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Gene ontology annotation as text categorization: An empirical study

Kazuhiro Seki, Javed Mostafa
2008 Information Processing & Management  
This paper explores an effective application of text categorization methods to this highly practical problem in biology.  ...  As a first step, we attempt to tackle the automatic GO annotation task posed in the Text Retrieval Conference (TREC) 2004 Genomics Track.  ...  Therefore, each article, gene pair can be treated as a "document" or "text" in the sense of text categorization.  ... 
doi:10.1016/j.ipm.2008.05.003 fatcat:qef2huauxvcujl3crtqqcplmqy

Data-poor categorization and passage retrieval for Gene Ontology Annotation in Swiss-Prot

Frédéric Ehrler, Antoine Geissbühler, Antonio Jimeno, Patrick Ruch
2005 BMC Bioinformatics  
Results: Our system achieved the best recall and precision combination both for passage retrieval and text categorization as evaluated by official evaluators.  ...  In the context of the BioCreative competition, where training data were very sparse, we investigated two complementary tasks: 1) given a Swiss-Prot triplet, containing a protein, a GO (Gene Ontology) term  ...  Acknowledgements We would like to thank Christine Chichester as well as the reviewers for their valuable comments.  ... 
doi:10.1186/1471-2105-6-s1-s23 pmid:15960836 pmcid:PMC1869016 fatcat:skxxgsbww5akjn3zpkazil2s6i

Learning-Free Text Categorization [chapter]

Patrick Ruch, Robert Baud, Antoine Geissbühler
2003 Lecture Notes in Computer Science  
In this paper, we report on the fusion of simple retrieval strategies with thesaural resources in order to perform large-scale text categorization tasks.  ...  Preliminary results show that performances of the hybrid system are significantly improved as compared to each single system.  ...  Acknowledgements The study has been partially sponsored by the European Union (IST Grant 2001-33260, see and the Swiss National Foundation (Grant 3200-065228).  ... 
doi:10.1007/978-3-540-39907-0_28 fatcat:obv4ztgiajht5bfzt77z5b44cu

An Improved Approach for Topic Ontology Based Categorization of Blogs Using Support Vector Machine

2012 Journal of Computer Science  
Conclusion: This study has effectively improved the classification of blogs based on topic ontology assisted SVM. Experiments showed the effectiveness of the blog categorization.  ...  Tags, page contents were collected as inputs from the blogs and the blogs were categorized using Support Vector Machine (SVM) algorithm.  ...  Text filtering: Categorizing the flow of received documents transmission in an asynchronous way by an information creator to an information customer (Sebastiani, 2002) .  ... 
doi:10.3844/jcssp.2012.251.258 fatcat:ehaunzbaijhbllqvrzr463vhh4

Automatic categorization of diverse experimental information in the bioscience literature

Ruihua Fang, Gary Schindelman, Kimberly Auken, Jolene Fernandes, Wen Chen, Xiaodong Wang, Paul Davis, Mary Tuli, Steven J Marygold, Gillian Millburn, Beverley Matthews, Haiyan Zhang (+3 others)
2012 BMC Bioinformatics  
, gene expression, gene product interaction, overexpression phenotype, gene interaction, and gene structure correction.  ...  During the biocuration process, a critical first step is to identify from all published literature the papers that contain results for a specific data type the curator is interested in annotating.  ...  PWS is an Investigator with the Howard Hughes Medical Institute.  ... 
doi:10.1186/1471-2105-13-16 pmid:22280404 pmcid:PMC3305665 fatcat:pgt5hyh44rdzhlfxdn2tc5hvfa

Automated Patent Categorization and Guided Patent Search using IPC as Inspired by MeSH and PubMed

Daniel Eisinger, George Tsatsaronis, Markus Bundschus, Ulrich Wieneke, Michael Schroeder
2013 Journal of Biomedical Semantics  
These additional query components are extracted from different sources such as patent text, IPC definitions, external vocabularies and co-occurrence data.  ...  First and foremost, I want to thank both my academic supervisor Michael Schroeder and my Roche supervisor Ulrich Wieneke for the scientific and financial support I received as well as the positive work  ...  All resulting patent documents are also annotated with relevant terms from MeSH as well as the Gene Ontology and a protein database, making faceted browsing based on completely different aspects of the  ... 
doi:10.1186/2041-1480-4-s1-s3 pmid:23734562 pmcid:PMC3632996 fatcat:mqdxpiitgzbx3akonwwzfq2edq

