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    1. Detection of gene interactions based on syntactic relations.

      Detection of gene interactions based on syntactic relations. J Biomed Biotechnol. 2008;2008:371710 Authors: Kim MY Interactions between proteins and genes are considered essential in the description of biomolecular phenomena, and networks of interactions are applied in a system's biology approach. Recently, many studies have sought to extract information from biomolecular text using natural language processing technology. Previous studies have asserted that linguistic information is useful for improving the detection of gene interactions. In particular, syntactic relations among linguistic information are good for detecting gene interactions. However, previous systems give a reasonably good precision but poor recall. To ...
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      Mentions: Seoul Korea
    2. CoagMDB: a database analysis of missense mutations within four conserved domains in five vitamin K-dependent coagulation serine proteases using a text-mining tool.

      Related Articles CoagMDB: a database analysis of missense mutations within four conserved domains in five vitamin K-dependent coagulation serine proteases using a text-mining tool. Hum Mutat. 2008 Mar;29(3):333-44 Authors: Saunders RE, Perkins SJ Central repositories of mutations that combine structural, sequence, and phenotypic information in related proteins will facilitate the diagnosis and molecular understanding of diseases associated with them. Coagulation involves the sequential activation of serine proteases and regulators in order to yield stable blood clots while maintaining hemostasis. Five coagulation serine proteases-factor VII (F7), factor IX (F9), factor X (F10), protein C (PROC), and thrombin (F2 ...
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    3. Towards a systematic evaluation of protein mutation extraction systems.

      Related Articles Towards a systematic evaluation of protein mutation extraction systems. J Bioinform Comput Biol. 2007 Dec;5(6):1339-59 Authors: Witte R, Baker CJ The development of text analysis systems targeting the extraction of information about mutations from research publications is an emergent topic in biomedical research. Current systems differ in both scope and approach, thus preventing a meaningful comparison of their performance and therefore possible synergies. To overcome this evaluation bottleneck, we developed a comprehensive framework for the systematic analysis of mutation extraction systems, precisely defining tasks and corresponding evaluation metrics, that will allow a comparison of existing ...
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    4. Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (umls).

      Related Articles Mining biomedical data using MetaMap Transfer (MMtx) and the Unified Medical Language System (UMLS). Methods Mol Biol. 2007;408:153-69 Authors: Osborne JD, Lin S, Zhu L, Kibbe WA Detailed instruction is described for mapping unstructured, free text data into common biomedical concepts (drugs, diseases, anatomy, and so on) found in the Unified Medical Language System using MetaMap Transfer (MMTx). MMTx can be used in applications including mining and inferring relationship between concepts in MEDLINE publications by transforming free text into computable concepts. MMTx is in general not designed to be an end-user program; therefore, a simple analysis ...
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    5. Multi-class classification of cancer stages from free-text histology reports using support vector machines.

      Related Articles Multi-class classification of cancer stages from free-text histology reports using support vector machines. Conf Proc IEEE Eng Med Biol Soc. 2007;2007:5140-3 Authors: Nguyen A, Moore D, McCowan I, Courage MJ Multi-class machine learning techniques using support vector machines (SVM) are proposed to classify the TNM stage of lung cancer patients from analysis of their free-text histology reports. Stages obtained automatically can be used for retrospective population-level studies of lung cancer outcomes. While the system could in principle be applied to stage different cancer types, the paper focuses on staging lung cancer due to data availability. Experiments ...
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    6. Ontology-based vector space model and fuzzy query expansion to retrieve knowledge on medical computational problem solutions.

      Related Articles Ontology-based vector space model and fuzzy query expansion to retrieve knowledge on medical computational problem solutions. Conf Proc IEEE Eng Med Biol Soc. 2007;2007:3794-7 Authors: Bratsas C, Koutkias V, Kaimakamis E, Bamidis P, Maglaveras N Medical Computational Problem (MCP) solving is related to medical problems and their computerized algorithmic solutions. In this paper, an extension of an ontology-based model to fuzzy logic is presented, as a means to enhance the information retrieval (IR) procedure in semantic management of MCPs. We present herein the methodology followed for the fuzzy expansion of the ontology model, the fuzzy query ...
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    7. Towards ontology-driven navigation of the lipid bibliosphere.

      Related Articles Towards ontology-driven navigation of the lipid bibliosphere. BMC Bioinformatics. 2008;9 Suppl 1:S5 Authors: Baker CJ, Kanagasabai R, Ang WT, Veeramani A, Low HS, Wenk MR BACKGROUND: The indexing of scientific literature and content is a relevant and contemporary requirement within life science information systems. Navigating information available in legacy formats continues to be a challenge both in enterprise and academic domains. The emergence of semantic web technologies and their fusion with artificial intelligence techniques has provided a new toolkit with which to address these data integration challenges. In the emerging field of lipidomics such navigation challenges ...
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    8. Introduction of enhancement technologies into the intensive care service, Royal Prince Alfred Hospital, Sydney.

