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Quantitative data on referring expressions in biomedical abstracts

Michael Poprat, Udo Hahn
2007 Proceedings of the Workshop on BioNLP 2007 Biological, Translational, and Clinical Language Processing - BioNLP '07   unpublished
We report on an empirical study that deals with the quantity of different kinds of referring expressions in biomedical abstracts.  ...  In this study we present the first comprehensive overview of various kinds of referring expressions that occur in biomedical abstracts.  ...  This contradictoriness and the lack of statistics on referring expressions induced us to collect our own data in order to obtain a consistent and meaningful overview.  ... 
doi:10.3115/1572392.1572427 fatcat:bbbjel2i55eftdx5pp2hk5nztm

PaperRobot: Incremental Draft Generation of Scientific Ideas

Qingyun Wang, Lifu Huang, Zhiying Jiang, Kevin Knight, Heng Ji, Mohit Bansal, Yi Luan
2019 Proceedings of the 57th Annual Meeting of the Association for Computational Linguistics  
Turing Tests, where a biomedical domain expert is asked to compare a system output and a human-authored string, show PaperRobot generated abstracts, conclusion and future work sections, and new titles  ...  to generate a title for a follow-on paper.  ...  The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the U.S. Government.  ... 
doi:10.18653/v1/p19-1191 dblp:conf/acl/WangHJKJBL19 fatcat:uha6e4bf4nhp3f53gil2fj7dsu

State of reporting of primary biomedical research: a scoping review protocol

Guowei Li, Lawrence Mbuagbaw, Zainab Samaan, Yanling Jin, Ikunna Nwosu, Mitchell A H Levine, Jonathan D Adachi, Lehana Thabane
2017 BMJ Open  
In this study based on evidence from systematic reviews and surveys that have evaluated the reporting issues in primary biomedical studies, we aim to conduct a scoping review with focuses on (1) the state-of-the-art  ...  extent of adherence to the emerging reporting guidelines in primary biomedical research, (2) the inconsistency between protocols or registrations and full reports and (3) the disagreement between abstracts  ...  Comparator reference Reporting guidelines Protocols or registrations Full reports Main data collected Adherence to the items listed in guidelines Inconsistent reporting on study-validity-related  ... 
doi:10.1136/bmjopen-2016-014749 pmid:28360252 pmcid:PMC5372137 fatcat:bxbdiwiuifdr3cvwd4y5vs7oii

Quantitative Imaging Biomarker Ontology (QIBO) for Knowledge Representation of Biomedical Imaging Biomarkers

Andrew J. Buckler, M. Ouellette, J. Danagoulian, G. Wernsing, Tiffany Ting Liu, Erica Savig, Baris E. Suzek, Daniel L. Rubin, David Paik
2013 Journal of digital imaging  
However, quantitative imaging biomarker data and knowledge are not standardized, representing a critical barrier to accumulating medical knowledge based on quantitative imaging data.  ...  Our results established the utility of QIBO in enabling integrated analysis of quantitative imaging data.  ...  We would also like to acknowledge Yi Liu of the Biomedical Informatics Program at Stanford University annotating linked terms in QIBO shared with Disease Ontology.  ... 
doi:10.1007/s10278-013-9599-2 pmid:23589184 pmcid:PMC3705004 fatcat:czuz7iswincb7bf2dump4whrca

SparkText: Biomedical Text Mining on Big Data Framework

Zhan Ye, Ahmad P. Tafti, Karen Y. He, Kai Wang, Max M. He, Vladimir B. Bajic
2016 PLoS ONE  
Results In this study, we designed and developed an efficient text mining framework called Spark-Text on a Big Data infrastructure, which is composed of Apache Spark data streaming and machine learning  ...  Conclusions This study demonstrates the potential for mining large-scale scientific articles on a Big Data infrastructure, with real-time update from new articles published daily.  ...  and extracted from biomedical text data.  ... 
doi:10.1371/journal.pone.0162721 pmid:27685652 pmcid:PMC5042555 fatcat:z6nmmvjdzjc6zfhmp5pnvhgjni

A critical review of PASBio's argument structures for biomedical verbs

K Bretonnel Cohen, Lawrence Hunter
2006 BMC Bioinformatics  
Propositional representations of biomedical knowledge are a critical component of most aspects of semantic mining in biomedicine. However, the proper set of propositions has yet to be determined.  ...  Here, we quantitatively evaluate several dimensions of the initial PASBio propositional structure repository.  ...  We therefore provide quantitative data on the following: the distribution of arity of argument sets, distribution of thematic role types versus individual thematic roles in the argument sets, violations  ... 
doi:10.1186/1471-2105-7-s3-s5 pmid:17134478 pmcid:PMC1764449 fatcat:karftpmu5fhwlnmwvnobooc2em

Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online)

Chun-Nan Hsu, Jin-Mei Lai, Chia-Hung Liu, Huei-Hun Tseng, Chih-Yun Lin, Kuan-Ting Lin, Hsu-Hua Yeh, Ting-Yi Sung, Wen-Lian Hsu, Li-Jen Su, Sheng-An Lee, Chang-Han Chen (+7 others)
2007 BMC Bioinformatics  
The significant advances in microarray and proteomics analyses have resulted in an exponential increase in potential new targets and have promised to shed light on the identification of disease markers  ...  In fact, many differentially expressed gene sets in EHCO could form interaction networks (e.g. HBV-associated HCC network) by using available human protein-protein interaction datasets.  ...  We are grateful to National Center for High-performance Computing for providing supports in this project.  ... 
doi:10.1186/1471-2105-8-66 pmid:17326819 pmcid:PMC1828168 fatcat:bredj7xrcrajvbbujgmt35z6wa

