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Automated labeling of bibliographic data extracted from biomedical online journals

Jongwoo Kim, Daniel X. Le, George R. Thoma, Tapas Kanungo, Elisa H. Barney Smith, Jianying Hu, Paul B. Kantor
2003 Document Recognition and Retrieval X  
A prototype system has been designed to automate the extraction of bibliographic data (e.g., article title, authors, abstract, affiliation and others) from online biomedical journals to populate the National  ...  Results from experiments conducted with 1,149 medical articles from forty-seven journal issues are presented.  ...  bibliographic data from paper-based biomedical journals.  ... 
doi:10.1117/12.476047 dblp:conf/drr/KimLT03 fatcat:d63h5lijjfhrrp6nm2o2q2htja

Automatic Extraction of Bibliographic Information from Biomedical Online Journal Articles Using a String Matching Algorithm

Jongwoo Kim, D.X. Le, G.R. Thoma
2006 19th IEEE Symposium on Computer-Based Medical Systems (CBMS'06)  
A system has been developed to extract bibliographic data (grant numbers and databank accession numbers) from online biomedical journal articles for the National Library of Medicine's MEDLINE database  ...  Rule-based algorithms and a string matching algorithm are proposed to extract the bibliographic data from HTML-formatted articles.  ...  The production of this database relies on different methods: the automatic extraction of bibliographic data from scanned (paper) journals, from online journals in HTML, PDF, and XML formats, as well as  ... 
doi:10.1109/cbms.2006.55 dblp:conf/cbms/KimLT06 fatcat:m2niqt7z6rdqxhxtfdrrxnojgi

Hybrid approach combining contextual and statistical information for identifying MEDLINE citation terms

In Cheol Kim, Daniel X. Le, George R. Thoma, Berrin A. Yanikoglu, Kathrin Berkner
2008 Document Recognition and Retrieval XV  
There is a strong demand for developing automated tools for extracting pertinent information from the biomedical literature that is a rich, complex, and dramatically growing resource, and is increasingly  ...  online biomedical documents.  ...  ACKNOWLEDGMENT This research was supported by the Intramural Research Program of the National Library of Medicine, National Institutes of Health.  ... 
doi:10.1117/12.766660 dblp:conf/drr/KimLT08 fatcat:qanpol4akng3lckaobdxaqpev4

Hypotheses generation as supervised link discovery with automated class labeling on large-scale biomedical concept networks

Jayasimha Katukuri, Ying Xie, Vijay V Raghavan, Ashish Gupta
2012 BMC Genomics  
We further model link discovery as a classification problem carried out on a training data set automatically extracted from two network snapshots taken in two consecutive time duration.  ...  We extract the relevant information from the biomedical literature corpus and generate a concept network and concept-author map on a cluster using Map-Reduce framework.  ...  Acknowledgements This article has been published as part of BMC Genomics Volume 13 Supplement 3, 2012  ... 
doi:10.1186/1471-2164-13-s3-s5 pmid:22759614 pmcid:PMC3394427 fatcat:3bwuez2qgbdudpyh3iuh6xiqoi

Biomedical text summarization to support genetic database curation: using Semantic MEDLINE to create a secondary database of genetic information

T. Elizabeth Workman, Marcelo Fiszman, John F Hurdle, Thomas C Rindflesch
2010 Journal of the Medical Library Association  
extracted from the primary literature.  ...  A gold standard was produced using records from Genetics Home Reference and Online Mendelian Inheritance in Man. Genes in text found by the system were compared to the gold standard.  ...  Outcomes from separate groups of research studies, represented as bibliographic text, could be compared.  ... 
doi:10.3163/1536-5050.98.4.003 pmid:20936065 pmcid:PMC2947139 fatcat:4gy4a6c5undsfpm32flvjes3b4

A structural SVM approach for reference parsing

Xiaoli Zhang, Jie Zou, Daniel X Le, George R Thoma
2011 BMC Bioinformatics  
Automated extraction of bibliographic data, such as article titles, author names, abstracts, and references is essential to the affordable creation of large citation databases.  ...  References, typically appearing at the end of journal articles, can also provide valuable information for extracting other bibliographic data.  ...  The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2105/12?issue=S3.  ... 
doi:10.1186/1471-2105-12-s3-s7 pmid:21658294 pmcid:PMC3111593 fatcat:jfnd6ba66javvmkotl2yjchyh4

A Structural SVM Approach for Reference Parsing

Xiaoli Zhang, Jie Zou, Daniel X. Le, George R. Thoma
2010 2010 Ninth International Conference on Machine Learning and Applications  
Automated extraction of bibliographic data, such as article titles, author names, abstracts, and references is essential to the affordable creation of large citation databases.  ...  References, typically appearing at the end of journal articles, can also provide valuable information for extracting other bibliographic data.  ...  The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2105/12?issue=S3.  ... 
doi:10.1109/icmla.2010.77 dblp:conf/icmla/ZhangZLT10 fatcat:zu6n6rlzrvckploymcm75lx34i

Methods and Trends in Information Retrieval in Big Data Genomic Research

2019 VOLUME-8 ISSUE-10, AUGUST 2019, REGULAR ISSUE  
There was a surge of genomic information from the different literature and the production of genome datasets that catapulted the development of several tools for analyzing and presenting new found knowledge  ...  in the biomedical and genome research.  ...  These applications automate the extraction of information for proteins, genes, functional relationships to domain research through published articles, journals or text documents.  ... 
doi:10.35940/ijitee.i1109.0789s219 fatcat:j2uramagd5a75jusrcor75w7ue

