NCBI Entrez API Guide for Advanced Bioinformatics

Advanced NCBI.
The Entrez API
https://github.com/lindenb/courses
Pierre Lindenbaum
@yokofakun
pierre.lindenbaum@univ-nantes.fr
http://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/cour

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 ” http :// en . w i k i p e d i a . org / wiki /Main page”
wget −O − ” http :// en . w i k i p e d i a . org / wiki /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

Formats
Genbank
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−1992
DEFINITION Blue Whale heavy s a t e l l i t e DNA.
ACCESSION X53813 X17460
VERSION X53813 .1 GI :25
KEYWORDS s a t e l l i t e DNA.
SOURCE Balaenoptera musculus ( Blue whale )
ORGANISM Balaenoptera musculus
Eukaryota ; Metazoa ; Chordata ; Craniata ; V e r t e br a t a ; Euteleostomi ;
Mammalia ; E u 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 ;
M y s t i c e t i ; B a l a e n o p t e r i d a e ; Balaenoptera .
REFERENCE 1 ( bases 1 to 422)
AUTHORS Arnason ,U. and Widegren ,B.
TITLE Composition and chromosomal l o c a l i z a t i o n of cetacean 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 blue whale ,
Balaenoptera musculus
JOURNAL Chromosoma 98 (5) , 323−329 (1989)
PUBMED 2612291
COMMENT See a l s o <X52700−2> f o r 1 ,760 bp common cetacean component c l o n e s
and <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 Location / Q u a l i f i e r s
source 1 . . 4 2 2
/ organism=”Balaenoptera musculus ”
/ mol type=”genomic DNA”
/ d b 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”
ORIGIN
1 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 gPierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/cour

Formats
ASN.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” ,
source {
org {
taxname ” Balaenoptera musculus ” ,
common ” Blue whale ” ,
db {
{
db ” taxon ” ,
tag
i d 9771 } } ,
orgname {
name
b i no m i al {
genus ” Balaenoptera ” ,
s p e c i e s ” musculus ” } ,
l i n e a g e ” Eukaryota ; Metazoa ; Chordata ; Craniata ; Ve r t e b r a t a ;
Euteleostomi ; Mammalia ; E u 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 ;
M y s t i c e t i ; B a l a e n o p t e r i d a e ; Balaenoptera ” ,
gcode 1 ,
mgcode 2 ,
d i v ”MAM” } } ,
subtype {Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/cour

Formats
ASN.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 n d e d n 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 ,
topology 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 ,
create−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 ,
create−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 ,
primary−a c c e s s i o n V i s i b l e S t r i n g OPTIONAL ,
entry−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 ,
other−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 ,
source V i s i b l e S t r i n g OPTIONAL ,
organism 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 ,
struc−comments SEQUENCE OF INSDStrucComment OPTIONAL ,
primary 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 ,Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/cour

Formats
ASN.1 (tools)
DATATOOL
Generate C++ data storage classes based on ASN.1 serialization
streams.
Convert data between ASN.1, XML and JSON formats.

Formats
XML
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. ncbi . nlm . nih . gov/ dtd /NCBI G
<GBSet>
<GBSeq>
<GBSeq locus>X53813</ GBSeq locus>
<GBSeq length>422</ GBSeq length>
<GBSeq strandedness>double</ GBSeq strandedness>
<GBSeq moltype>DNA</GBSeq moltype>
<GBSeq topology>l i n e a r</ GBSeq topology>
<GBSeq division>MAM</ GBSeq division>
<GBSeq update−date>22−JUN−1992</GBSeq update−date>
<GBSeq create−date>13−JUL−1990</ GBSeq create−date>
<G B S e q d e f i n i t i o n>Blue Whale heavy s a t e l l i t e DNA</ G B S e q 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 accession−v e r s i o n>X53813 .1</ GBSeq accession−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>Balaenoptera musculus ( Blue whale )</ GBSeq source>
<GBSeq organism>Balaenoptera musculus</ GBSeq organism>
<GBSeq taxonomy>Eukaryota ; Metazoa ; Chordata ; Craniata ; V e r t eb r a t a ; Euteleostomi ; Mam
a c t y l a ; Cetacea ; M y s t i c e t i ; B a l a e n o p t e r i d a e ; Balaenoptera</GBSeq taxonomy>Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/cour

