Survey of Natural Language Processing Techniques in Bioinformatics <s> Retrieving References. <s> We have developed Textpresso, a new text-mining system for scientific literature whose capabilities go far beyond those of a simple keyword search engine. Textpresso's two major elements are a collection of the full text of scientific articles split into individual sentences, and the implementation of categories of terms for which a database of articles and individual sentences can be searched. The categories are classes of biological concepts (e.g., gene, allele, cell or cell group, phenotype, etc.) and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., biological process, etc.). Together they form a catalog of types of objects and concepts called an ontology. After this ontology is populated with terms, the whole corpus of articles and abstracts is marked up to identify terms of these categories. The current ontology comprises 33 categories of terms. A search engine enables the user to search for one or a combination of these tags and/or keywords within a sentence or document, and as the ontology allows word meaning to be queried, it is possible to formulate semantic queries. Full text access increases recall of biological data types from 45% to 95%. Extraction of particular biological facts, such as gene-gene interactions, can be accelerated significantly by ontologies, with Textpresso automatically performing nearly as well as expert curators to identify sentences; in searches for two uniquely named genes and an interaction term, the ontology confers a 3-fold increase of search efficiency. Textpresso currently focuses on Caenorhabditis elegans literature, with 3,800 full text articles and 16,000 abstracts. The lexicon of the ontology contains 14,500 entries, each of which includes all versions of a specific word or phrase, and it includes all categories of the Gene Ontology database. Textpresso is a useful curation tool, as well as search engine for researchers, and can readily be extended to other organism-specific corpora of text. Textpresso can be accessed at http://www.textpresso.org or via WormBase at http://www.wormbase.org. <s> BIB001 </s> Survey of Natural Language Processing Techniques in Bioinformatics <s> Retrieving References. <s> This paper describes the application of IBM TAKMI® for Biomedical Documents to facilitate knowledge discovery from the very large text databases characteristic of life science and healthcare applications. This set of tools, designated MedTAKMI, is an extension of the TAKMI (Text Analysis and Knowledge MIning) system originally developed for text mining in customer-relationship-management applications. MedTAKMI dynamically and interactively mines a collection of documents to obtain characteristic features within them. By using multifaceted mining of these documents together with biomedically motivated categories for term extraction and a series of drill-down queries, users can obtain knowledge about a specific topic after seeing only a few key documents. In addition, the use of natural language techniques makes it possible to extract deeper relationships among biomedical concepts. The MedTAKMI system is capable of mining the entire MEDLINE® database of 11 million biomedical journal abstracts. It is currently running at a customer site. <s> BIB002 </s> Survey of Natural Language Processing Techniques in Bioinformatics <s> Retrieving References. <s> BackgroundResearchers who use MEDLINE for text mining, information extraction, or natural language processing may benefit from having a copy of MEDLINE that they can manage locally. The National Library of Medicine (NLM) distributes MEDLINE in eXtensible Markup Language (XML)-formatted text files, but it is difficult to query MEDLINE in that format. We have developed software tools to parse the MEDLINE data files and load their contents into a relational database. Although the task is conceptually straightforward, the size and scope of MEDLINE make the task nontrivial. Given the increasing importance of text analysis in biology and medicine, we believe a local installation of MEDLINE will provide helpful computing infrastructure for researchers.ResultsWe developed three software packages that parse and load MEDLINE, and ran each package to install separate instances of the MEDLINE database. For each installation, we collected data on loading time and disk-space utilization to provide examples of the process in different settings. Settings differed in terms of commercial database-management system (IBM DB2 or Oracle 9i), processor (Intel or Sun), programming language of installation software (Java or Perl), and methods employed in different versions of the software. The loading times for the three installations were 76 hours, 196 hours, and 132 hours, and disk-space utilization was 46.3 GB, 37.7 GB, and 31.6 GB, respectively. Loading times varied due to a variety of differences among the systems. Loading time also depended on whether data were written to intermediate files or not, and on whether input files were processed in sequence or in parallel. Disk-space utilization depended on the number of MEDLINE files processed, amount of indexing, and whether abstracts were stored as character large objects or truncated.ConclusionsRelational database (RDBMS) technology supports indexing and querying of very large datasets, and can accommodate a locally stored version of MEDLINE. RDBMS systems support a wide range of queries and facilitate certain tasks that are not directly supported by the application programming interface to PubMed. Because there is variation