1. Finding the needle in your DNAstack Ana Teresa Freitas Ciência 2010 – Encontro com a Ciência e Tecnologia em Portugal FIL, July 7, 2010
KDBIO Group

2. Finding the Needle

3. Biology 2.0
Economist, June 2010

4. The new law
Computing has increased in potency according to Moore’s law
It double in power roughly every two years
Sequencing the Human genome took 13 years and $3 billion
Now, Illumina can read the genome in 8 days and $10.000
Pacific Biosciences has a technology that in 3 years’ time will be able to map a human genome in 15 minutes for less than $1,000
Economist, June 2010

5. RefSeq GenBank UniGene Biological databases C GA ATT GA C GA C ATT GA
Curators
RefSeq
TATAGCCG
ACGTGC
TATAGCCG
AGCTCCGATA
CCGATGACAA
ATTGACTA
CGTGA
TTGACA
Labs
TTGACA
ACGTGC
TTGACA
Genome
Assembly
TATAGCCG
CGTGA
ATTGACTA
ACGTGC
TATAGCCG
CGTGA
CGTGA
TATAGCCG
ATTGACTA
ATTGACTA
ATTGACTA
ATTGACTA
TATAGCCG
TTGACA
TATAGCCG
TATAGCCG
TATAGCCG
TATAGCCG
ATT C
GenBank GA
UniGene AT C C
ATT C
Algorithms GA
ATT GA GA
ATT GA C GA
ATT GA C GA C
ATT GA

6. NIH NIG EMBL GenBank EMBL DDBJ Entrez NCBI Submissions Updates
Francis Ouellette
August 3rd, 1999
NIH
Entrez
NCBI
GenBank
Submissions
Updates
Submissions
Updates
EMBL
DDBJ
EBI
CIB
NIG
Submissions
Updates
SRS
EMBL
getentry
Lecture 2.0

7. So why do biologists care?

8. Database proliferation
Three main reasons
Database proliferation
Hundreds at the moment
More and more scientific discoveries result from inter-database analysis and mining
Rising complexity of required data-combinations
E.g. translational medicine: “from bench to bedside” (genomic data vs. clinical data)
Proliferation = great and rapid increase in numbers; Grid = a network of evenly space horizontal and vertical lines (rooster);
Semantic = related to the meaning;

10. Research at the KDBIO group
Algorithms on Strings, Trees and Graphs
Programming and Database Systems
Machine Learning
Understanding
genetic regulatory networks
Sequence analysis
Genome analysis
Whole genome sequencing and re-sequencing
Gene expression analysis
Haplotype inference
Genotype-phenotype
linkage
Discovery of motifs in DNA and RNA
Improving clinical diagnosis
Genotyping methods
Modeling of metabolic networks
Inference and modeling of regulation networks
Information systems
KDBIO Group

11. YEASTRACT www.yeastract.com

12. YEASTRACT USERS
YEASTRACT
KNOWLEDGE
not DATA

13. http://geneglob.inesc-id.pt/public/home.jsf PTDC/AGR-GPL/66564/2006
(Jorge Paiva PI, IICT)

14. SDLink
Web-based data management system
Management and analysis of heterogeneous
clinical and biological data
Linked Data
“… a recommended best practice for exposing, sharing, and connecting pieces of data, information, and knowledge on the Semantic Web using URIs and RDF."
KDBIO Group

15. Semantic model prototype
Harnessing Genetics and Imaging to Improve Diagnosis and Management of Hypertrophic Cardiomyopathy in Portugal
PTDC/SAU-GMG/112538/2009
(submitted, Alexandra Fernandes PI, CQE IST)

16. Biology 2.0 Computer Sc 2.0 Web 2.0 Medicine 2.0
DNA,

17. KDBIO Group Members 8 PhDs Ana Teresa Freitas Arlindo Oliveira
Susana Vinga
Sara Madeira
Paulo Fonseca
Sara Silva
Alexandre Francisco
Luís Russo
3 Invited researchers
João Carriço
Jonas Almeida
Marie-France Sagot
12 PhD Students
11 Graduate fellowships