Formats
XML (DTD)
http://www.ncbi.nlm.nih.gov/dtd/NCBI_GBSeq.mod.dtd
<!ELEMENT GBSeq (
GBSeq locus ,
GBSeq length ,
GBSeq strandedness ? ,
GBSeq moltype ,
GBSeq topology ? ,
GBSeq division ,
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 definition ,
GBSeq primary−a c c e s s i o n ? ,
GBSeq entry−v e r s i o n ? ,
GBSeq accession−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 project ? ,
GBSeq keywords ? ,
GBSeq segment ? ,
GBSeq source ? ,
GBSeq organism ? ,
GBSeq taxonomy ? ,
GBSeq references ? ,
GBSeq comment ? ,
GBSeq comment−s e t ? ,
GBSeq struc−comments ? ,
( . . . )

E-Utilities

GI

GI
http://www.ncbi.nlm.nih.gov/news/
03-02-2016-phase-out-of-GI-numbers/ : ”NCBI is phasing
out sequence GIs - use Accession.Version instead!”

E-Utilities
Set of seven server-side programs that provide a stable interface to
the 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/ ”Entrez
Direct (EDirect) is an advanced method for accessing the NCBI’s
set 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.”

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

EInfo
XML Ouput
https:
//eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi
<e I n f o R e s u l t>
<DbList>
<DbName>pubmed</DbName>
<DbName>p r o t e i n</DbName>
<DbName>nuccore</DbName>
<DbName>n u c l e o t i d e</DbName>
<DbName>nucgss</DbName>
<DbName>nucest</DbName>
<DbName>s t r u c t u r e</DbName>
<DbName>genome</DbName>
<DbName>assembly</DbName>
<DbName>gcassembly</DbName>
<DbName>genomeprj</DbName>
<DbName>b i o p r o j e c t</DbName>
<DbName>biosample</DbName>
<DbName>biosystems</DbName>
<DbName>b l a s t d b i n f o</DbName>Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/cour

EInfo
JSON Ouput
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/einfo.
fcgi?retmode=json
{
” header ”: {
” 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 ”: {
” d b l i s t ”: [
”pubmed” ,
” p r o t e i n ” ,
” nuccore ” ,
( . . . )
” unigene ” ,
” g e n c o l l ” ,
” gtr ”
]
}
}Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/cour

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

EInfo
Statistics 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>
<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</ D e s c r i p t i o n>
<DbBuild>Build130805 −2117m.4</ DbBuild>
<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>
<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</ D e s c r i p t i o n>
<TermCount>0</TermCount>
<IsDate>N</ IsDate>
Y
<SingleToken>Y</ SingleToken>
<H i e r a r c h y>N</ H i e r a r c h y>
<IsHidden>Y</ IsHidden>
</ F i e l d>
<F i e l d>
( . . . )

EInfo
Statistics for Pubmed
fcgi?db=pubmed&retmode=json
{
” header ”: {
” 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 ”: {
” d b 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 ” ,
” d b b u i l d ”: ” Build160921 −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” ,
” fullname ”: ” A l l F i e l d s ” ,
” d e s c r i p t i o n ”: ” A l l terms 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 u m 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” ,
” fullname ”: ”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/cour

EInfo
With 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 by
a single text query.

