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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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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
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