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Finding biomedical categories in Medline®

Lana Yeganova, Won Kim, Donald C Comeau, W John Wilbur
In this paper we describe and compare two methods for automatically learning meaningful biomedical categories in Medline.  ...  We study and compare these two alternative sets of terms to identify semantic categories in Medline. We find that both approaches produce reasonable terms as potential categories.  ...  Authors' contributions WJW suggested the study and all authors equally participated in the design of the study. LY and WK implemented the methods. LY and DCC drafted the manuscript.  ... 
doi:10.1186/2041-1480-3-s3-s3 pmid:23046816 pmcid:PMC3465206 fatcat:o6rbgojjmvfdbofcekz4ao5ify

Classifying Biomedical Text Abstracts Based On Hierarchical 'Concept' Structure

Rozilawati Binti Dollah, Masaki Aono
2011 Zenodo  
Then, we enrich the OHSUMED disease hierarchy before adapting it to ontology alignment process for finding probable concepts or categories.  ...  In this paper, we present an approach for classifying a collection of biomedical text abstracts downloaded from Medline database with the help of ontology alignment.  ...  ACKNOWLEDGMENT This work was supported in part by Global COE Program "Frontiers of Intelligent Sensing" from the Ministry of Education, Culture, Sports, Science and Technology, Japan.  ... 
doi:10.5281/zenodo.1080995 fatcat:zjjn3mx6z5ax5jkvvxl72w5suq

Multilingual Named-Entity Recognition from Parallel Corpora

Andreea Bodnari, Aurélie Névéol, Özlem Uzuner, Pierre Zweigenbaum, Peter Szolovits
2013 Conference and Labs of the Evaluation Forum  
., English, French, and Spanish) and is tailored to the biomedical domain. For each language, we design a supervised knowledge-based CRF model with rich biomedical and general domain information.  ...  We use the sentence alignment of the parallel corpora, the word alignment generated by the GIZA++[8] tool, and Wikipedia-based word alignment in order to transfer system predictions made by individual  ...  In this study, we present a system for extracting structured information from multilingual biomedical corpora.  ... 
dblp:conf/clef/BodnariNUZS13 fatcat:6gg5sqncsjervc52ldtlumuz6u

Predicting MeSH Beyond MEDLINE

Adam K. Kehoe, Vetle I. Torvik, Matthew B. Ross, Neil R. Smalheiser
2017 Proceedings of the 1st Workshop on Scholarly Web Mining - SWM '17  
When applied to PubMedCentral papers, NIH grants, and USPTO patents we find that these two sources of information produce largely disjoint sets of related MEDLINE records, albeit with some overlap in MeSH  ...  Here, we present MeSHier, a tool for assigning MeSH terms to biomedical documents based on abstract similarity and references to MEDLINE records.  ...  Acknowledgments Research reported in this publication was supported in part by NIH National Institute on Aging P01AG039347.  ... 
doi:10.1145/3057148.3057155 pmid:30417176 pmcid:PMC6221467 dblp:conf/wsdm/KehoeTRS17 fatcat:z5xh3j2mfbaifpbtm3hsztw4da

A text-mining system for knowledge discovery from biomedical documents

N. Uramoto, H. Matsuzawa, T. Nagano, A. Murakami, H. Takeuchi, K. Takeda
2004 IBM Systems Journal  
In their work life-science researchers typically use MEDLINE, 8 a bibliography database that covers the biomedical area.  ...  Note that hierarchical category definitions are shared by both the informationextraction and the runtime-server preprocessing components. MEDLINE-a collection of biomedical documents.  ... 
doi:10.1147/sj.433.0516 fatcat:6bbopwoknrenldcwtxpime2pfy

FACTA: a text search engine for finding associated biomedical concepts

Y. Tsuruoka, J. Tsujii, S. Ananiadou
2008 Bioinformatics  
FACTA is a text search engine for MEDLINE abstracts, which is designed particularly to help users browse biomedical concepts (e.g. genes/proteins, diseases, enzymes and chemical compounds) appearing in  ...  The user can also view snippets from MEDLINE to get textual evidence of associations between the query terms and the concepts.  ...  Text mining complements biomedical databases by providing researchers with a convenient way to find such information from the literature.  ... 
doi:10.1093/bioinformatics/btn469 pmid:18772154 pmcid:PMC2572701 fatcat:tvehiphoybcnne7mg6zm2wopde

Open Biomedical Ontology-based Medline exploration

Weijian Xuan, Manhong Dai, Barbara Mirel, Jean Song, Brian Athey, Stanley J Watson, Fan Meng
2009 BMC Bioinformatics  
to MeSH and Gene Ontology trees, we believe the use of multiple ontologies from the Open Biomedical Ontology can greatly help researchers to explore literature from different perspectives as well as to  ...  quickly locate the most relevant Medline records for further investigation.  ...  A biomedical researcher will want to identify quickly which ontological categories in one of more ontology contain retrieved articles.  ... 
doi:10.1186/1471-2105-10-s5-s6 pmid:19426463 pmcid:PMC2679406 fatcat:6tlpqsg34zaqbophjqaurnudey

Author keywords in biomedical journal articles

Aurélie Névéol, Rezarta Islamaj Doğan, Zhiyong Lu
2010 AMIA Annual Symposium Proceedings  
In this paper, we describe the growth of author keywords in biomedical journal articles and present a comparative study of author keywords and MeSH(®) indexing terms assigned by MEDLINE indexers to PubMed  ...  As an information retrieval system, PubMed(®) aims at providing efficient access to documents cited in MEDLINE(®).  ...  In the biomedical domain, MEDLINE ® indexers use indexing terms from the Medical Subject Headings (MeSH ® ) thesaurus to summarize the content of articles in the MEDLINE database.  ... 
pmid:21347036 pmcid:PMC3041277 fatcat:qa4ljnjbpjgyzhp7xwvkdpmxnq