GQuery
Example
$ c u r l ” h t t p s :// e u t i l s . ncbi . nlm . nih . gov/ gquery ? term=t y r a n n o s a u r u s%20rex&retmode
=xml”
<R e s u l t>
<Term>t y r a n n o s a u r u s rex</Term>
<eGQueryResult>
<ResultItem><DbName>pubmed</DbName><MenuName/><Count>41</Count><Status>
Ok</ Status></ ResultItem>
<ResultItem><DbName>pmc</DbName><MenuName/><Count>160</Count><Status>Ok<
/ Status></ ResultItem>
<ResultItem><DbName>mesh</DbName><MenuName/><Count>15</Count><Status>Ok<
<ResultItem><DbName>books</DbName><MenuName/><Count>179</Count><Status>
Ok</ Status></ ResultItem>
<ResultItem><DbName>pubmedhealth</DbName><MenuName/><Count>21</Count><
Status>Ok</ Status></ ResultItem>
<ResultItem><DbName>omim</DbName><MenuName/><Count>10</Count><Status>Ok<
<ResultItem><DbName>omia</DbName><MenuName/><Count>0</Count><Status>Term
or Database i s not found</ Status></ ResultItem>
<ResultItem><DbName>n c b i s e a r c h</DbName><MenuName/><Count>1</Count><
Status>Ok</ Status></ ResultItem>
<ResultItem><DbName>nuccore</DbName><MenuName/><Count>0</Count><Status>
Term or Database i s not found</ Status></ ResultItem>
( . . . )

GQuery
Transforming 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 ’ encoding=”UTF−8” ?>
2 <x s l : s t y l e s h e e t x m 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 ”/>
4
5 <x s l : t e m p l a t e match=”/”><html><body>
6 <x s l : a p p l y −templates s e l e c t=” R e s u l t ”/>
7 </body></ html></ x s l : t e m p l a t e>
8
9 <x s l : t e m p l a t e match=” R e s u l t ”>
10 <t a b l e><c a p t i o n><x s l : v a l u e −of s e l e c t=”Term”/></ c a p t i o n>
11 <t r><th>Database</ th><th>Count</ th><th>Status</ th></ t r>
12 <x s l : a p p l y −templates s e l e c t=” eGQueryResult / ResultItem ”/>
13 </ t a b l e>
14 </ x s l : t e m p l a t e>
15
16 <x s l : t e m p l a t e match=” ResultItem ”>
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. ncbi . nlm . nih . gov/<x s l : v a l u e −of s e l e c t=”
DbName”/>?cmd=se arch&amp ; term=<x s l : v a l u e −of s e l e c t=” t r a n s l a t e (/ R e 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 −of s e l e c t=”DbName”/></a></ td>
21 <td><x s l : v a l u e −of s e l e c t=”Count”/></ td>
22 <td><x s l : v a l u e −of s e l e c t=” Status ”/></ td>
23 </ t r>
24 </ x s l : t e m p l a t e>
25
26 </ x s l : s t y l e s h e e t>

GQuery
Transforming to HTML
$ c u r l ” h t t p s :// e u t i l s . ncbi . nlm . nih . gov/ gquery ? term=t y r a n n o s a u r u s%20rex&retmode
=xml” |
x s l t p r o c gquery2html . x s l −
<html>
<body>
<t a b l e>
<caption>t y r a n n o s a u r u s rex</ caption>
<t r>
<th>Database</ th>
<th>Count</ th>
<th>Status</ th>
</ t r>
<t r>
<td>
<a h r e f=” h t t p s ://www. ncbi . nlm . nih . gov/pubmed?cmd=s earch&amp ; term=t y r a n n o s a u r u s
</ td>
<td>41</ td>
<td>Ok</ td>
</ t r>
<t r>
<td>
<a h r e f=” h t t p s ://www. ncbi . nlm . nih . gov/pmc?cmd=searc h&amp ; term=t y r a n n o s a u r u s+re
</ td>
<td>160</ td>
<td>Ok</ td>
</ t r>
<t r>
<td>
<a h r e f=” h t t p s ://www. ncbi . nlm . nih . gov/mesh?cmd=sea rch&amp ; term=t y r a n n o s a u r u s+r
</ td>
<td>15</ td>Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/cour

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 History
server
Combines or limits UID datasets stored on the History server
Sorts sets of UIDs

ESearch
Syntax
Base URL https:
//eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi

ESearch
Searching for ’Mammuthus primigenius’
c u r l ” h t t p s :// e u t i l s . ncbi . nlm . nih . 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=n u c l e o t i d e&
term=%22Mammuthus%20 p r i m i g e n i u s%22%5BORGN%5D” |
x m l l i n t −−format −
<e Sea rc hR esu lt>
<Count>684</Count>
<RetMax>20</RetMax>
<RetStart>0</ RetStart>

