Advanced NCBI

Advanced NCBI.The Entrez API

https://github.com/lindenb/courses

Pierre Lindenbaum@yokofakun

[email protected]://plindenbaum.blogspot.com

Institut du Thorax. Nantes. France

September 27, 2016

Pierre Lindenbaum@yokofakun [email protected] http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/courses


https://twitter.com/yokofakun

mailto:[email protected]

http://plindenbaum.blogspot.com





NCBI ? What about EBI, ENSEMBL, ...






What will be covered today? :

File formats...

EInfo, GQuery, ESearch , Esummary, EFetch..

processing XML answer with XSLT: HTML, SVG, R...

generating a java parser for dbSNP.

NCBI EBot

using standalone BLAST






CURL

c u r l ” h t t p : / / en . w i k i p e d i a . o rg / w i k i / Main page ”wget −O − ” h t t p : / / en . w i k i p e d i a . o rg / w i k i / Main page ”






XML






XSLT






XSLTPROC

x s l t p r o c s t y l e s h e e t . x s l f i l e . xml > r e s u l t . xml






JSON






Formats






FormatsGenbank

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.

fcgi?db=nucleotide&id=25&rettype=gb

LOCUS X53813 422 bp DNA l i n e a r MAM 22−JUN−1992DEFINITION Blue Whale heavy s a t e l l i t e DNA.ACCESSION X53813 X17460VERSION X53813 . 1 GI : 25KEYWORDS s a t e l l i t e DNA.SOURCE Ba l a enop t e r a muscu lus ( Blue whale )

ORGANISM Ba la enop t e r a muscu lusEukaryota ; Metazoa ; Chordata ; C r an i a t a ; Ve r t e b r a t a ; Eu t e l e o s t om i ;Mammalia ; Eu t h e r i a ; L a u r a s i a t h e r i a ; C e t a r t i o d a c t y l a ; Cetacea ;My s t i c e t i ; B a l a e nop t e r i d a e ; Ba l a enop t e r a .

REFERENCE 1 ( ba se s 1 to 422)AUTHORS Arnason ,U. and Widegren ,B .TITLE Compos i t ion and chromosomal l o c a l i z a t i o n o f c e t acean h i g h l y

r e p e t i t i v e DNA with s p e c i a l r e f e r e n c e to the b l u e whale ,Ba l a enop t e r a muscu lus

JOURNAL Chromosoma 98 (5 ) , 323−329 (1989)PUBMED 2612291

COMMENT See a l s o <X52700−2> f o r 1 ,760 bp common ce tacean component c l o n e sand <X52703−6>,<X53811−4> f o r the 422 bp heavy s a t e l l i t e c l o n e s .

FEATURES Loca t i on / Q u a l i f i e r ss ou r c e 1 . . 4 2 2

/ organ i sm=”Ba l a enop t e r a muscu lus ”/mo l type=”genomic DNA”/ db x r e f=”taxon :9771”/ c l o n e=”7”

m i s c f e a t u r e 1 . . 4 2 2/ note=”heavy s a t e l l i t e DNA”

ORIGIN1 t a g t t a t t c a a c c t a t c c c a c t c t c t a g a t a c c c c t t a g c acgtaaagga a t a t t a t t t g

61 ggggtccagc ca tggagaa t ag t t t a ga c a c tagga tgag ataaggaaca c a c c c a t t c t121 aaagaaatca c a t t a g g a t t c t c t t t t t a a g c t g t t c c t t aaaacac tag ag t c t t a gaa181 a t c t a t t g g a ggcagaagca gtcaagggta g c c t aggg t t agggt taggc t t a ggg t t a g241 gg t t aggg ta cggc t taggg t a c t g t t t c g gggaggggtt caggtacggc g taggg ta tg301 gg t t a ggg t t agggt taggg t t a g t g t t a g gg t t agggc t cgg t t t aggg t a cggg t t ag361 ga t t aggg ta cg tg t t aggg t t aggg tagg g c t t a g g g t t agggtacgtg t t a ggg t t a g421 gg

//


https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=25&rettype=gb

FormatsASN.1


fcgi?db=nucleotide&id=25

Seq−e n t r y : := seq {i d {

embl {a c c e s s i o n ”X53813” ,v e r s i o n 1 } ,

g i 25 } ,d e s c r {

t i t l e ”Blue Whale heavy s a t e l l i t e DNA” ,s ou r c e {

org {taxname ” Ba l a enop t e r a muscu lus ” ,common ”Blue whale ” ,db {{

db ” taxon ” ,tag

i d 9771 } } ,orgname {

nameb i nom i a l {

genus ” Ba l a enop t e r a ” ,s p e c i e s ”muscu lus ” } ,

l i n e a g e ” Eukaryota ; Metazoa ; Chordata ; C r an i a t a ; Ve r t e b r a t a ;Eu t e l e o s t om i ; Mammalia ; Eu t h e r i a ; L a u r a s i a t h e r i a ; C e t a r t i o d a c t y l a ; Cetacea ;My s t i c e t i ; B a l a e nop t e r i d a e ; Ba l a enop t e r a ” ,

gcode 1 ,mgcode 2 ,d i v ”MAM” } } ,

sub type {{


https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=25






FormatsASN.1 (schema)

http:

//www.ncbi.nlm.nih.gov/data_specs/asn/insdseq.asn

INSDSeq : := SEQUENCE {l o c u s V i s i b l e S t r i n g ,l e n g t h INTEGER ,s t r a nd edn e s s V i s i b l e S t r i n g OPTIONAL ,moltype V i s i b l e S t r i n g ,t opo l ogy V i s i b l e S t r i n g OPTIONAL ,d i v i s i o n V i s i b l e S t r i n g ,update−date V i s i b l e S t r i n g ,c r e a t e−date V i s i b l e S t r i n g OPTIONAL ,update−r e l e a s e V i s i b l e S t r i n g OPTIONAL ,c r e a t e−r e l e a s e V i s i b l e S t r i n g OPTIONAL ,d e f i n i t i o n V i s i b l e S t r i n g ,pr imary−a c c e s s i o n V i s i b l e S t r i n g OPTIONAL ,ent ry−v e r s i o n V i s i b l e S t r i n g OPTIONAL ,a c c e s s i o n−v e r s i o n V i s i b l e S t r i n g OPTIONAL ,othe r−s e q i d s SEQUENCE OF INSDSeqid OPTIONAL ,secondary−a c c e s s i o n s SEQUENCE OF INSDSecondary−accn OPTIONAL,p r o j e c t V i s i b l e S t r i n g OPTIONAL ,keywords SEQUENCE OF INSDKeyword OPTIONAL ,segment V i s i b l e S t r i n g OPTIONAL ,s ou r c e V i s i b l e S t r i n g OPTIONAL ,organ i sm V i s i b l e S t r i n g OPTIONAL ,taxonomy V i s i b l e S t r i n g OPTIONAL ,r e f e r e n c e s SEQUENCE OF INSDReference OPTIONAL ,comment V i s i b l e S t r i n g OPTIONAL ,comment−s e t SEQUENCE OF INSDComment OPTIONAL ,s t r u c−comments SEQUENCE OF INSDStrucComment OPTIONAL ,p r imary V i s i b l e S t r i n g OPTIONAL ,source−db V i s i b l e S t r i n g OPTIONAL ,database−r e f e r e n c e V i s i b l e S t r i n g OPTIONAL ,f e a t u r e−t a b l e SEQUENCE OF INSDFeature OPTIONAL ,f e a t u r e−s e t SEQUENCE OF INSDFeatureSet OPTIONAL ,sequence V i s i b l e S t r i n g OPTIONAL , −− Opt i ona l f o r con t i g , wgs , e t c .c o n t i g V i s i b l e S t r i n g OPTIONAL ,a l t−seq SEQUENCE OF INSDAltSeqData OPTIONAL

}


http://www.ncbi.nlm.nih.gov/data_specs/asn/insdseq.asn

http://www.ncbi.nlm.nih.gov/data_specs/asn/insdseq.asn





FormatsASN.1 (tools)

DATATOOLGenerate C++ data storage classes based on ASN.1 serialization

streams.Convert data between ASN.1, XML and JSON formats.






FormatsXML


fcgi?db=nucleotide&id=25&retmode=xml

<?xml v e r s i o n=” 1 .0 ”?><!DOCTYPE GBSet PUBLIC ”−//NCBI//NCBI GBSeq/EN” ” h t t p : //www. ncb i . nlm . n i h . gov/ dtd /NCBI GBSeq . dtd ”><GBSet>

<GBSeq><GBSeq locus>X53813</GBSeq locus><GBSeq length>422</GBSeq length><GBSeq st randedness>doub l e</GBSeq st randedness><GBSeq moltype>DNA</GBSeq moltype><GBSeq topology> l i n e a r</GBSeq topology><GBSeq d i v i s i o n>MAM</ GBSeq d i v i s i o n><GBSeq update−date>22−JUN−1992</GBSeq update−date><GBSeq create−date>13−JUL−1990</GBSeq create−date><GBSeq d e f i n i t i o n>Blue Whale heavy s a t e l l i t e DNA</ GBSeq d e f i n i t i o n><GBSeq primary−a c c e s s i o n>X53813</GBSeq primary−a c c e s s i o n><GBSeq access ion−v e r s i o n>X53813 . 1</GBSeq access ion−v e r s i o n><GBSeq other−s e q i d s>

<GBSeqid>emb |X53813 . 1 |</GBSeqid><GBSeqid>g i |25</GBSeqid>

</GBSeq other−s e q i d s><GBSeq secondary−a c c e s s i o n s>

<GBSecondary−accn>X17460</GBSecondary−accn></GBSeq secondary−a c c e s s i o n s><GBSeq keywords>