Visualization of the Meridian System Based on Biomedical Information about Acupuncture Treatment

In-Seon Lee, Soon-Ho Lee, Song-Yi Kim, Hyejung Lee, Hi-Joon Park, Younbyoung Chae
2013 Evidence-Based Complementary and Alternative Medicine  
We suggest a new model for the visualization of a data-driven 3D meridian system of biomedical information about the meridians and acupoints.  ...  We found that both local and distal acupoints were used to treat low-back pain in clinical trials based on the meridian theory.  ...  However, these illustrations do not deal with biomedical information based on clinical data; instead, they express theoretical or abstract meanings of the meridian system.  ... 
doi:10.1155/2013/872142 pmid:23781270 pmcid:PMC3679759 fatcat:t5waeqwd65acjkt2by76ztv6je

Ten tips for a text-mining-ready article: How to improve automated discoverability and interpretability

Robert Leaman, Chih-Hsuan Wei, Alexis Allot, Zhiyong Lu
2020 PLoS Biology  
Data-driven research in biomedical science requires structured, computable data. Increasingly, these data are created with support from automated text mining.  ...  A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts.  ...  PubRe-Check provides two primary functions, as shown in the screenshot of its results on a synthetic abstract in Fig 2.  ... 
doi:10.1371/journal.pbio.3000716 pmid:32479517 fatcat:iecgq45umvfzfark4fv7kyg3qq

Hairpins in bookstacks: Information retrieval from biomedical text

H. Shatkay
2005 Briefings in Bioinformatics  
She works in the area of machine learning and its application to biomedical data.  ...  She is an active member of the biomedical text-mining community, and one of the first researchers in the area of text mining and information retrieval for bioinformatics.  ...  in most current biomedical text mining work, as described below, to focus on abstracts rather than on full-text articles.  ... 
doi:10.1093/bib/6.3.222 pmid:16212771 fatcat:2liwpccfq5dhza5mmdw66q7m2m

Impact assessment of oncology literature published in Serbia

Vladimir Baltic
2005 Archive of Oncology  
The number of inhabitants in Serbia is given in millions and gross domestic products (GDP) is expressed in million of US dollars; both parameters did not include data on Kosovo and Metohija (5).  ...  RESULTS: Quantitative analysis showed that 2,468 biomedical articles were published in Serbia.  ...  Acknowledgements I would like to thank Sabine Terziae, Branislava Vujaklija, Ljiljana ®egarac and Stanka Mateja¹ev for their help in manuscript preparation.  ... 
doi:10.2298/aoo0502059b fatcat:6hxubufydjgenkglzeuwufvofq

A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge

Trevor Cohen, Kirk Roberts, Anupama E. Gururaj, Xiaoling Chen, Saeid Pournejati, George Alter, William R. Hersh, Dina Demner-Fushman, Lucila Ohno-Machado, Hua Xu
2017 Database: The Journal of Biological Databases and Curation  
However, there are a number of barriers to the re-use of such datasets, which are distributed across a broad array of dataset repositories, focusing on different data types and indexed using different  ...  In this paper, we describe the design and generation of a benchmark for information retrieval of biomedical datasets, which was developed and used for the 2016 bioCADDIE Dataset Retrieval Challenge.  ...  YPED currently handles LCMS, MudPIT, ICAT, iTRAQ, SILAC, 2D Gel and DIGE, Label Free Quantitation (Progenesis), Label Free Quantitation (Skyline), MRM analysis and SWATH This repository contains data sets  ... 
doi:10.1093/database/bax061 pmid:29220453 pmcid:PMC5737202 fatcat:an22yuduwbbv5jq5txc77b6rzq

Classifying Negative Findings in Biomedical Publications

Bei Yu, Daniele Fanelli
2014 Proceedings of BioNLP 2014  
This paper proposes an NLP approach for automatically classifying negated sentences in biomedical abstracts as either reporting negative findings or not.  ...  data set.  ...  in Wnt expression per se are unlikely to be the cause of the observed dysregulation of β-catenin expression in DD" (PMC1564412).  ... 
doi:10.3115/v1/w14-3403 dblp:conf/bionlp/YuF14 fatcat:q4wxb7nfwfhohl5auck6e7rbha

Functional gene clustering via gene annotation sentences, MeSH and GO keywords from biomedical literature

Jeyakumar Natarajan, Jawahar Ganapathy
2007 Bioinformation  
Vital information about genes is available electronically from biomedical literature in the form of full texts and abstracts.  ...  data format.  ...  Results and Discussion: Evaluation To obtain a quantitative measure on the performance of the various keyword encoding schemes, we developed a text corpus of 200 manually annotated abstracts based on two  ... 
doi:10.6026/97320630002185 pmid:18305827 pmcid:PMC2241933 fatcat:6m3o7d5pz5gtdfrojicgnqvhky

Facilitating biomedical researchers' interrogation of electronic health record data: Ideas from outside of biomedical informatics

Gregory W. Hruby, Konstantina Matsoukas, James J. Cimino, Chunhua Weng
2016 Journal of Biomedical Informatics  
We show the current progress in biomedical informatics mainly lies in support for query execution and information modeling, primarily due to emphases on infrastructure development for data integration  ...  We suggest that cross-disciplinary translational research between biomedical informatics and information science can benefit our research in facilitating efficient data access in life sciences.  ...  In the context of EHR data interrogation, the PICO framework can be potentially a good starting point for supporting the expression of biomedical researchers' EHR data need.  ... 
doi:10.1016/j.jbi.2016.03.004 pmid:26972838 pmcid:PMC4837021 fatcat:m5evutghufd4xjibxisl6c4igu
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