Vision Talk

“If it is not in Wikipedia, it probably does not exist.”

Jimmy Wales used to say that about Google when Google still existed.

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

A Proleptic View on Science Communication in the early 21st century

In those days there was:Too much to read: so what happened ?

a LANDSLIDE…..

• From Reading to Consulting

• From Reading to Meta Analysis

• From Writing to Knowledge Representations

• To Central AND Community Annotation

Rejected Papers and Unpublished

results

Rejected proposals

Knowledgegeneration

Hypothesisgeneration

2006 Management of Science (work flow)

proposal

Peer Review

manuscript

Project

Paper

Enriched(annotated)Knowledge

RoughExperimental

Data= Text-semantic tagging= Semantic matching= currently heavily under-used

Believe it or not: In the early 21st century

• The ‘article’ was the unit of communication• There were centralised institutions calculating ‘impact’

– per article – or even per entire journal

• Web sites were not counted • Some publishers still asked money for the reading of

scientific articles• Articles did endlessly repeat already established

knowledge• Hardly any of this mostly redundant information was

interlinked semantically.• Web-publishing was still largely conceived as ‘putting

dead PDFs of articles on the Internet’

“Textmining”Writing:•Legal Plagiarism•Ambiguity•Delay

Future (hope)

Papyrust

1,000,000papers

Meta-Analysis

META-ANALYSIS2005

292Genes

Ambiguity 1: Synonyms

• Facilitating networks of information. van Mulligen EM, Diwersy M, Schmidt M, Buurman H, Mons BProceedings of AMIA Symposium 2000, 868-72

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

Then…we had nomenclature committees……

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

Early this century

Some historic quotes from the nomenclature committee period(Most committees now extinct.)

Biologists would rather share their toothbrush than their gene nameunless it is the same name for a different gene.

Now every-one is so convinced about the importance of standards that everyone creates their own.

Craig Venter is fishing up more new protein sequences by himselfevery day than SwissProt can annotate with 70 people in a year.

So…….

• People started to try and recover things as simple as concepts from text, link them and use them for meta-analysis and annotation.

• Imagine what you had to do to achieve this simple task in these days

• (some companies even charged money for it)

• 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

2002: First order semantic enrichment

The Knowlet

2nd order S.E.

As the population of Africa rapidly urbanizes it may be possible to protect large populations from malaria by controlling aquatic stages of mosquitoes. Here we present a baseline evaluation of the ability of community members to detect mosquito larval habitats with minimal training and supervision in the first weeks of an operational urban malaria control program. METHODS: The Urban Malaria Control Programme of Dar es Salaam recruited and provided preliminary training to teams of Community-Owned Resource Persons (CORPs) who performed weekly surveys of mosquito breeding sites. Two trained mosquito biologists accompanied each of these teams for one week and evaluated the sensitivity of this system for detecting potential Anopheles habitats. RESULTS: Overall, 42.4% of 986 habitats surveyed by an inspection team had previously been identified by CORPs. Agricultural habitats were detected less often than other habitats (30.8 % detected, Odds Ratio [95%CI ] = 0.46 [0.29-0.73], P = 0.001). Non-agricultural artificial habitats were less suitable than other habitats (29.3 % occupancy, OR= 0.69 [0.46-1.03], P=0.066) but still constituted 45% (169/289) of occupied habitats because of their abundance (51 % of all habitats). CONCLUSIONS: The levels of coverage achieved by modestly trained and supported CORPs at the start of the Dar es Salaam UMCP were insufficient to enable effective suppression of malaria transmission through larval control. Further operational research is required to develop surveillance systems that are practical, affordable, effective and acceptable so that community-based integrated vector management can be implemented in cities across

Malaria is transmitted by Mosquitoes of the

Genus Anopheles

.Source: Wiki-diseases

 

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

2006 A matrix of associative distances

meta-analysis

HierarchicalClusteringACSMDSEtc.

An old picture from a publication by Schuemie and Supekar in 2007

• REGISTRATION (1X)

• Unique Author ID• E-mail Adress• PHP/userpage• People Knowlets

• Unique concept ID• Language variants• Homonyms• Definitions (brief)• Object Knowlets

Science Wiki’s• UID from WiktionaryZ• Research information• Talk-page• Liquid Threads• Object Knowlets

• UID from WiktionaryZ• Articles about UID’s• Encyclopaedic/ NPOV• Anonymous allowed

0 02

8 8

14

17

28

25

34

16

34

41

29

26

22

1715 14

79 9

12 12 1213

2 2

0

5

10

15

20

25

30

35

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45

1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005

www.dmd.nl paper 1 paper 2

Fingerprints

Knowlet 

Association Matrix Meta-analysis

Expert Challenge

WikiZ/PExpert comments

Peer to Peer Review

Final Approval

U.W. Fingerprint

Update

old papers

Protein A

0.1

0.4

0.9

Traditional publications or modern annotations

Solid

Liquid

Gas

1st order Semantic enrichment

ReductionFalse Positives

DiscussionVoting in Wiki

Meta-analysisProximity measures

Proposals to Data bases ?

Central Annotation