Medical Document Classification Based on MeSH

Abdullah Muhammad Alghoson
2014 2014 47th Hawaii International Conference on System Sciences  
I collected a corpus of 50 full-text journal articles (N=50) from MEDLINE, which were already indexed by experts based on MeSH.  ...  One of the most challenging projects in information systems is extracting information from unstructured texts, including medical document classification.  ...  Funding: Scholarship granted by the King Abdulaziz University in Jeddah, Saudi Arabia.  ... 
doi:10.1109/hicss.2014.324 dblp:conf/hicss/Alghoson14 fatcat:5f3kicaolbedhb4pm3gxrd344q

Natural Language Processing and Unsupervised Learning: It's Significance on Biomedical Literature

Kanika Gupta, Ashok Kumar
2018 International Journal of Current Research and Review  
arising in the biomedical research and would also help in the development of new hypothesis.  ...  categorizes current work in biomedical information and entities extraction.  ...  Authors also acknowledge the immense help received from the scholars whose articles are cited and included in references of this manuscript.  ... 
doi:10.31782/ijcrr.2018.10143 fatcat:n56phwi4mfa4jkwgutik5r64ze

Machine Learning based Methodology Process Model to Handle Healthcare Information

K. Subrahmanyam, G. Bala Bharath Reddy, T.V.L. Manisha, K. Raga Poojitha, B. Yashaswi
2019 Sun International Journal of Engineering and Basic Sciences  
The used mechanism can be incorporated with any medical management program to make better medical care decision for a human control program can instantly use mining techniques to get biomedical details  ...  Primary employment to display what Natural Language Process Handling (NLP) and Machine Learning methods used for reflection of information and what category methods are appropriate for identifying & identifying  ...  The tagger is specifically updated for biomedical written text such as Medline abstracts.  ... 
doi:10.30558/ijebs.20180201001 fatcat:lokfbuykpvfo7nr7gcgrcei4n4

Finding potentially new multimorbidity patterns of psychiatric and somatic diseases: exploring the use of literature-based discovery in primary care research

Rein Vos, Sil Aarts, Erik van Mulligen, Job Metsemakers, Martin P van Boxtel, Frans Verhey, Marjan van den Akker
2014 JAMIA Journal of the American Medical Informatics Association  
In a more detailed analysis, the number of citations in Medline was mapped to four categories: N=0, N=1-9, N=10-49, and N ≥ 50 citations in Medline.  ...  Whereas there are no cases in the category N=0 (figure 5), 10 of the 11 cases which the experts find causally possible associations are prominent in the categories of very low and modest number of citations  ... 
doi:10.1136/amiajnl-2012-001448 pmid:23775174 pmcid:PMC3912726 fatcat:kv5aukuyznaynaz7luw4k5nn7m

Research articles on volunteering in biomedical journals: a MEDLINE-based bibliometric analysis

Bo-Ren Cheng, Hsiao-Ting Chang, Ming-Hwai Lin, Tzeng-Ji Chen, Li-Fang Chou, Shinn-Jang Hwang
2020 Journal of International Medical Research  
However, there few are extensive surveys examining the trend and scope of research on volunteering in biomedical areas.  ...  In the current study, we aimed to identify the publication trend of research on volunteering in the biomedical literature, to analyze the categories of journals that have published research articles on  ...  In contrast, although only 20 journals of palliative care are indexed in MEDLINE, the number of volunteering articles published in these journals ranked ninth among all subject categories.  ... 
doi:10.1177/0300060520903616 pmid:32090648 fatcat:a5xzutod2feirlhypdxrud4qyi

Anne O'Tate: A tool to support user-driven summarization, drill-down and browsing of PubMed search results

Neil R Smalheiser, Wei Zhou, Vetle I Torvik
2008 Journal of Biomedical Discovery and Collaboration  
Results: In this paper, we present Anne O'Tate, a web-based tool that processes articles retrieved from PubMed and displays multiple aspects of the articles to the user, according to pre-defined categories  ...  such as the "most important" words found in titles or abstracts; topics; journals; authors; publication years; and affiliations.  ...  Categories defined by MEDLINE fields To give a typical example of how the MEDLINE fields may assist in categorizing search results for further analysis, consider how a user might seek to gain an overview  ... 
doi:10.1186/1747-5333-3-2 pmid:18279519 pmcid:PMC2276193 fatcat:xb4pfrp2gjdmblkjaavdlgilsq


Kamal Kumar, Mathew J. Palakal, Snehasis Mukhopadhyay, Mathew J. Stephens, Huian Li
2004 Proceedings of the 2004 ACM symposium on Applied computing - SAC '04  
from over 4600 biomedical journals worldwide and to develop an interactive knowledge network for users to access this secondary knowledge (BioMap) along with its primary databases such as the MEDLINE.  ...  an initial set of 30,000 MEDLINE abstracts.  ...  The research reported in this paper was supported in part by National Science Foundation Information Technology Research grant number NSF-IIS/ITR 0081944 and NIH BISTI grant, NIH-NIGMS P20 GM66402.  ... 
doi:10.1145/967900.967927 dblp:conf/sac/KumarPMSL04 fatcat:2usbpchpzbfadlrhki5ionnqqu
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