Finding Out About(Biology)

Transcription

1 1 Finding Out About(Biology)

2 2 Keywords in Evolutionary Biology [Key words]... serve as conduits for unacknowledged, unbidden, and often unwelcome traffic between worlds. Indeed, it is precisely because of the large overlap between forms of scientific thought and forms of societal thought that ``keywords''---terms whose meanings chronically and insistently traverse the boundaries between ordinary and technical discourse ---can serve not simply as indicators of either social meanings and social change OR scientific meaning and scientific change, but as indicators of the ongoing traffic BETWEEN social and scientific meaning and, accordingly, between social and scientific change.

3 3 Documents + Sequence Query Retrieval I n t e r f a c e Proteins Sim Genes TGFß Sim Pax3 Documents Annotate RPTK BMP4 UNC5 Hox1a Notch MLH1 SRD5h1 Sim

4 4 Preview

5 5 Mixing many voices

6 6 Use of previous writing

7 7 Co-citation a a b x x b Coupling Cocitation

8 8 Science

9 9 Bibliometrics Citing paper Cited paper

10 10 Citing paper Classic Research front w hardness(field) w Cited paper Analysis [D. d.s.price] Review article

11 11 Inverting bibliographic pointers

12 12 Law

13 13 Legal background

14 14 Explicit marking of citation valence by authors cf. but cf.

15 15 Shepards analysis of judges treatment

16 16 Historical feature Code Description Comments A affirmed Same case affirmed on appeal. CC connected case Different case from cited case... CF certiorari filed DE denied DM dismissed Appeal from same case dismissed. GR granted IN US cert denied Certiorari denied by U.S. Supreme Court. US cert dismissed Certiorari dismissed by U.S. Supreme Court. US reh denied Rehearing denied by U.S. Supreme Court. US reh dismissed Rehearing dismissed by U.S. Supreme Court. M modified Same case modified on appeal. MI mandate issed NP not published PD petition denied PG petition granted R reversed Same case reversed on appeal. S superseded Substitution for former opinion. SC same case V vacated Same case vacated.

17 17 Treatment Code Description Comments C criticized Soundness of decision or reasoning in cited case criticized D distinguished Case at bar different either in law or fact from case cited E explained Statement of import of decision in cited case. EX examiner's decision F followed Cited as controlling. H harmonized Apparent inconsistency explained and shown not to exist. J dissenting Citation in dissenting opinion. L limited Refusal to extend decision of cited case O overruled Ruling in cited case expressly overruled. P parallel Citing case substantially alike or on all fours Q questioned Soundness of decision or reasoning in cited case questioned.

18 18 Reduced dimensionality

19 19 Swanson's Arrowsmith

20 20 Google s Page rank

21 21 Hubs & Authorities [Kleinberg 98] S T

22 22 ABORTION example w_{2} URL TITLE Abortion and Reproductive Rights Internet Resources Welcome to Planned Parenthood Abortion Clinics OnLine IPPF Home Page The National Abortion Federation Life WEB Healing after Abortion members.aol.com/pladvocate/ The Right Side of the Web

23 23

24 24 Summary

25 25 Extraction methods

26 26 Morphological analysis

27 27 Other approaces

28 28 EDGAR

29 29 BioMed Visualization

30 30 PubMed

31 31 Entrez- overview

32 32 Term strength

33 33 STKE

34 34 Relation details Relation Information: Source Node: Glycogen Synthase Kinase-3 Target Node: beta-catenin in Pathway Xenopus egg Wnt/beta-catenin Relation Authority: Randall T Moon Sign: - Method: covalent modification : serine/threonine Reliability: Demonstrated Description: Xgsk-3 phosphorylates Xenopus beta-catenin at a specific amino terminal site (Yost). The efficiency is likely enhanced by Axin. This phosphorylation targets beta-catenin to interact with beta-trcp, which in turn leads to its being ubiquitinated and thus degraded by the proteosome. Mutation of the consensus GSK-3 phosphorylation site leads to hyperactivity of beta-catenin signaling in both embryos and in multiple human cancers. View References: Literature Literature References: Yost, C., Torres, M., Miller, J.R., Huang, E., Kimelman, D., and Moon, R.T. (1996) The axis-inducing activity, stability, and subcellular distribution of beta-catenin is regulated in Xenopus embryos by glycogen synthase kinase 3. Genes Dev 10: [Medline]

