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The Rat Genome Database, update 2007--Easing the path from disease to data and back again

S. N. Twigger, M. Shimoyama, S. Bromberg, A. E. Kwitek, H. J. Jacob
2007 Nucleic Acids Research  
The disease curation efforts combined with normal curation activities have served to greatly increase the content of the database, particularly for biological information, including gene ontology, disease  ...  In addition to improving the features and database content, community outreach has been expanded to demonstrate how investigators can leverage the resources at RGD to facilitate their research and to elicit  ...  ACKNOWLEDGEMENTS In addition to the listed authors RGD is built and maintained by the following group of dedicated people: Jiali Chen, Weihong Jin, Nataliya Nenasheva, Rajni Nigam, Andrew Patzer, Victoria  ... 
doi:10.1093/nar/gkl988 pmid:17151068 pmcid:PMC1761441 fatcat:2zdfnka2dfh7fgggb5ulwxznti

FSim: A Novel Functional Similarity Search Algorithm and Tool for Discovering Functionally Related Gene Products

Qiang Hu, ZhiGang Wang, ZhengGuo Zhang
2014 BioMed Research International  
FSim is a flexible tool to analyze functional gene groups based on the GO annotation databases.  ...  During the analysis of genomics data, it is often required to quantify the functional similarity of genes and their products based on the annotation information from gene ontology (GO) with hierarchical  ...  Acknowledgments The authors wish to thank Dr. Walter N. Moss (Yale University) for reading the paper and for the comments on this work.  ... 
doi:10.1155/2014/509149 pmid:25184141 pmcid:PMC4145548 fatcat:yhj4p2ut5nfo7ozk5bjb3a252m

Mouse Genome Database: From sequence to phenotypes and disease models

Janan T. Eppig, Joel E. Richardson, James A. Kadin, Cynthia L. Smith, Judith A. Blake, Carol J. Bult
2015 Genesis  
The Mouse Genome Database (MGD, www. informatics.jax.org) is the international scientific database for genetic, genomic, and biological data on the laboratory mouse to support the research requirements  ...  Among the key data sets MGD supports are: the complete catalog of mouse genes and genome features, comparative homology data for mouse and vertebrate genes, the authoritative set of Gene Ontology (GO)  ...  MGD's mouse GO annotations are contributed to the GO Consortium Gene Ontology database, resulting in their wide distribution to other resources and use in large-scale functional analyses.  ... 
doi:10.1002/dvg.22874 pmid:26150326 pmcid:PMC4545690 fatcat:fv3rrn7kk5ccliujtdbbsyzm5a

A database for orphan genes in Poaceae

Chensong Yao, Hanwei Yan, Xiaodan Zhang, Rongfu Wang
2017 Experimental and Therapeutic Medicine  
In the present study, a Poaceae orphan genes database (POGD; http://bioinfo.ahau.edu.cn/pogd) was established to serve as a user-friendly web interface for entry browsing, searching and downloading orphan  ...  Basic Local Alignment Search Tool and comparative analyses were also provided on the website.  ...  Furthermore, the database provides online tools for sequence similarity searches such as BLAST.  ... 
doi:10.3892/etm.2017.4918 pmid:28966675 pmcid:PMC5615222 fatcat:rgpsbxs26jgzlgzwyrpvrne7xm

Gene Expression Analysis to Mine Highly Relevant Gene Data in Chronic Diseases and Annotating its GO Terms

J. Bell, S. Vigila
2018 EAI Endorsed Transactions on Energy Web  
The proposed method uses term Similarity measures to compare two or more gene ontology terms.  ...  the gene ontology annotations taken from bioinformatics database.  ...  Conclusion Gene association of gene ontology terms is a challenging task in gene ontology analysis. The efficient implementation of statistical analysis tools using GO are analyzed and validated.  ... 
doi:10.4108/eai.13-7-2018.164821 fatcat:jamba3374fb4ldk2jrsgzewydq

OMIT: Dynamic, Semi-Automated Ontology Development for the microRNA Domain

Jingshan Huang, Jiangbo Dang, Glen M. Borchert, Karen Eilbeck, He Zhang, Min Xiong, Weijian Jiang, Hao Wu, Judith A. Blake, Darren A. Natale, Ming Tan, Franca Fraternali
2014 PLoS ONE  
As a special class of short non-coding RNAs, microRNAs (a.k.a. miRNAs or miRs) have been reported to perform important roles in various biological processes by regulating respective target genes.  ...  Therefore, we propose in this paper an innovative ontology development methodology.  ...  Acknowledgments The authors would like to thank Dr. Jeffrey Todd McDonald and Ms. Leyue Wang for their help in the project.  ... 
doi:10.1371/journal.pone.0100855 pmid:25025130 pmcid:PMC4099014 fatcat:hsy3rgtu7bb7vkrtu3nv6k3fee

Biomedical Informatics [chapter]

C David Page, Sriraam Natarajan
2017 Encyclopedia of Machine Learning and Data Mining  
Terminologies/ontologies The Gene Ontology Consortium created and maintains the GO, a group of three ontologies: molecular function, biological process and cellular component.  ...  Considering the large number of online scientific information searching tools and their large spectrum of type of information retrieved, do you think that any online tool needs to provide links to other  ... 
doi:10.1007/978-1-4899-7687-1_30 fatcat:45z6hsbczvaj3ajx3c3xf3bfpm

Novel semantic similarity measure improves an integrative approach to predicting gene functional associations

