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Integr8 and Genome Reviews: integrated views of complete genomes and proteomes

P. Kersey
2004 Nucleic Acids Research  
For over 190 species, Integr8 provides access to general information, recent publications, and a detailed statistical overview of the genome and proteome of the organism.  ...  Integr8 is a new web portal for exploring the biology of organisms with completely deciphered genomes.  ...  the Genome Reviews files, enabling the provision of a consistent view of the genome and proteome of each organism.  ... 
doi:10.1093/nar/gki039 pmid:15608201 pmcid:PMC539993 fatcat:ekaypo4iz5bnxm4sjhc2u2hfs4

Integrating Genomic and Proteomic Data: The Integr8 Project

Manuela Pruess, Paul Kersey, Rolf Apweiler
2004 Journal of Integrative Bioinformatics  
Thus, a framework exists that allows for new kinds of data to be integrated, and an entity-centric view of complete genomes and proteomes is offered.  ...  SummaryIntegr8 ( has been developed to provide an integration layer for the exploitation of genomic and proteomic data.  ...  the Genome Reviews files, enabling the provision of a consistent view of the genome and proteome of each organism.  ... 
doi:10.1515/jib-2004-9 fatcat:7m7r4o7yj5h4hki3ep2a3yowzy

The European Bioinformatics Institute's data resources: towards systems biology

C. Brooksbank
2004 Nucleic Acids Research  
Genomic and post-genomic biological research has provided fine-grain insights into the molecular processes of life, but also threatens to drown biomedical researchers in data.  ...  The European Bioinformatics Institute's (EBI's) databases and tools have evolved to meet the changing needs of molecular biologists: since we last wrote about our services in the 2003 issue of Nucleic  ...  The data in Genome Reviews have been incorporated into Integr8 ( (6), a new portal for completely sequenced genomes and their predicted proteomes that utilizes cross-links between  ... 
doi:10.1093/nar/gki026 pmid:15608238 pmcid:PMC539980 fatcat:ccwgkwuws5fsjaz7zp7i5jfjzy

TEMBLOR – Perspectives of EBI Database Services

Henning Hermjakob, Rolf Apweiler
2002 Comparative and Functional Genomics  
The Integr8 component will enable text-, structure-and sequence-based searches against a gene-centric view of all completed genomes.  ...  The TEMBLOR project will provide a highly integrated view of genomic and proteomic data (Integr8) by drawing on databases maintained at major bioinformatics centres in Europe (Table 1) .  ... 
doi:10.1002/cfg.133 pmid:18628871 pmcid:PMC2447230 fatcat:mm66zbhv4rcy5lfi6722twzf54

The use of multiple hierarchically independent gene ontology terms in gene function prediction and genome annotation

Yiannis A I Kourmpetis, Ate van der Burgt, Marco C A M Bink, Cajo J F Ter Braak, Roeland C H J van Ham
2007 In Silico Biology  
By consequence, probabilistic methods that aim to predict gene function automatically through integration of diverse genomic datasets, and that employ the GO, must be able to predict such multiple terms  ...  In this study we quantify the usage of multiple and hierarchically independent GO terms in the curated genome annotations of seven well-studied species.  ...  The use of multiple hierarchically independent Gene Ontology terms in gene function prediction and genome annotation References  ... 
pmid:18467770 fatcat:n3akgt72gnedhesigzti5zxfia

The human phylome

Jaime Huerta-Cepas, Hernán Dopazo, Joaquín Dopazo, Toni Gabaldón
2007 Genome Biology  
A phylome, the complete collection of all gene phylogenies in a genome, constitutes a valuable source of information, but its use in large genomes still constitutes a technical challenge.  ...  We find support for at least one, and probably two, rounds of whole genome duplications before vertebrate radiation.  ...  Part of this study is funded by grants from the Spanish Science Ministry BFU2006-15413-C02-02 and Generalitat Valenciana GV06/080 and the National Institute of Bioinformatics a platform of Genoma España  ... 
doi:10.1186/gb-2007-8-6-r109 pmid:17567924 pmcid:PMC2394744 fatcat:b3btzemx3ncyhkkunyucv2jkeu

Conference Report: The ESF Programme on Integrated Approaches for Functional Genomics. Workshop on 'Data Integration in Functional Genomics and Proteomics'

Pierre-Alain Binz, Annette Martin, Mike Taussig, Antoine de Daruvar
2002 Comparative and Functional Genomics  
We are also grateful to the Medical Faculty of the Geneva University, which provided the conference rooms and infrastructure.  ...  The organisers would like to thank the ESF for financing the workshop and Geneva Bioinformatics, GeneProt and LION bioscience for generous sponsorship.  ...  It will provide a highly integrated view of genomic and proteomic data (Integr8) by drawing on databases maintained at major bioinformatics centres in Europe, and by creating new and important resources  ... 
doi:10.1002/cfg.134 pmid:18628884 pmcid:PMC2447244 fatcat:4cv3i55wozfibb6htdzebfpxma

Page 38 of Genetics Vol. 179, Issue 1 [page]

2008 Genetics  
PETRYSZAK et al., 2005 Integr8 and Genome Reviews: integrated views of com- plete genomes and proteomes. Nucleic Acids Res. 33: D297- D302. KUMAR, S., K. TAMURA and M.  ...  SEOIGHE, C., and C. GEHRING, 2004 Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome. Trends Genet. 20: 461-464 SHAKED, H., N. Avivi-RAGoLsky and A. A.  ... 