Categorization of Lung Mesenchymal Cells in Development and Fibrosis

Xue Liu, Simon C. Rowan, Jiurong Liang, Changfu Yao, Guanling Huang, Nan Deng, Ting Xie, Di Wu, Yizhou Wang, Ankita Burman, Tanyalak Parimon, Zea Borok (+8 others)
2021 iScience  
All mesenchymal subpopulations contributed to matrix gene expression in fibrosis.  ...  They are increasingly recognized as highly heterogeneous, but there is no consensus on subpopulations or discriminative markers for each subtype.  ...  Ontology database.  ... 
doi:10.1016/j.isci.2021.102551 pmid:34151224 pmcid:PMC8188567 fatcat:kpijb7jbyncfdoo3tdn2vz5grq

Gene induction and categorical reprogramming during in vitro human endometrial fibroblast decidualization

2001 Physiological Genomics  
induction and categorical reprogramming during in vitro human endometrial fibroblast decidualization.  ...  Human decidual fibroblasts undergo a differentiative commitment to the acquisition of endocrine, metabolic, and structural cell functions in a process known as decidualization.  ...  This work was also supported by an infrastructure grant to the University of Cincinnati College of Medicine from the Howard Hughes Medical Institute.  ... 
doi:10.1152/physiolgenomics.00061.2001 pmid:11773600 fatcat:x45avcr2efhbnn7hvmw77zfxs4

Biomarker detection and categorization in ribonucleic acid sequencing meta-analysis using Bayesian hierarchical models

Tianzhou Ma, Faming Liang, George C. Tseng
2016 Journal of the Royal Statistical Society, Series C: Applied Statistics  
A naive approach to combine multiple RNA-seq studies is to apply differential analysis tools such as edgeR and DESeq to each study and then combine the summary statistics of p-values or effect sizes by  ...  Meta-analysis combining multiple transcriptomic studies increases statistical power and accuracy in detecting differentially expressed genes.  ...  After we obtained the DE genes from each approach, we performed pathway enrichment analysis using Fisher's exact test based on the Gene Ontology (GO) database to annotate the identified genes (Khatri  ... 
doi:10.1111/rssc.12199 pmid:28785119 pmcid:PMC5543999 fatcat:xwbgbzxwifd2lawyelqx6jmoli

Report on the TREC 2004 Experiment: Genomics Track

Patrick Ruch, Christine Chichester, Gilles Cohen, Frédéric Ehrler, Paul Fabry, Johan Marty, Henning Müller, Antoine Geissbühler
2004 Text Retrieval Conference  
categorization task (task II: triage and annotation).  ...  For these tasks we attempted to adapt a Gene Ontology categorizer, which showed very effective results in the context of the BioCreative challenge, where training data were very sparse.  ...  Acknowledgments The study reported in this paper has been supported by the SNF (MEDTAG, Grant 3200-065228.01 and an EU/OFES grant (SemanticMining, IST Grant 507505/03.0399).  ... 
dblp:conf/trec/RuchCCEFMMG04 fatcat:673vpokfrrbenif5o4ryrnqz6u


Manaswini Pradhan
In recent times, bioinformatics plays an increasingly important role in the study of advanced biology.  ...  An extensive review of the prevailing literature related to gene prediction is presented along with classification by utilizing an assortment of techniques.  ...  [62] have offered an analytical method for categorizing the gene expression data.  ... 

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.  ...  The second approach uses any scalable machine learning techniques to generate a model trained on the Gene Ontology Annotation (GOA) database.  ... 
doi:10.1007/978-1-4939-3743-1_6 pmid:27812936 fatcat:qegtjj5flvbqpj4evpe3zttb24

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

Thresholding Strategies for Text Classifiers: TREC 2005 Biomedical Triage Task Experiments

Luo Si, Tapas Kanungo
2005 Text Retrieval Conference  
Then a subset of the test documents was identified as positive instances by selecting the top-k documents of the ranked lists. Deciding on the ideal value for k requires a good thresholding strategy.  ...  The research presented in this paper is partially supported by an ARDA grant under Phase II of the AQUAINT program.  ...  Algorithm Description The triage task can be seen as a text categorization problem. Text categorization algorithms first extract useful features from text data.  ... 
dblp:conf/trec/SiK05 fatcat:lkzacbbxcjfkhgrbo2kk52hwca

Ontological discovery environment: A system for integrating gene–phenotype associations

Erich J. Baker, Jeremy J. Jay, Vivek M. Philip, Yun Zhang, Zuopan Li, Roumyana Kirova, Michael A. Langston, Elissa J. Chesler
2009 Genomics  
Gene sets are annotated with several levels of metadata, including community ontologies, while gene set translations compare models across species.  ...  serve as inputs.  ...  , depression, or mania emerge as a part of the empirically created ontology.  ... 
doi:10.1016/j.ygeno.2009.08.016 pmid:19733230 pmcid:PMC2783409 fatcat:ovgsv6gryffulacpgtrkhee4im
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