バイオメトリクス授業資料 iwatawiki lec13 s

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MEDLINE

Jensen et al. (2006) Nat Rev Genet 7: 119 2

2

•  5

2008 ₃

• 

• 

•  PubMed/MEDLINE

•  MeSH term

• 

• 

•  ^(GO)

•  MEDIE

•  Swanson

• 

4

• 

• 

– 

– 

(Jensen et al. (2006) Nat Rev 7: 119)

5

•  InformaOon retrieval ^:

– 

•  EnOty recogniOon ^:

– 

•  InformaOon extracOon ^:

– 

•  Text mining (Knowledge discovery) ^:

–  A-B B-C A-C

•  IntegraOon ^:

–  QTL

Jensen et al. (2006) Nat Rev 7: 119

6

MEDLINE PubMed

•  MEDLINE NaOonal Library of

Medicine; NLM

•  1946 39 60 ;

91% 5,600

1900 2012 7

•  PubMed MEDLINE

7

•  PubMed

–  binary search

Google MeSH term

–  vector search

Related citaOons

8

MeSH term

(Medical Subject Headings)

•  NLM

•  2011 ^26,142 descriptors

177,000

• 

Salt-tolerance Saline-Tolerance Salt-Adap0on

⁹

Seeds Cotyledon Endosperm

MeSH term

10

PubMed

MeSH term

MeSH term

11

•  a idf

– 

–  7 (term frequency) ^{d t}

•  7(d, t) = nt / Wd

n_t t W_d d

–  idf (inverse document frequency): ^t

•  idf(t)=log₂(N/w_i) + 1

N w_i t

–  ^{d x}

x_dt = 7(d, t) × idf(t)

5 10 15 20

01234

Index

log(1:20, 2)

12

• 

•  ^{x y}

•  α

sim(x, y) = ^{∑ x i y i}

x _i ²

∑ ∑ ^{y i 2}

13

(2)

TextPresso

•  Textpresso ( hgp://www.textpresso.org/):

– 

– 

– 

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Natural Language Processing: NLP

• 

morphological analysis

: ; cats = cat + s

syntaOc analysis

:

semanOc analysis discourse analysis

1999 . 15

•  semanOc analysis

• 

• 

•  ontology

1999 .

16

Gene Ontology (GO)

• 

• 

•  hgp://www.geneontology.org/

GO term

17

GO term

18

Go term

biological process cellular component

molecular funcOon

3

GO term

(Directed Acyclic Graph: DAG)

19

(TextPresso )

Muller et al. (2004) PLoS Biology 2: e309

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Textpresso

•  ^Recall

Precision

Muller et al. PLoS Biol 2(11): e309 ²¹ hgp://www.textpresso.org/

precision recall

tp fp

fn tn

Precision ₌ ^tp

tp + fp

Recall ₌ ^tp

tp + fn

F = 2 × ^{Precision × Recall}

Precision _{+ Recall}

F

F

22

Textpresso

Muller et al. PLoS Biol 2(11): e309 2 ‘‘regulaOon’’

‘‘associaOon’’

₂₃

•  ^10%

‘‘Neither pdk-1(gf) nor akt-1(gf) suppressed the

Hyp phenotype of age-1(mg44).’’

•  ^{context 70%}

‘‘lin-35 and lin-53, two genes that antagonize a C.

elegans pathway, encode proteins similar to Rb and

its binding protein RbAp48.’’

→

Muller et al. PLoS Biol 2(11): e309 ²⁴

MEDIE

•  MEDIE (hgp://www.nactem.ac.uk/medie/)

•  semanOc query

What causes cancer?

25

Ananiadou et al. TRENDS in Biotechnology 24: 571 ²⁶

MEDIE

27

(4)

Swanson

Arrowsmith hgp://arrowsmith.psych.uic.edu/

A C

B1, B2, B3, B4

A-C

Undiscovered public knowledge

Swanson Fig.1

MEDLINE (1)

(A) (C) (2)

(A) (C) (3)

C(A)

Biomedical Digital Libraries 2006, 3:2 ₂₈

Arrowsmith

hgp://arrowsmith.psych.uic.edu/arrowsmith_uic/index.html ²⁹

Smalheiser (2009) Computer Methods and Programs in Biomedicine 94: 190–197

A = microRNA, C = Xist

Xist (X-inacOve specific transcript)

30

“Disorder”

31

A C

32

co- occurrence

Jensen et al. (2006) Nat Rev Genet 7: 119

von Mering (2005)Nuc Acids Res 33: D433

NLP

b c

33

(5)

Korbel et al. (2005) PLoS Biology 3: e134

92 (I’’)

172,967 -

I 224,754

11,026OG I’

34

[ - ], [

]

35

G2D (Genes to Disease)

hgp://g2d2.ogic.ca/

G2D

Gene Ontology term

Tremblay 2008 PLoS One 3: e2907 2 Teber et al. 2009 BMC BioinformaOcs 10: S69 G2D

36

G2D PHENOTYPE

1.  ^{OMIM ID}

2. 

3.  OMIM

MeSH term

C,

4.  MEDLINE

MeSH D GO

term GO

5.  RefSeq ^GO

6.  ^RefSeq

(2) BLAST

7. 

①

②

1, 2

③ ④

⑤

⑥

⑦

37

OMIM

MEDLINE , MEDLINE MeSH term

C,

MEDLINE

GO term MeSH C D

RefSeq

BLAST

38

2010

主成分 分析

生物 統計 ^{理解 階層 説明}

例 応用 データ 必要

実験 研究 ^計算

系統 高い 興味深い 非常 フーリエ 形 表現

楽しい お願い バーコード レポート 大変 アルゴリズム ^{意味 方法}

レジュメ 手法 授業 数学 話

!"

内容 面白い 数式 難しい ^{多い 解説}

良い #$% 解析

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!"#$%&'()&*+',-'./

*+,-./012304567849 8

:;<=*/

RMeCab

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