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

<T r a n s l a t i o n S e t>
<T r a n s l a t i o n>Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/cour

ESearch
Searching for ’Mammuthus primigenius’ (JSON)
c u r l ” h t t p s :// e u t i l s . ncbi . nlm . nih . 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=n u c l e o t i d e
&term=%22Mammuthus%20 p r i m i g e n i u s%22%5BORGN%5D&retmode=j s o n ”
{
” header ”: {
” 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” ,Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/cour

ESearch
the retmax parameter
term=%22Mammuthus%20 p r i m i g e n i u s%22%5BORGN%5D&retmax=2” |
<Count>684</Count>
<RetMax>2</RetMax>

<Id>507866428</ Id>
<Id>124056416</ Id>

<T r a n s l a t i o n>
<From>”Mammuthus p r i m i g e n i u s ” [ORGN]</From>
<To>”Mammuthus p r i m 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>
<T r a n s l a t i o n S t a c k>
<TermSet>
<Term>”Mammuthus p r i m i g e n i u s ” [ Organism ]</Term>
<F i e l d>Organism</ F i e l d>
<Count>684</Count>
<Explode>Y</ Explode>
</TermSet>
<OP>GROUP</OP>
</ T r a n s l a t i o n S t a c k>
<QueryTranslation>”Mammuthus p r i m i g e n i u s ” [ Organism ]</ QueryTranslation>
</ e Se ar ch Res ul t>

ESearch
the retstart parameter
term=%22Mammuthus%20 p r i m i g e n i u s%22%5BORGN%5D&retmax=3&r e t s t a r t =100” |
<Count>684</Count>
<RetMax>3</RetMax>

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

<T r a n s l a t i o n>
<From>”Mammuthus p r i m i g e n i u s ” [ORGN]</From>
<To>”Mammuthus p r i m 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>
<TermSet>
<Term>”Mammuthus p r i m i g e n i u s ” [ Organism ]</Term>
<F i e l d>Organism</ F i e l d>
<Count>684</Count>
<Explode>Y</ Explode>
</TermSet>
<OP>GROUP</OP>
<QueryTranslation>”Mammuthus p r i m i g e n i u s ” [ Organism ]</ QueryTranslation>

ESearch
rettype=retcount
term=%22Mammuthus%20 p r i m i g e n i u s%22%5BORGN%5D&r e t t y p e=count ” |
<eSearchResult>
<Count>684</Count>
</ eSearchResult>

ESearch
sort=Date Released
c u r l −s ” h t t p s :// e u t i l s . ncbi . nlm . nih . 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=
n u c l e o t i d e&term=%22Mammuthus%20 p r i m i g e n i u s%22%5BORGN%5D&s o r t=Date+Released ”
<eSearchResult><Count>811</Count><RetMax>20</RetMax>
<Id>1033204644</ Id>
<Id>1033204658</ Id>
<Id>1033204672</ Id>
<Id>1033204686</ Id>
<Id>1033204729</ Id>
<Id>1033204771</ Id>
<Id>1033204785</ Id>
<Id>1033204799</ Id>
<Id>1033204813</ Id>
<Id>1033204827</ Id>
<Id>1033204871</ Id>
<Id>1033205124</ Id>
<Id>1033205194</ Id>

ESummary

ESummary
Syntax
Returns document summaries (DocSums) for a list of input
UIDs
Returns DocSums for a set of UIDs stored on the Entrez
History server

