing, (  ...  Our research is examining the methods for extracting numerical (number of patients, age, gender distribution) and textual (adverse reactions) information from tables in the clinical literature.  ...  any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.  ... 
doi:10.1007/s10032-019-00317-0 fatcat:d3nh4c6to5gntap2zk4vlppvxq

iASiS Open Data Graph: Automated Semantic Integration of Disease-Specific Knowledge [article]

Anastasios Nentidis, Konstantinos Bougiatiotis, Anastasia Krithara, Georgios Paliouras
2020 arXiv   pre-print
Identifying and extracting specific information is a challenging task and computational analysis of knowledge bases can be valuable in this direction.  ...  In biomedical research, unified access to up-to-date domain-specific knowledge is crucial, as such knowledge is continuously accumulated in scientific literature and structured resources.  ...  Our goal is not to create a new text mining tool, but rather to create a framework where any such tool can be incorporated to extract biomedical entities and relations from text for enriching a unified  ... 
arXiv:1912.08633v2 fatcat:djs6dt5lubctbfgc7uurqvt66e

An Ontology-Enabled Natural Language Processing Pipeline for Provenance Metadata Extraction from Biomedical Text (Short Paper) [chapter]

Joshua Valdez, Michael Rueschman, Matthew Kim, Susan Redline, Satya S. Sahoo
2016 Lecture Notes in Computer Science  
Extraction of structured information from biomedical literature is a complex and challenging problem due to the complexity of biomedical domain and lack of appropriate natural language processing (NLP)  ...  In this paper, we describe an effective approach to extract provenance metadata from published biomedical research literature using an ontology-enabled NLP platform as part of the Provenance for Clinical  ...  Acknowledgments This work is supported in part by the NIH-NIBIB Big Data to Knowledge (BD2K) 1U01EB020955 and NIH-NHLBI R24 HL114473 grants.  ... 
doi:10.1007/978-3-319-48472-3_43 pmid:28664200 pmcid:PMC5486409 fatcat:54vkrp3d5rgibi4futtjh4m3nu

A Review of Towered Big-Data Service Model for Biomedical Text-Mining Databases

Alshreef Abed, Jingling Yuan, Lin Li
2017 International Journal of Advanced Computer Science and Applications  
Subsequently, in a traditional database system (structured data), managing and extracting useful information from unstructured-biomedical data is a tedious job.  ...  Text mining can help us mine information and knowledge from a mountain of text, and is now widely applied in biomedical research.  ...  Few of the previous studies have proposed a framework for identifying key information components from biomedical text documents, such as [55] , [82] and [74] , [84] .  ... 
doi:10.14569/ijacsa.2017.080804 fatcat:juylimcz4jdbhmifhrz6so7ciq

Combining gene sequence similarity and textual information for gene function annotation in the literature

Luo Si, Danni Yu, Daisuke Kihara, Yi Fang
2008 Information retrieval (Boston)  
Information extraction techniques have been proposed to obtain the function information of genes and proteins in the biomedical literature.  ...  However, the performance of most information extraction techniques of function annotation in the biomedical literature is not satisfactory due to the large variability in the expression of concepts in  ...  from curated databases, can be extracted from text literature.  ... 
doi:10.1007/s10791-008-9053-0 fatcat:vxlvdeza2rbjfmcx2hvuosc7py

Linked open data-based framework for automatic biomedical ontology generation

Mazen Alobaidi, Khalid Mahmood Malik, Susan Sabra
2018 BMC Bioinformatics  
For concept extraction, evaluation shows an average F-measure of 58.12% for CDR corpus and 81.68% for SemMedDB; F-measure of 65.26% and 77.44% for biomedical taxonomic relation extraction using datasets  ...  Conclusion: This paper has presented LOD-ABOG framework which shows that current LOD sources and technologies are a promising solution to automate the process of biomedical ontology generation and extract  ...  Methods Our methodology for automated ontology generation from biomedical literatures is graphically depicted in Fig. 1 . A concise description of all LOD-ABOG modules is given in Table 2 .  ... 
doi:10.1186/s12859-018-2339-3 pmid:30200874 pmcid:PMC6131949 fatcat:drrkhq63zbeung3sssq2htltq4

Biomedical Document Retrieval for Clinical Decision Support System

Jainisha Sankhavara
2018 Proceedings of ACL 2018, Student Research Workshop  
In this work, we are focusing on biomedical document retrieval from literature for clinical decision support systems.  ...  The availability of huge amount of biomedical literature have opened up new possibilities to apply Information Retrieval and NLP for mining documents from them.  ...  The tasks of named entity recognition and relation and event extraction, summarization, question answering, and literature based discovery are outlined in Biomedical text mining: a survey of recent progress  ... 
doi:10.18653/v1/p18-3012 dblp:conf/acl/Sankhavara18 fatcat:ggpycr4cfvckrl7j4ddy733hum

Literature mining for context-specific molecular relations using multimodal representations (COMMODAR)

Jaehyun Lee, Doheon Lee, Kwang Hyung Lee
2020 BMC Bioinformatics  
In this paper, we propose COMMODAR, a machine learning-based literature mining framework for context-specific molecular relations using multimodal representations.  ...  The construction of context-specific relational resources vastly relies on laborious manual extraction from unstructured literature.  ...  About this supplement This article has been published as part of BMC Bioinformatics, Volume 21 Supplement 5, 2020: Proceedings of the 13th International Workshop on Data and Text Mining in Biomedical Informatics  ... 
doi:10.1186/s12859-020-3396-y pmid:33106154 fatcat:s3oha7endfcqhnxifzdckxxi5a

