1. 2010/05/27
kaneko.satoko(at)ocha.ac.jp

2. Web API
Web API (TogoWS)
EMBOSS Dotplot

3. Web API
Web API
Google Chart API
Google Chart API
Google Chart API

4. Web API
A P I
Web API HTTP
Google Chart API
Google Chart API ( )
URL

5. Google Chart API
:
?
&
chs: Chart size *
chs=< >x< >
*: (pixel)
chd: Chart data
chd=t:< >
chd=t:< >|< >|< >
1 X Y
chd=t:< 1 X >|< 1 Y >|< 2 X >|< 2 Y
>

6. Google Chart API
:
( )
( )
( )
( )
( )

7. Google Chart API
chco:Colors
chco=FF0000,00FF00
*
( )
*
.

8. Google Chart API 1
(Y )
h[p://chart.apis.google.com/chart?chs=300x300&chd=t:10,15,4,60,45|30,23,73,24,87
&cht=lc&chco=ff0000,00ff00
Safari URL
|
[enter]

9. Google Chart API 2
h[p://chart.apis.google.com/chart?chs=200x200&chd=t:20,40,60|15,25,40&cht=s
20 15
40 25
60 40
20 40 60 15 25 40
X |Y |
20 40 60 15 25 40|25,50,75

10. Google Chart API 3
h[p://chart.apis.google.com/chart?chs=300x300&chd=t:50,25,15,6,4&cht=p
3D
h[p://chart.apis.google.com/chart?chs=300x300&chd=t:50,25,15,6,4&cht=p3
3D
chl=< 1>|< 2>|< n>
chl=Italy|Spain|France|Germany|Greece|UK
h[p://chart.apis.google.com/chart?chs=460x230&chd=t:35,34,12,12,6,1&cht=p
&chl=Italy|Spain|France|Germany|Greece|UK ( )

11. Google Chart API 4
7
3 3 (A B C )
4 A B
5 A C
6 B C
7
h[p://chart.apis.google.com/chart?chs=200x200&chd=t:100,80,50,20,20,10,5&cht=v
(A, B, C, AB, AC, BC, ABC)
o "h[p://chart.apis.google.com/chart?chs=200x200&chd=t:
100,100,50,20,20,10,5&cht=v"
( )

12. 1) X Y
1 0 10 2 0 30 3 0 20
25 15 3 23 20 50
50 4 6 73 40 30
8 60 9 24 9 50
1,2,3
2) B A C
1) 2 2
|0,20,40,90|20,50,30,50 lxy 11 99 ,0034ff
2) h[p://chart.apis.google.com/chart?chs=300x300&chd=t:40,100,20,50,0,50,50&cht=v

13. Web API
TogoWS
TogoWS
SOAP( ( ) )/REST
REST

14. TogoWS
NCBI Ensembl

15. TogoWS
Services: TogoWS
SOAP: Simple Object Access Protocol
→
REST: Representalonal State Transfer
URL

16. TogoWS: REST –Entry retrieval‐
xml: Extensible Markup Language
tag
json: JavaScript Object Notalon
JavaScript
gff: 'Gene‐Finding Format' or 'General Feature Format'
CDS molf
h[p://togows.dbcls.jp/entry/
database
h[p://togows.dbcls.jp/entry/ncbi‐nucleolde?fields
( definilon, features, references, seq )

17. TogoWS: REST Entry retrieval (1)
LOCUS
h[p://togows.dbcls.jp/entry/ebi‐uniprot/MKRN1_MOUSE,MKRN1_HUMAN
h[p://togows.dbcls.jp/entry/ebi‐uniprot/MKRN1_MOUSE,MKRN1_HUMAN.fasta
h[p://togows.dbcls.jp/entry/ncbi‐nucleolde/MKRN1_MOUSE/seq
ACCESSION Number
h[p://togows.dbcls.jp/entry/ncbi‐nucleolde/NM_173335
h[p://togows.dbcls.jp/entry/ncbi‐nucleolde/NM_173335.fasta
h[p://togows.dbcls.jp/entry/ncbi‐nucleolde/NM_173335/seq
GI (GenInfo Idenlfier)
h[p://togows.dbcls.jp/entry/ncbi‐nucleolde/27545435