in hardware, software, and network infrastructures across sites, we cannot predict the exact time required for a user to load MEDLINE, but our results suggest that performance of the software is reasonable. Our database schemas and conversion software are publicly available at http://biotext.berkeley.edu. <s> BIB003 </s> Survey of Natural Language Processing Techniques in Bioinformatics <s> Retrieving References. <s> The rapid growth of the biological text data repository makes it difficult for human beings to access required information in a convenient and effective manner. The problem arises due to the fact that most of the information is embedded within unstructured or semi-structured text that computers cannot interpret very easily. In this paper we have presented an ontology-based Biological Information Extraction and Query Answering (BIEQA) System, which initiates text mining with a set of concepts stored in a biological ontology, and thereafter mines possible biological relations among those concepts using NLP techniques and co-occurrence-based analysis. The system extracts all frequently occurring biological relations among a pair of biological concepts through text mining. A mined relation is associated to a fuzzy membership value, which is proportional to its frequency of occurrence in the corpus and is termed a fuzzy biological relation. The fuzzy biological relations extracted from a text corpus along with other relevant information components like biological entities occurring within a relation, are stored in a database. The database is integrated with a query-processing module. The query-processing module has an interface, which guides users to formulate biological queries at different levels of specificity. <s> BIB004 </s> Survey of Natural Language Processing Techniques in Bioinformatics <s> Retrieving References. <s> Traditional Information Extraction (IE) takes a relation name and hand-tagged examples of that relation as input. Open IE is a relationindependent extraction paradigm that is tailored to massive and heterogeneous corpora such as the Web. An Open IE system extracts a diverse set of relational tuples from text without any relation-specific input. How is Open IE possible? We analyze a sample of English sentences to demonstrate that numerous relationships are expressed using a compact set of relation-independent lexico-syntactic patterns, which can be learned by an Open IE system. What are the tradeoffs between Open IE and traditional IE? We consider this question in the context of two tasks. First, when the number of relations is massive, and the relations themselves are not pre-specified, we argue that Open IE is necessary. We then present a new model for Open IE called O-CRF and show that it achieves increased precision and nearly double the recall than the model employed by TEXTRUNNER, the previous stateof-the-art Open IE system. Second, when the number of target relations is small, and their names are known in advance, we show that O-CRF is able to match the precision of a traditional extraction system, though at substantially lower recall. Finally, we show how to combine the two types of systems into a hybrid that achieves higher precision than a traditional extractor, with comparable recall. <s> BIB005 </s> Survey of Natural Language Processing Techniques in Bioinformatics <s> Retrieving References. <s> GeneCards (www.genecards.org) is a comprehensive, authoritative compendium of annotative information about human genes, widely used for nearly 15 years. Its gene-centric content is automatically mined and integrated from over 80 digital sources, resulting in a web-based deep-linked card for each of >73 000 human gene entries, encompassing the following categories: protein coding, pseudogene, RNA gene, genetic locus, cluster and uncategorized. We now introduce GeneCards Version 3, featuring a speedy and sophisticated search engine and a revamped, technologically enabling infrastructure, catering to the expanding needs of biomedical researchers. A key focus is on gene-set analyses, which leverage GeneCards’ unique wealth of combinatorial annotations. These include the GeneALaCart batch query facility, which tabulates user-selected annotations for multiple genes and GeneDecks, which identifies similar genes with shared annotations, and finds set-shared annotations by descriptor enrichment analysis. Such set-centric features address a host of applications, including microarray data analysis, cross-database annotation mapping and gene-disorder associations for drug targeting. We highlight the new Version 3 database architecture, its multi-faceted search engine, and its semi-automated quality assurance system. Data enhancements include an expanded visualization of gene expression patterns in normal and cancer tissues, an integrated alternative splicing pattern display, and augmented multi-source SNPs and pathways sections. GeneCards now provides direct links to gene-related research reagents such as antibodies, recombinant proteins, DNA clones and inhibitory RNAs and features gene-related drugs and compounds lists. We also portray the GeneCards Inferred Functionality Score annotation landscape tool for scoring a gene’s functional information status. Finally, we delineate examples of applications and collaborations that have benefited from the GeneCards suite. ::: ::: Database URL: www.genecards.org <s> BIB006 </s> Survey of Natural Language Processing Techniques in Bioinformatics <s> Retrieving References. <s> Motivation: The MEDLINE database, consisting of over 19 million publication records, is the primary source