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ApiDB WorkshopIntroductionJessica Kissinger

June 26, 2006

Life Sciences Towers

A TowerB Tower

C Tower

ParkingLot

C128

B116Restroom

Logistics

• Please, always wear your name tag• There are no “stupid” questions• Please do all exercises, they are cumulative• Please attend all sessions, they are fairly

organism independent• Arrange for assistance in the evenings to get

help with your particular research needs• Read “Getting the most out of bioinformatics

resources” before class tomorrow• Building locked in evening ~7PM. Use C tower

door

InstructorsSee Course book for names and contact

informationApiDB Co-PI’sAll Database ManagersExpert usersDatabase programmersData Visualization students

Center for Tropical and Emerging Global Diseases(CTEGD) at UGA

17 interdisciplinary faculty and their laboratories Cross-college and Institute (4), cross-department (7) Center, under the

Office of the Vice President for Research (OVPR) To pursue cutting edge research on tropical and emerging global

diseases, and train students in this field

CTEGD’s Goals• Become a preeminent center for research and education in parasitic

and other diseases in the world (our peers say we are getting close)• Translate research results into medical and public health interventions

for people at risk of these diseases (this is a long-range goal)• Promote global and biomedical research and educational programs at

the University of Georgia (we are working with others to accomplish this)

Training is a large part of CTEGD’s missionWe all teach and train undergraduates, graduate students and postdocs

CTEGD has been awarded 4 Training Grants to fund students (3 NIH, 1 Fdn)

www.ctegd.uga.edu

Faculty College/School Department______________Diseases Studied_____________

Don Champagne Agri.& Environ. Sci. Entomology Malaria; Chagas’ diseaseMike Strand Agri. & Environ. Sci Entomology Parasitoid wasps; Innate immunityDan Colley Arts and Sciences Microbiology Schistosomiasis (human &mouse)Jessie Kissinger Arts and Sciences Genetics Apicomplexa; Malaria; Crypto; Chagas’Roberto Docampo Arts and Sciences Cellular Biology Malaria; Leishmanisis; Chagas’diseaseSilvia Moreno Arts and Sciences Cellular Biology Toxoplasmosis; LeishmaniasisKojo Mensa-Wilmot Arts and Sciences Cellular Biol. African trypanosomes; LeishmaniasisBoris Striepen Arts and Sciences Cellular Biol. Toxoplasmosis; CryptosporidiosisRick Tarleton Arts and Sciences Cellular Biol. Chagas’ disease (human & mouse)Harry Dickerson Veterinary Medicine Infectious Dis. Ichthyophthirius multifilis (Ich) of fishJulie Moore Veterinary Medicine Infectious Dis. Malaria (human & mouse)David Peterson Veterinary Medicine Infectious Dis. MalariaPejman Rohani Institute of Ecology Ecology Infectious disease transmission

Adjunct/Associate FacultyYnes Ortega (Griffin) Agri & Environ. Sci. Food Sci. & Tech. Cyclosporiasis; CryptosporidiosisPat Lammie (CDC) Arts and Sciences Cellular Biol. Lymphatic filariasisVictor Tsang (CDC) Arts and Sciences Cellular Biol. Cysticercosis; SchistosomiasisMark Brown Agri. & Environ. Sci. Entomology Malaria; Vector biology

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Training is a large part of CTEGD’s mission We all teach and train undergraduates, graduate students and post-doctoral

fellows[so far,1 MCG MD/PhD candidate is training within the CTEGD]

CTEGD has an NIAID/NIH T32 institutional training grant to support graduatestudents & post-docs here at UGA

CTEGD has an Ellison Medical Foundation international exchange traininggrant to send and bring undergraduates, graduate students and post-docsto and from UGA

CTEGD has 2 FIC/NIH D43 institutional training grants: 1 with Brazil (bioinformatics), 1 with Kenya (Kenyan graduate students & post-docs in Kenya and at UGA)

Countries in which CTEGD faculty:Have ongoing programsKenya, Argentina, Brazil, Peru, Haiti, Guyana

Have active contactsGhana, Guatemala, Mali, Japan, Egypt

Introduction

• Data integration and databases• NIH Bioinformatic Resource Centers (BRC’s)• Databases and Queries• Some History of the Apicompelxan databases• Federation• Our software• Workshop specifics

Issues facing our community

• Data preservation• Data curation• Data access• Data integration

Bacterial Viral Parasitic

Genetics

Immunology

Proteomic

Microarray

Genomics

Host

Experimental systems

Pathogen Vector

Host

Infectious Disease Paradigm

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RADESTclusteringand assembly

DoTS

Genomic alignmentand comparativeSequence analysis

Identify coordinateregulation

Linking Biological and ComputationalData to solve real problems

GUS

The daily routine

Genes Proteins Micro-array

BUILD YOUR QUERY, FIND A TESTABLE RESULT!