<GBKeyword> s a t e l l i t e DNA</GBKeyword></GBSeq keywords><GBSeq source>Ba laenop t e r a muscu lus ( Blue whale )</GBSeq source><GBSeq organism>Ba laenop t e r a muscu lus</GBSeq organism><GBSeq taxonomy>Eukaryota ; Metazoa ; Chordata ; C r an i a t a ; Ve r t e b r a t a ; Eu t e l e o s t om i ; Mammalia ; Eu t h e r i a ; L a u r a s i a t h e r i a ; C e t a r t i o d

a c t y l a ; Cetacea ; My s t i c e t i ; B a l a e nop t e r i d a e ; Ba l a enop t e r a</GBSeq taxonomy><GBSeq r e f e r ence s>


https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=25&retmode=xml

FormatsXML (DTD)

http://www.ncbi.nlm.nih.gov/dtd/NCBI_GBSeq.mod.dtd

<!ELEMENT GBSeq (GBSeq locus ,GBSeq length ,GBSeq s t randedness ? ,GBSeq moltype ,GBSeq topology ? ,GBSeq d i v i s i on ,GBSeq update−date ,GBSeq create−date ? ,GBSeq update−r e l e a s e ? ,GBSeq create−r e l e a s e ? ,GBSeq de f i n i t i o n ,GBSeq primary−a c c e s s i o n ? ,GBSeq entry−v e r s i o n ? ,GBSeq access ion−v e r s i o n ? ,GBSeq other−s e q i d s ? ,GBSeq secondary−a c c e s s i o n s ? ,GBSeq pro j ec t ? ,GBSeq keywords ? ,GBSeq segment ? ,GBSeq source ? ,GBSeq organism ? ,GBSeq taxonomy ? ,GBSeq r e f e r ence s ? ,GBSeq comment ? ,GBSeq comment−s e t ? ,GBSeq struc−comments ? ,( . . . )


http://www.ncbi.nlm.nih.gov/dtd/NCBI_GBSeq.mod.dtd

E-Utilities






GI






GI

http://www.ncbi.nlm.nih.gov/news/

03-02-2016-phase-out-of-GI-numbers/ : ”NCBI is phasingout sequence GIs - use Accession.Version instead!”


http://www.ncbi.nlm.nih.gov/news/03-02-2016-phase-out-of-GI-numbers/

http://www.ncbi.nlm.nih.gov/news/03-02-2016-phase-out-of-GI-numbers/





E-Utilities

Set of seven server-side programs that provide a stable interface tothe search, retrieval, and linking functions of the Entrez system,

using a fixed URL syntax.The output provided by the E-Utilities is in XML format,

sometimes JSON, (...)






Entrez Direct

http://www.ncbi.nlm.nih.gov/books/NBK179288/ ”EntrezDirect (EDirect) is an advanced method for accessing the NCBI’sset of interconnected databases (publication, sequence, structure,gene, variation, expression, etc.) from a UNIX terminal window.

Functions take search terms from command-line arguments.Individual operations are combined to build multi-step queries.

Record retrieval and formatting normally complete the process.”


http://www.ncbi.nlm.nih.gov/books/NBK179288/





EInfo






EInfo

Provides a list of the names of all valid Entrez databases.Provides statistics for a single database, including lists of indexing

fields and available link names.






EInfo

Base URL:https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi


https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi





EInfoXML Ouput

https:

//eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi

<e I n f o R e s u l t><D bLi s t>

<DbName>pubmed</DbName><DbName>p r o t e i n</DbName><DbName>n u c c o r e</DbName><DbName>n u c l e o t i d e</DbName><DbName>n u c g s s</DbName><DbName>n u c e s t</DbName><DbName>s t r u c t u r e</DbName><DbName>genome</DbName><DbName>a s s e m b l y</DbName><DbName>g c a s s e m b l y</DbName><DbName>genomepr j</DbName><DbName>b i o p r o j e c t</DbName><DbName>b i o s a m p l e</DbName><DbName>b i o s y s t e m s</DbName><DbName>b l a s t d b i n f o</DbName><DbName>books</DbName><DbName>cdd</DbName><DbName>c l i n v a r</DbName>

( . . . )

EInfoJSON Ouput

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.

fcgi?retmode=json

{” h e a d e r ” : {

” t y p e ” : ” e i n f o ” ,” v e r s i o n ” : ” 0 . 3 ”

} ,” e i n f o r e s u l t ” : {

” d b l i s t ” : [”pubmed ” ,” p r o t e i n ” ,” n u c c o r e ” ,

( . . . )” u n i g e n e ” ,” g e n c o l l ” ,” g t r ”

]}

}Pierre Lindenbaum@yokofakun [email protected] http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/courses

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?retmode=json

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?retmode=json





EInfo

Return statistics for a given Entrez database:https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?

db=DbName


https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=DbName

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=DbName





EInfoStatistics for Pubmed


fcgi?db=pubmed

<?xml v e r s i o n=” 1 .0 ”?><e I n f o R e s u l t>

<DbInfo><DbName>pubmed</DbName><MenuName>PubMed</MenuName><De s c r i p t i o n>PubMed b i b l i o g r a p h i c r e c o r d</ De s c r i p t i o n><DbBui ld>Bui ld130805−2117m.4</DbBui ld><Count>22974581</Count><LastUpdate>2013/08/06 08 :33</ LastUpdate><F i e l d L i s t>

( . . . )<F i e l d>

<Name>UID</Name><FullName>UID</FullName><De s c r i p t i o n>Unique number a s s i g n e d to p u b l i c a t i o n</ De s c r i p t i o n><TermCount>0</TermCount>NY<S ing l eToken>Y</ S ing l eToken><H i e r a r c h y>N</ H i e r a r c h y>Y

</ F i e l d><F i e l d>

( . . . )


https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pubmed

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pubmed

EInfoStatistics for Pubmed


fcgi?db=pubmed&retmode=json

{” heade r ” : {

” type ” : ” e i n f o ” ,” v e r s i o n ” : ”0 .3”

} ,” e i n f o r e s u l t ” : {

” db i n f o ” : {”dbname ” : ”pubmed” ,”menuname ” : ”PubMed” ,” d e s c r i p t i o n ” : ”PubMed b i b l i o g r a p h i c r e c o r d ” ,” dbbu i l d ” : ”Bui ld160921−2207m.6” ,” count ” : ”26470199” ,” l a s t u p d a t e ” : ”2016/09/22 16 :32” ,” f i e l d l i s t ” : [

{”name ” : ”ALL” ,” f u l l n ame ” : ” A l l F i e l d s ” ,” d e s c r i p t i o n ” : ” A l l te rms from a l l s e a r c h a b l e f i e l d s ” ,” termcount ” : ”179424126” ,” i s d a t e ” : ”N” ,” i s n um e r i c a l ” : ”N” ,” s i n g l e t o k e n ” : ”N” ,” h i e r a r c h y ” : ”N” ,” i s h i d d e n ” : ”N”

} ,{

”name ” : ”UID” ,” f u l l n ame ” : ”UID” ,” d e s c r i p t i o n ” : ”Unique number a s s i g n e d to p u b l i c a t i o n ” ,

( . . . )Pierre Lindenbaum@yokofakun [email protected] http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/courses

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pubmed&retmode=json

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi?db=pubmed&retmode=json





EInfoWith entrez-direct

$ e i n f o −dbs$ e i n f o −db pubmed






GQuery






GQuery

Provides the number of records retrieved in all Entrez databases bya single text query.






GQueryExample

$ c u r l ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ gquery ? term=ty r anno s au r u s%20r e x&retmode=xml”

<Re su l t><Term>t y r a nno s au r u s r e x</Term><eGQueryResu l t>

<Resu l t I t em><DbName>pubmed</DbName><MenuName/><Count>41</Count><Sta tu s>Ok</ S ta tu s></ Re su l t I t em>

<Resu l t I t em><DbName>pmc</DbName><MenuName/><Count>160</Count><Sta tu s>Ok</ S ta tu s></ Re su l t I t em>

<Resu l t I t em><DbName>mesh</DbName><MenuName/><Count>15</Count><Sta tu s>Ok</ S ta tu s></ Re su l t I t em>

<Resu l t I t em><DbName>books</DbName><MenuName/><Count>179</Count><Sta tu s>Ok</ S ta tu s></ Re su l t I t em>

<Resu l t I t em><DbName>pubmedhealth</DbName><MenuName/><Count>21</Count><Sta tu s>Ok</ S ta tu s></ Re su l t I t em>

<Resu l t I t em><DbName>omim</DbName><MenuName/><Count>10</Count><Sta tu s>Ok</ S ta tu s></ Re su l t I t em>

<Resu l t I t em><DbName>omia</DbName><MenuName/><Count>0</Count><Sta tu s>Termor Database i s not found</ S ta tu s></ Re su l t I t em>

<Resu l t I t em><DbName>n c b i s e a r c h</DbName><MenuName/><Count>1</Count><Sta tu s>Ok</ S ta tu s></ Re su l t I t em>

<Resu l t I t em><DbName>nucco re</DbName><MenuName/><Count>0</Count><Sta tu s>Term or Database i s not found</ S ta tu s></ Re su l t I t em>

( . . . )

GQueryTransforming to HTML using XSLT

The XSLT stylesheet. https://raw.githubusercontent.com/

lindenb/courses/master/about.ncbi/gquery2html.xsl

1 <?xml v e r s i o n=’ 1 .0 ’ encod ing=”UTF−8” ?>2 <x s l : s t y l e s h e e t xm l n s : x s l= ’ h t t p : //www.w3 . org /1999/XSL/Transform ’ v e r s i o n=’ 1 .0 ’>3 <x s l : o u t p u t method=”html ”/>45 <x s l : t em p l a t e match=”/”><html><body>6 <x s l : a p p l y−t emp l a t e s s e l e c t=” Re su l t ”/>7 </body></html></ x s l : t em p l a t e>89 <x s l : t em p l a t e match=” Re su l t ”>

10 <t a b l e><c ap t i o n><x s l : v a l u e−o f s e l e c t=”Term”/></ c ap t i o n>11 <t r><th>Database</ th><th>Count</ th><th>Sta tu s</ th></ t r>12 <x s l : a p p l y−t emp l a t e s s e l e c t=” eGQueryResu l t / Re su l t I t em ”/>13 </ t a b l e>14 </ x s l : t em p l a t e>1516 <x s l : t em p l a t e match=” Re su l t I t em ”>17 <t r>18 <td><a>19 <x s l : a t t r i b u t e name=” h r e f ”>h t t p : //www. ncb i . nlm . n i h . gov/<x s l : v a l u e−o f s e l e c t=”

