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GoPubMed: exploring PubMed with the Gene Ontology

A. Doms, M. Schroeder
2005 Nucleic Acids Research  
We introduce GoPubMed, a web server which allows users to explore PubMed search results with the Gene Ontology (GO), a hierarchically structured vocabulary for molecular biology.  ...  Fourth, exploring PubMed abstracts with GoPubMed is useful as it shows definitions of GO terms without the need for further look up. GoPubMed is online at www.gopubmed.org.  ...  ACKNOWLEDGEMENTS We kindly thank the reviewers for their comments, which helped to improve the paper. We gratefully acknowledge support of the EU project REWERSE (IST-2004-506779).  ... 
doi:10.1093/nar/gki470 pmid:15980585 pmcid:PMC1160231 fatcat:dvwi7cnzvfeyffosvz7gax5zxa

GoPubMed: ontology-based literature search applied to Gene Ontology and PubMed

Ralph Delfs, Andreas Doms, Alexander Kozlenkov, Michael Schroeder
2004 German Conference on Bioinformatics  
We develop and implement GoP-ubMed, which submits keywords to PubMed, extracts GeneOntology-terms from the retrieved abstracts, and presents the relevant sub-ontology for browsing.  ...  To address this problem we introduce ontology-based literature search, which structures search results thorugh the categories of an ontology.  ...  Acknowledgment: We gratefully acknowledge support of the EU projects BioGrid (IST-2002-38344) and REWERSE (IST-2004-06779).  ... 
dblp:conf/gcb/DelfsDKS04 fatcat:o5vgzx24hrehvivog2rffwlm5a

Semantic Analysis of Macedonian Medical Abstracts Indexed in the PubMed Database using GoPubMed

2013 Macedonian Journal of Medical Sciences  
GO2PUB was developed to automatically enrich PubMed queries with gene names, symbols and synonyms annotated by a Gene Ontology (GO) term of interest or one of its descendants.  ...  Fourth, exploring PubMed abstracts with GoPubMed is useful as it shows definitions of GO terms without the need for further look up. GoPubMed is online at www.gopubmed.org [11, 12] .  ... 
doi:10.3889/mjms.1857-5773.2013.0260 fatcat:pbwx36ln5bd3xecfkett7pgq6q

Thinking PubMed: an Innovative System for Mental Health Domain

Maja Hadzic, Russel D'Souza, Fedja Hadzic, Tharam Dillon
2008 2008 21st IEEE International Symposium on Computer-Based Medical Systems  
In this paper we present Thinking PubMed as a system that results from synergy of ontology and data mining technologies and performs intelligent information searches using the domain ontology.  ...  Specific and targeted searches are very difficult with current search engines as they look for the specific string of letters within the text rather than its meaning.  ...  the Gene Ontology to perform its searches, searching for gene-related topics are highly efficient with the GOPubMed.  ... 
doi:10.1109/cbms.2008.20 dblp:conf/cbms/HadzicDHD08 fatcat:aanc6fx3ebaa3k42ras7nb4cee

A Maximum-Entropy approach for accurate document annotation in the biomedical domain

George Tsatsaronis, Natalia Macari, Sunna Torge, Heiko Dietze, Michael Schroeder
2012 Journal of Biomedical Semantics  
A fundamental step in these approaches is the annotation of documents with ontology concepts, which can also be seen as a classification task.  ...  Previous studies have shown that the usage of ontologies makes it possible to process document and query information at the semantic level, which greatly improves the search for the relevant information  ...  Some representative examples of such search engines for the biomedical domain are: (a) GoPubMed 1 which uses the Gene Ontology (GO) and the Medical Subject Headings (MeSH) as background knowledge for indexing  ... 
doi:10.1186/2041-1480-3-s1-s2 pmid:22541593 pmcid:PMC3337257 fatcat:ftaxggw2cjebvd26epq26ofn6i

BMExpert: Mining MEDLINE for Finding Experts in Biomedical Domains Based on Language Model

Beichen Wang, Xiaodong Chen, Hiroshi Mamitsuka, Shanfeng Zhu
2015 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
Experimental results show that BMExpert outperformed three existing biomedical expert finding services: JANE, GoPubMed, and eTBLAST, with respect to both MAP (mean average precision) and P@50 (Precision  ...  With the rapid development of biomedical sciences, a great number of documents have been published to report new scientific findings and advance the process of knowledge discovery.  ...  S.Z. would like to thank the China Scholarship Council for the financial support on his visit at University of Illinois at Urbana-Champaign.  ... 
doi:10.1109/tcbb.2015.2430338 pmid:26671801 fatcat:rgssjssvwbfhlo24tbqv43irme

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  ...  Results: We developed an ontology-based interactive Medline exploration solution called PubOnto to enable the interactive exploration and filtering of search results through the use of multiple ontologies  ...  After fitness-to-purpose and usability improvements are implemented, we will conduct comparative user performance evaluations with systems such as PubMed and GoPubMed with the aim of establishing the benefits  ... 
doi:10.1186/1471-2105-10-s5-s6 pmid:19426463 pmcid:PMC2679406 fatcat:6tlpqsg34zaqbophjqaurnudey

A user-centred evaluation framework for the Sealife semantic web browsers

Helen Oliver, Gayo Diallo, Ed de Quincey, Dimitra Alexopoulou, Bianca Habermann, Patty Kostkova, Michael Schroeder, Simon Jupp, Khaled Khelif, Robert Stevens, Gawesh Jawaheer, Gemma Madle
2009 BMC Bioinformatics  
Results: It was found that the evaluation framework used successfully elicited users' perceptions of the three distinct SWBs. The results indicate that the browser with the most mature and  ...  Furthermore, little attention has been given to evaluating semantic browsers with real users to demonstrate the enhancements and obtain valuable feedback.  ...  HPA supported by Dave Keech and Oliver Vass; Heiko Dietze of the Bioinformatics Group in Dresden for supplying the web server logs for Group A2;  ... 
doi:10.1186/1471-2105-10-s10-s14 pmid:19796398 pmcid:PMC2755822 fatcat:n2qowuzm4raqxnf5wus76j7bua

