1,271 research outputs found

    Extraction of Transcript Diversity from Scientific Literature

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    Transcript diversity generated by alternative splicing and associated mechanisms contributes heavily to the functional complexity of biological systems. The numerous examples of the mechanisms and functional implications of these events are scattered throughout the scientific literature. Thus, it is crucial to have a tool that can automatically extract the relevant facts and collect them in a knowledge base that can aid the interpretation of data from high-throughput methods. We have developed and applied a composite text-mining method for extracting information on transcript diversity from the entire MEDLINE database in order to create a database of genes with alternative transcripts. It contains information on tissue specificity, number of isoforms, causative mechanisms, functional implications, and experimental methods used for detection. We have mined this resource to identify 959 instances of tissue-specific splicing. Our results in combination with those from EST-based methods suggest that alternative splicing is the preferred mechanism for generating transcript diversity in the nervous system. We provide new annotations for 1,860 genes with the potential for generating transcript diversity. We assign the MeSH term “alternative splicing” to 1,536 additional abstracts in the MEDLINE database and suggest new MeSH terms for other events. We have successfully extracted information about transcript diversity and semiautomatically generated a database, LSAT, that can provide a quantitative understanding of the mechanisms behind tissue-specific gene expression. LSAT (Literature Support for Alternative Transcripts) is publicly available at http://www.bork.embl.de/LSAT/

    Building a protein name dictionary from full text: a machine learning term extraction approach

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    BACKGROUND: The majority of information in the biological literature resides in full text articles, instead of abstracts. Yet, abstracts remain the focus of many publicly available literature data mining tools. Most literature mining tools rely on pre-existing lexicons of biological names, often extracted from curated gene or protein databases. This is a limitation, because such databases have low coverage of the many name variants which are used to refer to biological entities in the literature. RESULTS: We present an approach to recognize named entities in full text. The approach collects high frequency terms in an article, and uses support vector machines (SVM) to identify biological entity names. It is also computationally efficient and robust to noise commonly found in full text material. We use the method to create a protein name dictionary from a set of 80,528 full text articles. Only 8.3% of the names in this dictionary match SwissProt description lines. We assess the quality of the dictionary by studying its protein name recognition performance in full text. CONCLUSION: This dictionary term lookup method compares favourably to other published methods, supporting the significance of our direct extraction approach. The method is strong in recognizing name variants not found in SwissProt

    Two learning approaches for protein name extraction

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    Cataloged from PDF version of article.Protein name extraction, one of the basic tasks in automatic extraction of information from biological texts, remains challenging. In this paper, we explore the use of two different machine learning techniques and present the results of the conducted experiments. in the first method, Bigram language model is used to extract protein names. In the latter, we use an automatic rule learning method that can identify protein names located in the biological texts. In both cases, we generalize protein names by using hierarchically categorized syntactic token types. We conducted our experiments on two different datasets. our first method based on Bigram language model achieved an F-score of 67.7% on the YAPEX dataset and 66.8% on the GENIA corpus. The developed rule learning method obtained 61.8% F-score value on the YAPEX dataset and 61.0% on the GENIA corpus. The results of the comparative experiments demonstrate that both techniques are applicable to the task of automatic protein name extraction, a prerequisite for the large-scale processing of biomedical literature. (C) 2009 Elsevier Inc. All rights reserved

    Mining Host-Pathogen Interactions

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    OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature

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    <p>Abstract</p> <p>Background</p> <p>Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases such as dbSNP, clues about the functional and phenotypic consequences of the variations are generally found in biomedical literature. The identification of the relevant documents and the extraction of the information from them are hampered by the large size of literature databases and the lack of widely accepted standard notation for biomedical entities. Thus, automatic systems for the identification of citations of allelic variants of genes in biomedical texts are required.</p> <p>Results</p> <p>Our group has previously reported the development of OSIRIS, a system aimed at the retrieval of literature about allelic variants of genes <url>http://ibi.imim.es/osirisform.html</url>. Here we describe the development of a new version of OSIRIS (OSIRISv1.2, <url>http://ibi.imim.es/OSIRISv1.2.html</url>) which incorporates a new entity recognition module and is built on top of a local mirror of the MEDLINE collection and HgenetInfoDB: a database that collects data on human gene sequence variations. The new entity recognition module is based on a pattern-based search algorithm for the identification of variation terms in the texts and their mapping to dbSNP identifiers. The performance of OSIRISv1.2 was evaluated on a manually annotated corpus, resulting in 99% precision, 82% recall, and an F-score of 0.89. As an example, the application of the system for collecting literature citations for the allelic variants of genes related to the diseases intracranial aneurysm and breast cancer is presented.</p> <p>Conclusion</p> <p>OSIRISv1.2 can be used to link literature references to dbSNP database entries with high accuracy, and therefore is suitable for collecting current knowledge on gene sequence variations and supporting the functional annotation of variation databases. The application of OSIRISv1.2 in combination with controlled vocabularies like MeSH provides a way to identify associations of biomedical interest, such as those that relate SNPs with diseases.</p

    Named Entity Recognition for the Estonian Language

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    Käesoleva töö raames uuriti eestikeelsetes tekstides nimega üksuste tuvastamise probleemi (NÜT) kasutades masinõppemeetodeid. NÜT süsteemi väljatöötamisel käsitleti kahte põhiaspekti: nimede tuvastamise algoritmi valikut ja nimede esitusviisi. Selleks võrreldi maksimaalse entroopia (MaxEnt) ja lineaarse ahela tinglike juhuslike väljade (CRF) masinõppemeetodeid. Uuriti, kuidas mõjutavad masinõppe tulemusi kolme liiki tunnused: 1) lokaalsed tunnused (sõnast saadud informatsioon), 2) globaalsed tunnused (sõna kõikide esinemiskontekstide tunnused) ja 3) väline teadmus (veebist saadud nimede nimekirjad). Masinõppe algoritmide treenimiseks ja võrdlemiseks annoteeriti käsitsi ajakirjanduse artiklitest koosnev tekstikorpus, milles märgendati asukohtade, inimeste, organisatsioonide ja ehitise-laadsete objektide nimed. Eksperimentide tulemusena ilmnes, et CRF ületab oluliselt MaxEnt meetodit kõikide vaadeldud nimeliikide tuvastamisel. Parim tulemus, 0.86 F1 skoor, saavutati annoteeritud korpusel CRF meetodiga, kasutades kombinatsiooni kõigist kolmest nime esitusvariandist. Vaadeldi ka süsteemi kohanemisvõimet teiste tekstižanridega spordi domeeni näitel ja uuriti võimalusi süsteemi kasutamiseks teistes keeltes nimede tuvastamisel.In this thesis we study the applicability of recent statistical methods to extraction of named entities from Estonian texts. In particular, we explore two fundamental design challenges: choice of inference algorithm and text representation. We compare two state-of-the-art supervised learning methods, Linear Chain Conditional Random Fields (CRF) and Maximum Entropy Model (MaxEnt). In representing named entities, we consider three sources of information: 1) local features, which are based on the word itself, 2) global features extracted from other occurrences of the same word in the whole document and 3) external knowledge represented by lists of entities extracted from the Web. To train and evaluate our NER systems, we assembled a text corpus of Estonian newspaper articles in which we manually annotated names of locations, persons, organisations and facilities. In the process of comparing several solutions we achieved F1 score of 0.86 by the CRF system using combination of local and global features and external knowledge

    Meat: A Novel

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    An English-language translation of a Russian novel that appeared in the Soviet thick journal Novyi Mir in three installments during February, March, and April of 1936
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