DbName”/>?cmd=sea r ch&amp ; term=<x s l : v a l u e−o f s e l e c t=” t r a n s l a t e (/ Re s u l t /Term, ’ ’ , ’+ ’ ) ”/></ x s l : a t t r i b u t e>

20 <x s l : v a l u e−o f s e l e c t=”DbName”/></a></ td>21 <td><x s l : v a l u e−o f s e l e c t=”Count”/></ td>22 <td><x s l : v a l u e−o f s e l e c t=” Sta tu s ”/></ td>23 </ t r>24 </ x s l : t em p l a t e>2526 </ x s l : s t y l e s h e e t>


https://raw.githubusercontent.com/lindenb/courses/master/about.ncbi/gquery2html.xsl

https://raw.githubusercontent.com/lindenb/courses/master/about.ncbi/gquery2html.xsl

GQueryTransforming to HTML

$ c u r l ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ gquery ? term=ty r anno s au r u s%20r e x&retmode=xml” |\

x s l t p r o c gquery2html . x s l −

<html><body>

<t a b l e><capt i on>t y r a nno s au r u s r e x</ capt i on><t r>

<th>Database</ th><th>Count</ th><th>Sta tu s</ th>

</ t r><t r>

<td><a h r e f=” h t t p s : //www. ncb i . nlm . n i h . gov/pubmed?cmd=sea r ch&amp ; term=ty r anno s au r u s+r e x ”>pubmed</a>

</ td><td>41</ td><td>Ok</ td>

</ t r><t r>

<td><a h r e f=” h t t p s : //www. ncb i . nlm . n i h . gov/pmc?cmd=sea r c h&amp ; term=ty r anno s au r u s+r e x ”>pmc</a>

</ td><td>160</ td><td>Ok</ td>

</ t r><t r>

<td><a h r e f=” h t t p s : //www. ncb i . nlm . n i h . gov/mesh?cmd=sea r ch&amp ; term=ty r anno s au r u s+r e x ”>mesh</a>

</ td><td>15</ td>Pierre Lindenbaum@yokofakun [email protected] http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/courses

ESearch






ESearch

Provides a list of UIDs matching a text query

Posts the results of a search on the History server

Downloads all UIDs from a dataset stored on the Historyserver

Combines or limits UID datasets stored on the History server

Sorts sets of UIDs






ESearchSyntax

Base URL https:

//eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi


https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi





ESearchSearching for ’Mammuthus primigenius’

c u r l ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e s e a r c h . f c g i ?db=nu c l e o t i d e&term=%22Mammuthus%20p r im i g e n i u s%22%5BORGN%5D” |\

xm l l i n t −−fo rmat −

<eSea r c hRe su l t><Count>684</Count><RetMax>20</RetMax><Re tS t a r t>0</ Re tS t a r t>

507866428</ Id>124056416</ Id>383843869</ Id>383843867</ Id>383843865</ Id>383843863</ Id>383843861</ Id>383843859</ Id>383843857</ Id>383843855</ Id>383843853</ Id>383843851</ Id>383843849</ Id>383843847</ Id>383843845</ Id>157367690</ Id>157367676</ Id>157367662</ Id>157367648</ Id>157367634</ Id>

<Tr a n s l a t i o n S e t>

<T r a n s l a t i o n><From>”Mammuthus p r im i g e n i u s ” [ORGN]</From><To>”Mammuthus p r im i g e n i u s ” [ Organism ]</To>

</ T r a n s l a t i o n></ T r a n s l a t i o n S e t><Tran s l a t i o nS t a c k>

<TermSet><Term>”Mammuthus p r im i g e n i u s ” [ Organism ]</Term><F i e l d>Organism</ F i e l d><Count>684</Count><Exp lode>Y</ Exp lode>

</TermSet><OP>GROUP</OP>

</ T r a n s l a t i o nS t a c k><Que r yT ran s l a t i o n>”Mammuthus p r im i g e n i u s ” [ Organism ]</ Que r yT ran s l a t i o n>

</ eSea r chRe su l t>

ESearchSearching for ’Mammuthus primigenius’ (JSON)

c u r l ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e s e a r c h . f c g i ?db=nu c l e o t i d e&term=%22Mammuthus%20p r im i g e n i u s%22%5BORGN%5D&retmode=j s o n ”

{” heade r ” : {

” type ” : ” e s e a r c h ” ,” v e r s i o n ” : ”0 .3”

} ,” e s e a r c h r e s u l t ” : {

” count ” : ”811” ,” retmax ” : ”20” ,” r e t s t a r t ” : ”0” ,” i d l i s t ” : [

”1059791223” ,”198241525” ,”198241523” ,”198241521” ,”198241519” ,”198241517” ,”198241515” ,”198241513” ,”198241511” ,”198241509” ,”198241507” ,”198241505” ,”198241503” ,”198241501” ,”198241499” ,”198241497” ,”198241495” ,”198241493” ,”198241491” ,”198241489”

] ,” t r a n s l a t i o n s e t ” : [

{” from ” : ”\”Mammuthus p r im i g e n i u s \”[ORGN]” ,” to ” : ”\”Mammuthus p r im i g e n i u s \”[ Organism ]”

}] ,” t r a n s l a t i o n s t a c k ” : [

{” term ” : ”\”Mammuthus p r im i g e n i u s \”[ Organism ] ” ,” f i e l d ” : ”Organism ” ,” count ” : ”811” ,” exp l ode ” : ”Y”

} ,”GROUP”

] ,” q u e r y t r a n s l a t i o n ” : ”\”Mammuthus p r im i g e n i u s \”[ Organism ]”

}}






ESearchthe retmax parameter

c u r l ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e s e a r c h . f c g i ?db=nu c l e o t i d e&term=%22Mammuthus%20p r im i g e n i u s%22%5BORGN%5D&retmax=2” |\



507866428</ Id>124056416</ Id>

ESearchthe retstart parameter

c u r l ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e s e a r c h . f c g i ?db=nu c l e o t i d e&term=%22Mammuthus%20p r im i g e n i u s%22%5BORGN%5D&retmax=3&r e t s t a r t =100” |\



300810656</ Id>300810655</ Id>300810654</ Id>

ESearchrettype=retcount

c u r l ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e s e a r c h . f c g i ?db=nu c l e o t i d e&term=%22Mammuthus%20p r im i g e n i u s%22%5BORGN%5D&r e t t y p e=count ” |\


<e S e a r c h R e s u l t><Count>684</ Count>

</ e S e a r c h R e s u l t>

ESearchsort=Date Released

c u r l −s ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e s e a r c h . f c g i ?db=nu c l e o t i d e&term=%22Mammuthus%20p r im i g e n i u s%22%5BORGN%5D&s o r t=Date+Re l ea s ed ”


<e S e a r c h R e s u l t><Count>811</ Count><RetMax>20</RetMax><R e t S t a r t>0</ R e t S t a r t>103320464410332046581033204672103320468610332047291033204771103320478510332047991033204813103320482710332048711033205124103320519410332052081033205222103320523610332052641033205390( . . . )

ESummary






ESummarySyntax

Returns document summaries (DocSums) for a list of inputUIDs

Returns DocSums for a set of UIDs stored on the EntrezHistory server






ESummarySyntax

Base URL: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=(DB)&id=(TERM)


https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=(DB)&id=(TERM)

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=(DB)&id=(TERM)





ESummaryRetrieve nucleotide gi=507866428

$ c u r l ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s /esummary . f c g i ?db=nu c l e o t i d e&i d =507866428”

<eSummaryResult><DocSum>507866428</ Id>KC524742</ Item>Mammuthus p r im i g e n i u s i s o l a t e CME2005/915 myog lob in (Mb) gene , p a r t i a l cds</ Item>g i |507866428 | gb |KC524742 . 1 | [ 5 0 7866428 ]</ Item>507866428</ Item>2013/06/15</ Item>2013/06/21</ Item>0</ Item>37349</ Item>9042</ Item> l i v e</ Item></ Item><! [CDATA[ ] ]></ Item></DocSum></ eSummaryResult>

ESummaryRetrieve nucleotide gi=507866428 in JSON

$ c u r l ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s /esummary . f c g i ?db=nu c l e o t i d e&i d =507866428& retmode=j s o n ”

{” heade r ” : {

” type ” : ”esummary ” ,” v e r s i o n ” : ”0 .3”

} ,” r e s u l t ” : {

” u i d s ” : [”507866428”

] ,”507866428”: {

” u id ” : ”507866428” ,” c ap t i o n ” : ”KC524742 ” ,” t i t l e ” : ”Mammuthus p r im i g e n i u s i s o l a t e CME2005/915 myog lob in (Mb) gene , p a r t i a l cds ” ,” e x t r a ” : ” g i |507866428 | gb |KC524742 . 1 | ” ,” g i ” : 507866428 ,” c r e a t e d a t e ” : ”2013/06/15” ,” updatedate ” : ”2013/06/21” ,” f l a g s ” : ”” ,” t a x i d ” : 37349 ,” s l e n ” : 9042 ,” b iomol ” : ” genomic ” ,”moltype ” : ”dna ” ,” t opo l ogy ” : ” l i n e a r ” ,” sou rcedb ” : ” i n s d ” ,” s e g s e t s i z e ” : ”” ,” p r o j e c t i d ” : ”0” ,

( . . . )






ESummaryRetrieve snp rs25

$ c u r l ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s /esummary . f c g i ?db=snp&i d=25”

