next generation semantic support technology barend mons cd40 ligand and tumor necro sis factor...
TRANSCRIPT
![Page 1: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/1.jpg)
Next generation semantic support technology
Barend Mons
CD40 ligand and tumor necrosis factor alpha, the cells acquire a mature phenotype of dendritic cells that is characterized by up-regulation of human leukocy
te antigen (CD80, CD86, CD40and CD54 and appearance of CD83. These
KnewCo
![Page 2: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/2.jpg)
Too much to read: major trends foreseen:
• From Reading to Consulting
• From Reading to Meta Analysis
• From Writing to Knowledge Representations
![Page 3: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/3.jpg)
textmining
PLEASE !
Writing =ambiguity
Future (hope)
Papyrust
![Page 4: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/4.jpg)
What is needed
• Disambiguate Text and tag/link concepts
• Meta-analyse information at concept level
• Provide meta-analysed information
• Support Information Based Knowledge Discovery (especially new associations)
![Page 5: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/5.jpg)
1,000,000papers
Meta-Analysis
META-ANALYSISResearch
292Genes
![Page 6: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/6.jpg)
TERM Pubmed ScholarGoogle Concept Based
Bovine Spongiform E 2073 5,640 1673
Mad cow disease 1676 3,160 1682
CD154 2479 4,390 2812
CD40L 2771 20,800 2849
TNFSF5 2273 116 2751
EBV 12357 80,500 8154
Epstein Barr virus 20761 99,000 8154
Human Herpes virus 4 15025 78,400 8154
Word Based is NOT good enough
![Page 7: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/7.jpg)
Tag-As-You-Type, Tag-As-You-Like
![Page 8: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/8.jpg)
Ambiguity 1: Synonyms
• Facilitating networks of information. van Mulligen EM, Diwersy M, Schmidt M, Buurman H, Mons BProceedings of AMIA Symposium 2000, 868-72
![Page 9: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/9.jpg)
Ambiguity 2: Homonyms
PSAProstate Specific AntigenPSoriatic Arthritisalpha-2,8-PolySialic AcidPolySubstance AbusePicryl Sulfonic AcidPolymeric Silicic AcidPartial Sensory AgnosiaPoultry Science Association
• Distribution of information in biomedical abstracts and full-text publications, Schuemie MJ, Weeber M, Schijvenaars BJ, van Mulligen EM, van der Eijk CC, Jelier R, Mons B, Kors JA, Bioinformatics 2004 Nov 1, 20:2597-604
![Page 10: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/10.jpg)
But…we have nomenclature committees now……
DEFB4DEFB4defensin, beta 4defensin, beta 4SAP1SAP1, HBD-2, DEFB-2, DEFB102, DEFB2, HBD-2, DEFB-2, DEFB102, DEFB2
ELK4ELK4ELK4, ETS-domain protein (SRF accessory protein 1)ELK4, ETS-domain protein (SRF accessory protein 1) SAP1SAP1
PSAPPSAPproposin (variant Gaucher disease and variant proposin (variant Gaucher disease and variant metachromatic leukodystrophy)metachromatic leukodystrophy)SAP1SAP1, GLBA, GLBA
PRESENT
![Page 11: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/11.jpg)
292 genes > 1 million papers115 genes have a homonym problem (40 %)
• Dbp – D site albumin promoter binding protein
– PubMed: 1015 hits, including <diastolic blood pressure>– After disambiguation: 124 relevant hits
• Prp – proliferin related protein
– 2971 hits <platelet rich plasma>, <prion protein>
– Relevant hits: 7
• After disambiguation: 60.000 papers ( << 10 % is relevant)
PRESENT
Junk ? or Jewels ?Junk ? or Jewels ?
![Page 12: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/12.jpg)
Fingerprints (CFP’s)
C19881 0.99C92992 0.67C02002 0.66C99229 0.44C00392 0.33C93939 0.21
consolidated knowledge
PRESENT
![Page 13: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/13.jpg)
The Knowlet
• Contextual annotation of web pages for interactive browsing, van Mulligen E, Diwersy M, Schijvenaars B, Weeber M, van der Eijk CC, Jelier R, Schuemie M, Kors J, Mons B, Medinfo 2004, 11:94-8• Which gene did you mean?, Mons B, BMC Bioinformatics 2005 Jun 7, 6:142
![Page 14: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/14.jpg)
Creating Reference Knowlets
PSA Prostate Specific Antigen
PSA Psoriatic Arthritis
ReferenceKnowlet
ReferenceKnowlet
![Page 15: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/15.jpg)
Context matching
PSA ??
Prostate Specific Antigen
Psoriatic Arthritis
ReferenceKnowlet
ReferenceKnowlet
New text
93 % correct in ‘Worst Case Scenario’98 % overall….
• Thesaurus-based disambiguation of gene symbols. Schijvenaars BJ, Mons B, Weeber M, Schuemie MJ, van Mulligen EM, Wain HM, Kors JABMC Bioinformatics 2005 Jun 16, 6:149•Word sense disambiguation in the biomedical domain: an overview. Schuemie MJ, Kors JA, Mons B, Journal of Computational Biology 2005 Jun, 12:554-65
x
![Page 16: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/16.jpg)
person organisation Object 1
gene
Object 2
disease
Object 3
drug
> 15 million Knowlets from PubMed etc.
