Limits...
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.

Show MeSH
PharmGKB Irinotecan Pathway. View of a model human liver cell showing blood, bile, and intestinal compartments, indicating tissue-specific involvement of genes in the irinotecan pathway. Drugs are depicted by purple boxes, transporter genes by turquoise ovals and genes coding for metabolic enzymes by blue ovals. Available at: http://www.pharmgkb.org/search/pathway/irinotecan/liver.jsp.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2238877&req=5

Figure 4: PharmGKB Irinotecan Pathway. View of a model human liver cell showing blood, bile, and intestinal compartments, indicating tissue-specific involvement of genes in the irinotecan pathway. Drugs are depicted by purple boxes, transporter genes by turquoise ovals and genes coding for metabolic enzymes by blue ovals. Available at: http://www.pharmgkb.org/search/pathway/irinotecan/liver.jsp.

Mentions: Historically, many pharmacogenetic studies have focused on single genes involved in drug side-effects. There is now a growing interest in how pathways of interacting genes can affect both drug metabolism and drug response. PharmGKB pathways are drug-centered, depicting candidate genes for pharmacogenetics and pharmacogenomics studies and they provide the means to connect separate data sets to represent the current knowledge as a cohesive snapshot. Pathways are created based on community interest and involvement/contributions. The diagrams have information content in the shape and color of the icons that represent whether the component is a gene, drug, metabolic intermediate, etc. (Figure 4). The pathways are interactive: clicking on a gene takes the user to the gene page from which available genotype and phenotype data and literature citations can be found. Drugs and metabolites are represented by rectangles. Clicking on a drug takes the user to the drug page from which available phenotype data and literature citations can be found. Clicking on a golden arrow presents the user with phenotype data that support a relationship. In addition to the pathway diagram, a summary is provided to describe the content of the graphic. The pathways are generated by collaboration of investigators and represent a consensus of the opinions of the authors. Currently, these pathways are constructed by hand as graphic images and updated by the scientific community every 2 years. Dates of pathway release and updates are posted on the pathway pages.Figure 4.


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 Irinotecan Pathway. View of a model human liver cell showing blood, bile, and intestinal compartments, indicating tissue-specific involvement of genes in the irinotecan pathway. Drugs are depicted by purple boxes, transporter genes by turquoise ovals and genes coding for metabolic enzymes by blue ovals. Available at: http://www.pharmgkb.org/search/pathway/irinotecan/liver.jsp.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 4: PharmGKB Irinotecan Pathway. View of a model human liver cell showing blood, bile, and intestinal compartments, indicating tissue-specific involvement of genes in the irinotecan pathway. Drugs are depicted by purple boxes, transporter genes by turquoise ovals and genes coding for metabolic enzymes by blue ovals. Available at: http://www.pharmgkb.org/search/pathway/irinotecan/liver.jsp.
Mentions: Historically, many pharmacogenetic studies have focused on single genes involved in drug side-effects. There is now a growing interest in how pathways of interacting genes can affect both drug metabolism and drug response. PharmGKB pathways are drug-centered, depicting candidate genes for pharmacogenetics and pharmacogenomics studies and they provide the means to connect separate data sets to represent the current knowledge as a cohesive snapshot. Pathways are created based on community interest and involvement/contributions. The diagrams have information content in the shape and color of the icons that represent whether the component is a gene, drug, metabolic intermediate, etc. (Figure 4). The pathways are interactive: clicking on a gene takes the user to the gene page from which available genotype and phenotype data and literature citations can be found. Drugs and metabolites are represented by rectangles. Clicking on a drug takes the user to the drug page from which available phenotype data and literature citations can be found. Clicking on a golden arrow presents the user with phenotype data that support a relationship. In addition to the pathway diagram, a summary is provided to describe the content of the graphic. The pathways are generated by collaboration of investigators and represent a consensus of the opinions of the authors. Currently, these pathways are constructed by hand as graphic images and updated by the scientific community every 2 years. Dates of pathway release and updates are posted on the pathway pages.Figure 4.

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