Global mapping of gene/protein interactions in PubMed abstracts: A framework and an experiment with P53 interactions

Xin Li, Hsinchun Chen, Zan Huang, Hua Su, Jesse D. Martinez
2007 Journal of Biomedical Informatics  
In this paper, we propose a comprehensive framework for constructing and analyzing large-scale gene functional networks based on the gene/protein interactions extracted from biomedical literature repositories  ...  Recent advances in text mining tools have made it possible to automatically extract such documented interactions from free-text literature.  ...  Acknowledgment This work was supported by: NIH/NLM, 1 R33 LM07299-01, 2003-2005, ''Genescene: a Toolkit for Gene Pathway Analysis.''  ... 
doi:10.1016/j.jbi.2007.01.001 pmid:17317333 pmcid:PMC2047827 fatcat:wl3xjzdf4vcqfpwnk473q5lts4

Repeat: a framework to assess empirical reproducibility in biomedical research

Leslie D. McIntosh, Anthony Juehne, Cynthia R. H. Vitale, Xiaoyan Liu, Rosalia Alcoser, J. Christian Lukas, Bradley Evanoff
2017 BMC Medical Research Methodology  
The tool (RepeAT) was developed through a multi-phase process that involved coding and extracting recommendations and practices for improving reproducibility from publications and reports across the biomedical  ...  Preliminary results in manually processing 40 scientific manuscripts indicate components of the proposed framework with strong inter-rater reliability, as well as directions for further research and refinement  ...  Louis Center for Biomedical Informatics Github repository: and within the RepeAT project's Open Science Framework repository: ppnwa/.  ... 
doi:10.1186/s12874-017-0377-6 pmid:28923006 pmcid:PMC5604503 fatcat:jxoghd7ixffmdmvfybyucwn7ve

A Novel Framework for Biomedical Text Mining

Janyl Jumadinova, Oliver Bonham-Carter, Hanzhong Zheng, Michael Camara, Dejie Shi
2020 Journal on Big Data  
Text mining has emerged as an effective method of handling and extracting useful information from the exponentially growing biomedical literature and biomedical databases.  ...  biomedical information through text mining paradigm.  ...  Similar to the overarching theme of these tools, our framework is able to extract information from scientific publications, find similarities and build relationships between keywords in the literature.  ... 
doi:10.32604/jbd.2020.010090 fatcat:mobdvmwqyfhf5cx2fbi5zezclu

A New Biomedical Passage Retrieval Framework for Laboratory Medicine: Leveraging Domain-specific Ontology, Multilevel PRF, and Negation Differential Weighting

Keejun Han, Hyoeun Shim, Mun Y. Yi
2018 Journal of Healthcare Engineering  
In this paper, we present a novel CDS search framework designed for passage retrieval from biomedical textbooks in order to support clinical decision-making using laboratory test results.  ...  Our study results indicate that the proposed CDS search framework specifically designed for passage retrieval of biomedical literature represents a practically viable choice for clinicians as it supports  ...  Second, passage-level indexes for biomedical textbooks should be made for our biomedical literature retrieval. e indexes convert the literature into a set of passages for quick access to relevant information  ... 
doi:10.1155/2018/3943417 pmid:30675333 pmcid:PMC6323463 fatcat:diyx7wyfgre7feemjasxdzo57q

Ultra-low-power biomedical circuit design and optimization: Catching the don't cares

Xin Li, Ronald D. Shawn Blanton, Pulkit Grover, Donald E. Thomas
2014 2014 International Symposium on Integrated Circuits (ISIC)  
In this paper, we describe a radically new design framework for ultra-low-power biomedical circuit design and optimization.  ...  The efficacy of the proposed framework is demonstrated by a case study of brain computer interfaces (BCIs).  ...  CONCLUSIONS In this paper, we describe a new design framework for ultra-low-power biomedical circuits.  ... 
doi:10.1109/isicir.2014.7029551 dblp:conf/isicir/0001BGT14 fatcat:uqrv7ukdqnah5bhaqn437j5us4

Ultra-Low-Power Biomedical Circuit Design and Optimization: Catching the Don't Cares [chapter]

Xin Li, Ronald D. (Shawn) Blanton, Pulkit Grover, Donald E. Thomas
2017 Emerging Technology and Architecture for Big-data Analytics  
In this paper, we describe a radically new design framework for ultra-low-power biomedical circuit design and optimization.  ...  The efficacy of the proposed framework is demonstrated by a case study of brain computer interfaces (BCIs).  ...  CONCLUSIONS In this paper, we describe a new design framework for ultra-low-power biomedical circuits.  ... 
doi:10.1007/978-3-319-54840-1_7 fatcat:fkd2ldel4bfrtgx2gukwy3zcg4

DTMiner: identification of potential disease targets through biomedical literature mining

Dong Xu, Meizhuo Zhang, Yanping Xie, Fan Wang, Ming Chen, Kenny Q. Zhu, Jia Wei
2016 Bioinformatics  
Given the rapid growth of biomedical literature, automatic relation extraction, a crucial technology in biomedical literature mining, has shown great potential to support research of gene-related diseases  ...  The framework incorporates name entity recognition (NER), which identifies occurrences of genes and diseases in texts, association detection whereby we extract and evaluate features from gene-disease pairs  ...  Conclusion In this paper, we proposed a framework for the automatic extraction of gene-disease relation from biomedical literature.  ... 
doi:10.1093/bioinformatics/btw503 pmid:27506226 pmcid:PMC5181534 fatcat:4hg7z5lr3rcknet5zpaj6z4g7m
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