18. TogoWS: REST Entry retrieval (2)
PubMed
& PMID:1840504
h[p://togows.dbcls.jp/entry/ncbi‐pubmed/1840504
h[p://togows.dbcls.jp/entry/ncbi‐pubmed/1840504/au
h[p://togows.dbcls.jp/entry/ncbi‐pubmed/1840504/abstract
h[p://togows.dbcls.jp/entry/ncbi‐pubmed/1840504/mesh
PMID:17438280
h[p://togows.dbcls.jp/entry/ncbi‐pubmed/17438280
h[p://togows.dbcls.jp/entry/ncbi‐pubmed/17438280/au
h[p://togows.dbcls.jp/entry/ncbi‐pubmed/17438280/abstract
h[p://togows.dbcls.jp/entry/ncbi‐pubmed/17438280/mesh
* mesh
MeSH (Medical Subject Headings) NLM
NLM MEDLINE 10 15
MeSH

19. TogoWS: REST –Database search‐
keyword
h[p://togows.dbcls.jp/search/
database
query
offset, limit hit

20. TogoWS: REST Database search
h[p://togows.dbcls.jp/search/[database]/[query+string]/[offset, limit]
h[p://togows.dbcls.jp/search/ebi‐uniprot/olfactory/
h[p://togows.dbcls.jp/search/ebi‐uniprot/olfactory/count
h[p://togows.dbcls.jp/search/ebi‐uniprot/olfactory+rat/
h[p://togows.dbcls.jp/search/ebi‐uniprot/olfactory+rat/1,20
h[p://togows.dbcls.jp/search/ebi‐biomodels/olfactory
h[p://togows.dbcls.jp/search/ncbi‐omim/olfactory
h[p://togows.dbcls.jp/search/kegg‐enzyme/carboxylesterase
h[p://togows.dbcls.jp/search/ncbi‐omim/carboxylesterase
h[p://togows.dbcls.jp/search/kegg‐orthology/carboxylesterase
h[p://togows.dbcls.jp/search/kegg‐reaclon/carboxylesterase
h[p://togows.dbcls.jp/search/ebi‐go/carboxylesterase
h[p://togows.dbcls.jp/search/ncbi‐cdd/carboxylesterase
(cdd: conserved domain database)

21. Dotplot (2)
Dotplot (2)
dotplot
Dotplot (3)

22. Dotplot 5' alignment
1 alignment 10kb
pairwise alignment
rat 7 Olr1082 60kb(12192676‐12231066)
dotplot Olr1082

23. FTP
$ cd ~/bin
$lyp yp://yp.ensembl.org/pub/current_fasta/ra[us_norvegicus/dna/
lyp> mget Ra[us_norvegicus.RGSC3.4.57.dna.chromosome.7.fa.gz
lyp>quit
$gzip –d Ra[us_norvegicus.RGSC3.4.57.dna.chromosome.7.fa.gz
(60kb)
ruby
CotEditor .rb
.rb
$ruby

24. #ruby
#
1
#
# genome_seq
#
12192676 #
60000 #
#genome_seq [ , ]
geneseq *ruby 0 ‐1
#geneseq
Chr7_Olr1082 # Chr7_Olr1082
#geneseq
out.close

25. $cd ~/bin
$ruby get_seq.rb Ra[us_norvegicus.RGSC3.4.57.dna.chromosome.7.fa
2 ruby
Ra[us_norvegicus.RGSC3.4.57.dna.chromosome.7.fa
get_seq.rb
$less Ra[us_norvegicus.RGSC3.4.57.dna.chromosome.7.fa
less
fp.gets( )
q

26. dotmatcher
dotmatcher
dotplot
Ensembl annotalon
$cd ~/bin
$ 610 Chr7_Olr1082 Chr7_Olr1082
50 50 Olr1082.out #

27. Olr1082
Olr1082 40kb Olr1083
annotalon
Olr1082
2 2
Olr1082
Olr1083
1 2 3 4 1 4
Delelon
1 2 3 4
1 2 3 2 3 4
Duplicalon

28. Dotplot (3)
dotplot
mouse 7 synteny
rat human
rearrangement

29. Makorin1 mouse, rat, human
‐Makorin1 Rab19 50kb(human
80kb) dotmatcher
Makorin1
‐Localon Synteny
(Makorin1 annotalon )
mouse chromosome[ ]: ( )
rat chromosome[ ]: ( )
human chromosome[ ]: ( )
get_seq.rb
mouse rat mouse human dotmatcher
(windowsize 100 threshold 30 plot )

30. mouse rat exon, intron
mouse human CDS
intron
exon
human
rat
mouse mouse

31. Web API (Google Chart API, TogoWS (REST))
ruby
dotplot
TogoWS(SOAP)