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DETECTING GENE RELATIONS FROM MEDLINE ABSTRACTS

M. STEPHENS, M. PALAKAL, S. MUKHOPADHYAY, R. RAJE, J. MOSTAFA
2000 Biocomputing 2001  
In this article, we present a simple analysis and knowledge discovery method that can identify related genes as well as their shared functionality (if any) based on a collection of relevant retrieved relevant  ...  MEDLINE documents.  ...  Acknowledgement This project is supported in part by a grant from the NSF Digital Libraries Initiative Phase 2 grant IIS-9817572 and Elli Lilly & Company.  ... 
doi:10.1142/9789814447362_0047 fatcat:iw4dbovltfgftghluvzfv6ld4u

RANKING GENE-DRUG RELATIONSHIPS IN BIOMEDICAL LITERATURE USING LATENT DIRICHLET ALLOCATION

YONGHUI WU, MEI LIU, W. JIM ZHENG, ZHONGMING ZHAO, HUA XU
2011 Biocomputing 2012  
Our approach consists of three steps: 1) recognize gene and drug entities in MEDLINE abstracts; 2) extract candidate gene-drug pairs based on different levels of co-occurrence, including abstract level  ...  We systematically evaluated these methods by using a gold standard data set of gene-drug relations derived from PharmGKB.  ...  Alan Aronson at NLM for making MetaMapped corpus available, and the PharmGKB team for the gold standard PGx relations.  ... 
doi:10.1142/9789814366496_0041 fatcat:v7gih4dywne57lg3fzekwdfvf4

Mining functional information associated with expression arrays

Christian Blaschke, Juan C. Oliveros, Alfonso Valencia
2001 Functional & Integrative Genomics  
expression clusters by mining collections of Medline abstracts.  ...  We propose here a strategy, implemented in a system called GEISHA (gene expression information system for human analysis) and able to detect biological terms significantly associated to different gene  ...  We also thank the referees of this paper for their constructive and very valuable comments and the members of the Protein Design Group (CNB-CSIC) for the discussions on text analysis and related topics  ... 
doi:10.1007/s101420000036 pmid:11793245 fatcat:miwwge66xjcczcdz6bacpe5arm

Automatic extraction of mutations from Medline and cross-validation with OMIM

D. Rebholz-Schuhmann
2004 Nucleic Acids Research  
This is 27% of all PSM±gene pairs in OMIM and 91% of those pairs from OMIM which co-occur in at least one Medline abstract.  ...  From a sample of 100 abstracts we estimated the recall for the identi®cation of mutation±gene pairs to 35% at a precision of 93%.  ...  ACKNOWLEDGEMENTS This work has been supported by grants from the German Ministry of Research (BMBF-Project 0312385,`BioPath') and was embedded into the Text Mining Group of the research department at LION  ... 
doi:10.1093/nar/gkh162 pmid:14704350 pmcid:PMC373272 fatcat:kmz4veg7m5dgdpqs7moqfbpoiy

Gene annotation from scientific literature using mappings between keyword systems

A. J. Perez, C. Perez-Iratxeta, P. Bork, G. Thode, M. A. Andrade
2004 Bioinformatics  
Results: To support this task, we present a procedure to derive keywords from the set of scientific abstracts related to a gene.  ...  We tested the system by annotating genes of the SWISS-PROT database with keywords derived from the abstracts linked to their entries (stored in the MEDLINE database of scientific references).  ...  ACKNOWLEDGEMENTS We are also grateful to the developers and maintainers of SWISS-PROT, MeSH terms and Gene Ontology terms, to Helmut Schmid (IMS, Stuttgart University) for the implementation and public  ... 
doi:10.1093/bioinformatics/bth207 pmid:15059832 fatcat:uzhcz2xzzfdn7gh5b4olmejeby

Finding relevant references to genes and proteins in Medline using a Bayesian approach

J. E. Leonard, J. B. Colombe, J. L. Levy
2002 Bioinformatics  
We hypothesize that abstracts and titles that discuss the same gene or protein use similar words.  ...  Results: We analyzed the entire set of Medline records from 1966 to late 2001, and scored each gene and protein reference using a Bayesian estimated probability (EP) based on word frequency in a training  ...  SYSTEM AND METHODS In order to validate our hypothesis, we developed a system for detecting gene and protein symbols in Medline entries, and for determining the relevance of each Medline entry to the gene  ... 
doi:10.1093/bioinformatics/18.11.1515 pmid:12424124 fatcat:lkx74e35sfgk7ibzmxvg53a36u

Can Bibliographic Pointers for Known Biological Data Be Found Automatically? Protein Interactions as a Case Study

Christian Blaschke, Alfonso Valencia
2001 Comparative and Functional Genomics  
used information retrieval technology to search automatically for sentences in Medline abstracts that support these 851 DIP interactions.  ...  A positive finding is the capacity of the IE system to identify new relations between proteins, even in a set of proteins previously characterized by human experts.  ...  (Rindflesch et al., 1999 , Rindflesch et al., 2000 detect binding relations between proteins and relations between genes and cells by using external knowledge systems (the UMLS MetaThesaurus from the  ... 
doi:10.1002/cfg.91 pmid:18628915 pmcid:PMC2447212 fatcat:6by6iwbibfgizbpq7fban443yy

