Advanced NCBI

Advanced NCBI.The Entrez API

https://github.com/lindenb/courses

Pierre Lindenbaum@yokofakun

pierre.lindenbaum@univ-nantes.frhttp://plindenbaum.blogspot.com

Institut du Thorax. Nantes. France

September 27, 2016

Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/courses

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

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 ”

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

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

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 {{

FormatsASN.1 (schema)

//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

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>

</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>

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 ? ,( . . . )

E-Utilities

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

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

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.”

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.

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

EInfoXML Ouput

https:

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

<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 pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/courses

Return statistics for a given Entrez database: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>

( . . . )

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 pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/courses

EInfoWith entrez-direct

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

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”

<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>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>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>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>

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 −

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

</ t r><t r>

</ td><td>15</ td>Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/courses

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

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 −

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>

<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>

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)

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)

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

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>

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>

</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