Combining SVM classifiers to identify investigator name zones in biomedical articles

Jongwoo Kim, Daniel X. Le, George R. Thoma, Christian Viard-Gaudin, Richard Zanibbi
2012 Document Recognition and Retrieval XIX  
This paper describes an automated system to label zones containing Investigator Names (IN) in biomedical articles, a key item in a MEDLINE® citation.  ...  The correct identification of these zones is necessary for the subsequent extraction of IN from these zones.  ...  ACKNOWLEDGMENT This research was supported by the Intramural Research Program of the National Institutes of Health, National Library of Medicine, and Lister Hill National Center for Biomedical Communications  ... 
doi:10.1117/12.910517 dblp:conf/drr/KimLT12 fatcat:sbf26m46urckbkndy7temfrqpm

Text-mined fossil biodiversity dynamics using machine learning

Bjørn Tore Kopperud, Scott Lidgard, Lee Hsiang Liow
2019 Proceedings of the Royal Society of London. Biological Sciences  
Here, we extract observations of fossils and their inferred ages from unstructured text in books and scientific articles using machine-learning approaches.  ...  We believe our automated pipeline, that greatly reduced the time required to compile our dataset, can help others compile similar data for other taxa.  ...  We thank Olja Toljagić for help with labelling the candidates, Bjö rn Berning, Dennis P. Gordon, Paul D.  ... 
doi:10.1098/rspb.2019.0022 pmid:31014224 pmcid:PMC6501925 fatcat:t6ukabuxb5ddjns3fbvcji4psu

Exploring use of images in clinical articles for decision support in evidence-based medicine

Sameer Antani, Dina Demner-Fushman, Jiang Li, Balaji V. Srinivasan, George R. Thoma, Berrin A. Yanikoglu, Kathrin Berkner
2008 Document Recognition and Retrieval XV  
captions for modality and 76.6% accuracy combining captions and image data for utility on 743 images from articles over 2 years from a clinical journal.  ...  Our results indicated that automatic augmentation of bibliographic references with relevant images was feasible.  ...  in biomedical journal articles with text or symbols on them.  ... 
doi:10.1117/12.766778 dblp:conf/drr/AntaniDLST08 fatcat:5eks2ywmtjfqjgyslvykgtlum4

Automatically Finding Images for Clinical Decision Support

Dina Demner-Fushman, Sameer Antani, Mohammad-Reza Siadat, Hamid Soltanian-Zadeh, Farshad Fotouhi, and Kost Elisevich
2007 Seventh IEEE International Conference on Data Mining Workshops (ICDMW 2007)  
We selected 2004 --2005 issues of the British Journal of Oral and Maxillofacial Surgery, manually annotating 743 images by utility and modality (radiological, photo, etc.)  ...  Our results indicate that automatic augmentation of bibliographic references with relevant images is feasible.  ...  As future work, we plan to automate extraction and labeling from analysis of HTML text, and cropping of sub-images from a multi-panel image.  ... 
doi:10.1109/icdmw.2007.12 dblp:conf/icdm/Demner-FushmanASSFE07 fatcat:jzj3k3puezb3jcpdtnzzxo7qx4

Wikidata and the bibliography of life

Roderic D. M. Page
2022 PeerJ  
This article argues that Wikidata can be that database as it has flexible and sophisticated models of bibliographic information, and an active community of people and programs ("bots") adding, editing,  ...  Biological taxonomy rests on a long tail of publications spanning nearly three centuries.  ...  I am grateful to David Shotton, John Mittermeier, and an anonymous reviewer for their helpful critiques of the manuscript.  ... 
doi:10.7717/peerj.13712 pmid:35821898 pmcid:PMC9271275 fatcat:qev477rnwna3vdalba3abpvnki

Two Level Self-Supervised Relation Extraction From Medline Using UMLS

Huda Banuqitah, Fathy Eassa, Kamal Jambi, Maysoon Abulkhair
2016 International Journal of Data Mining & Knowledge Management Process  
of biomedical entities, such as disease, drugs,etc.MEDLINE is a huge database of biomedical research papers which remain a significantly underutilized source of biological information.  ...  The model uses a Self-supervised Approach for Relation Extraction (RE) by constructing enhanced training examples using information from UMLS.  ...  MEDLINE is one example of the online bibliographic database from a biomedical domain that contains more than 22 million biomedicine journal articles [1] .  ... 
doi:10.5121/ijdkp.2016.6302 fatcat:wctvqzwozjbb5deshlajclrdey

Brede Tools and Federating Online Neuroinformatics Databases

Finn Årup Nielsen
2013 Neuroinformatics  
The databases rely on simple formats and allow other online tools to reuse their content.  ...  As open science neuroinformatics databases the Brede Database and Brede Wiki seek to make distribution and federation of their content as easy and transparent as possible.  ...  where automated algorithms extract coordinates from a database based on neuroanatomical label (Nielsen et al, 2006) .  ... 
doi:10.1007/s12021-013-9183-4 pmid:23666785 fatcat:xjltp6ttqngafgtowmjff4g2ae
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