From reading to

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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.

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OPEN ACCESSOn our way to Information Overload ?
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Too much to read major trends foreseen

• From Reading to Consulting
• From Reading to Meta-analysis
• From Text to Knowledge Representations

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Fingerprints (CFPs)
PRESENT
consolidated knowledge
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The Early Evolution of Fingerprint Manipulation
PRESENT
add
add
Articles, books
organization fingerprint
contents fingerprints
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PRESENT
content, people, organisations

• Publications
• Molecular Databases
• Image databases
• Patents
• Events
• Calls

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An example of e-Vamp
PRESENT
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META-ANALYSIS
Research
Meta-Analysis
Enlightened Nonsense
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PRESENT
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PRESENT
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The big problem
PRESENT

• The TLA

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Protein names.
PRESENT
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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.
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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)
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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
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Across species The problem gets worse
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Creating reference fingerprints
PSA Prostate Specific Antigen
reference fingerprint
PSA Psoriatic Arthritis
reference fingerprint
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Collect fingerprints for each meaning
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Context matching
PSA Prostate Specific Antigen
PSA
PSA Psoriatic Arthritis
Not-In-Thesaurus
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Results

• LF/SF dataset
• Upto 99 accuracy
• OMIM annotation
• Upto 93
• OMIM PubMed references
• Upto 90

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META-ANALYSIS
Research
Meta-Analysis
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Research
New Drug discovery ?
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Future (hope)
PLEASE !
Papyrust
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Knowledge Maps Medline Bioterrorism Map 2001
Future