      Related Articles Introduction of enhancement technologies into the intensive care service, Royal Prince Alfred Hospital, Sydney. HIM J. 2008;37(1):40-5 Authors: Ryan A, Patrick J, Herkes R In order to achieve the full potential of information technology in healthcare, information systems must have the ability to share and exchange data, which requires the support of standardised medical terminology, such as Systematised Nomenclature of Medicine--Clinical Terms (SNOMED-CT). The Royal Prince Alfred Intensive Care Service and the School of Information Technologies, University of Sydney have been collaborating for over two years, developing pioneering software initiatives for clinical information systems (CIS ...
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    9. A cluster-based approach for semantic similarity in the biomedical domain.

      Related Articles A cluster-based approach for semantic similarity in the biomedical domain. Conf Proc IEEE Eng Med Biol Soc. 2006;1:2713-7 Authors: Al-Mubaid H, Nguyen HA We propose a new cluster-based semantic similarity/distance measure for the biomedical domain within the framework of UMLS. The proposed measure is based mainly on the cross-modified path length feature between the concept nodes, and two new features: (1) the common specificity of two concept nodes, and (2) the local granularity of the clusters. We also applied, for comparison purpose, five existing general English ontology-based similarity measures into the biomedical domain within UMLS ...
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    10. Comparing usability of matching techniques for normalising biomedical named entities.

      Related Articles Comparing usability of matching techniques for normalising biomedical named entities. Pac Symp Biocomput. 2008;:628-39 Authors: Wang X, Matthews M String matching plays an important role in biomedical Term Normalisation, the task of linking mentions of biomedical entities to identifiers in reference databases. This paper evaluates exact, rule-based and various string-similarity-based matching techniques. The matchers are compared in two ways: first, we measure precision and recall against a gold-standard dataset and second, we integrate the matchers into a curation tool and measure gains in curation speed when they were used to assist a curator in normalising protein and ...
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    11. An Executable Survey Of Advances In Biomedical Named Entity Recognition.

      Related Articles BANNER: an executable survey of advances in biomedical named entity recognition. Pac Symp Biocomput. 2008;:652-63 Authors: Leaman R, Gonzalez G There has been an increasing amount of research on biomedical named entity recognition, the most basic text extraction problem, resulting in significant progress by different research teams around the world. This has created a need for a freely-available, open source system implementing the advances described in the literature. In this paper we present BANNER, an open-source, executable survey of advances in biomedical named entity recognition, intended to serve as a benchmark for the field. BANNER is implemented ...
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    12. An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology.

      Related Articles An open source infrastructure for managing knowledge and finding potential collaborators in a domain-specific subset of PubMed, with an example from human genome epidemiology. BMC Bioinformatics. 2007;8:436 Authors: Yu W, Yesupriya A, Wulf A, Qu J, Khoury MJ, Gwinn M BACKGROUND: Identifying relevant research in an ever-growing body of published literature is becoming increasingly difficult. Establishing domain-specific knowledge bases may be a more effective and efficient way to manage and query information within specific biomedical fields. Adopting controlled vocabulary is a critical step toward data integration and interoperability in any information system. We present an open ...
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    13. Linguistic analyses of natural written language: unobtrusive assessment of cognitive style in eating disorders.

      Related Articles Linguistic analyses of natural written language: unobtrusive assessment of cognitive style in eating disorders. Int J Eat Disord. 2007 Dec;40(8):711-7 Authors: Wolf M, Sedway J, Bulik CM, Kordy H OBJECTIVE: Linguistic style analysis is introduced as a method of nonreactive measurement of cognitive style in individuals with eating disorders (ED). METHOD: A journaling exercise was implemented on an ED inpatient unit. Thirty-four written essays collected from an unselected sample of 11 patients were analysed with the Linguistic Inquiry and Word Count, with regard to predefined text categories. At each session, self-report of participant well-being and ...
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    14. Natural language processing using online analytic processing for assessing recommendations in radiology reports.

      Related Articles Natural language processing using online analytic processing for assessing recommendations in radiology reports. J Am Coll Radiol. 2008 Mar;5(3):197-204 Authors: Dang PA, Kalra MK, Blake MA, Schultz TJ, Stout M, Lemay PR, Freshman DJ, Halpern EF, Dreyer KJ PURPOSE: The study purpose was to describe the use of natural language processing (NLP) and online analytic processing (OLAP) for assessing patterns in recommendations in unstructured radiology reports on the basis of patient and imaging characteristics, such as age, gender, referring physicians, radiology subspecialty, modality, indications, diseases, and patient status (inpatient vs outpatient). MATERIALS AND METHODS: A ...
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    15. Semantic tagging for medical knowledge tracking.

      Related Articles Semantic tagging for medical knowledge tracking. Conf Proc IEEE Eng Med Biol Soc. 2006;1:6257-60 Authors: Jang H, Song SK, Myaeng SH We propose a semantic tagger that provides high level concept information for phrases in clinical documents, which enriches medical information tracking system that support decision making or quality assurance of medical treatment. In this paper, we have tried to deal with patient records written by doctors rather than well-formed documents such as Medline abstracts. In addition, annotating clinical text on phrases semantically rather than syntactically has been attempted, which are at higher level granularity than ...
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    16. BioProber: software system for biomedical relation discovery from PubMed.

