Download hinv1

Two (Extreme) Stereotypes
Gene-originated research
Disease-originated research
"I don't care other genes (pathways).
Any disease welcome, as long as
relevant to my gene (pathway)."
"I don't care other diseases.
Any gene welcome, as long as
relevant to my disease."
Genespecific
DB
 Many reasons to integrate!
Diseasespecific
DB
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
Often off-line
Individual pts' raw data
Diversity of data
Difficult to digitize
Difficult to standardize
Inter-diseae merger makes little sense/
incentive
Needs: H-inv/ Dis Ed as an Initial Omnibus Port to Dis Info
Starting from a gene/ pathway…
Off-line
Diseasespecific
DB
Diseasespecific
DB
Diseasespecific
DB
Hinv
Multidisease
port
Diseasespecific
DB
Diseasespecific
DB
① Text mining with curation
② Summary exp data
(e.g. pooled samples?)
③ Link to dis-specific DB
Diseasespecific
DB
Diseasespecific
DB
Needs: H-inv/ Dis Ed as an Additional Annotation Base
Starting from each disease…
① Interpretation of identified
candidate genes/ loci
Diseasespecific
DB
② G-G interaction
③ Selection of candidate
genes/ markers
④ Acquisition of physical
clones for functional
assays
① (Unexpected)
relationship with other
phenotypes suggesting
(i) shared pathways
and/or (ii) shared lifestyle/ env factors
② Selection of candidate
genes/ markers
Diseasespecific
DB
Multidisease
port
Hinv
Diseasespecific
DB
Diseasespecific
DB
In Sum
 Strength of H-invitational DB, main body (my current understanding)
– FL-nature
– High-quolity sequences
– Most comprehensive collection in the world
– Availability of physical clones
– Powerful computational and human resources
– Integration with other genome-related databases
■To-do's for H-invitational DB, disease extension part (based on dis ed mtg)
– Gene-originated/ oriented research
• Comprehensive and extensive automatic text mining with first-level manual curation
for disease-related info
• Addition of disease-summary type wet data (e.g. exp profiling on pooled samples)
• Link with disease-specific DBs
– Disease-originated/ oriented research
• Tools for: Dis→Genes →Best annotation in the world (strength/mission of main
body)
• Tools for: Dis→Genes →Relationship with other phenotypes (other dis, life-style)
• Tools for candidate gene selection (strength/mission of main body and dis ed part)
Dr. Gojobori's Option Catalog
① Disease-specific DB, focused to few diseases,
but with in-depth info.
② Broad disease coverage, with a text-book level info
(no patients' data)
③ Clinical info DB on few diseases, more clinical practiceoriented (incl. patients' data)
④ Expression profiling DB with insights in gene regulation
network for tailor-made medicine
⑤ Probability-based disease gene info DB for gene mapping and
for genotype-phenotype prediction in clinical medicine
⑥ Focusing on a particular cohort
Eventually, all gene- and all human phenotype (incl.
disease)- DBs will be combined seamlessly and in unity.
2/4/03 Strategic Meeting Agreement
WG D1
WG D2
WG D3
WG D20
③ Clin
info DB
③ Clin
info DB
③ Clin
info DB
③ Clin
info DB
⑤ Prob
⑤ Prob
⑤ Prob
⑤ Prob
genotypephenotype
genotypephenotype
genotypephenotype
genotypephenotype
⑥ SNP/MS ⑥ SNP/MS ⑥ SNP/MS
Unidirectional
data flow
H-inv,
Dis ed
④ Exp
profile
DB
④ Exp
profile
DB
④ Exp
profile
DB
⑥ SNP/MS
④ Exp
profile
DB
② H-inv version of Clinical Synopsis in OMIM
based on automatic text mining with manual curation
H-inv
Publication
Publication