<eSummaryResult><DocSum>25</ Id>25</ Item></ Item></ Item>0 .4913</ Item></ Item>0</ Item></ Item></ Item>THSD7A</ Item>221981</ Item>NM 015204 . 2 , NT 007819 .17</ Item>7</ Item>1</ Item>1000GENOMES, BGI , BL ,BUSHMAN,COMPLETE GENOMICS,CSHL−HAPMAP,GMI , ILLUMINA−UK,KWOK,PERLEGEN,SSMP,TISHKOFF</ Item>i n t r on−v a r i a n t</ Item>by−1000G, by−c l u s t e r , by−f r equency , by−hapmap</ Item>t r u e</ Item>f a l s e</ Item>HGVS=NC 000007 .13 : g .11584142T&gt ;C , NG 027670 . 1 : g .292683A&gt ;G, NM 015204 . 2 : c .1454−1398A&gt ;G, NT 007819 .17 : g .11574142T&gt ;C|SEQ=TCTGTGAGCTTCTGCATGCAATCCT[A/G]TGCAATTGGAATTTGATAGTCCTTT|GENE=THSD7A:221981</ Item>50</ Item>0</ Item>9606</ Item>2 5 | 2 | 0 | 1 | 1 | 1 | 7 | NT 007819 .17 |11574141 |11584142 |THSD7A|0 . 499848 |0 . 00872267 | | 51 |1 | 1 |36 | 13 8 | 0 | | | T:2178 :0 .4913</ Item>36</ Item>138</ Item>2000−09−19 17 :02</ Item>2013−06−21 14 :17</ Item></ Item>computed , h y b r i d i z e , sequence , unknown</ Item></ Item>ILLUMINA−UK| h t t p : //www. i l l um i n a . com/HumanGenomeNA18507 000019106 NCBI36 . 1 ch r7 11550667</ Item>654151077</ Item>7 11584142</ Item>R</ Item>snp</ Item>7 :11584142</ Item>NT 007819 .17 :11574142</ Item></ Item>325952</ Item></DocSum></ eSummaryResult>

ESummaryRetrieve pubmed pmid=7939126

$ c u r l ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s /esummary . f c g i ?db=pubmed&i d =7939126”

<eSummaryResult><DocSum>7939126</ Id>1994 Apr</ Item></ Item>S l e ep</ Item>Broughton R</ Item>B i l l i n g s R</ Item>Ca r tw r i gh t R</ Item>Doucette D</ Item>Edmeads J</ Item>Edwardh M</ Item>Er v i n F</ Item>Orchard B</ Item>H i l l R</ Item>Tu r r e l l G</ Item></ Item>Tu r r e l l G</ Item>Homic ida l somnambul ism: a ca se r e p o r t .</ Item>17</ Item>3</ Item>253−64</ Item>Eng l i s h</ Item></ Item>7809084</ Item>0161−8105</ Item>1550−9109</ Item>Jou r na l A r t i c l e</ Item></ Item>PubMed − i ndexed f o r MEDLINE</ Item>ppub l i s h</ Item>7939126</ Item>7939126</ Item>7939126</ Item></ Item>1994/04/01 00 :00</ Item>1994/04/01 00 :01</ Item>1994/04/01 00 :00</ Item></ Item></ Item>1</ Item>4</ Item>S l e ep</ Item></ Item>1994 Apr ; 1 7 ( 3 ) :253−64</ Item></DocSum></ eSummaryResult>

EFetch






EFetchSyntax

Base URL: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=(db)&id=(ID)


https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=(db)&id=(ID)

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=(db)&id=(ID)





EFetchRetrieve nucleotide gi=507866428 as ASN.1

Default https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=507866428

Seq−e n t r y : := s e t {c l a s s nuc−p ro t ,d e s c r {

source {genome genomic ,org {

taxname ”Mammuthus p r im i g e n i u s ” ,common ” woo l l y mammoth” ,db {{

db ” taxon ” ,tag

i d 37349 } } ,orgname {

nameb i nom i a l {

genus ”Mammuthus” ,s p e c i e s ” p r im i g e n i u s ” } ,

mod {{








EFetchRetrieve nucleotide gi=507866428 as Fasta


fcgi?db=nucleotide&id=507866428&rettype=fasta

>g i |507866428 | gb |KC524742 . 1 | Mammuthus p r im i g e n i u s i s o l a t e CME2005/915 myog lob in(Mb) gene , p a r t i a l cds

GCACTTGCTTTTTTTGTCTTCTTCAGACCACGACATGGGACTCAGCGACGGGGAATGGGAGTTGGTGTTGAAAACCTGGGGGAAAGTGGAGGCTGACATCCCGGGCCATGGGCTGGAAGTCTTCGTCAGGTAAAGGAAGAAATCCTGTGGCCCCCATCACCCACCCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN


https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=507866428&rettype=fasta

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=507866428&rettype=fasta





EFetchRetrieve nucleotide gi=507866428 as TinySeq

https:

//eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?

db=nucleotide&id=507866428&rettype=fasta&retmode=xml

<?xml v e r s i o n=” 1 .0 ”?><!DOCTYPE TSeqSet PUBLIC ”−//NCBI//NCBI TSeq/EN”<TSeqSet>

<TSeq><TSeq seqtype v a l u e=” n u c l e o t i d e ”/><TSeq g i>507866428</TSeq g i><TSeq accver>KC524742 . 1</TSeq accver><TSeq tax id>37349</TSeq tax id><TSeq orgname>Mammuthus p r im i g e n i u s</TSeq orgnam<TSeq d e f l i n e>Mammuthus p r im i g e n i u s i s o l a t e CME2<TSeq length>9042</TSeq length><TSeq sequence>GCACTTGCTTTTTTTGTCTTCTTCAGACCACGA

</TSeq></TSeqSet>


https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=507866428&rettype=fasta&retmode=xml

EFetchRetrieve nucleotide gi=507866428 as Genbank-xml


fcgi?db=nucleotide&id=507866428&retmode=xml

<GBSeq><GBSeq locus>KC524742</GBSeq locus><GBSeq length>9042</GBSeq length><GBSeq st randedness>doub l e</GBSeq st randedness><GBSeq moltype>DNA</GBSeq moltype><GBSeq topology> l i n e a r</GBSeq topology><GBSeq d i v i s i o n>MAM</ GBSeq d i v i s i o n><GBSeq update−date>21−JUN−2013</GBSeq update−date><GBSeq create−date>15−JUN−2013</GBSeq create−date><GBSeq d e f i n i t i o n>Mammuthus p r im i g e n i u s i s o l a t e CME2005/915 myog lob in (Mb) gene , p a r t i a l cds</ GBSeq d e f i n i t i o n><GBSeq primary−a c c e s s i o n>KC524742</GBSeq primary−a c c e s s i o n><GBSeq access ion−v e r s i o n>KC524742 . 1</GBSeq access ion−v e r s i o n><GBSeq other−s e q i d s>

<GBSeqid>gb |KC524742 . 1 |</GBSeqid><GBSeqid>g i |507866428</GBSeqid>

</GBSeq other−s e q i d s><GBSeq source>Mammuthus p r im i g e n i u s ( woo l l y mammoth)</GBSeq source><GBSeq organism>Mammuthus p r im i g e n i u s</GBSeq organism>

( . . . )

EFetchRetrieve nucleotide gi=507866428 as Genbank


fcgi?db=nucleotide&id=507866428&rettype=gb

LOCUS KC524742 9042 bp DNA l i n e a r MAM 21−JUN−2013DEFINITION Mammuthus p r im i g e n i u s i s o l a t e CME2005/915 myog lob in (Mb) gene ,

p a r t i a l cds .ACCESSION KC524742VERSION KC524742 . 1 GI :507866428KEYWORDS .SOURCE Mammuthus p r im i g e n i u s ( woo l l y mammoth)

ORGANISM Mammuthus p r im i g e n i u sEukaryota ; Metazoa ; Chordata ; C r an i a t a ; Ve r t e b r a t a ; Eu t e l e o s t om i ;Mammalia ; Eu t h e r i a ; A f r o t h e r i a ; P robo s c i d ea ; E l e phan t i d a e ;Mammuthus .

REFERENCE 1 ( ba se s 1 to 9042)AUTHORS Mirceta , S . , S ignore ,A .V . , Burns , J .M. , Cos s i n s ,A .R . , Campbel l ,K. L .

and Berenbr ink ,M.TITLE Evo l u t i o n o f mammalian d i v i n g c a p a c i t y t r a c e d by myog lob in net

s u r f a c e cha rgeJOURNAL Sc i e n c e 340 (6138) , 1234192 (2013)PUBMED 23766330

REFERENCE 2 ( ba se s 1 to 9042)AUTHORS Signore ,A .V . , Campbel l ,K. L . and Poinar ,H.N.TITLE D i r e c t Submis s i onJOURNAL Submitted (09−JAN−2013) B i o l o g i c a l Sc i ence s , U n i v e r s i t y o f

Manitoba , 50 S i f t o n Road , Winnipeg , Manitoba R3T2N2 , CanadaCOMMENT ##Assembly−Data−START##

Sequenc ing Technology : : Sanger d i d eoxy s equenc i ng##Assembly−Data−END##

FEATURES Loca t i on / Q u a l i f i e r ssource 1 . . 9 042

/ organ i sm=”Mammuthus p r im i g e n i u s ”/mo l type=”genomic DNA”/ i s o l a t e=”CME2005/915”/ d b x r e f=” taxon :37349 ”/ t i s s u e t y p e=”bone”

gene <35..>9042/gene=”Mb”

mRNA j o i n ( <35 . .129 ,5627 . .5849 ,8979 . . >9042)/ gene=”Mb”/ product=”myog lob in ”

CDS j o i n (35 . . 129 , 5627 . . 5849 , 8979 . . >9042 )

EFetchEfetch works with the ACCESSION NUMBERS


fcgi?db=nucleotide&id=KC524742&rettype=gb

LOCUS KC524742 9042 bp DNA l i n e a r MAM 21−JUN−2013DEFINITION Mammuthus p r im i g e n i u s i s o l a t e CME2005/915 myog lob in (Mb) gene ,

p a r t i a l cds .ACCESSION KC524742VERSION KC524742 . 1 GI :507866428KEYWORDS .SOURCE Mammuthus p r im i g e n i u s ( woo l l y mammoth)

ORGANISM Mammuthus p r im i g e n i u sEukaryota ; Metazoa ; Chordata ; C r an i a t a ; Ve r t e b r a t a ; Eu t e l e o s t om i ;Mammalia ; Eu t h e r i a ; A f r o t h e r i a ; P robo s c i d ea ; E l e phan t i d a e ;Mammuthus .