of information for biomedicine and health questions. Although the database itself has been growing rapidly, the search paradigm of MEDLINE has remained largely unchanged. ::: ::: Results: Here, we propose a new system for exploring the entire MEDLINE collection, represented by two unique features: (i) interactive: providing instant feedback to users' query letter by letter, and (ii) fuzzy: allowing approximate search. We develop novel index structures and search algorithms to make such a search model possible. We also develop incremental-update techniques to keep the data up to date. ::: ::: Availability: Interactive and fuzzy searching algorithms for exploring MEDLINE are implemented in a system called iPubMed, freely accessible over the web at http://ipubmed.ics.uci.edu/ and http://tastier.cs.tsinghua.edu.cn/ipubmed/ ::: ::: Contact:chenli@ics.uci.edu; xhx@ics.uci.edu <s> BIB007 </s> Survey of Natural Language Processing Techniques in Bioinformatics <s> Retrieving References. <s> Manually curating knowledge from biomedical literature into structured databases is highly expensive and time-consuming, making it difficult to keep pace with the rapid growth of the literature. There is therefore a pressing need to assist biocuration with automated text mining tools. Here, we describe PubTator, a web-based system for assisting biocuration. PubTator is different from the few existing tools by featuring a PubMed-like interface, which many biocurators find familiar, and being equipped with multiple challenge-winning text mining algorithms to ensure the quality of its automatic results. Through a formal evaluation with two external user groups, PubTator was shown to be capable of improving both the efficiency and accuracy of manual curation. PubTator is publicly available at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/Demo/PubTator/. <s> BIB008 </s> Survey of Natural Language Processing Techniques in Bioinformatics <s> Retrieving References. <s> One effective way to improve the state of the art is through competitions. Following the success of the Critical Assessment of protein Structure Prediction (CASP) in bioinformatics research, a number of challenge evaluations have been organized by the text-mining research community to assess and advance natural language processing (NLP) research for biomedicine. In this article, we review the different community challenge evaluations held from 2002 to 2014 and their respective tasks. Furthermore, we examine these challenge tasks through their targeted problems in NLP research and biomedical applications, respectively. Next, we describe the general workflow of organizing a Biomedical NLP (BioNLP) challenge and involved stakeholders (task organizers, task data producers, task participants and end users). Finally, we summarize the impact and contributions by taking into account different BioNLP challenges as a whole, followed by a discussion of their limitations and difficulties. We conclude with future trends in BioNLP challenge evaluations. <s> BIB009 </s> Survey of Natural Language Processing Techniques in Bioinformatics <s> Retrieving References. <s> The use of crowdsourcing to solve important but complex problems in biomedical and clinical sciences is growing and encompasses a wide variety of approaches. The crowd is diverse and includes online marketplace workers, health information seekers, science enthusiasts and domain experts. In this article, we review and highlight recent studies that use crowdsourcing to advance biomedicine. We classify these studies into two broad categories: (i) mining big data generated from a crowd (e.g. search logs) and (ii) active crowdsourcing via specific technical platforms, e.g. labor markets, wikis, scientific games and community challenges. Through describing each study in detail, we demonstrate the applicability of different methods in a variety of domains in biomedical research, including genomics, biocuration and clinical research. Furthermore, we discuss and highlight the strengths and limitations of different crowdsourcing platforms. Finally, we identify important emerging trends, opportunities and remaining challenges for future crowdsourcing research in biomedicine. <s> BIB010
A considerable amount of bioscience literature has been published. Searching for interacting proteins and examining the relationship between genes and diseases are only two application cases. Text mining technology is required to obtain answers to many other bioscience and bioinformatics problems in various databases, such as PubMed. Biological literature mining and related problem solving have to cope with two major problems, namely, recognizing name entities and extracting relations. These problems are mainly solved by (1) methods based on linguistic analysis BIB001 , (2) methods based on dictionaries BIB002 , (3) machine learning methods  BIB005 , and (4) statistical methods BIB004 . Several important databases are also selected with text mining. STRING  and BioGRID  are built for proteinprotein interaction with literature mining. For predicting gene function, PubTator BIB008 and GeneCards BIB006 are important databases using text mining techniques. Related works were reviewed in detail in Huang and Lu's work BIB009 recently. As the development of crowdsource, artificial text searching and mining can also be helpful for biomedicine literature collection BIB010 . Moreover, converting PubMed database into an Extensible Markup Language relational database BIB003 and a fuzzy search of papers and author names through short-term matching are also current research hot spots BIB007 .