Automated semantic annotation of rare disease cases: a case study

M. Taboada, H. Rodriguez, D. Martinez, M. Pardo, M. J. Sobrido
2014 Database: The Journal of Biological Databases and Curation  
with similar clinical characteristics.  ...  Results: Our results confirm that it is possible to automatically identify new relevant case reports with a high precision and to annotate them with a satisfactory quality (74% F-measure).  ...  Acknowledgement The authors thank Veró nica Á lvarez for assistance with implementations.  ... 
doi:10.1093/database/bau045 pmid:24903515 pmcid:PMC4207225 fatcat:pguzshyv3bdvlc7di3pynwphlm

Automated semantic annotation of rare disease cases: a case study

Maria Taboada, Hadriana Rodríguez, Diego Martínez, María Pardo, María Jesús Sobrido
2015 Database: The Journal of Biological Databases and Curation  
Motivation: As the number of clinical reports in the peer-reviewed medical literature keeps growing, there is an increasing need for online search tools to find and analyze publications on patients with  ...  Results: Our results confirm that it is possible to automatically identify new relevant case reports with a high precision and to annotate them with a satisfactory quality (74% F-measure).  ...  GoPubMed ( 2 ) is a successful search engine for biomedical texts, based on the background knowledge of the Gene Ontology (GO) (3) and MeSH.  ... 
doi:10.1093/database/bav107 pmid:26568328 pmcid:PMC4644219 fatcat:7tnsx6inyja6jhqcdlqonu4l4y

Bi2SoN

Benjamin Köhncke, Sascha Tönnies, Wolf-Tilo Balke
2012 Proceedings of the 12th ACM/IEEE-CS joint conference on Digital Libraries - JCDL '12  
The resulting prototype was presented to a group of domain experts who confirmed that the system delivers suitable results supporting the scientists by their literature search.  ...  The knowledge from different data sources is combined and further used for, e.g. synonym enrichment of the query term.  ...  With GoPubMed [2] it exists a portal allowing users to explore PubMed search results with a hierarchically structured vocabulary for molecular biology, the Gene Ontology [3] .  ... 
doi:10.1145/2232817.2232888 dblp:conf/jcdl/KohnckeTB12 fatcat:tz6g4cmutbcybafysawrlsbs5y

TPX: Biomedical literature search made easy

Thomas Joseph, Vangala G Saipradeep, Ganesh Sekar Venkat Raghavan, Rajgopal Srinivasan, Aditya Rao, Sujatha Kotte, Naveen Sivadasan
2012 Bioinformation  
TPX is a web-based PubMed search enhancement tool that enables faster article searching using analysis and exploration features.  ...  The tool allows contextual exploration of knowledge sources by providing concept association maps derived from the MEDLINE repository.  ...  TPX, with the ability to point to external websites in addition to local repositories is a step towards faster, personalized biomedical literature analysis. [3], Gene Ontology [4] and other sources like  ... 
doi:10.6026/97320630008578 pmid:22829734 pmcid:PMC3398782 fatcat:qzgjtsswcrhl5oqtaspzqzuplu

Categorization of services for seeking information in biomedical literature: a typology for improvement of practice

J.-j. Kim, D. Rebholz-Schuhmann
2008 Briefings in Bioinformatics  
Biomedical researchers have to efficiently explore the scientific literature, keeping the focus on their research.  ...  This goal can only be achieved if the available means for accessing the literature meet the researchers' retrieval needs and if they understand how the tools filter the perpetually increasing number of  ...  This work was sponsored by the EC STREP project ''BOOTStrep'' (FP6-028099, www.bootstrep.org).  ... 
doi:10.1093/bib/bbn032 pmid:18660511 fatcat:tt5jtdj4yfg43k7dbhuhwjy26y

Semedico: A Comprehensive Semantic Search Engine for the Life Sciences

Erik Faessler, Udo Hahn
2017 Proceedings of ACL 2017, System Demonstrations  
SEMEDICO excels with an ad-hoc search approach which directly reflects relevance in terms of information density of entities and relations among them (events) and, a truly unique feature, ranks interaction  ...  SEMEDICO is a semantic search engine designed to support literature search in the life sciences by integrating the semantics of the domain at all stages of the search process-from query formulation via  ...  GOPUBMED (Doms and Schroeder, 2005) integrates the Medical Subject Headings (MESH), 1 GENE ONTOLOGY (GO) 2 and UNIPROT. 3 It allows to browse PUBMED citations taxonomically structured by the MESH and  ... 
doi:10.18653/v1/p17-4016 dblp:conf/acl/FaesslerH17 fatcat:folqg7czdbdsdo5z6uqfnw2e5a

BioLit: integrating biological literature with databases

J. L. Fink, S. Kushch, P. R. Williams, P. E. Bourne
2008 Nucleic Acids Research  
Specifically, these metadata include database identifiers and ontology terms found within the full text of the article.  ...  BioLit is a web server which provides metadata describing the semantic content of all open access, peer-reviewed articles which describe research from the major life sciences literature archive, PubMed  ...  Jeff Milton, and Joe Mulvaney for assistance with system administration and installation of the PDB clone. Project funding was provided by National Science Foundation Award # 0544575.  ... 
doi:10.1093/nar/gkn317 pmid:18515836 pmcid:PMC2447735 fatcat:d2utaoxvzzaovelv3e6oqpswx4
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