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

ESummary
Retrieve nucleotide gi=507866428
$ c u r l ” h t t p s :// e u t i l s . ncbi . nlm . nih . gov/ e n t r e z / e u t i l s /esummary . f c g i ?db=
n u c l e o t i d e&i d =507866428”
<eSummaryResult>
<DocSum>
<Id>507866428</ Id>
<Item Name=” Caption ” Type=” S t r i n g ”>KC524742</ Item>
<Item Name=” T i t l e ” Type=” S t r i n g ”>Mammuthus p r i m i g e n i u s i s o l a t e CME2005/915 myoglobin (Mb
<Item Name=” Extra ” Type=” S t r i n g ”>g i |507866428| gb | KC524742 . 1 | [ 5 0 7 8 6 6 4 2 8 ]</ Item>
<Item Name=” Gi ” Type=” I n t e g e r ”>507866428</ Item>
<Item Name=” CreateDate ” Type=” S t r i n g ”>2013/06/15</ Item>
<Item Name=”UpdateDate” Type=” S t r i n g ”>2013/06/21</ Item>
<Item Name=” Flags ” Type=” I n t e g e r ”>0</ Item>
<Item Name=” TaxId ” Type=” I n t e g e r ”>37349</ Item>
<Item Name=” Length ” Type=” I n t e g e r ”>9042</ Item>
<Item Name=” Status ” Type=” S t r i n g ”>l i v e</ Item>
<Item Name=” ReplacedBy ” Type=” S t r i n g ”></ Item>
<Item Name=”Comment” Type=” S t r i n g ”><! [CDATA[ ] ]></ Item>
</DocSum>
</ eSummaryResult>

ESummary
Retrieve nucleotide gi=507866428 in JSON
$ c u r l ” h t t p s :// e u t i l s . ncbi . nlm . nih . gov/ e n t r e z / e u t i l s /esummary . f c g i ?db=
n u c l e o t i d e&i d =507866428& retmode=j s o n ”
{
” header ”: {
” type ”: ”esummary ” ,
” v e r s i o n ”: ”0.3”
} ,
” r e s u l t ”: {
” u i d s ”: [
”507866428”
] ,
”507866428”: {
” uid ”: ”507866428” ,
” c a p t i o n ”: ”KC524742 ” ,
” t i t l e ”: ”Mammuthus p r i m i g e n i u s i s o l a t e CME2005/915 myoglobin (Mb) gene , p a r
” 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 ,
” biomol ”: ” genomic ” ,
” moltype ”: ”dna ” ,
” topology ”: ” l i n e a r ” ,
” sourcedb ”: ” i n s d ” ,
” s e g s e t s i z e ”: ”” ,
” p r o j e c t i d ”: ”0” ,
( . . . )

ESummary
Retrieve snp rs25
$ c u r l ” h t t p s :// e u t i l s . ncbi . nlm . nih . 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>
<Id>25</ Id>
<Item Name=”SNP ID” Type=” I n t e g e r ”>25</ Item>
<Item Name=”Organism” Type=” S t r i n g ”></ Item>
<Item Name=”ALLELE ORIGIN” Type=” S t r i n g ”></ Item>
<Item Name=”GLOBAL MAF” Type=” S t r i n g ”>0.4913</ Item>
<Item Name=”GLOBAL POPULATION” Type=” S t r i n g ”></ Item>
<Item Name=”GLOBAL SAMPLESIZE” Type=” I n t e g e r ”>0</ Item>
<Item Name=”SUSPECTED” Type=” S t r i n g ”></ Item>
<Item Name=”CLINICAL SIGNIFICANCE” Type=” S t r i n g ”></ Item>
<Item Name=”GENE” Type=” S t r i n g ”>THSD7A</ Item>
<Item Name=”LOCUS ID” Type=” I n t e g e r ”>221981</ Item>
<Item Name=”ACC” Type=” S t r i n g ”>NM 015204 . 2 , NT 007819 .17</ Item>
<Item Name=”CHR” Type=” S t r i n g ”>7</ Item>
<Item Name=”WEIGHT” Type=” I n t e g e r ”>1</ Item>
<Item Name=”HANDLE” Type=” S t r i n g ”>1000GENOMES, BGI , BL ,BUSHMAN,COMPLETE GENOMICS, CSHL−HAPM
<Item Name=”FXN CLASS” Type=” S t r i n g ”>intron−v a r i a n t</ Item>
<Item Name=”VALIDATED” Type=” S t r i n g ”>by−1000G, by−c l u s t e r , by−frequency , by−hapmap</ Item>
<Item Name=”GTYPE” Type=” S t r i n g ”>t r u e</ Item>
<Item Name=”NONREF” Type=” S t r i n g ”>f a l s e</ Item>
<Item Name=”DOCSUM” Type=” S t r i n g ”>HGVS=NC 000007 .13 :g .11584142T&gt ; C, NG 027670 .1 :g .29268
<Item Name=”HET” Type=” I n t e g e r ”>50</ Item>
<Item Name=”SRATE” Type=” I n t e g e r ”>0</ Item>
<Item Name=”TAX ID” Type=” I n t e g e r ”>9606</ Item>
<Item Name=”CHRRPT” Type=” S t r i n g ”>2 5 | 2 | 0 | 1 | 1 | 1 | 7 | NT 007819 .17|11574141|11584142|THSD7A|0
<Item Name=”ORIG BUILD” Type=” I n t e g e r ”>36</ Item>
<Item Name=”UPD BUILD” Type=” I n t e g e r ”>138</ Item>
<Item Name=”CREATEDATE” Type=” S t r i n g ”>2000−09−19 17 :02</ Item>Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/cour