35 35 Problems with STKE

36 36 Emerging issues

37 37 Gerstein s letter There is, however, a third approach for annotating the human genome (providing at least the putative start, stop, and structure of each gene) that is, in a sense, already extant: extend the capabilities of the biological science literature. The current journal system is decentralized, yet most research articles adhere to common standards that make them ideal for annotation: (i) Each article associates a bit of annotation with a distinct time and place and with specific, responsible parties. (ii) Attentive scholarly referencing and footnoting provide a way to connect bits of annotation and allow for continuous "updates." (iii) Peer review and editing provide a proven quality-control mechanism. (iv) Publication is an established indicator of scientific productivity; consequently, scientists already have an incentive to provide the information, whereas database submissions are often regarded as a chore.

38 38 Gerstein s letter (cont.) The main drawback of current journal article formats is that they are not very "computer-parseable," or suitable for bulk annotation of thousands of genes. However, by adding sections of highly structured text to each article (that is, extended keywords and using a controlled vocabulary ) and linking subparts of an article to relevant database identifiers, one can envision how a "literature annotation standard" could readily be interpreted by computers. Furthermore, if an article could be linked to a large "supplementary materials" data file with simple annotations for many genes (for example, lists of all the membrane proteins in the Caenorhabditis elegans genome), one would have a mechanism for bulk annotation. Further standardization could be achieved if the article described defined ways in which the data file might be updated over time and if the supplementary materials were refereed and evaluated with the text of the article.

39 39 Learning to annotate Query Documents Retrieval RelFbk + # - I n t e r f a c e Proteins Sim Genes TGFß Sim Pax3 Annotate RPTK BMP4 UNC5 Hox1a Notch MLH1 SRD5h1 Sim

40 40 Quality assurance mechanisms

41 41 Confused document semantics

42 42 WWW decouples CONTEXT

43 43 Users queries are PORTALS! " #! " # $ # % & $ ' ' ' ( ( # ) * +, -. / ) * +, -. / , +., 1 ) 7 +., / :. 4. / 4 1 ;

44 44 Publishing tricks for the Web

45 45 Medical DEDUCTION meets data-mining INDUCTION

46 46 ABDUCTION

47 47 Knowledge representation alternatives ) < / + +, = > 3. / 4 1 )? / / =, > > 3, - > +. =, 1 ;. 4 3, + > A 3. / 4 1 ) B C D E ) D E F F ) * > 3 G H? ) 1,, I. 4 8, 4 J > K, + ; L M / = 1 4, 1 1 ;?, =, 2 ; D > J J, K, + ; L > 0 3 4, + ; N N N

48 48 Cell lineage... Gamete C Developmental time "Mature" phenotype Morphogenic field (C)

49 OO modeled as grammar Gamete Special start symbol g 0 -> A B A A -> D C -> A B B B -> E F Each mitosis described by rewrite rule for non-terminals A,B,C,... g 1 g 2 g 3 A -> D C B -> E F A -> K L D C E F Developmental time g 4 S -> r t "Mature" phenotype Morphogenic field (C) S -> r t A string composed of all terminals a,b,c,...

50 50 Knowledge representation alternatives ) < / + +, = > 3. / 4 1 INFERENTIAL STRENGTH )? / / =, > > 3, - > +. =, 1 ;. 4 3, + > A 3. / 4 1 ) B C D E ) D E F F ) * > 3 G H? ) 1,, I. 4 8, 4 J > K, + ; L M / = 1 4, 1 1 ;?, =, 2 ; D > J J, K, + ; L > 0 3 4, + ; N N N

51 51 The need for lexical hooks into genomic data