CSIRO at 2017 TREC Precision Medicine Track

Vincent Nguyen, Sarvnaz Karimi, Sara Falamaki, Diego Mollá Aliod, Cécile Paris, Stephen Wan
2017 Text Retrieval Conference  
We submitted five runs for the scientific abstracts collection (MEDLINE and Cancer Proceedings), and five runs for the clinical trials collection.  ...  Our results show that boosting the gene variant in the query increases the relevance of the retrieved results.  ...  We performed negation detection using the NegEx algorithm implemented in MetamapLite, which detected medically related negated terms.  ... 
dblp:conf/trec/NguyenKFAPW17 fatcat:zl6e3szjdrbvnc6xrzlsrgegwu

GeneNarrator: Mining the Literaturome for Relations Among Genes

Jing Ding, Daniel Berleant, Jun Xu, Kenton Juhlin, Eve Wurtele, Andy Fulmer
2009 Journal of Proteomics & Bioinformatics  
Given a list of genes, GeneNarrator collects abstracts about them from PubMed, then clusters the abstracts into functional topics in a first clustering stage.  ...  In the second clustering stage, the genes are clustered into groups based on similarities in their distributions of occurrence across topics.  ...  DocBuilder retrieves MEDLINE abstracts that are related to at least one of the user-provided genes.  ... 
doi:10.4172/jpb.1000096 fatcat:efhbpvauvfcfnah4ofqnyzegqi

Extracting Information Automatically from Biological Literature

Christian Blaschke, Robert Hoffmann, Juan Carlos Oliveros, Alfonso Valencia
2001 Comparative and Functional Genomics  
Suiseki Suiseki was designed as an integrated system for the extraction of protein interactions from Medline abstracts [5] .  ...  The steps followed by Suiseki are: (a) download of Medline abstracts (or local access); (b) part-ofspeech tagging for the detection of protein names; (c) detection of protein name synonyms; (d) determination  ... 
doi:10.1002/cfg.102 pmid:18629239 pmcid:PMC2448400 fatcat:bsdlw4w3eza7jhoznqw4ricczq

Medline search engine for finding genetic markers with biological significance

W. Xuan, P. Wang, S. J. Watson, F. Meng
2007 Bioinformatics  
Our goal is to develop a web-based tool that facilitates the mining of Medline literature related to genetic studies and gene/protein function studies.  ...  or association between genetic markers and diseases (3) integrating marker genomic location data from different databases to enable the retrieval of Medline records related to markers in the same linkage  ...  When a cytoband pattern detected is ambiguous, we calculate the weighted sum of such feature terms in an abstract.  ... 
doi:10.1093/bioinformatics/btm375 pmid:17823133 fatcat:efpaszqxh5gm7fp2y4klimr4bu

TXTGate: profiling gene groups with text-based information

Patrick Glenisson, Bert Coessens, Steven Van Vooren, Janick Mathys, Yves Moreau, Bart De Moor
2004 Genome Biology  
By means of tailored vocabularies, term- as well as gene-centric views are offered on selected textual fields and MEDLINE abstracts used in LocusLink and the Saccharomyces Genome Database.  ...  We implemented a framework called TXTGate that combines literature indices of selected public biological resources in a flexible text-mining system designed towards the analysis of groups of genes.  ...  Acknowledgements This research was supported by grants from the Research Council K.U.  ... 
doi:10.1186/gb-2004-5-6-r43 pmid:15186494 pmcid:PMC463076 fatcat:iijxrcxvr5hffkpfnpwl4hbhvq

Inferring Higher Functional Information for RIKEN Mouse Full-Length cDNA Clones With FACTS

T. Nagashima
2003 Genome Research  
Text-inferred information was extracted from keyword-based retrievals of MEDLINE abstracts and by matching of gene or protein names to OMIM, BIND, and DIP database entries.  ...  Much biological knowledge can be gleaned from MEDLINE records and their references.  ...  Emphasis was placed on detecting the cause of query results with no match or excessive matches to MEDLINE abstracts.  ... 
doi:10.1101/gr.1019903 pmid:12819151 pmcid:PMC403704 fatcat:erzymgcaq5cihazysmmaoblwom

Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information

James W Cooper, Aaron Kershenbaum
2005 BMC Bioinformatics  
This paper reports a scalable method for the discovery of protein-protein interactions in Medline abstracts, using a combination of text analytics, statistical and graphical analysis, and a set of easily  ...  This combination of linguistic and statistical approaches appears to provide the highest precision and recall thus far reported in detecting protein-protein relations using text analytic approaches.  ...  Acknowledgements We thank Bhavani Iyer for writing the XML extractor from our database representation, Eric Brown for the use of his DictMatcher code for detecting dictionary terms, and Bob Mack for numerous  ... 
doi:10.1186/1471-2105-6-143 pmid:15941473 pmcid:PMC1164402 fatcat:v6rz6xmjxbecrbbx4ofgfen5dy

miRiaD: A Text Mining Tool for Detecting Associations of microRNAs with Diseases

Samir Gupta, Karen E. Ross, Catalina O. Tudor, Cathy H. Wu, Carl J. Schmidt, K. Vijay-Shanker
2016 Journal of Biomedical Semantics  
Results: miRiaD was applied to the entire Medline corpus, identifying 8301 PMIDs with miR-disease associations.  ...  These abstracts and the miR-disease associations are available for browsing at http://biotm.cis.udel.edu/miRiaD.  ...  Next we assessed precision and recall of relations for randomly selected sentences from Medline abstracts.  ... 
doi:10.1186/s13326-015-0044-y pmid:27216254 pmcid:PMC4877743 fatcat:lan2a7blv5c5xijtug6pnxhd3m
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