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An application of text categorization methods to gene ontology annotation

Kazuhiro Seki, Javed Mostafa
2005 Proceedings of the 28th annual international ACM SIGIR conference on Research and development in information retrieval - SIGIR '05  
This paper describes an application of IR and text categorization methods to a highly practical problem in biomedicine, specifically, Gene Ontology (GO) annotation.  ...  As a first step toward automatic GO annotation, we aim to assign GO domain codes given a specific gene and an article in which the gene appears, which is one of the task challenges at the TREC 2004 Genomics  ...  This paper introduces a successful application of general IR and text categorization methods to this evolving field of research targeting biomedical texts.  ... 
doi:10.1145/1076034.1076060 dblp:conf/sigir/SekiM05 fatcat:kbomr47p6vfkvkix4majlrzxf4

Text analytics for life science using the Unstructured Information Management Architecture

R. Mack, S. Mukherjea, A. Soffer, N. Uramoto, E. Brown, A. Coden, J. Cooper, A. Inokuchi, B. Iyer, Y. Mass, H. Matsuzawa, L. V. Subramaniam
2004 IBM Systems Journal  
methods and a suite of prototype application-enabling engines for supporting certain types of biomedical text-mining applications.  ...  Entity extractors are annotators that identify the location of an entity name in a text and categorize the name relative to one or more knowledge resources like MeSH and UMLS** (Unified Medical Language  ...  His current research interests include statistical natural language processing, text and data mining, and bioinformatics.  ... 
doi:10.1147/sj.433.0490 fatcat:altfinouzbdy7mrcqx2kzdzecy

Ontologies and Knowledge Graphs in Oncology Research

Marta Contreiras Silva, Patrícia Eugénio, Daniel Faria, Catia Pesquita
2022 Cancers  
paradigm, support the application of Artificial Intelligence methods to unlock new knowledge from a holistic view of the available large volumes of heterogeneous data.  ...  In total, our review encompasses 141 published works, which we categorized under 14 hierarchical categories according to their usage of ontologies and knowledge graphs.  ...  The immense potential of ontologies and the knowledge graph paradigm to support cancer research data management and analysis is increasingly recognized by the oncology research community as an essential  ... 
doi:10.3390/cancers14081906 pmid:35454813 pmcid:PMC9029532 fatcat:t6erzohmvnextkix4infnk7kza

Overview of the gene regulation network and the bacteria biotope tasks in BioNLP'13 shared task

Robert Bossy, Wiktoria Golik, Zorana Ratkovic, Dialekti Valsamou, Philippe Bessières, Claire Nédellec
2015 BMC Bioinformatics  
BB'13 extends the typology of BB'11 to a large diversity of biotopes, as defined by the OntoBiotope ontology.  ...  Moving beyond a list of gene interactions, the goal of the GRN task is to build a gene regulation network from the extracted gene interactions.  ...  Declaration The publication costs of this article were funded by the Institut National  ... 
doi:10.1186/1471-2105-16-s10-s1 pmid:26202448 pmcid:PMC4511173 fatcat:keakzqti2bftpdbtaoi6nhv2pu

Text Mining in Cancer Gene and Pathway Prioritization

Yuan Luo, Gregory Riedlinger, Peter Szolovits
2014 Cancer Informatics  
We explain the relatively slow progress of text mining in gene prioritization, identify several challenges to current text mining methods, and highlight a few directions where more effective text mining  ...  Prioritization of cancer implicated genes has received growing attention as an effective way to reduce wet lab cost by computational analysis that ranks candidate genes according to the likelihood that  ...  PSZ contributed to the analysis and categorization of text mining methods in gene and pathway prioritization. All authors reviewed and approved of the final manuscript.  ... 
doi:10.4137/cin.s13874 pmid:25392685 pmcid:PMC4216063 fatcat:mtk6jnyvxjbntedeioojlmrq3u

Text mining in life sciences [chapter]

J. Fluck, H. Deneke, C. Gieger
2005 Text Mining and its Applications to Intelligence, CRM and Knowledge Management  
Text mining provides the methods to automatically retrieve and extract information contained in free text.  ...  Furthermore a structured representation formalized by ontologies is required to combine the extracted knowledge with other sources.  ...  We discuss which methods are used today and which steps need to be taken to make text mining usable for a broader range of applications in life sciences. 2 Text mining -current state Methodical development  ... 
doi:10.2495/978-1-85312-995-7/17 fatcat:l55iiv3op5hqhpsd5nfz4yxc7y

GOGrapher: A Python library for GO graph representation and analysis

Brian Muller, Adam J Richards, Bo Jin, Xinghua Lu
2009 BMC Research Notes  
The Gene Ontology is the most commonly used controlled vocabulary for annotating proteins.  ...  ., a graph-based multi-label text classifier for protein annotation.  ...  Ontology and Annotation Files The library is also capable of using ontology definition and annotation data files from the Gene Ontology Consortium.  ... 
doi:10.1186/1756-0500-2-122 pmid:19583843 pmcid:PMC2714316 fatcat:op5i44xuqfet3m7cl4iprms7ge

Multi-Label Classification using an Ontology

Yaya TRAORE, Sadouanouan MALO, Didier BASSOLE, Abdoulaye SERE
2019 International Journal of Advanced Computer Science and Applications  
This paper studies the problem of Multi-label classification in the context of web pages categorization. The categories are defined in an ontology.  ...  During these last few years, the problem of multilabel classification (ML) has been studied in several domains, such as text categorization.  ...  Uniprot.org web site is an example of semantic web platform where web pages are annotated by keywords (tags) and classes (categories) of gene ontology (GO).  ... 
doi:10.14569/ijacsa.2019.0101264 fatcat:jjn4uxjphbbptkxd3fa2muehxe

Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction

Julien Gobeill, Imad Tbahriti, Frédéric Ehrler, Anaïs Mottaz, Anne-Lise Veuthey, Patrick Ruch
2008 BMC Bioinformatics  
The second extraction scheme (GOEx) uses an automatic text categorizer to estimate the density of Gene Ontology categories in every sentence; thus providing a full ranking of all possible candidate GeneRiFs  ...  Conclusions: Argumentative representation levels and conceptual density estimation using Gene Ontology contents appear complementary for functional annotation in proteomics.  ...  Acknowledgements This study is supported by the Swiss National Science Foundation thanks to the EAGL project (Engine for question-Answering in Genomics 3252B0-105755).  ... 
doi:10.1186/1471-2105-9-s3-s9 pmid:18426554 pmcid:PMC2352866 fatcat:gso7ix72qjexfkoey62n6wkrzq

The SOFG Anatomy Entry List (SAEL): An Annotation Tool for Functional Genomics Data

Helen Parkinson, Stuart Aitken, Richard A. Baldock, Jonathan B. L. Bard, Albert Burger, Terry F. Hayamizu, Alan Rector, Martin Ringwald, Jeremy Rogers, Cornelius Rosse, Christian J. Stoeckert, Duncan Davidson
2004 Comparative and Functional Genomics  
A great deal of data in functional genomics studies needs to be annotated with low-resolution anatomical terms.  ...  It can be used directly for annotation in the contexts described above. Importantly, each term is linked to the corresponding term in each of the major anatomy ontologies.  ...  The text of this paper is based on a presentation given by Helen Parkinson at the ISMB Bio-ontologies meeting in Glasgow, 30 July 2004.  ... 
doi:10.1002/cfg.434 pmid:18629134 pmcid:PMC2447422 fatcat:tnz6p7mgcnclhjqh7xwusotmky

TogoGenome/TogoStanza: modularized Semantic Web genome database

Toshiaki Katayama, Shuichi Kawashima, Shinobu Okamoto, Yuki Moriya, Hirokazu Chiba, Yuki Naito, Takatomo Fujisawa, Hiroshi Mori, Toshihisa Takagi
2019 Database: The Journal of Biological Databases and Curation  
TogoGenome also serves as an interface to conduct semantic comparative genomics by which a user can observe pan-organism or organism-specific genes based on the functional aspect of gene annotations and  ...  TogoGenome provides a semantic-faceted search system by gene functional annotation, taxonomy, phenotypes and environment based on the relevant ontologies.  ...  We would also like to thank the participants of the BioHackathon series and the RDF summits for developing the FALDO and its applications.  ... 
doi:10.1093/database/bay132 pmid:30624651 pmcid:PMC6323299 fatcat:fvt7ckeipjdxvlzogtlhzufw4a

Text Mining to Support Gene Ontology Curation and Vice Versa [chapter]

Patrick Ruch
2016 Msphere  
We review a decade of efforts to improve the automatic assignment of Gene Ontology (GO) descriptors, the reference ontology for the characterization of genes and gene products.  ...  To illustrate the high potential of this approach, we compare the performances of an automatic text categorizer and show a large improvement of +225 % in both precision and recall on benchmarked data.  ...  Subheading 3 presents the text mining methods developed to support the assignment of GO descriptors to a gene or a gene product based on the content of some published articles.  ... 
doi:10.1007/978-1-4939-3743-1_6 pmid:27812936 fatcat:qegtjj5flvbqpj4evpe3zttb24

Biomedical ontologies in action: role in knowledge management, data integration and decision support

O Bodenreider
2008 IMIA Yearbook of Medical Informatics  
Ontologies play an important role in biomedical research through a variety of applications.  ...  Barriers to the use of ontologies in biomedical applications are discussed.  ...  Acknowledgments This research was supported in part by the Intramural Research Program of the National Institutes of Health (NIH), National Library of Medicine (NLM).  ... 
pmid:18660879 pmcid:PMC2592252 fatcat:axl74koixzbffmfi6m3txvlwqu

Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support

O. Bodenreider
2008 IMIA Yearbook of Medical Informatics  
Conclusions Ontologies play an important role in biomedical research through a variety of applications.  ...  Barriers to the use of ontologies in biomedical applications are discussed.Geissbuhler A, Kulikowski C, editors. IMIA Year book of Medical Informatics 2008.  ...  Acknowledgments This research was supported in part by the Intramural Research Program of the National Institutes of Health (NIH), National Library of Medicine (NLM).  ... 
doi:10.1055/s-0038-1638585 fatcat:r7vz4bruq5fpxa5nhhgcxohd2e

Automated Methods Enable Direct Computation on Phenotypic Descriptions for Novel Candidate Gene Prediction

Ian R. Braun, Carolyn J. Lawrence-Dill
2020 Frontiers in Plant Science  
Moreover, NLP methods for generating vector representations of phenotypes are scalable to large quantities of text because they require no human input.  ...  We compared resulting phenotype similarity measures to those derived from manually curated data to determine the performance of each method.  ...  The result of applying these three annotation methods was a set of ontology terms from PATO, PO, GO, and ChEBI assigned to each text description.  ... 
doi:10.3389/fpls.2019.01629 pmid:31998331 pmcid:PMC6965352 fatcat:chcjhodaunbmtnvmnegbtdr3pi
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