REFERENCE 1 ( ba se s 1 to 9042)AUTHORS Mirceta , S . , S ignore ,A .V . , Burns , J .M. , Cos s i n s ,A .R . , Campbel l ,K. L .

and Berenbr ink ,M.TITLE Evo l u t i o n o f mammalian d i v i n g c a p a c i t y t r a c e d by myog lob in net

s u r f a c e cha rgeJOURNAL Sc i e n c e 340 (6138) , 1234192 (2013)PUBMED 23766330

REFERENCE 2 ( ba se s 1 to 9042)AUTHORS Signore ,A .V . , Campbel l ,K. L . and Poinar ,H.N.TITLE D i r e c t Submis s i onJOURNAL Submitted (09−JAN−2013) B i o l o g i c a l Sc i ence s , U n i v e r s i t y o f

Manitoba , 50 S i f t o n Road , Winnipeg , Manitoba R3T2N2 , CanadaCOMMENT ##Assembly−Data−START##

Sequenc ing Technology : : Sanger d i d eoxy s equenc i ng##Assembly−Data−END##

FEATURES Loca t i on / Q u a l i f i e r ssource 1 . . 9 042

/ organ i sm=”Mammuthus p r im i g e n i u s ”/mo l type=”genomic DNA”/ i s o l a t e=”CME2005/915”/ d b x r e f=” taxon :37349 ”/ t i s s u e t y p e=”bone”

gene <35..>9042/gene=”Mb”

mRNA j o i n ( <35 . .129 ,5627 . .5849 ,8979 . . >9042)/ gene=”Mb”/ product=”myog lob in ”

CDS j o i n (35 . . 129 , 5627 . . 5849 , 8979 . . >9042 )


https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=KC524742&rettype=gb

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=KC524742&rettype=gb

EFetchUsing the WebEnv parameter.

Web environment string returned from a previous ESearch, EPostor ELink call. When provided, ESearch will post the results of thesearch operation to this pre-existing WebEnv.






Searching extinct species in the NCBI taxonomy (’extinct[PROP]’)c u r l ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e s e a r c h . f c g i ?usehistory=y&db=

taxonomy&term=e x t i n c t%5BPROP%5D”

<eSea r c hRe su l t><Count>145</Count><RetMax>20</RetMax><Re tS t a r t>0</ Re tS t a r t><QueryKey>1</QueryKey><WebEnv>NCID 1 75550312 130.14.18.34 9001 1375948145 325582538</WebEnv>

1225531</ Id>1225530</ Id>1211276</ Id>1211275</ Id>1027716</ Id>948961</ Id>943952</ Id>867394</ Id>867393</ Id>748142</ Id>748141</ Id>741158</ Id>703576</ Id>703571</ Id>703559</ Id>693865</ Id>686441</ Id>665113</ Id>659069</ Id>656807</ Id>

<Tr a n s l a t i o n S e t /><Tran s l a t i o nS t a c k>

<TermSet><Term>e x t i n c t [PROP]</Term><F i e l d>PROP</ F i e l d><Count>145</Count><Exp lode>N</ Exp lode>


</ T r a n s l a t i o nS t a c k><Que r yT ran s l a t i o n>e x t i n c t [PROP]</ Que r yT ran s l a t i o n>

Fetch the extinct species in the NCBI taxonomy (’extinct[PROP]’)using the WebEnv parameter.

$ c u r l ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e f e t c h . f c g i ?db=taxonomy&query key=1&WebEnv=NCID 1 75550312 130.14.18.34 9001 1375948145 325582538&retmode=xml”

<TaxaSet><Taxon><TaxId>1225531</TaxId><Sc i e n t i f i cName>Equus ovodov i</ S c i e n t i f i cName><OtherNames>

<Synonym>Equus ( Sussemionus ) ovodov i</Synonym><Name>

<ClassCDE>a u t h o r i t y</ClassCDE><DispName>Equus ovodov i Eisenmann &amp ; Se rge j , 2011</DispName>

</Name></OtherNames><ParentTax Id>1225530</ParentTax Id><Rank>s p e c i e s</Rank><D i v i s i o n>Mammals</ D i v i s i o n><Genet icCode>

<GCId>1</GCId><GCName>Standard</GCName>

</Genet icCode><MitoGenet icCode>( . . . . )

EPOST






EPost

Uploads a list of UIDs to the Entrez History server

Appends a list of UIDs to an existing set of UID lists attachedto a Web Environment






EPostPost gi to epost

Get a list of gis of extincts animals:

wget −O − ’ h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e s e a r c h . f c g i ?db=taxonomy&term=e x t i n c t [PROP]& retmax=1000 ’ |\

xm l l i n t −fo rmat − |\grep ’< Id>’ |\cut −d ’< ’ −f 2 |\cut −d ’> ’ −f 2|\t r ”\n” ” , ”

output:

1860150 ,1860149 ,1849957 ,1825730 ,1825729 ,1636722 ,1607772 ,1607771 ,1607767 ,1607757 ,1607756 ,1597978 ,1582057 ,1566623 ,1563127 ,1563126 ,1563125 ,1563124 ,1563123 ,1563122 ,1563121 ,1563120 ,1560315 ,1560314 ,1543223 ,1542494 ,1542469 ,1530197 ,1524889 ,1523245 ,1513476 ,1513474 ,1503129 ,1453604 ,1425170 ,1415635 ,1295174 ,1225531 ,1225530 ,1211276 ,1211275 ,1027716 ,948961 ,943952 ,867394 ,867393 ,748142 ,748141 ,741158 ,703576 ,703571 ,703559 ,693865 ,686441 ,665113 ,659069 ,656807 ,647691 ,647690 ,643746 ,643745 ,643744 ,643742 ,577682 ,572106 ,572105 ,572104 ,572099 ,572098 ,570943 ,570942 ,570941 ,551196 ,544298 ,523825 ,523824 ,523822 ,523821 ,523820 ,518692 ,518691 ,518689 ,475185 ,436495 ,436494 ,436493 ,436488 ,402889 ,399386 ,399178 ,386524 ,379504 ,363580 ,363579 ,363578 ,363571 ,339614 ,339612 ,339609 ,330944 ,330640 ,330639 ,330638 ,330637 ,330636 ,328612 ,314500 ,307641 ,304335 ,272462 ,268291 ,251263 ,251094 ,251093 ,239970 ,239969 ,237965 ,230980 ,230979 ,227166 ,227165 ,223567 ,222863 ,222862 ,216182 ,216181 ,201717 ,201716 ,192211 ,188536 ,187135 ,187134 ,187133 ,187132 ,187131 ,187118 ,184920 ,180214 ,180178 ,180177 ,180176 ,180175 ,180174 ,173935 ,166505 ,148923 ,147494 ,147466 ,147464 ,136416 ,136415 ,126594 ,126429 ,115942 ,107030 ,103864 ,94623 ,92649 ,92648 ,89252 ,89250 ,63631 ,63221 ,54568 ,54500 ,54497 ,54366 ,54365 ,48784 ,46906 ,39097 ,39053 ,39051 ,37349 ,37348 ,37185 ,27445 ,27444 ,20678 ,13266 ,13140 ,9619 ,9275 ,9274 ,9273 ,8818 ,8817 ,8815 ,8813 ,8812 ,8811 ,8810 ,8367 ,3409

EPostPost gi to epost

wget −O − ’ h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / epo s t . f c g i ?db=taxonomy&WebEnd=NCID 1 15435144 130 . 1 4 . 2 2 . 2 1 59001 1474637318 669113391 0MetA0 S MegaStore F 1&i d=1860150 ,1860149 ,1849957 ,1825730 ,1825729 ,1636722 ,1607772. . . ”

Output:

<?xml v e r s i o n=” 1 .0 ”?><!DOCTYPE ePo s tRe su l t PUBLIC ”−//NLM//DTD ePos tResu l t , 11 May 2002//EN” ” h t t p : //

www. ncb i . nlm . n i h . gov/ e n t r e z / query /DTD/ ePost 020511 . dtd ”><ePo s tRe su l t><QueryKey>1</QueryKey><WebEnv>NCID 1 15467192 130 . 1 4 . 2 2 . 2 1 5

9001 1474637456 570452194 0MetA0 S MegaStore F 1</WebEnv></ ePo s tRe su l t>

EPostSearching in the WebEnv

Search Homo Sapiens in WebEnv ?

c u r l −s ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e s e a r c h . f c g i ?db=taxonomy&term=Homo%20Sapiens&u s e h i s t o r y=y&WebEnv=NCID 1 75550312 130 . 1 4 . 1 8 . 3 49001 1375948145 325582538&que r y k ey=1”

<eSea r c hRe su l t><Count>0</Count><RetMax>0</RetMax><Re tS t a r t>0</ Re tS t a r t><QueryKey>8</QueryKey><WebEnv>NCID 1 75550312 130 . 1 4 . 1 8 . 3 4 9001 1375948145 325582538</WebEnv><Tr a n s l a t i o n S e t /><Tran s l a t i o nS t a c k>

<OP>GROUP</OP><TermSet>

<Term>homo s a p i e n s [ A l l Names ]</Term><F i e l d>A l l Names</ F i e l d><Count>0</Count><Exp lode>N</ Exp lode>

</TermSet><OP>AND</OP>

</ T r a n s l a t i o nS t a c k><Que r yT ran s l a t i o n>(#2) AND homo s a p i e n s [ A l l Names ]</ Que r yT ran s l a t i o n>

EPostSearching in the WebEnv

Search Tyranosaurus in WebEnv ?

