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Gene name identification and normalization using a model organism database

Alexander A. Morgan, Lynette Hirschman, Marc Colosimo, Alexander S. Yeh, Jeff B. Colombe
2004 Journal of Biomedical Informatics  
We focused on listing the normalized form of genes and gene products discussed in an article. We broke this into two steps: gene mention tagging in text, followed by normalization of gene names.  ...  Biology has now become an information science, and researchers are increasingly dependent on expert-curated biological databases to organize the findings from the published literature.  ...  This track focused on the normalized gene list task using data from three model organism databases (mouse, fly, and yeast).  ... 
doi:10.1016/j.jbi.2004.08.010 pmid:15542014 fatcat:f2r63l3ecfhrtjxm2eo2omfxvq

Overview of BioCreAtIvE: critical assessment of information extraction for biology

Lynette Hirschman, Alexander Yeh, Christian Blaschke, Alfonso Valencia
2005 BMC Bioinformatics  
The first dealt with extraction of gene or protein names from text, and their mapping into standardized gene identifiers for three model organism databases (fly, mouse, yeast).  ...  The assessment provided state-of-the-art performance results for a basic task (gene name finding and normalization), where the best systems achieved a balanced 80% precision / recall or better, which potentially  ...  Acknowledgements The work of AV and CB was funded by the European Commission as part of the E-BioSci and ORIEL projects, contract numbers QLRI-CT  ... 
doi:10.1186/1471-2105-6-s1-s1 pmid:15960821 pmcid:PMC1869002 fatcat:kktugbhkrzgwvnnwuo7jxszkaq

Human chromosome 21/Down syndrome gene function and pathway database

Oleksii Nikolaienko, Cao Nguyen, Linda S. Crinc, Krzysztof J. Cios, Katheleen Gardiner
2005 Gene  
To aid the Down syndrome and chromosome 21 community, and researchers interested in the study of any chromosome 21 gene or ortholog, we are developing a comprehensive chromosome 21-specific database with  ...  These data are dispersed among diverse databases, and the variety of formats and locations, plus their often rapid growth, makes access and assimilation a daunting task.  ...  and the Ministry of Education and Training -Vietnam (CN).  ... 
doi:10.1016/j.gene.2005.07.019 pmid:16310977 fatcat:tim6m7ggnfgdvh5ktyekhznpju

ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization

Jian Sang, Zhennan Wang, Man Li, Jiabao Cao, Guangyi Niu, Lin Xia, Dong Zou, Fan Wang, Xingjian Xu, Xiaojiao Han, Jinqi Fan, Ye Yang (+8 others)
2017 Nucleic Acids Research  
in both model and nonmodel organisms.  ...  Unlike extant related databases that focus on qPCR primers in model organisms (mainly human and mouse), ICG features harnessing collective intelligence in community integration of internal control genes  ...  ACKNOWLEDGEMENTS We thank a number of users for reporting bugs and providing suggestions as well as the anonymous reviewers for their valuable comments on this work.  ... 
doi:10.1093/nar/gkx875 pmid:29036693 pmcid:PMC5753184 fatcat:kok3jdphqva6boxmelu4kznzau

Quantitative Assessment of Dictionary-based Protein Named Entity Tagging

H. Liu, Z.-Z. Hu, M. Torii, C. Wu, C. Friedman
2006 JAMIA Journal of the American Medical Informatics Association  
Several other databases were also included including several model organism databases, HUGO, and ENZYME etc. Terms obtained from the annotation fields comprised the Raw Dictionary.  ...  A critical step for biological literature mining is biological named entity tagging (BNET) that identifies names mentioned in text and normalizes them with entries in biological databases.  ...  The data for the normalization task of BioCreAtive (Task 1B) 31 were prepared using a gene list associated with the full journal articles found in the model organism databases, i.e., SGD (yeast), 32  ... 
doi:10.1197/jamia.m2085 pmid:16799122 pmcid:PMC1561801 fatcat:slluxn6gknhx5hpvexewpnr47a

Improved mutation tagging with gene identifiers applied to membrane protein stability prediction

Rainer Winnenburg, Conrad Plake, Michael Schroeder
2009 BMC Bioinformatics  
In order to link mutations to their proteins, we utilize a named entity recognition algorithm for the identification of gene names co-occurring in the abstract, and establish links based on sequence checks  ...  The automated retrieval and integration of information about protein point mutations in combination with structure, domain and interaction data from literature and databases promises to be a valuable approach  ...  Acknowledgements We thank Frank Dressel and Dirk Labudde from TU Dresden and FH Mittweida for their work on the prediction of stabilizing regions in membrane proteins and the helpful comments on the application  ... 
doi:10.1186/1471-2105-10-s8-s3 pmid:19758467 pmcid:PMC2745585 fatcat:i2xqvejgrra35eln6wutviepsq

One model per entity: using hundreds of machine learning models to recognize and normalize biomedical names in text

Victor Bellon, Raul Rodriguez-Esteban
2017 Proceedings of the Biomedical NLP Workshop  
We explored a new approach to named entity recognition based on hundreds of machine learning models, each trained to distinguish a single entity, and showed its application to gene name identification  ...  The rationale for our approach, which we named "one model per entity" (OMPE), was that increasing the number of models would make the learning task easier for each individual model.  ...  Gene name identification (GNI) is the combination of gene name recognition and normalization (GNR + GNN) (see the framework by Krauthammer and Nenadic (2004) ).  ... 
doi:10.26615/978-954-452-044-1_007 dblp:conf/ranlp/BellonR17 fatcat:uwhum2pm3jhztf5yp4apmbqzc4