GO PATH

ArrayGene + Array Array + PATH

Data

The benefits of data integration

• Queries spanning data types become possible• Systems approaches become become tractable

for the average researcher• Re-analyses become possible• Patterns and trends become discoverable

– Commonalities in pathogen strategies?– Host response?

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BRC’s

• http://www.niaid.nih.gov/dmid/genomes/brc/default.htm

• www.niaid.nih.gov/dmid/genomes/brc/awards.htm

• http://www.brc-central.org

NIAID Bioinformatics Resource Centers forBiodefense and Emerging or Re-Emerging

Infectious Diseases• Owen White:TIGR• David Roos: UPenn• Frank Collins: UND• Rick Stevens: U of C• Elliot Lefkowitz: UAB• Richard Scheuermann, UTSMC• Bruno Sobral:VBI• John Greene:SRA

www.niaid.nih.gov/dmid/genomes/brc/default.htm

Category A• Bacillus anthracis, Clostridium

botulinum, Francisella tularensis• Variola major virus, Arenavirus, Hanta

virus, Rift Valley fever virus, Ebolavirus, Marburg virus, Dengue virus

• Yersinia pestis

Category B

• Burkholderia mallei, B. pseudomallei, Clostridium perfringens• Toxoplasma gondii, Cryptosporidium parvum• Staphylococcus aureus, pathogenic vibrios, Listeria monocytogenes,

Campylobacter jejuni• California encephalitis group virus, Kyasanar forest disease virus,

Omsk hemorrhagic fever virus, West Nile virus, Alphavirus• Giardia lamblia, Entamoeba histolytica, Microsporidia, Ricinus

communis• Diarrhaegenic E. coli, Yersinia enterocolitica, Shigella, Salmonella• Rickettsiae species, Brucella species, Coxiella burnetii, Calicivirus,

Hepatitis A virus

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Category C• Plasmodium species• Anopheles gambiae, Aedes Aegypti, An. Funestus, Culex pipiens,

Ixodes scapularis• Streptococcus pyogenes, Streptococcus pneumoniae• Hantaan virus, Puumala virus, Crimean-Congo hemorrhagic fever virus,

Yellow fever virus, Tick-borne encephalitis, Nipah virus, Equinemorbillivirus

• Multi-drug resistant Mycobacterium tuberclosis, Influenza virus• Rabies virus, Coronavirus

ApiDB overview

• ApiDB (Apicomplexan Databases) is an NIHBRC

• It is an umbrella database that talks to thethree component database, CryptoDB,PlasmoDB and ToxoDB

• ApiDB has tools and queries to supportunified apicomplexan studies of sequence,orthologous genes and biochemical pathways

What is a database?

• In its simplest form, it is a collection ofdata

• Computational databases can be– “flat file”– Relational– Object oriented

Lots of “flat” Data Files

General searches vs a Query

• General searches of flat files, like “find” inWord or web page content searches at yahooor Google look for the appearance of wordwithin some text and in the case of websearches, return the entire page containingthe found item

• Queries are structured searches of storedterms or features contained in a structureddatabase, usually relational. What is returned,depends on what is asked.

Relational Schema

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What is a Tool?

• Tools operate outside of the relationalframework. They usually function on flatfiles. Examples are BLAST, pubcrawler,custom motif tool, PlasmoAP, CYCpathway tools

• Sometimes the results from tools canbe stored in a relations data base forlater searches

What are external resources?

• Resources outside the ApiDB family ofdatabases

• Examples include, NCBI Genbank,KEGG metabolic database, OrthoMCL-DB, web site of data donors, WHO website etc.

A Little History

• PlasmoDB• ToxoDB• CryptoDB• ApiDB

PlasmoDB was born in June 2000

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ApiDB.org

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Our Software Tools

• GUS schema– http://gusdb.org

• WDK (Web Development Kit)– http://gusdb.org/wdk

• The Databases:– http://PlasmoDB.org– http://ToxoDB.org– http://CryptoDB.org– http://orthomcl.cbil.upenn.edu/cgi-

bin/OrthoMclWeb.cgi

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We need your help

• How do you, the user, logical sort dataand expect to find it in the databases?

• Intro and exit surveys• Query sorting exercise• Interactive studies of computer usage• Interviews• Suggestions and feed back

Course Exercises• Course computers -

– use the same computer for the entire workshop– Login = apicomplex (click on name)– Password = daydabaz23– Open a browser (Safari, Firefox)

• Printing - select print from your browser orapplication. The lab laser printer is pre-configured. We have supplied the printer with3-hole punch paper so you can keep resultsin your binder if you choose to do so

Course Web Site

– http://apidb.org/static/workshop2006/schedule.php• The web site (exercises and and answers)

will remain posted to facilitate your transfer ofinformation. It is not necessary to printeverything.

Acknowledgements

• Funders– NIH - ApiDB Contract

HHSN26600400037C– Burroughs Wellcome Fund

• ApiDB Team– ToxoDB and PlasmoDB Team at UPENN– CryptoDB and ApiDB Team at UGA