Databases and software for the comparison of prokaryotic genomes

D. Field
2005 Microbiology  
The explosion in the number of complete genomes over the past decade has spawned a new and exciting discipline, that of comparative genomics.  ...  This article reviews progress towards the development of computational tools and databases for organizing and extracting biological meaning from the comparison of large collections of genomes.  ...  /GMINE/ Integr8 Access to species descriptions, literature, statistical analysis and summary information about proteomes NCBI Genome Projects Organism-specific overviews that function  ... 
doi:10.1099/mic.0.28006-0 pmid:16000703 fatcat:p5bgkzdv2zfaleuywsrftkgrry

Annotation, comparison and databases for hundreds of bacterial genomes

Claudine Médigue, Ivan Moszer
2007 Research in Microbiology  
This paper reviews advances in the development of bacterial annotation and comparative analysis tools, and progress in the design of novel database structures for the integration of heterogeneous biological  ...  and loops in closely related bacterial genomes ACT Comparative genome analysis and visualization tools for multiple genome alignments CGAT Research in Microbiology  ...  ) Integrated views of complete genomes and proteomes RefSeq Curated non-redundant sequence database of genomes, transcripts  ... 
doi:10.1016/j.resmic.2007.09.009 pmid:18031997 fatcat:bfw4zslyw5bgrdtrxhozk2uc7e

The European Bioinformatics Institute's data resources

Catherine Brooksbank, Graham Cameron, Janet Thornton
2009 Nucleic Acids Research  
The European Bioinformatics Institute (EMBL-EBI) is unique in Europe and is one of only two organisations worldwide providing access to a comprehensive, integrated set of these collections.  ...  Here, we describe how the EMBL-EBI's biomolecular databases are evolving to cope with increasing levels of submission, a growing and diversifying user base, and the demand for new types of data.  ...  of thousands of scientists who have submitted data and annotation to the shared data collections.  ... 
doi:10.1093/nar/gkp986 pmid:19934258 pmcid:PMC2808956 fatcat:lha7vmv3fnhipb7kunhmvunveu

The UniProt-GO Annotation database in 2011

E. C. Dimmer, R. P. Huntley, Y. Alam-Faruque, T. Sawford, C. O'Donovan, M. J. Martin, B. Bely, P. Browne, W. Mun Chan, R. Eberhardt, M. Gardner, K. Laiho (+43 others)
2011 Nucleic Acids Research  
UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views.  ...  Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model  ...  ACKNOWLEDGEMENTS The UniProt Consortium would like to thank all collaborating annotation groups that have enabled inclusion of their annotation data in the UniProt-GOA annotation view.  ... 
doi:10.1093/nar/gkr1048 pmid:22123736 pmcid:PMC3245010 fatcat:gdeuk363knfv5ozq2q7tn254aa

Biological Data Resources at the EMBL-EBI

Rodrigo Lopez
2008 Revista Colombiana de Biotecnología  
The aims of this note are to introduce the reader to these resources and briefly outline training and education activities which may be of interest to students as well as academic staff in general.  ...  The EBI has been maintaining core data resources in molecular biology for 15 years and is notionally custodian to the largest collection of databases and services in Life Sciences in Europe.  ...  This one provides easy access to integrated information about deciphered genomes and their corresponding proteomes.  ... 
doaj:1181789ff05043988701f7c984425c83 fatcat:aoqiuavzcreutlry6vbuzaoxhm

Strepto-DB, a database for comparative genomics of group A (GAS) and B (GBS) streptococci, implemented with the novel database platform 'Open Genome Resource' (OGeR)

Johannes Klein, Richard Münch, Ilona Biegler, Isam Haddad, Ida Retter, Dieter Jahn
2008 Nucleic Acids Research  
Strepto-DB identifies the homologous proteins deduced from the genomes of interest. It allows for the elucidation of the GAS and GBS core-and pan-genomes via genome-wide comparisons.  ...  The system automatically creates the dedicated relational database and web interface and imports an arbitrary number of genomes derived from standardized genome files.  ...  ACKNOWLEDGEMENTS We would like to thank Bernd Hoppe for excellent technical assistance and financial management.  ... 
doi:10.1093/nar/gkn674 pmid:18854354 pmcid:PMC2686516 fatcat:ifc7t5r3mbe5bcrgurzfzxyxfu

EpoDB: An erythropoiesis gene expression database in progress [chapter]

Fidel Salas, Juergen Haas, Christian J. Stoeckert, G. Christian Overton
1996 Lecture Notes in Computer Science  
on amino acids (from Berlin Free Univ.)  Delta Mass -Db of mass of Post Proteome analysis are facilitated by projects such as the freely available EU funded Integr8 (  ...  Archaea  List of complete archaeal proteomes in Swiss-Prot (HAMAP)  A.pernix -Aeropyrum pernix K1 genome db  AfDB -Archaeoglobus fulgidus genome db at TIGR  Halobacterium NRC-1 -Halobacterium strain  ... 
doi:10.1007/bfb0033203 fatcat:ltcxl5dva5ecxik7tati4wy6bm
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