ESummary
Retrieve pubmed pmid=7939126
$ c u r l ” h t t p s :// e u t i l s . ncbi . nlm . nih . 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>
<Id>7939126</ Id>
<Item Name=”PubDate” Type=”Date”>1994 Apr</ Item>
<Item Name=”EPubDate” Type=”Date”></ Item>
<Item Name=” Source ” Type=” S t r i n g ”>Sleep</ Item>
<Item Name=” A u t h o r L i s t ” Type=” L i s t ”>
<Item Name=” Author ” Type=” S t r i n g ”>Broughton R</ Item>
<Item Name=” Author ” Type=” S t r i n g ”>B i l l i n g s R</ Item>
<Item Name=” Author ” Type=” S t r i n g ”>Cartwright R</ Item>
<Item Name=” Author ” Type=” S t r i n g ”>Doucette D</ Item>
<Item Name=” Author ” Type=” S t r i n g ”>Edmeads J</ Item>
<Item Name=” Author ” Type=” S t r i n g ”>Edwardh M</ Item>
<Item Name=” Author ” Type=” S t r i n g ”>Ervin F</ Item>
<Item Name=” Author ” Type=” S t r i n g ”>Orchard B</ Item>
<Item Name=” Author ” Type=” S t r i n g ”>H i l l R</ Item>
<Item Name=” Author ” Type=” S t r i n g ”>T u r r e l l G</ Item>
</ Item>
<Item Name=” LastAuthor ” Type=” S t r i n g ”>T u r r e l l G</ Item>
<Item Name=” T i t l e ” Type=” S t r i n g ”>Homicidal somnambulism: a case r e p o r t .</ Item>
<Item Name=”Volume” Type=” S t r i n g ”>17</ Item>
<Item Name=” I s s u e ” Type=” S t r i n g ”>3</ Item>
<Item Name=” Pages ” Type=” S t r i n g ”>253−64</ Item>
<Item Name=” LangList ” Type=” L i s t ”>
<Item Name=”Lang” Type=” S t r i n g ”>E n g l i s h</ Item>
</ Item>
<Item Name=”NlmUniqueID” Type=” S t r i n g ”>7809084</ Item>
<Item Name=”ISSN” Type=” S t r i n g ”>0161−8105</ Item>
<Item Name=”ESSN” Type=” S t r i n g ”>1550−9109</ Item>Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/cour

EFetch

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

EFetch
Retrieve 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 ::= set {
c l a s s nuc−prot ,
d e s c r {
source {
genome genomic ,
org {
taxname ”Mammuthus p r i m i g e n i u s ” ,
common ” woolly mammoth” ,
db {
{
db ” taxon ” ,
tag
i d 37349 } } ,
orgname {
name
b i no m i al {
genus ”Mammuthus” ,
s p e c i e s ” p r i m i g e n i u s ” } ,
mod {
{

EFetch
Retrieve nucleotide gi=507866428 as Fasta
fcgi?db=nucleotide&id=507866428&rettype=fasta
>g i |507866428| gb | KC524742 . 1 | Mammuthus p r i m i g e n i u s i s o l a t e CME2005/915 myoglobin
(Mb) gene , p a r t i a l cds
GCACTTGCTTTTTTTGTCTTCTTCAGACCACGACATGGGACTCAGCGACGGGGAATGGGAGTTGGTGTTG
AAAACCTGGGGGAAAGTGGAGGCTGACATCCCGGGCCATGGGCTGGAAGTCTTCGTCAGGTAAAGGAAGA
AATCCTGTGGCCCCCATCACCCACCCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