$ c u r l −s ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e s e a r c h . f c g i ?db=taxonomy&term=Tyrannosaurus&u s e h i s t o r y=y&WebEnv=NCID 1 75550312 130 . 1 4 . 1 8 . 3 49001 1375948145 325582538&que r y k ey=1”

<eSea r c hRe su l t><Count>1</Count><RetMax>1</RetMax><Re tS t a r t>0</ Re tS t a r t><QueryKey>9</QueryKey><WebEnv>NCID 1 75550312 130 . 1 4 . 1 8 . 3 4 9001 1375948145 325582538</WebEnv>

436494</ Id><Tr a n s l a t i o n S e t /><Tran s l a t i o nS t a c k>

<OP>GROUP</OP><TermSet>

<Term>Tyrannosaurus [ A l l Names ]</Term><F i e l d>A l l Names</ F i e l d><Count>1</Count><Exp lode>N</ Exp lode>

</TermSet><OP>AND</OP>

</ T r a n s l a t i o nS t a c k><Que r yT ran s l a t i o n>(#2) AND Tyrannosaurus [ A l l Names ]</ Que r yT ran s l a t i o n>

EDirect: combining tools






Piping Edirect

e s e a r c h −db taxonomy −q u e r y ” T y r a n n o s a u r u s ” | \e f e t c h −fo rmat xml






Piping Edirect

e s e a r c h −db pubmed −q u e r y ” T y r a n n o s a u r u s ” | \e f i l t e r −mindate 2005 | \e f e t c h −fo rmat docsum | \x t r a c t −p a t t e r n DocumentSummary \−e l em en t M e d l i n e C i t a t i o n /PMID \−e l em en t I d S o r t F i r s t A u t h o r






Elink






Elink

Returns UIDs linked to an input set of UIDs in either thesame or a different Entrez database

Returns UIDs linked to other UIDs in the same Entrezdatabase that match an Entrez query

Checks for the existence of Entrez links for a set of UIDswithin the same database

Lists the available links for a UID

Lists LinkOut URLs and attributes for a set of UIDs

Lists hyperlinks to primary LinkOut providers for a set of UIDs

Creates hyperlinks to the primary LinkOut provider for a singleUID






Elink

Base URL:https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi


https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi





ELinkSearching the pubmed records associated to sequence gi:507866428

h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e l i n k . f c g i ? dbfrom=nu c l e o t i d e&db=pubmed&i d =507866428&cmd=n e i g h b o r s c o r e

<eL i n kRe s u l t><L inkSe t>

<DbFrom>nucco re</DbFrom>

507866428</ Id><LinkSetDb>

<DbTo>pubmed</DbTo><LinkName>nuccore pubmed</LinkName><L ink>

23766330</ Id><Score>0</ Score>

</ L ink></LinkSetDb>

</ L inkSe t></ eL i n kRe s u l t>

$ c u r l −s ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e f e t c h . f c g i ?db=pubmed&i d =23766330& r e t t y p e=med l i ne&retmode=t e x t ”

PMID− 23766330TI − Evo l u t i o n o f mammalian d i v i n g c a p a c i t y t r a c e d by myog lob in net s u r f a c e

cha rge .PG − 1234192LID − 10.1126/ s c i e n c e .1234192 [ do i ]

Transformations






EfetchTransforming to SVG

Using the stylesheethttps://github.com/lindenb/xslt-sandbox/blob/master/

stylesheets/bio/ncbi/gb2svg.xsl

x s l t p r o c <( c u r l ” h t t p s : // raw . g i t hub . com/ l i n d e n b / x s l t−sandbox /master / s t y l e s h e e t s/ b i o / ncb i / gb2svg . x s l ” ) \

” h t t p s : //www. ncb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e f e t c h . f c g i ?db=nu c l e o t i d e&i d=14971102&retmode=xml&r e t t y p e=gbc”


https://github.com/lindenb/xslt-sandbox/blob/master/stylesheets/bio/ncbi/gb2svg.xsl

https://github.com/lindenb/xslt-sandbox/blob/master/stylesheets/bio/ncbi/gb2svg.xsl

1 <?xml v e r s i o n=” 1 .0 ” encod ing=”UTF−8”?>2 <s v g : s v g xm ln s : s v g=” h t t p : //www.w3 . org /2000/ svg ” h e i g h t=”121” width=”920” s t y l e=”

s t r oke−wid th : 1px ; ”>3 <s v g : t i t l e>Human r o t a v i r u s segment 7 NSP3 gene , complete cds</ s v g : t i t l e>4 <s v g : d e f s>5 <s v g : l i n e a r G r a d i e n t x1=”0%” y1=”0%” x2=”0%” y2=”100%” i d=” grad ”>6 <s v g : s t o p o f f s e t=”5%” stop−c o l o r=” b l a ck ”/>7 <s v g : s t o p o f f s e t=”50%” stop−c o l o r=”whitesmoke ”/>8 <s v g : s t o p o f f s e t=”95%” stop−c o l o r=” b l a ck ”/>9 </ s v g : l i n e a r G r a d i e n t>

10 <s v g : l i n e a r G r a d i e n t x1=”0%” y1=”0%” x2=”0%” y2=”100%” i d=”v e r t i c a l b o d y g r a d i e n t ”>

11 <s v g : s t o p o f f s e t=”5%” stop−c o l o r=”wh i t e ”/>12 <s v g : s t o p o f f s e t=”95%” stop−c o l o r=” l i g h t g r a y ”/>13 </ s v g : l i n e a r G r a d i e n t>14 </ s v g : d e f s>15 <s v g : s t y l e type=” t e x t / c s s ”/>16 <s v g : g>17 <s v g : g t r an s f o rm=” t r a n s l a t e (0 , 0 ) ”>18 <s v g : r e c t x=”0” y=”0” width=”920” h e i g h t=”120” f i l l =” u r l (#

v e r t i c a l b o d y g r a d i e n t ) ” s t r o k e=” b l a c k ”/>19 <s v g : t e x t s t y l e=” c o l o r : r e d ; font−s i z e : 3 5 p x ; ” x=”10” y=”35”>Human r o t a v i r u s

segment 7 NSP3 gene , complete cds</ s v g : t e x t>20 <s v g : g>21 <s v g : r e c t x=”10” y=”40” width=”900” h e i g h t=”18” s t y l e=” f i l l : u r l (#grad ) ;

s t r o k e : b l a c k ; ” t i t l e=” 1 . . 1 074 ”/>22 <s v g : t e x t y=”54” x=”460” tex t−anchor=”midd le ”><s v g : t s p a n s t y l e=” font−

we i g h t : b o l d ; ”>s ou r c e</ s v g : t s p a n><s v g : t s p a n xm l n s : x s i=” h t t p : //www.w3. org /2001/XMLSchema−i n s t a n c e ” xm l n s : x l i n k=” h t t p : //www.w3 . org /1999/x l i n k ” font−we ight=” bo ld ”>organ i sm</ s v g : t s p a n>:Human r o t a v i r u s A <s v g : t s p a n xm l n s : x s i=” h t t p : //www.w3 . org /2001/XMLSchema−i n s t a n c e ”xm l n s : x l i n k=” h t t p : //www.w3 . org /1999/ x l i n k ” font−we ight=” bo ld ”>mol type</ s v g : t s p a n>: genomic RNA <s v g : t s p a n xm l n s : x s i=” h t t p : //www.w3 . org /2001/XMLSchema−i n s t a n c e ” xm l n s : x l i n k=” h t t p : //www.w3 . org/1999/ x l i n k ” font−we ight=” bo ld ”>s t r a i n</ s v g : t s p a n>:M <s v g : t s p a nxm l n s : x s i=” h t t p : //www.w3 . org /2001/XMLSchema−i n s t a n c e ” xm l n s : x l i n k=”h t t p : //www.w3 . org /1999/ x l i n k ” font−we ight=” bo ld ”>segment</ s v g : t s p a n>: 7 <s v g : t s p a n xm l n s : x s i=” h t t p : //www.w3 . org /2001/XMLSchema−i n s t a n c e” xm l n s : x l i n k=” h t t p : //www.w3 . org /1999/ x l i n k ” font−we ight=” bo ld ”>c l o n e</ s v g : t s p a n>:M0</ s v g : t e x t>

23 </ s v g : g>24 <s v g : g>25 <s v g : r e c t x=”10” y=”60” width=”27.6794035414725 ” h e i g h t=”18” s t y l e=”

f i l l : u r l (#grad ) ; s t r o k e : b l a c k ; ” t i t l e=” 1 . . 3 4 ”/>26 <s v g : t e x t y=”74” x=”39.6794035414725 ” tex t−anchor=” s t a r t ”>27 <s v g : t s p a n s t y l e=” font−we i g h t : b o l d ; ”>5 ’UTR</s vg : t s pan>28 </s v g : t e x t>29 </svg :g>30 <svg :g>31 <s v g : r e c t x=”38.5181733457595” y=”80” width =”781.733457595526” h e i g h t

=”18” s t y l e=” f i l l : u r l (#grad ) ; s t r o k e : b l a c k ; ” t i t l e =”35..967”/>32 <s v g : t e x t y=”94” x=”429.384902143523” tex t−anchor=”midd le”><s v g : t s p a n

s t y l e=”font−we i g h t : b o l d ;”>CDS</s vg : t s pan><s v g : t s p a n xm l n s : x s i=”h t t p : //www.w3 . org /2001/XMLSchema−i n s t a n c e ” xm l n s : x l i n k=”h t t p : //www.w3 . org /1999/ x l i n k ”font−we ight=”bo ld”>codon s t a r t</s vg : t s pan>: 1 <s v g : t s p a n xm l n s : x s i=”h t t p : //www.w3 . org /2001/XMLSchema−i n s t a n c e ” xm l n s : x l i n k=”h t t p : //www.w3 . org /1999/x l i n k ” font−we ight=”bo ld”>product</s vg : t s pan>:NSP3 <s v g : t s p a n xm l n s : x s i=”h t t p : //www.w3 . org /2001/XMLSchema−i n s t a n c e ” xm l n s : x l i n k=”h t t p : //www.w3 . org/1999/ x l i n k ” font−we ight=”bo ld”>p r o t e i n i d </s vg : t s pan>:AAK74116.1</ s v g : t e x t>

33 </svg :g>34 <svg :g>35 <s v g : r e c t x=”821.090400745573” y=”100” width =”88.909599254427” h e i g h t

=”18” s t y l e=” f i l l : u r l (#grad ) ; s t r o k e : b l a c k ; ” t i t l e =”968..1074”/>36 <s v g : t e x t y=”114” x=”819.090400745573” tex t−anchor=”end”>37 <s v g : t s p a n s t y l e=”font−we i g h t : b o l d ;”>3 ’UTR</ s v g : t s p a n>38 </ s v g : t e x t>39 </ s v g : g>40 <s v g : r e c t x=”0” y=”0” width=”920” h e i g h t=”120” f i l l =”none” s t r o k e=” b l a ck ”/

>41 </ s v g : g>42 </ s v g : g>43 </ s v g : s v g>

EfetchTransforming to R

$ c u r l −s ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e s e a r c h . f c g i ?db=pubmed&term=Tyrannosaurus&u s e h i s t o r y=t r u e ” | xm l l i n t −−fo rmat −