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID

Sun Kim, Rezarta Islamaj Doğan, Andrew Chatr-Aryamontri, Christie S. Chang, Rose Oughtred, Jennifer Rust, Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou, Sérgio Matos, André Santos, David Campos (+23 others)
2016 Database: The Journal of Biological Databases and Curation  
., Chatr-Aryamontri, A. et al. BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID.  ...  . • Task 2, 'Species/organism NER'-Identification and normalization of species/organism names.  ...  A submitted run contains predicted text, e.g. gene/ protein/organism names or PPI/GI passages, optionally with normalized IDs for gene/protein/organism names.  ... 
doi:10.1093/database/baw121 pmid:27589962 pmcid:PMC5009341 fatcat:bqe4o77fizadhf5e3xese3i23y

Cry-Bt identifier: A biological database for PCR detection of Cry genes present in transgenic plants

Vinay Kumar Singh, Sonu Ambwani, Soma Marla, Anil Kumar
2009 Bioinformation  
The tool designed based on relational database model enables easy retrieval of information from the database with simple user queries.  ...  We describe the development of a user friendly tool that would assist in the retrieval of information relating to Cry genes in transgenic crops.  ...  Programs written in PHP enabled database search using keywords like `organism name`, `Gene name`, `Gene Id.` and `Gene & Protein Sequences` of Cry-Bt genes.  ... 
doi:10.6026/97320630004182 pmid:20461155 pmcid:PMC2859572 fatcat:pqj2cgh635bzngvqdeibziao4q

Fantastic databases and where to find them: Web applications for researchers in a rush

Gerda Cristal Villalba, Ursula Matte
2021 Genetics and Molecular Biology  
, and comparative analysis between human and model organisms.  ...  To show the databases at work, we present a a case study using ACE2 as example of a gene to be investigated. The analysis and the complete list of databases is available in the following website .  ...  .: 148615/2018-0) and UM (Process no.: 312714/2018-1). We also thank FIPE/ HCPA (Project Number 2019-0761) for financial support.  ... 
doi:10.1590/1678-4685-gmb-2020-0203 pmid:33821874 fatcat:owkdaqz2nngb5a2zcqbccxnvpe

Metabolic Network Modeling for Rational Drug Design against Candida albicans [chapter]

Rashi Verma, Dibyabhaba Pradhan, Harpreet Singh, Arun Kumar Jain, Luqman Ahmad Khan
2021 Infectious diseases  
Thus, the chapter details current advancement in model construction, target identification and validation.  ...  To overcome the concern, genome scale metabolic model construction provides a promising platform that allows novel target identification in combination with subtractive genome analysis.  ...  Creation of new database Database creation is the first step of draft model construction that requires the information like unique identifier, database name, taxonomy of organism and database storage type  ... 
doi:10.5772/intechopen.96749 fatcat:hwifr5d4vzh3lh7ysgdmdm7cry

Gene name extraction using FlyBase resources

Alex Morgan, Lynette Hirschman, Alexander Yeh, Marc Colosimo
2003 Proceedings of the ACL 2003 workshop on Natural language processing in biomedicine -  
tor), a model organism for genetics research: http://www.flybase.org. 2 Of course most of these early references in FlyBase are not in electronic form.  ...  The FlyBase database has been in existence since 1993. 3  ...  We used resources available in the FlyBase model organism database; these resources include a curated lists of genes and the articles from which the entries were drawn, together a synonym lexicon.  ... 
doi:10.3115/1118958.1118959 dblp:conf/bionlp/MorganHYC03 fatcat:y5br6vlv5rfdtll2byszlnipd4

Gene and protein nomenclature in public databases

Katrin Fundel, Ralf Zimmer
2006 BMC Bioinformatics  
Various organism-specific or general public databases aim at organizing knowledge about genes and proteins. These databases can be used for deriving gene and protein name dictionaries.  ...  of all used names referring to a given gene or protein.  ...  This work was funded by projects BEX (Sanofi-Aventis, Frankfurt) and BOA (German ministry for research and education, grant 01GG9824).  ... 
doi:10.1186/1471-2105-7-372 pmid:16899134 pmcid:PMC1560172 fatcat:n56wp6k6ajdspchk2toalqbsyq

SPRENO: a BioC module for identifying organism terms in figure captions

Hong-Jie Dai, Onkar Singh
2018 Database: The Journal of Biological Databases and Curation  
The other is a convolutional neural network (CNN) model trained by learning both the context and the distance information of the target organism mention.  ...  In this study, we present our species identification tool SPRENO (Species Recognition and Normalization), which is established for recognizing organism terms mentioned in figure captions and linking them  ...  of abbreviations of species names and the use of common English names instead of Latin names to refer to an organism.  ... 
doi:10.1093/database/bay048 pmid:29873706 pmcid:PMC6007219 fatcat:leki4amzwrehrajfb56vrwugzy

LimiTT: link miRNAs to targets

Julia Bayer, Carsten Kuenne, Jens Preussner, Mario Looso
2016 BMC Bioinformatics  
This issue is aggravated for niche model organisms, where validated miRNAs and MTIs both have to be transferred from well described model organisms.  ...  The integrated mapping to homologous target identifiers enables the identification of MTIs not only for standard models, but for niche model organisms as well.  ...  MirTarBase and StarBase are completely free for noncommercial use.  ... 
doi:10.1186/s12859-016-1070-1 pmid:27170328 pmcid:PMC4866021 fatcat:3hsbie5rznegvpwapct3ud53pu
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