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Literature DB >> 14728234

Semantic relations asserting the etiology of genetic diseases.

Thomas C Rindflesch¹, Bisharah Libbus, Dimitar Hristovski, Alan R Aronson, Halil Kilicoglu.

Abstract

Considerable research is being directed at extracting molecular biology information from text. Particularly challenging in this regard is to identify relations between entities, such as protein-protein interactions or molecular pathways. In this paper we present a natural language processing method for extracting causal relations between genetic phenomena and diseases. After presenting the results of preliminary evaluation, we suggest the use of a graphical display application for viewing the semantic predications produced by the system.

Entities: Disease

Mesh：

Year: 2003 PMID： 14728234 PMCID： PMC1480275

Source DB: PubMed Journal: AMIA Annu Symp Proc ISSN： 1559-4076

18 in total

1. GENIES: a natural-language processing system for the extraction of molecular pathways from journal articles.

Authors: C Friedman; P Kra; H Yu; M Krauthammer; A Rzhetsky
Journal: Bioinformatics Date: 2001 Impact factor: 6.937

2. Robust relational parsing over biomedical literature: extracting inhibit relations.

Authors: J Pustejovsky; J Castaño; J Zhang; M Kotecki; B Cochran
Journal: Pac Symp Biocomput Date: 2002

3. Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program.

Authors: A R Aronson
Journal: Proc AMIA Symp Date: 2001

4. Supporting discovery in medicine by association rule mining in Medline and UMLS.

Authors: D Hristovski; J Stare; B Peterlin; S Dzeroski
Journal: Stud Health Technol Inform Date: 2001

5. Identification of key concepts in biomedical literature using a modified Markov heuristic.

Authors: W H Majoros; G M Subramanian; M D Yandell
Journal: Bioinformatics Date: 2003-02-12 Impact factor: 6.937

6. Exploring text mining from MEDLINE.

Authors: Padmini Srinivasan; Thomas Rindflesch
Journal: Proc AMIA Symp Date: 2002

7. Tagging gene and protein names in biomedical text.

Authors: Lorraine Tanabe; W John Wilbur
Journal: Bioinformatics Date: 2002-08 Impact factor: 6.937

8. Toward information extraction: identifying protein names from biological papers.

Authors: K Fukuda; A Tamura; T Tsunoda; T Takagi
Journal: Pac Symp Biocomput Date: 1998

9. Automatic Indexing of Documents from Journal Descriptors: A Preliminary Investigation.

Authors: Susanne M Humphrey
Journal: J Am Soc Inf Sci Date: 1999

10. Protein structures and information extraction from biological texts: the PASTA system.

Authors: R Gaizauskas; G Demetriou; P J Artymiuk; P Willett
Journal: Bioinformatics Date: 2003-01 Impact factor: 6.937

31 in total

1. Integrating a hypernymic proposition interpreter into a semantic processor for biomedical texts.

Authors: Marcelo Fiszman; Thomas C Rindflesch; Halil Kilicoglu
Journal: AMIA Annu Symp Proc Date: 2003

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

Authors: T Elizabeth Workman; Marcelo Fiszman; John F Hurdle; Thomas C Rindflesch
Journal: J Med Libr Assoc Date: 2010-10

3. Using text to build semantic networks for pharmacogenomics.

Authors: Adrien Coulet; Nigam H Shah; Yael Garten; Mark Musen; Russ B Altman
Journal: J Biomed Inform Date: 2010-08-17 Impact factor: 6.317

4. Visualizing information across multidimensional post-genomic structured and textual databases.

Authors: Ying Tao; Carol Friedman; Yves A Lussier
Journal: Bioinformatics Date: 2004-12-14 Impact factor: 6.937

5. MachineProse: an ontological framework for scientific assertions.

Authors: Deendayal Dinakarpandian; Yugyung Lee; Kartik Vishwanath; Rohini Lingambhotla
Journal: J Am Med Inform Assoc Date: 2005-12-15 Impact factor: 4.497

6. Semantic classification of biomedical concepts using distributional similarity.

Authors: Jung-Wei Fan; Carol Friedman
Journal: J Am Med Inform Assoc Date: 2007-04-25 Impact factor: 4.497

Review 7. Recent progress in automatically extracting information from the pharmacogenomic literature.

Authors: Yael Garten; Adrien Coulet; Russ B Altman
Journal: Pharmacogenomics Date: 2010-10 Impact factor: 2.533

8. Semantic relations for interpreting DNA microarray data.

Authors: Dimitar Hristovski; Andrej Kastrin; Borut Peterlin; Thomas C Rindflesch
Journal: AMIA Annu Symp Proc Date: 2009-11-14

9. Comparing a Rule Based vs. Statistical System for Automatic Categorization of MEDLINE Documents According to Biomedical Specialty.

Authors: Susanne M Humphrey; Aurélie Névéol; Julien Gobeil; Patrick Ruch; Stéfan J Darmoni; Allen Browne
Journal: J Am Soc Inf Sci Technol Date: 2009-12-01

10. HypertenGene: extracting key hypertension genes from biomedical literature with position and automatically-generated template features.

Authors: Richard Tzong-Han Tsai; Po-Ting Lai; Hong-Jie Dai; Chi-Hsin Huang; Yue-Yang Bow; Yen-Ching Chang; Wen-Harn Pan; Wen-Lian Hsu
Journal: BMC Bioinformatics Date: 2009-12-03 Impact factor: 3.169