$ c u r l −s ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e f e t c h . f c g i ?db=pubmed&u s e h i s t o r y=t r u e&WebEnv=NCID 1 52434791 130 . 1 4 . 2 2 . 2 1 59001 1375957034 1619786167&que r y k ey=1&retmode=xml”






1 <?xml v e r s i o n=’ 1 .0 ’ encod ing=”UTF−8” ?>2 <x s l : s t y l e s h e e t xm l n s : x s l= ’ h t t p : //www.w3 . org /1999/XSL/Transform ’ v e r s i o n=’ 1 .0 ’>3 <x s l : o u t p u t method=” t e x t ”/>456 <x s l : t em p l a t e match=”/”>7 date2count &l t ;− l i s t ( )8 <x s l : a p p l y−t emp l a t e s s e l e c t=”/PubmedArt i c l eSet / PubmedArt i c l e [ Med l i n eC i t a t i o n /

DateCreated /Year ] ”/>9 d f &l t ;− data . f rame (

10 Year=as . i n t e g e r ( names ( date2count ) ) ,11 Count=u n l i s t ( date2count )12 )13 png ( ’ j e te rpubmed . png ’ )14 p l o t ( d f )15 t i t l e ( ’ pubmed: count ( a r t i c l e s )=f ( y ea r ) ’ )16 dev . o f f ( )17 </ x s l : t em p l a t e>1819 <x s l : t em p l a t e match=”PubmedArt i c l e ”>20 <x s l : v a r i a b l e name=” yea r ” s e l e c t=”Med l i n eC i t a t i o n /DateCreated /Year ”/>21 date2count [ [ ”<x s l : v a l u e−o f s e l e c t=”$ yea r ”/>” ] ] & l t ;− i f e l s e ( i s . n u l l ( da te2count [ [

”<x s l : v a l u e−o f s e l e c t=”$ yea r ”/>” ] ] ) ,1 ,1+ date2count [ [ ”<x s l : v a l u e−o f s e l e c t=”$ yea r ”/>” ] ] )

22 </ x s l : t em p l a t e>2324 </ x s l : s t y l e s h e e t>

$ c u r l ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e f e t c h . f c g i ?db=pubmed&u s e h i s t o r y=t r u e&WebEnv=NCID 1 52434791 130 . 1 4 . 2 2 . 2 1 59001 1375957034 1619786167&que r y k ey=1&retmode=xml” |\

x s l t p r o c pubmed2rs ta t s . x s l −

date2count <− l i s t ( )

da te2count [ [ ”2013” ] ] <− i f e l s e ( i s . n u l l ( date2count [ [ ”2013” ] ] ) ,1 ,1+ date2count [ [ ”2013” ] ] )





( . . )df <− data . frame (Year=as . i n t e g e r (names ( date2count ) ) ,Count=u n l i s t ( date2count ))png ( ’ j e te rpubmed . png ’ )p l o t ( df )t i t l e ( ’ pubmed : count ( a r t i c l e s )=f ( y ea r ) ’ )dev . o f f ( )


$ c u r l ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e f e t c h . f c g i ?db=pubmed&u s e h i s t o r y=t r u e&WebEnv=NCID 1 52434791 130 . 1 4 . 2 2 . 2 1 59001 1375957034 1619786167&que r y k ey=1&retmode=xml” |\

x s l t p r o c pubmed2rs ta t s . x s l − |\R −−no−save






Generating a JAVA parser






Using the XML schemaXML Schema for dbSNP

ftp://ftp.ncbi.nlm.nih.gov/snp/specs/docsum_3.4.xsd

<?xml v e r s i o n=” 1 .0 ” encod ing=”UTF−8”?><xsd : schema xm ln s : x s d=” h t t p : //www.w3 . org /2001/XMLSchema” xmlns=” h t t p : //www. ncb i . nlm . n i h . gov/SNP/docsum” targetNamespace=” h t t p : //www. ncb i . nlm . n i h . gov/SNP/docsum” e lementFormDefault=” q u a l i f i e d ” a t t r i b u t eFo rmDe f a u l t=” u n q u a l i f i e d ”><x s d : e l emen t name=”ExchangeSet ”>

<x s d : a n n o t a t i o n><x sd :documenta t i on>Set o f dbSNP refSNP docsums , v e r s i o n 3 .4</ x sd :documenta t i on>

</ x s d : a n n o t a t i o n><xsd :complexType>

<x s d : s e qu en c e><x s d : e l emen t name=”SourceDatabase ” minOccurs=”0”>

<xsd :complexType><x s d : a t t r i b u t e name=” t a x I d ” type=” x s d : i n t ” use=” r e q u i r e d ”>

<x s d : a n n o t a t i o n><x sd :documenta t i on>NCBI taxonomy ID f o r v a r i a t i o n</ x sd :documenta t i on>

</ x s d : a n n o t a t i o n></ x s d : a t t r i b u t e><x s d : a t t r i b u t e name=” organ i sm ” type=” x s d : s t r i n g ” use=” r e q u i r e d ”>

<x s d : a n n o t a t i o n><x sd :documenta t i on>common name f o r s p e c i e s used as pa r t o f da tabase name .</ x sd :documenta t i on>

</ x s d : a n n o t a t i o n></ x s d : a t t r i b u t e><x s d : a t t r i b u t e name=”dbSnpOrgAbbr” type=” x s d : s t r i n g ”>

<x s d : a n n o t a t i o n><x sd :documenta t i on>organ i sm a b b r e v i a t i o n used i n dbSNP . </ x sd :documenta t i on>

</ x s d : a n n o t a t i o n></ x s d : a t t r i b u t e><x s d : a t t r i b u t e name=”gpipeOrgAbbr ” type=” x s d : s t r i n g ”>

<x s d : a n n o t a t i o n><x sd :documenta t i on>organ i sm a b b r e v i a t i o n used w i t h i n NCBI genome p i p e l i n e data dumps .</ x sd :documenta t i on>


ftp://ftp.ncbi.nlm.nih.gov/snp/specs/docsum_3.4.xsd

Using the XML schemaCompiling the XML Schema for dbSNP with XJC

$ x j c −d . ” f t p : // f t p . n cb i . nlm . n i h . gov/ snp/ spe c s /docsum 3 . 4 . xsd ”p a r s i n g a schema . . .c omp i l i n g a schema . . .h t t p s /www ncb i n lm n ih gov / snp/docsum/Assay . j a v ah t t p s /www ncb i n lm n ih gov / snp/docsum/Assembly . j a v ah t t p s /www ncb i n lm n ih gov / snp/docsum/BaseURL . j a v ah t t p s /www ncb i n lm n ih gov / snp/docsum/Component . j a v ah t t p s /www ncb i n lm n ih gov / snp/docsum/ExchangeSet . j a v ah t t p s /www ncb i n lm n ih gov / snp/docsum/FxnSet . j a v ah t t p s /www ncb i n lm n ih gov / snp/docsum/MapLoc . j a v ah t t p s /www ncb i n lm n ih gov / snp/docsum/Ob j e c tFac to r y . j a v ah t t p s /www ncb i n lm n ih gov / snp/docsum/Pr imarySequence . j a v ah t t p s /www ncb i n lm n ih gov / snp/docsum/Rs . j a v ah t t p s /www ncb i n lm n ih gov / snp/docsum/RsL inkout . j a v ah t t p s /www ncb i n lm n ih gov / snp/docsum/ RsSt ruc t . j a v ah t t p s /www ncb i n lm n ih gov / snp/docsum/Ss . j a v ah t t p s /www ncb i n lm n ih gov / snp/docsum/package−i n f o . j a v a







Search the non-genomic rs# in dbSNP.1 import h t t p s . www ncb i n lm n ih gov . snp . docsum .∗ ;2 import j a v a x . xml . b ind .∗ ;3 import j a v a x . xml . s t ream .∗ ;4 import j a v a x . xml . s t ream . e v en t s .∗ ;5 c l a s s ParseDbSnp6 {7 pub l i c s t a t i c vo id main ( S t r i n g [ ] a r g s ) throws Excep t i on8 {9 JAXBContext j a xbC t x t=JAXBContext . new In s tance ( ” h t t p s . www ncb i n lm n ih gov

. snp . docsum” ) ;10 Unmar sha l l e r u nma r s h a l l e r=j a xbC t x t . c r e a t eUnma r s h a l l e r ( ) ;11 XMLInputFactory i f a c t o r y = XMLInputFactory . new Ins tance ( ) ;12 XMLEventReader r= i f a c t o r y . createXMLEventReader ( System . i n ) ;13 wh i l e ( r . hasNext ( ) )14 {15 XMLEvent ev t=r . peek ( ) ;16 i f ( ! ( e v t . i s S t a r t E l emen t ( ) && ev t . a sS t a r tE l emen t ( ) . getName ( ) .

g e t Lo c a lPa r t ( ) . e q u a l s ( ”Rs” ) ) )17 {18 ev t=r . nex tEvent ( ) ;19 cont inue ;20 }2122 Rs r s=unma r s h a l l e r . unmarsha l ( r , Rs . c l a s s ) . ge tVa lue ( ) ;23 i f ( ” genomic ” . e qua l s ( r s . getMolType ( ) ) ) cont inue ;24 System . out . p r i n t l n ( ” r s ”+r s . g e tRs I d ( )+” ”+r s . getMolType ( ) ) ;25 }26 r . c l o s e ( ) ;27 }28 }







compile...$ j a v a c ParseDbSnp . j a v a h t t p s /www ncb i n lm n ih gov / snp/docsum/∗ . j a v a

and run...$ c u r l −s ” f t p : // f t p . n cb i . n i h . gov/ snp/ o rgan i sms /human 9606/XML/ ds ch1 . xml . gz” |\gunz ip −c |\j a v a ParseDbSnp

r s701 cDNArs860 cDNArs861 cDNArs862 cDNArs863 cDNArs864 cDNArs865 cDNArs866 cDNArs877 cDNArs878 cDNArs879 cDNArs880 cDNArs882 cDNArs883 cDNArs884 cDNArs885 cDNArs886 cDNArs913 cDNArs945 cDNArs946 cDNA( . . . )






