pathema burkholderia annotation jamboree: introduction to annotation jamboree

PATHEMA-BurkholderiaA CLADE SPECIFIC

BIOINFORMATICS RESOURCECENTER

http://pathema.jcvi.org

What is Pathema?

Pathema (http://pathema.jcvi.org)

A NIAID Bioinformatics Resource Center designed tosupport bio-defense and infectious disease research.

Pathema provides detailed curation of six target pathogens:

Category A priority pathogens:Bacillus anthracis, Clostridium botulinum

Category B priority pathogens:Burkholderia mallei, Burkholderia pseudomallei,Clostridium perfringens, Entamoeba histolytica

What is Pathema?

• An extensive library of literature and manually curated data

• A customized suite of sophisticated bioinformatics software

• Comparative analysis tools customized to retrieve, display,and compute results relevant to ongoing bio-defenseresearch

Overarching Goal: to provide core resources that willaccelerate scientific progress on understanding, detecting,diagnosing and treating Category A-C pathogens and otherpathogens involved in new and re-emerging infectiousdiseases.

All Bacillus (24)

B. anthracis (17)B. cereus (3)B. thuringiensis (2)B. subtilisB. pumilus

All Clostridium (25)

C. perfringens (9)

C. botulinum (9)C. difficileC. thermocellumC. acetobutylicumC. tetaniC. butyricumC. novyiC. phytofermentans

All Burkholderia (28)

B. mallei (11)B. pseudomallei (10)B. thailandensisB. cenocepaciaB. sp.B. phages (4)P. aeruginosaR. solanacearum

All Entamoeba (3)

E. histolyticaE. disparE. invadens

What is the future of Pathema?

We are relying on your feedback! Data exchange & integration Genome sequence analysis Custom data analysis Custom tool development

New Genome Sequences & Annotation Data

Clade-specific Pathema Workshops

! Clade-specific Annotation Jamborees ! Incorporate expert annotation & experimental references

AcknowledgementsP.I.: Granger SuttonFunding: NIAIDSubcontract: University of Maryland Baltimore, IGS

Informatics Engineers Informatics AnalystsTanja Davidsen (manager) Scott Durkin (manager)Erin Beck Ramana MadupuAlex Richter Susmita ShrivastavaKevin Galinsky Bob DodsonJay Sundarm Derek HarkinsSeth Schobel Lis Caler

Owen White (University of Maryland Baltimore)Anu Ganapathy YongMei ZhaoJosh Orvis Aaron GussmanKevin Galens Jonathon Crabtree

Jamboree OverviewDay 1: Prokaryotic Annotation Methodologies

• Gene Model & Functional Curation Introduction to ManateeDay 2:

Participant Presentations Burkholderia Training Exercises Burkholderia AnnotationDay 3: Burkholderia Annotation

Introductions Bioinformatics Project Manager

Lauren Brinkac lbrinkac@jcvi.org

Burkholderia InvestigatorBill Nierman wnierman@jcvi.org

Bioinformatics AnalystRamana Madupu rmadupu@jcvi.org

Bioinformatics AnalystDerek Harkins dharkins@jcvi.org

Pathema-Burkholderia burkholderia@jcvi.org