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The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge.

Hernandez-Boussard T, Whirl-Carrillo M, Hebert JM, Gong L, Owen R, Gong M, Gor W, Liu F, Truong C, Whaley R, Woon M, Zhou T, Altman RB, Klein TE - Nucleic Acids Res. (2007)

Bottom Line: PharmGKB's website is designed to effectively disseminate knowledge to meet the needs of our users.These changes allow us to capture more structured information on phenotypes for better cataloging and comparison of data.PharmGKB is available at www.pharmgkb.org.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.

ABSTRACT
PharmGKB is a knowledge base that captures the relationships between drugs, diseases/phenotypes and genes involved in pharmacokinetics (PK) and pharmacodynamics (PD). This information includes literature annotations, primary data sets, PK and PD pathways, and expert-generated summaries of PK/PD relationships between drugs, diseases/phenotypes and genes. PharmGKB's website is designed to effectively disseminate knowledge to meet the needs of our users. PharmGKB currently has literature annotations documenting the relationship of over 500 drugs, 450 diseases and 600 variant genes. In order to meet the needs of whole genome studies, PharmGKB has added new functionalities, including browsing the variant display by chromosome and cytogenetic locations, allowing the user to view variants not located within a gene. We have developed new infrastructure for handling whole genome data, including increased methods for quality control and tools for comparison across other data sources, such as dbSNP, JSNP and HapMap data. PharmGKB has also added functionality to accept, store, display and query high throughput SNP array data. These changes allow us to capture more structured information on phenotypes for better cataloging and comparison of data. PharmGKB is available at www.pharmgkb.org.

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PharmGKB phenotype data set. PharmGKB displays phenotype data. In the figure, there are five tabs: (i) Overview presents key indexing terms and a summary of the file, (ii) Publications points to key publication summaries, (iii) Column Headers defines the data present in the file and (iv) Individualized Data provides a data browser to look at the primary data. (v) External Data Links point to external data sources relevant to the data set, such as exon arrays stored in other databases.
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Figure 5: PharmGKB phenotype data set. PharmGKB displays phenotype data. In the figure, there are five tabs: (i) Overview presents key indexing terms and a summary of the file, (ii) Publications points to key publication summaries, (iii) Column Headers defines the data present in the file and (iv) Individualized Data provides a data browser to look at the primary data. (v) External Data Links point to external data sources relevant to the data set, such as exon arrays stored in other databases.

Mentions: The phenotype data set knowledge is available to the general public via an integrated tab-display (Figure 5). For all data sets in PharmGKB, genes, drugs, diseases and categories of pharmacogenetic evidence are tagged and indexed for querying. Curated phenotype data sets are reviewed and include meaningful phenotypic annotations related to pharmacogenomic research, from clinical-metabolite data to protein constructs. Genotype and/or phenotype data can be downloaded by clicking on arrows in the upper right corner of the webpage.Figure 5.


The pharmacogenetics and pharmacogenomics knowledge base: accentuating the knowledge.

Hernandez-Boussard T, Whirl-Carrillo M, Hebert JM, Gong L, Owen R, Gong M, Gor W, Liu F, Truong C, Whaley R, Woon M, Zhou T, Altman RB, Klein TE - Nucleic Acids Res. (2007)

PharmGKB phenotype data set. PharmGKB displays phenotype data. In the figure, there are five tabs: (i) Overview presents key indexing terms and a summary of the file, (ii) Publications points to key publication summaries, (iii) Column Headers defines the data present in the file and (iv) Individualized Data provides a data browser to look at the primary data. (v) External Data Links point to external data sources relevant to the data set, such as exon arrays stored in other databases.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238877&req=5

Figure 5: PharmGKB phenotype data set. PharmGKB displays phenotype data. In the figure, there are five tabs: (i) Overview presents key indexing terms and a summary of the file, (ii) Publications points to key publication summaries, (iii) Column Headers defines the data present in the file and (iv) Individualized Data provides a data browser to look at the primary data. (v) External Data Links point to external data sources relevant to the data set, such as exon arrays stored in other databases.
Mentions: The phenotype data set knowledge is available to the general public via an integrated tab-display (Figure 5). For all data sets in PharmGKB, genes, drugs, diseases and categories of pharmacogenetic evidence are tagged and indexed for querying. Curated phenotype data sets are reviewed and include meaningful phenotypic annotations related to pharmacogenomic research, from clinical-metabolite data to protein constructs. Genotype and/or phenotype data can be downloaded by clicking on arrows in the upper right corner of the webpage.Figure 5.

Bottom Line: PharmGKB's website is designed to effectively disseminate knowledge to meet the needs of our users.These changes allow us to capture more structured information on phenotypes for better cataloging and comparison of data.PharmGKB is available at www.pharmgkb.org.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.

ABSTRACT
PharmGKB is a knowledge base that captures the relationships between drugs, diseases/phenotypes and genes involved in pharmacokinetics (PK) and pharmacodynamics (PD). This information includes literature annotations, primary data sets, PK and PD pathways, and expert-generated summaries of PK/PD relationships between drugs, diseases/phenotypes and genes. PharmGKB's website is designed to effectively disseminate knowledge to meet the needs of our users. PharmGKB currently has literature annotations documenting the relationship of over 500 drugs, 450 diseases and 600 variant genes. In order to meet the needs of whole genome studies, PharmGKB has added new functionalities, including browsing the variant display by chromosome and cytogenetic locations, allowing the user to view variants not located within a gene. We have developed new infrastructure for handling whole genome data, including increased methods for quality control and tools for comparison across other data sources, such as dbSNP, JSNP and HapMap data. PharmGKB has also added functionality to accept, store, display and query high throughput SNP array data. These changes allow us to capture more structured information on phenotypes for better cataloging and comparison of data. PharmGKB is available at www.pharmgkb.org.

Show MeSH