NCBI EBot






NCBI EBotURL

https://www.ncbi.nlm.nih.gov/Class/PowerTools/eutils/

ebot/ebot.cgi


https://www.ncbi.nlm.nih.gov/Class/PowerTools/eutils/ebot/ebot.cgi

https://www.ncbi.nlm.nih.gov/Class/PowerTools/eutils/ebot/ebot.cgi





NCBI EBotSample output

#!/ u s r / b i n / p e r l( . . . )# PUBLIC DOMAIN NOTICE# Nat i o na l Cente r f o r B i o t e chno l ogy I n f o rma t i o nuse LWP: : S imple ;use LWP: : UserAgent ;use Net : : FTP ;

my $de l a y = 0 ;my $maxdelay = 3 ;my $base = ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s /” ;

$params{ ema i l} = ”nobody@nowhere . com” ;$params{db} = ” nuccore ” ;$params{ t o o l} = ” ebot ” ;$params{term} = ”Mammuthus+p r im i g e n i u s [ORGN] ” ;%params = e s e a r c h (%params ) ;

$params{retmode} = ”xml” ;$params{ o u t f i l e } = ” r e s u l t . xml” ;$params{ r e t t y p e} = ” na t i v e ” ;e f e t c h b a t c h (%params ) ;






BLAST






Standalone BlastDownloading

Standalone tools are available at ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

#add BLAST to your pathexport PATH=${PATH} : / path / to / ncb i−b l a s t −2.2.28+/ b i n


ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/

ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/





Standalone BlastDownload a sample

apis mellifera proteins

c u r l −o p r o t e i n . f a . gz \” f t p : // f t p . n cb i . n i h . gov/genomes/ A p i s m e l l i f e r a / p r o t e i n / p r o t e i n . f a . gz”

gunz ip p r o t e i n . f a . gz






Standalone BlastCreate a Blast database with makeblastdb

Getting help...

$ makeb lastdb −h e l p( . . . )−dbtype <S t r i n g , ‘ nuc l ’ , ‘ p rot ’>

M o l e c u l e type o f t a r g e t db− i n <F i l e I n >

I n p u t f i l e / d a t a b a s e nameD e f a u l t = ‘− ’

− i n p u t t y p e <S t r i n g , ‘ a s n 1 b i n ’ , ‘ a s n 1 t x t ’ , ‘ b l a s t d b ’ , ‘ f a s t a ’>Type o f the data s p e c i f i e d i n i n p u t f i l eD e f a u l t = ‘ f a s t a ’

( . . )

Standalone BlastCreate a Blast database with makeblastdb

Create the BLAST database:

$ makeb lastdb − i n p r o t e i n . f a −dbtype p r o t

B u i l d i n g a new DB, c u r r e n t t ime : 09/02/2013 1 8 : 2 9 : 3 8New DB name : p r o t e i n . f aNew DB t i t l e : p r o t e i n . f aSequence type : P r o t e i nKeep L i n k o u t s : TKeep MBits : TMaximum f i l e s i z e : 1000000000BAdding s e q u e n c e s from FASTA ; added 10570 s e q u e n c e s i n 1 .84458 s e c o n d s .






Standalone BlastQuery a Blast database with blastp

Get help:

$ b l a s t p −h e l p( . . . )−q u e r y <F i l e I n >

I n p u t f i l e nameD e f a u l t = ‘− ’

−db <S t r i n g>BLAST d a t a b a s e name

( . . . )

Standalone BlastBlast human EIF4G1 gi:187956781

$ c u r l ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e f e t c h . f c g i ?db=p r o t e i n&r e t t y p e=f a s t a&i d =187956781” |\

b l a s t p −db p r o t e i n . f a

Query= g i |187956781 | gb |AAI40897 . 1 | EIF4G1 p r o t e i n [Homo s a p i e n s ]( . . . )

Score ESequences p roduc i ng s i g n i f i c a n t a l i g nmen t s : ( B i t s ) Value

g i |328782175 | r e f |XP 394628 . 4 | PREDICTED : e u k a r y o t i c t r a n s l a t i o n . . . 189 4e−49g i |328779480 | r e f | XP 003249661 . 1 | PREDICTED : h y p o t h e t i c a l p r o t e i . . . 38 .1 0 .017g i |110762568 | r e f | XP 001121713 . 1 | PREDICTED : h y p o t h e t i c a l p r o t e i . . . 38 .1 0 .018

( . . . )> g i |328782175 | r e f |XP 394628 . 4 | PREDICTED : e u k a r y o t i c t r a n s l a t i o ni n i t i a t i o n f a c t o r 4 gamma 2− l i k e [ Ap i s m e l l i f e r a ]Length=899

Score = 189 b i t s (479) , Expect = 4e−49, Method : Compos i t i ona l mat r i x a d j u s t .I d e n t i t i e s = 115/319 (36%) , P o s i t i v e s = 175/319 (55%) , Gaps = 39/319 (12%)

Query 717 KEPRKIIATVLMTEDIKLNKAEKAWKPSS−−KRTAADKDRGEEDADGSKTQDLFRRVRSI 774++P + +++ +DI+ E+ W P S +R A + S+ +FR+VR I

Sb j c t 22 RKPSETTVGLVIKDDIRSLSTEQRWIPPSTLRRDALTPE−−−−−−−−SRNNFIFRKVRGI 73

Query 775 LNKLTPQMFQQLMKQVTQLAIDTEERLKGVIDLIFEKAISEPNFSVAYANMCRCL−−−−− 829LNKLTP+ F +L + + ++++ LKGVI LIFEKA+ EP +S YA +C+ L

Sb j c t 74 LNKLTPEKFAKLSNDLLNVELNSDVILKGVIFLIFEKALDEPKYSSMYAQLCKRLSDEAA 133

Query 830 −MALKVPTTEKPTVTVNFRKLLLNRCQKEFEKDKDDDEVFEKKQKEMDEAATAEERGRLK 888K E F LLL++C+ EFE E FE + DE EE

Sb j c t 134 NFEPKKALIESQKGQSTFTFLLLSKCRDEFENRSKASEAFENQ−−−−DELGPEEE−−−−− 184Pierre Lindenbaum@yokofakun [email protected] http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/courses





Standalone BlastBlast human EIF4G1 gi:187956781 , ouput XML

$ c u r l ” h t t p s : // e u t i l s . n cb i . nlm . n i h . gov/ e n t r e z / e u t i l s / e f e t c h . f c g i ?db=p r o t e i n&r e t t y p e=f a s t a&i d =187956781” |\

b l a s t p −db p r o t e i n . f a −outfmt 5

( . . . )<H i t h s p s>

<Hsp><Hsp num>1</Hsp num><Hsp b i t−s c o r e>189.119</Hsp b i t−s c o r e><Hsp sco r e>479</ Hsp sco r e><Hsp eva l ue>3.78314 e−49</ Hsp eva l ue><Hsp query−from>717</Hsp query−from><Hsp query−to>1017</Hsp query−to><Hsp h i t−from>22</Hsp h i t−from><Hsp h i t−to>319</Hsp h i t−to><Hsp query−f rame>0</Hsp query−f rame><Hsp h i t−f rame>0</Hsp h i t−f rame><Hs p i d e n t i t y>115</ H s p i d e n t i t y><Hs p p o s i t i v e>175</ H s p p o s i t i v e><Hsp gaps>39</Hsp gaps><Hsp a l i gn−l e n>319</ Hsp a l i gn−l e n><Hsp qseq>KEPRKIIATVLMTEDIKLNKAEKAWKPSS−−KRTAADKDRGEEDADGSKTQDLFRRVRSILNKLTPQMFQQLMKQVTQLAIDTEERLKGVIDLIFEKAISEPNFSVAYANMCRCL−−−−−−MALKVPTTEKPTVTVNFRKLLLNRCQKEFEKDKDDDEVFEKKQKEMDEAATAEERGRLKEELEEARD

IARRRSLGNIKFIGELFKLKMLTEAIMHDCVVKLL−−−−−−−−KNHDEESLECLCRLLTTIGKDLDFEKAKPRMDQYFNQMEKIIKEKKTSSRIRFMLQDVLDLRGSNWVPRRG−−DQGPKTIDQIHKEAE</Hsp qseq><Hsp hseq>RKPSETTVGLVIKDDIRSLSTEQRWIPPSTLRRDALTPE−−−−−−−−SRNNFIFRKVRGILNKLTPEKFAKLSNDLLNVELNSDVILKGVIFLIFEKALDEPKYSSMYAQLCKRLSDEAANFEPKKALIESQKGQSTFTFLLLSKCRDEFENRSKASEAFENQ−−−−DELGPEEE−−−−−−−−−ERRQ

VAKRKMLGNIKFIGELGKLGIVSETILHRCILQLLEKKRRRRSRGDTAEDIECLCQIMRTCGRILDSDKGRGLMDQYFKRMNSLAESRDLPLRIKFMLRDVIELRRDGWVPRKATSTEGPMPINQIRNDNE</Hsp hseq><Hsp m id l i n e>++P + +++ +DI+ E+ W P S +R A + S+ +FR+VR ILNKLTP+ F +L

+ + ++++ LKGVI LIFEKA+ EP +S YA +C+ L K E F LLL++C+ EFEE FE + DE EE ER +A+R+ LGNIKFIGEL KL +++E I+H C+++LL + E +ECLC+++ T G+ LD +K + MDQYF +M

+ + + RI+FML+DV++LR WVPR+ +GP I+QI + E</ Hsp m id l i n e></Hsp>

( . . . )Pierre Lindenbaum@yokofakun [email protected] http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/courses

NCBI URL-API Blast






NCBI URL-API Blast

https://www.ncbi.nlm.nih.gov/blast/Doc/urlapi.html

$ c u r l ” h t t p s : //www. ncb i . nlm . n i h . gov/ b l a s t / B l a s t . c g i ?CMD=Put&QUERY=PAERLMERKADIE&DATABASE=nr&PROGRAM=b l a s t p&FILTER=L&HITLIST SZE=500”

( . . . )

<!−−QBla s t I n f oBeg i nRID = 1NRYGX9K014RTOE = 29

QBlas t In foEnd−−>

( . . . )

The End






Advanced NCBI

Health & Medicine

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