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From reading to

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Homonyms. PSA. Prostate Specific Antigen. PSoriatic Arthritis ... Multiple genes, one homonym. DEFB4. defensin, beta 4. SAP1, HBD-2, DEFB-2, DEFB102, DEFB2 ... – PowerPoint PPT presentation

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Title: From reading to


1
From reading to
PRESENT
  • Text a source of confusion ?
  • Text Text Context Confusion
  • Text Text context Information
  • Context can be added through
  • Expert knowledge
  • Contextual disambiguation
  • Final aim communication at concept level.

2
OPEN ACCESSOn our way to Information Overload ?
3
Too much to read major trends foreseen
  • From Reading to Consulting
  • From Reading to Meta-analysis
  • From Text to Knowledge Representations

4
Fingerprints (CFPs)
PRESENT
consolidated knowledge
5
The Early Evolution of Fingerprint Manipulation
PRESENT
add
add
Articles, books
organization fingerprint
contents fingerprints
6
PRESENT
content, people, organisations
  • Publications
  • Molecular Databases
  • Image databases
  • Patents
  • Events
  • Calls

7
An example of e-Vamp
PRESENT
8
META-ANALYSIS
Research
Meta-Analysis
Enlightened Nonsense
9
PRESENT
10
PRESENT
11
(No Transcript)
12
The big problem
PRESENT
  • The TLA

13
Protein names.
PRESENT
14
Synonyms
Epidermal growth factor receptor El, DER, Egf,
Elp, flb, top, EGFR, EGFr, EgfR, egfr, C-erb,
D-Egf, Degfr, EGF-R, EK2-6, Egf-r, Elp-1, HD-33,
dEGFR, D-EGFR, Elp-B1, c-erbB, dEGFR1, CG10079,
CT28361, DER/top, DmHD-33, Ellipse, Torpedo,
top/DER, top/flb,DER/EGFR, l(2)57Ea, Elp-B1RB1,
l(2)05351, l(2)09261, l(2)57EFa, l(2)57DEFa, DER
flb, EGF Receptor, Torpedo/Egfr, Ellipse torpedo,
faint little ball.
15
Homonyms
PSA Prostate Specific Antigen PSoriatic
Arthritis alpha-2,8-PolySialic Acid PolySubstance
Abuse Picryl Sulfonic Acid Polymeric Silicic
Acid Partial Sensory Agnosia Poultry Science
Association
(Not-In-Thesaurus)
16
Multiple genes, one homonym
PRESENT
DEFB4 defensin, beta 4 SAP1, HBD-2, DEFB-2,
DEFB102, DEFB2 ELK4 ELK4, ETS-domain protein
(SRF accessory protein 1) SAP1 PSAP proposin
(variant Gaucher disease and variant
metachromatic leukodystrophy) SAP1, GLBA
17
Across species The problem gets worse
18
Creating reference fingerprints
PSA Prostate Specific Antigen
reference fingerprint
PSA Psoriatic Arthritis
reference fingerprint
19
Collect fingerprints for each meaning
20
Context matching
PSA Prostate Specific Antigen
PSA
PSA Psoriatic Arthritis
Not-In-Thesaurus
21
Results
  • LF/SF dataset
  • Upto 99 accuracy
  • OMIM annotation
  • Upto 93
  • OMIM PubMed references
  • Upto 90

22
META-ANALYSIS
Research
Meta-Analysis
23
Research
New Drug discovery ?
24
(No Transcript)
25
(No Transcript)
26
(No Transcript)
27
Future (hope)
PLEASE !
Papyrust
28
Knowledge Maps Medline Bioterrorism Map 2001
Future
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