Building an association matrix of large data sources
![Page 17: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/17.jpg)
Text (free or structured)
Resolving ambiguities (contextual reference concepts)
Concept Tagging and inserting appropriate links
Text Knowlet
Aggregation of Text Knowlets
Object Knowlets (people, diseases, drugs, genes)
Aggregation of Object Knowlets
Collection Knowlets ( category, pathway, Micro-array-gene-set )
Basic methodology:Concept Tagging, creation and systematic aggregation of Knowlets
![Page 18: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/18.jpg)
1
0.16 1
0.30 0.03 1
0.28 0.35 0.20 1
0.188
0.004 0.15 0.13 1
A matrix of associative distances
meta-analysis
HierarchicalClusteringACSMDSEtc.
![Page 19: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/19.jpg)
Meta-analysis 1: ACS
• Constructing an Associative Concept Space for Literature-based Discovery, van der Eijk CC, van Mulligen EM, Kors JA, Mons B, van den Berg JJournal of the American Society for Information Science and Technology 2004, 55(5): 436-444•Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes. Jelier R, Jenster G, Dorssers LC, van der Eijk CC, •van Mulligen EM, Mons B, Kors JA Bioinformatics 2005 May 1, 21:2049-58
![Page 20: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/20.jpg)
Meta Analysis 2: Hierarchical Clustering
![Page 21: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/21.jpg)
![Page 22: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/22.jpg)
200779_at200799_at200800_s_at201000_at201427_s_at201939_at202022_at202887_s_at203355_s_at203574_at203622_s_at204026_s_at204033_at204146_at204285_s_at204415_at205047_s_at205239_at208763_s_at208813_at208949_s_at209230_s_at209608_s_at210338_s_at212063_at212501_at212971_at213040_s_at213075_at213703_at217999_s_at218145_at218180_s_at218585_s_at218986_s_at219588_s_at219961_s_at221731_x_at222039_at222111_at35820_at
Q-norm
![Page 23: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/23.jpg)
Q-norm
![Page 24: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/24.jpg)
Q-norm
![Page 25: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/25.jpg)
Physiology Phosphorylation Lymphocyte Transformation Cell Cycle
Anatomy T-Lymphocytes Dendritic Cells Monocytes Lymph Nodes
Blood Platelets
Anatomy T-Lymphocytes Macrophages Fibroblasts Monocytes Neutrophils
PhysiologyImmunity, NaturalAntigen PresentationGenetic Predisposition to Disease Fibrinolysis
![Page 26: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/26.jpg)
Fingerprints
Knowlet
Association Matrix Meta-analysis
Expert Challenge
U.W.Expert comments
Peer to Peer Review
Final Approval
U.W. Fingerprint
Update
Literature
Protein A
The cycle of computer-assisted distributed annotation
![Page 27: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/27.jpg)
Key conceptselected
DAILY Feed
C= Suggested Experts
Invite to chat, etc.
Send e-mail (group)
Etc.
Accept
Block
Add
BLAST-over
A = Established Knowledge B = suggested Knowledge
D= Suggested PMID’s
![Page 28: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/28.jpg)
1996
![Page 29: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/29.jpg)
1997
![Page 30: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/30.jpg)
1998
![Page 31: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/31.jpg)
1999
![Page 32: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/32.jpg)
2000
![Page 33: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/33.jpg)
2001
![Page 34: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/34.jpg)
2002
![Page 35: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/35.jpg)
2003
![Page 36: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/36.jpg)
2004
![Page 37: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/37.jpg)
2005
![Page 38: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/38.jpg)
The Million Minds Approach
Semantic Tagging (distributed and central)
• Tag-as-you-Type/Like • Proposals-Projects (NIH, Wellcome Trust as environment)• Manuscripts-Papers (BMC, Plos, SciELO as test environment)
• Retrospective Tagging • Text (PubMed, projects, patents, open access journals, own papers!)
• Data base records (SwissProt, EntrezGene, GO, OMIM, BIND)
• Thesaurus Enrichment (with Wikipedia, U-Wiktionary)
• Semantic linking at concept level (All tagged resources)
![Page 39: Next generation semantic support technology Barend Mons CD40 ligand and tumor necro sis factor alpha, the cells acquire a mature phenotype of dendritic](https://reader036.vdocuments.mx/reader036/viewer/2022081519/56649e7f5503460f94b83bc4/html5/thumbnails/39.jpg)
Semantic Passport
B. Mons, PhDb.mons@ Erasmusmc.nl
Netherlands
• All output with clickbox
• Your Topics•Your concepts
• People•Similar•Complementary
• Semantic types (topics)•TextBlast output• Restricted to ‘logic’
•Resources• Medline• CRISP• CORDIS• LILACS• Others based on
•Sem.types• Metadata (country)
•Interactive tools• Add (missing papers/projects)•Invite colleagues•Etc.
Output 1 (confirm Focus)Maybe different panelsMinimal personal data
Act.SHARED CRISPCORDIS
Publ.MedlineSciELO
confirm
Semantic Passport