      Related Articles BioProber: software system for biomedical relation discovery from PubMed. Conf Proc IEEE Eng Med Biol Soc. 2006;1:5779-82 Authors: Jang H, Lim J, Lim JH, Park SJ, Lee KC The numbers of articles and journals that are published are increasing at a considerable rate, and the published information is growing continuously and fast. Because of this, researches to acquire knowledge automatically have been carried out in the areas of information retrieval, information extraction and text mining. Information retrieval approaches are good for specific topics that the number of related articles is small. But, if the number is ...
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    17. The AMIA 2006 Scientific Program Committee has retracted the following paper from the AMIA 2006 Proceedings: Comparative evaluation of accuracy of extraction of medication information from narrative physician notes by commercial and academic natural langu

      The AMIA 2006 Scientific Program Committee has retracted the following paper from the AMIA 2006 Proceedings: Comparative evaluation of accuracy of extraction of medication information from narrative physician notes by commercial and academic natural language processing software packages. AMIA Annu Symp Proc. 2006;:789-93 Authors: PMID: 18297753 [PubMed - in process]
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    18. Randomized controlled trial of an automated problem list with improved sensitivity.

      Related Articles Randomized controlled trial of an automated problem list with improved sensitivity. Int J Med Inform. 2008 Feb 14; Authors: Meystre SM, Haug PJ PURPOSE: To improve the completeness and timeliness of an electronic problem list, we have developed a system using Natural Language Processing (NLP) to automatically extract potential medical problems from clinical, free-text documents; these problems are then proposed for inclusion in an electronic problem list management application. METHODS: A prospective randomized controlled evaluation of the Automatic Problem List (APL) system in an intensive care unit and in a cardiovascular surgery unit is reported here. A total ...
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    19. Extraction of Protein Interaction Data: A Comparative Analysis of Methods in Use.

      Related Articles Extraction of Protein Interaction Data: A Comparative Analysis of Methods in Use. EURASIP J Bioinform Syst Biol. 2007;2007:53096 Authors: Jose H, Vadivukarasi T, Devakumar J Several natural language processing tools, both commercial and freely available, are used to extract protein interactions from publications. Methods used by these tools include pattern matching to dynamic programming with individual recall and precision rates. A methodical survey of these tools, keeping in mind the minimum interaction information a researcher would need, in comparison to manual analysis has not been carried out. We compared data generated using some of the selected ...
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      Mentions: India Bangalore
    20. Script and language identification in noisy and degraded document images.

      Related Articles Script and language identification in noisy and degraded document images. IEEE Trans Pattern Anal Mach Intell. 2008 Jan;30(1):14-24 Authors: Shijian L, Lim Tan C This paper reports an identification technique that detects scripts and languages of noisy and degraded document images. In the proposed technique, scripts and languages are identified through the document vectorization, which converts each document image into a document vector that characterizes the shape and frequency of the conta ned character or word images. Document images are vectorized by using vertical component cuts and character extremum points, which are both tolerant to ...
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    21. Comparison with manual registration reveals satisfactory completeness and efficiency of a computerized cancer registration system.

      Related Articles Comparison with manual registration reveals satisfactory completeness and efficiency of a computerized cancer registration system. J Biomed Inform. 2008 Feb;41(1):24-32 Authors: Contiero P, Tittarelli A, Maghini A, Fabiano S, Frassoldi E, Costa E, Gada D, Codazzi T, Crosignani P, Tessandori R, Tagliabue G Automated software for cancer registration, called Open Registry and developed by ourselves was adopted by the Varese (population-based) Cancer Registry starting from 1997. Since the use of automated cancer registration is increasing, it is important to assess the quality and completeness of the automated data being produced. In this study, we assessed ...
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    22. A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences.

      Related Articles A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences. J Biomed Inform. 2008 Feb;41(1):65-81 Authors: Othman RM, Deris S, Illias RM A genetic similarity algorithm is introduced in this study to find a group of semantically similar Gene Ontology terms. The genetic similarity algorithm combines semantic similarity measure algorithm with parallel genetic algorithm. The semantic similarity measure algorithm is used to compute the similitude strength between the Gene Ontology terms. Then, the parallel genetic algorithm is employed to perform batch retrieval and to accelerate the search in large search ...
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      Mentions: Gene Ontology
    23. Non-linear correlation of content and metadata information extracted from biomedical article datasets.

      Related Articles Non-linear correlation of content and metadata information extracted from biomedical article datasets. J Biomed Inform. 2008 Feb;41(1):202-16 Authors: Theodosiou T, Angelis L, Vakali A Biomedical literature databases constitute valuable repositories of up to date scientific knowledge. The development of efficient machine learning methods in order to facilitate the organization of these databases and the extraction of novel biomedical knowledge is becoming increasingly important. Several of these methods require the representation of the documents as vectors of variables forming large multivariate datasets. Since the amount of information contained in different datasets is voluminous, an open issue ...
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