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

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

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

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

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

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

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.

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.

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

Ontology-driven Isolate Submission Form

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

Using OBI and other OBO Foundry ontologies to capture phenotype data

Jie Zheng, Omar Harb

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