Fatemeh Vafaee, Daniela Rosu, Fiona Broackes-Carter, Igor Jurisica
2013 BMC Systems Biology  
We also provided extra supporting evidence for subset of the predicted functionally-associated pairs using an expert curated database of genes associated to autism spectrum disorders.  ...  GAP integrates different biological features using a novel taxonomy-based semantic similarity measure in predicting and prioritizing high-quality putative gene associations.  ...  The GO feature-set associated to each gene is retrieved by GoPubMed search engine by performing a knowledgebased semantic search to effectively identify ontology concepts in the texts of biomedical documents  ... 
doi:10.1186/1752-0509-7-22 pmid:23497449 pmcid:PMC3663825 fatcat:dheiggdiojax5b44p6rv6zqa2q

Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases

Olivier Tassy, Olivier Pourquié
2013 Nucleic Acids Research  
The function of genes is often evolutionarily conserved, and comparing the annotation of ortholog genes in different model organisms has proved to be a powerful predictive tool to identify the function  ...  Sophisticated querying tools provide unlimited ways to merge the information contained in Manteia along with the possibility of introducing custom user-designed biological questions into the system.  ...  We are grateful to Serge Uge, Guillaume Seith, Mike Newhouse and Brandon Young for the configuration and maintenance of the servers hosting the system.  ... 
doi:10.1093/nar/gkt807 pmid:24038354 pmcid:PMC3964984 fatcat:s2r7mzveivelhklbln4zy3gi2e

HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis

Wen-Ping Guo, Xiao-Bao Ding, Jie Jin, Hai-bo Zhang, Qiao-lei Yang, Peng-Cheng Chen, Heng Yao, L i Ruan, Yu-Tian Tao, Xin Chen
2021 Database: The Journal of Biological Databases and Curation  
This update of the HIR consists of 88 069 pairs of genes (23.2% functional interactions of HIR V2 are in common with the previous version of HIR), representing functional associations that are of strengths  ...  The gene set linkage analysis (GSLA) tool is developed based on the high-quality HIR V2 to identify the potential functional impacts of the observed transcriptomic changes, helping to elucidate their biological  ...  GSLA can classify an OTC as an established biological function if this OTC has strong functional associations with genes in the established biological process.  ... 
doi:10.1093/database/baab009 pmid:33677507 fatcat:2vlzsxq6fbgn7dzy7gkiwb7qk4

TargetMine, an Integrated Data Warehouse for Candidate Gene Prioritisation and Target Discovery

Yi-An Chen, Lokesh P. Tripathi, Kenji Mizuguchi, Vladimir Uversky
2011 PLoS ONE  
It enables complicated searches that are difficult to perform with existing tools and it also offers integration of custom annotations and in-house experimental data.  ...  Prioritising candidate genes for further experimental characterisation is a non-trivial challenge in drug discovery and biomedical research in general.  ...  We gather the genes mapped to the top N significant associations (where N = 1,2,3…, an adjustable value reflecting incrementally relaxed thresholds) retrieved from KEGG (A), GO Biological Process (B) and  ... 
doi:10.1371/journal.pone.0017844 pmid:21408081 pmcid:PMC3050930 fatcat:fvfqc77ymjfmlmviaqhb6wjkha

IntegromeDB: an integrated system and biological search engine

Michael Baitaluk, Sergey Kozhenkov, Yulia Dubinina, Julia Ponomarenko
2012 BMC Genomics  
With the growth of biological data in volume and heterogeneity, web search engines become key tools for researchers.  ...  data that are automatically retrieved from publicly available databases and web pages using biological ontologies.  ...  Acknowledgements This work was supported by the National Institute of Health grants R01GM084881 to MB and R01GM085325 to JP. Author details  ... 
doi:10.1186/1471-2164-13-35 pmid:22260095 pmcid:PMC3293773 fatcat:wrjk3un4urf2vd3psw4xpvozoe

GRONS: a comprehensive genetic resource of nicotine and smoking

Zhonghai Fang, Yichen Yang, Yanshi Hu, Ming D Li, Ju Wang
2017 Database: The Journal of Biological Databases and Curation  
for genes related to biological response to nicotine exposure, tobacco smoking related behaviors or diseases.  ...  genes associated with nicotine addiction.  ...  Acknowledgement We are grateful to the staff at Information Center of Tianjin Medical University for their support and help on managing the server. We also appreciate Mr. Xinhua Liu and Ms.  ... 
doi:10.1093/database/bax097 fatcat:vla7ie7jeffvnobcmvou6i6nve

Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate

S. Draghici
2003 Nucleic Acids Research  
Typically, in order to analyze a set of genes and create their functional profiles, one needs to search the literature and the various online databases.  ...  Searching various online databases is an enormous task as different databases refer to the same piece of information differently and complementary information about the same gene may be stored in many  ... 
doi:10.1093/nar/gkg624 pmid:12824416 pmcid:PMC169030 fatcat:rj4v4wtwirgslhbcprvlhkjkxi

Novelty Indicator for Enhanced Prioritization of Predicted Gene Ontology Annotations

Davide Chicco, Fernando Palluzzi, Marco Masseroli
2018 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
In this context, machine-learning algorithms able to predict and prioritize new biomolecular annotations are both effective and efficient, especially if compared with the time-consuming trials of biological  ...  We propose a novelty indicator able to state the level of "newness" (or "originality") of the annotations predicted for a specific gene to Gene Ontology terms, and to help prioritizing the most novel and  ...  the most efficient rate in correlating gene sequence similarities [32] [33] .  ... 
doi:10.1109/tcbb.2017.2695459 pmid:28436884 fatcat:l75ibw3ewzgu7buxeyauejsihy
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