EuPathDB –Eukaryotic Pathogen Database Resources
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Transcript of EuPathDB –Eukaryotic Pathogen Database Resources
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EuPathDB –Eukaryotic Pathogen Database Resources
Chris Stoeckert, Ph.D. Dept of Genetics and Penn Center for Bioinformatics,
University of Pennsylvania School of Medicine
IDO Workshop Dec. 8, 2010 BWI
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EuPathDB supports genomic research on Eukaryotic Protozoan Parasites
EuPathDB: a portal to eukaryotic pathogen databases.Aurrecoechea C, Brestelli J, Brunk BP, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer ET, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Srinivasamoorthy G, Stoeckert CJ Jr, Thibodeau R, Treatman C, Wang H.Nucleic Acids Res. 2010
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EuPathDB retreatAthens, Georgia
June 2009
EuPathDB: a portal to eukaryotic pathogen databases.Aurrecoechea C, Brestelli J, Brunk BP, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer ET, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Srinivasamoorthy G, Stoeckert CJ Jr, Thibodeau R, Treatman C, Wang H.Nucleic Acids Res. 2010
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EuPathDB metadata associated with genomic and post-genomic data is mostly free text with
some structure
• Gene annotations• User comments• Data sources• Study descriptions• Submission forms
![Page 5: EuPathDB –Eukaryotic Pathogen Database Resources](https://reader036.fdocuments.net/reader036/viewer/2022070412/56814955550346895db6a790/html5/thumbnails/5.jpg)
EuPathDB metadata associated with genomic and post-genomic data is mostly free text with
some structure
• Gene annotations• User comments• Data sources• Study descriptions• Submission forms
![Page 6: EuPathDB –Eukaryotic Pathogen Database Resources](https://reader036.fdocuments.net/reader036/viewer/2022070412/56814955550346895db6a790/html5/thumbnails/6.jpg)
EuPathDB metadata associated with genomic and post-genomic data is mostly free text with
some structure
• Gene annotations• User comments• Data sources• Study descriptions• Submission forms
![Page 7: EuPathDB –Eukaryotic Pathogen Database Resources](https://reader036.fdocuments.net/reader036/viewer/2022070412/56814955550346895db6a790/html5/thumbnails/7.jpg)
EuPathDB metadata associated with genomic and post-genomic data is mostly free text with
some structure
• Gene annotations• User comments• Data sources• Study descriptions• Submission forms
Opportunity for cross study integration and analysis if descriptions were standardized.
![Page 8: EuPathDB –Eukaryotic Pathogen Database Resources](https://reader036.fdocuments.net/reader036/viewer/2022070412/56814955550346895db6a790/html5/thumbnails/8.jpg)
EuPathDB metadata associated with genomic and post-genomic data is mostly free text with
some structure
• Gene annotations• User comments• Data sources• Study descriptions• Submission forms
Opportunity for cross study integration and analysis if descriptions were standardized.
![Page 9: EuPathDB –Eukaryotic Pathogen Database Resources](https://reader036.fdocuments.net/reader036/viewer/2022070412/56814955550346895db6a790/html5/thumbnails/9.jpg)
EuPathDB metadata associated with genomic and post-genomic data is mostly free text with
some structure
• Gene annotations• User comments• Data sources• Study descriptions• Submission forms
![Page 10: EuPathDB –Eukaryotic Pathogen Database Resources](https://reader036.fdocuments.net/reader036/viewer/2022070412/56814955550346895db6a790/html5/thumbnails/10.jpg)
Ontology-driven Isolate Submission Form
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Find T. brucei genes by phenotype based on RNAi knockdown and insufficiency studies.
TriTrypDB: a functional genomic resource for the Trypanosomatidae.Aslett M, Aurrecoechea C, Berriman M, Brestelli J, Brunk BP, Carrington M, Depledge DP, Fischer S, Gajria B, Gao X, Gardner MJ, Gingle A, Grant G, Harb OS, Heiges M, Hertz-Fowler C, Houston R, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Logan FJ, Miller JA, Mitra S, Myler PJ, Nayak V, Pennington C, Phan I, Pinney DF, Ramasamy G, Rogers MB, Roos DS, Ross C, Sivam D, Smith DF, Srinivasamoorthy G, Stoeckert CJ Jr, Subramanian S, Thibodeau R, Tivey A, Treatman C, Velarde G, Wang H.Nucleic Acids Res. 2010
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Using OBI and other OBO Foundry ontologies to capture phenotype data
Jie Zheng, Omar Harb
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EuPathDB and IDO• Using IDO (and other OBO Foundry ontologies) to capture
phenotypes– manifestations of disease
• severity • occurrences • smears of parasites• pathology
• Other use cases– host-parasite interactions
• specific host response• drug resistance and regimens • location(s) in host
– parasite biology• adhesion molecules • metabolic states• developmental stage(s)
• Synergy with other BRCs
D. Wirth