ABSTRACT
The Mouse Genome Database (MGD) forms the core of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a model organism database resource for the laboratory mouse. MGD provides essential integration of experimental knowledge for the mouse system with information annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genotype (sequence) through phenotype information, including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships among genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent improvements in MGD discussed here include the enhancement of phenotype resources, the re-development of the International Mouse Strain Resource, IMSR, the update of mammalian orthology datasets and the electronic publication of classic books in mouse genetics.
Subject(s)
Databases, Genetic , Genomics , Mice/genetics , Animals , Genes , Genome , Genotype , Internet , Mice, Mutant Strains , Phenotype , Systems Integration , User-Computer InterfaceABSTRACT
The Mouse Genome Database (MGD) is one component of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a community database resource for the laboratory mouse. MGD strives to provide a comprehensive knowledgebase about the mouse with experiments and data annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genetic, genotype (sequence) and phenotype information including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships between genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent developments in MGD discussed here include an extensive integration of the mouse sequence data and substantial revisions in the presentation, query and visualization of sequence data.
Subject(s)
Computational Biology , Databases, Genetic , Genome , Mice/genetics , Animals , Genomics , Information Storage and Retrieval , Internet , Molecular Biology , Phenotype , Terminology as TopicABSTRACT
Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.
Subject(s)
DNA, Complementary/genetics , Genomics , Mice/genetics , Transcription, Genetic/genetics , Alternative Splicing/genetics , Amino Acid Motifs , Animals , Chromosomes, Mammalian/genetics , Cloning, Molecular , Databases, Genetic , Expressed Sequence Tags , Genes/genetics , Genomics/methods , Humans , Membrane Proteins/genetics , Physical Chromosome Mapping , Protein Structure, Tertiary , Proteome/chemistry , Proteome/genetics , RNA, Antisense/genetics , RNA, Messenger/analysis , RNA, Messenger/genetics , RNA, Untranslated/analysis , RNA, Untranslated/genetics , Transcription Initiation SiteABSTRACT
Recently, Indonesia has experienced six major provincial, civil, armed conflicts. Underlying causes include the transmigration policy, sectarian disputes, the Asian economic crisis, fall of authoritarian rule, and a backlash against civil and military abuses. The public health impact involves the displacement nationwide of > 1.2 million persons. Violence in the Malukus, Timor, and Kalimantan has sparked the greatest population movements such that five provinces in Indonesia each now harbor > 100,000 internally displaced persons. With a background of government instability, hyperinflation, macroeconomic collapse, and elusive political solutions, these civil armed conflicts are ripe for persistence as complex emergencies. Indonesia has made substantial progress in domestic disaster management with the establishment of central administrative authority, strategic planning, and training programs. Nevertheless, the Indonesian experience reveals recurrent issues in international humanitarian health assistance. Clinical care remains complicated by absences of treatment protocols, inappropriate drug use, high procedural complication rates, and variable referral practices. Epidemiological surveillance remains complicated by unsettled clinical case definitions, non-standardized case management of diseases with epidemic potential, variable outbreak management protocols, and inadequate epidemiological analytic capacity. International donor support has been semi-selective, insufficient, and late. The militia murders of three UN staff in West Timor prompted the withdrawal of UN international staff from West Timor for nearly a year to date. Re-establishing rules of engagement for humanitarian health workers must address security, public health, and clinical threats.
