K2/Kleisli and GUS: Experiments in integrated access to genomic data sources

Davidson, Susan B.; Crabtree, Jonathan; Brunk, Brian P.; Schug, Jonathan; Tannen, Val; Overton, Gail; Stoeckert, Christian J.

doi:10.1147/sj.402.0512

Cited by 160 publications

(84 citation statements)

References 53 publications

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“…These clustered sequences were further grouped with their corresponding mRNAs in GenBank to generate "assemblies," which represent consensus sequences for a given transcript within each organism. To better facilitate comparative analyses, we used a relational database called GUS (Genomics Unified Schema; Davidson et al 2001). This apicomplexan EST database comprises the separate assemblies from each species along with their annotations and information on the EST sources.…”

Section: Gene Assemblies and Generation Of A Comparative Databasementioning

confidence: 99%

“…The clusters were assembled to form consensus sequences using the CAP4 algorithm (at http://www.paracel.com/publications/ cap4_092200.pdf). The CAP4 alignments were decomposed into constituent parts and stored in the GUS relational database housed at the Center for Bioinformatics, University of Pennsylvania (Davidson et al 2001). Assemblies were reverse complemented if assembly orientation was inconsistent with mRNA orientation and EST clone end assignment.…”

Section: Clustering and Assembly Of Est/mrna Sequencesmentioning

confidence: 99%

See 1 more Smart Citation

Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database

Li¹,

Brunk²,

Kissinger³

et al. 2003

Genome Res.

133

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Large-scale EST sequencing projects for several important parasites within the phylum Apicomplexa were undertaken for the purpose of gene discovery. Included were several parasites of medical importance (Plasmodium falciparum, Toxoplasma gondii) and others of veterinary importance (Eimeria tenella, Sarcocystis neurona, and Neospora caninum). A total of 55,192 ESTs, deposited into dbEST/GenBank, were included in the analyses. The resulting sequences have been clustered into nonredundant gene assemblies and deposited into a relational database that supports a variety of sequence and text searches. This database has been used to compare the gene assemblies using BLAST similarity comparisons to the public protein databases to identify putative genes. Of these new entries, ∼15%-20% represent putative homologs with a conservative cutoff of p < 10 −9 , thus identifying many conserved genes that are likely to share common functions with other well-studied organisms. Gene assemblies were also used to identify strain polymorphisms, examine stage-specific expression, and identify gene families. An interesting class of genes that are confined to members of this phylum and not shared by plants, animals, or fungi, was identified. These genes likely mediate the novel biological features of members of the Apicomplexa and hence offer great potential for biological investigation and as possible therapeutic targets.

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Section: Gene Assemblies and Generation Of A Comparative Databasementioning

confidence: 99%

Section: Clustering and Assembly Of Est/mrna Sequencesmentioning

confidence: 99%

Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database

Li¹,

Brunk²,

Kissinger³

et al. 2003

Genome Res.

133

View full text Add to dashboard Cite

show abstract

“…Moreover, as BioGuide is architecture-independent we are studying its use in different integration systems: browsers (SRS [7]) but also mediators (K2 [3]). …”

Section: Example Of Cgh Analysismentioning

confidence: 99%

“…Life sciences are continuously evolving so that the number and size of new sources providing specialized information in biological sciences have increased exponentially in the last few years, 3 as well as the number of tools required to carry out bioinformatics tasks. Scientists are therefore frequently faced with the problem of selecting sources and tools when interpreting their data.…”

Section: Introductionmentioning

confidence: 99%

A User-Centric Framework for Accessing Biological Sources and Tools

Cohen-Boulakia

Davidson

Froidevaux

2005

Lecture Notes in Computer Science

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Biologists face two problems in interpreting their experiments: the integration of their data with information from multiple heterogeneous sources and data analysis with bioinformatics tools. It is difficult for scientists to choose between the numerous sources and tools without assistance. Following a thorough analysis of scientists' needs during the querying process, we found that biologists express preferences concerning the sources to be queried and the tools to be used. Interviews also showed that the querying process itself -the strategy followed -differs between scientists. In response to these findings, we have introduced a user-centric framework allowing to specify various querying processes. Then we have developed the BioGuide system which helps the scientists to choose suitable sources and tools, find complementary information in sources, and deal with divergent data. It is generic in that it can be adapted by each user to provide answers respecting his/her preferences, and obtained following his/her strategies. Abstract. Biologists face two problems in interpreting their experiments: the integration of their data with information from multiple heterogeneous sources and data analysis with bioinformatics tools. It is difficult for scientists to choose between the numerous sources and tools without assistance. Following a thorough analysis of scientists' needs during the querying process, we found that biologists express preferences concerning the sources to be queried and the tools to be used. Interviews also showed that the querying process itself -the strategy followed -differs between scientists. In response to these findings, we have introduced a user-centric framework allowing to specify various querying processes. Then we have developed the BioGuide system which helps the scientists to choose suitable sources and tools, find complementary information in sources, and deal with divergent data. It is generic in that it can be adapted by each user to provide answers respecting his/her preferences, and obtained following his/her strategies.

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“…• in datawarehouses, e.g., GUS [2], data are imported from various sources and stored locally in a single format. A direct limitation of datawarehouses is that, unless the local version of the sources is updated regularly in the warehouse, query results are not necessarily up-to-date.…”

Section: Introductionmentioning

confidence: 99%

Automatic Methods for Integrating Biomedical Data Sources in a Mediator-Based System

Mougin

Burgun

Bodenreider

et al. 2008

Lecture Notes in Computer Science

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Abstract. The information needed by biologists and physicians for research purposes is distributed over many heterogeneous sources. Integration systems provide a single, centralized and homogeneous interface for users to query multiple information sources simultaneously. The major limitation of integration systems, including mediator-based systems, is that the tasks involved in their creation and maintenance remain mainly manual. To address this limitation, we developed automated methods for facilitating the creation of a mediator-based system. We first implemented an automatic method for acquiring the local schemas of the sources to be integrated. We derived the global schema from the UMLS. Finally, we proposed schema-and instance-based approaches to mapping data elements from the local schemas to the global schema. To illustrate the applicability of our methods, we created a mediator-based system integrating eleven biomedical sources. This prototype is operational, available on the Internet (http://www.med.univ-rennes1.fr/cgi-bin/mougin/These/system.pl) and its evolution is managed semi-automatically.

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K2/Kleisli and GUS: Experiments in integrated access to genomic data sources

Cited by 160 publications

References 53 publications

Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database

Gene Discovery in the Apicomplexa as Revealed by EST Sequencing and Assembly of a Comparative Gene Database

A User-Centric Framework for Accessing Biological Sources and Tools

Automatic Methods for Integrating Biomedical Data Sources in a Mediator-Based System

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