EFetch
Retrieve 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 gi>507866428</ TSeq gi>
<TSeq accver>KC524742 .1</ TSeq accver>
<TSeq taxid>37349</ TSeq taxid>
<TSeq orgname>Mammuthus p r i m i g e n i u s</TSeq orgnam
<T S e q d e f l i n e>Mammuthus p r i m 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>

EFetch
Retrieve 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 strandedness>double</ GBSeq strandedness>
<GBSeq moltype>DNA</GBSeq moltype>
<GBSeq topology>l i n e a r</ GBSeq topology>
<GBSeq division>MAM</ GBSeq division>
<GBSeq update−date>21−JUN−2013</GBSeq update−date>
<GBSeq create−date>15−JUN−2013</ GBSeq create−date>
<G B S e q d e f i n i t i o n>Mammuthus p r i m i g e n i u s i s o l a t e CME2005/915 myoglobin (Mb) gene , p a r t i
<GBSeq primary−a c c e s s i o n>KC524742</ GBSeq primary−a c c e s s i o n>
<GBSeq accession−v e r s i o n>KC524742 .1</ GBSeq accession−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 i m i g e n i u s ( woolly mammoth)</ GBSeq source>
<GBSeq organism>Mammuthus p r i m i g e n i u s</ GBSeq organism>
( . . . )

EFetch
Retrieve 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−2013
DEFINITION Mammuthus p r i m i g e n i u s i s o l a t e CME2005/915 myoglobin (Mb) gene ,
p a r t i a l cds .
ACCESSION KC524742
VERSION KC524742 .1 GI :507866428
KEYWORDS .
SOURCE Mammuthus p r i m i g e n i u s ( woolly mammoth)
ORGANISM Mammuthus p r i m i g e n i u s
Mammalia ; E u t h e r i a ; A f r o t h e r i a ; Proboscidea ; E l e p h a n t i d a e ;
Mammuthus .
AUTHORS Mirceta , S . , Signore ,A.V. , Burns , J .M. , Cossins ,A.R. , Campbell ,K. L .
and Berenbrink ,M.
TITLE E v o l u t i o n of mammalian d i v i n g c a p a c i t y t r a c e d by myoglobin net
s u r f a c e charge
JOURNAL Science 340 (6138) , 1234192 (2013)
PUBMED 23766330
AUTHORS Signore ,A.V. , Campbell ,K. L . and Poinar ,H.N.
TITLE D i r e c t Submission
JOURNAL Submitted (09−JAN−2013) B i o l o g i c a l Sciences , U n i v e r s i t y of
Manitoba , 50 S i f t o n Road , Winnipeg , Manitoba R3T2N2 , Canada
COMMENT ##Assembly−Data−START##
Sequencing Technology : : Sanger dideoxy sequencing
##Assembly−Data−END##
source 1 . . 9 0 4 2
/ organism=”Mammuthus p r i m i g e n i u s ”Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/cour

EFetch
Efetch 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−2013
DEFINITION Mammuthus p r i m i g e n i u s i s o l a t e CME2005/915 myoglobin (Mb) gene ,
p a r t i a l cds .
ACCESSION KC524742
VERSION KC524742 .1 GI :507866428
KEYWORDS .
SOURCE Mammuthus p r i m i g e n i u s ( woolly mammoth)
ORGANISM Mammuthus p r i m i g e n i u s
Mammalia ; E u t h e r i a ; A f r o t h e r i a ; Proboscidea ; E l e p h a n t i d a e ;
Mammuthus .
AUTHORS Mirceta , S . , Signore ,A.V. , Burns , J .M. , Cossins ,A.R. , Campbell ,K. L .
and Berenbrink ,M.
TITLE E v o l u t i o n of mammalian d i v i n g c a p a c i t y t r a c e d by myoglobin net
s u r f a c e charge
JOURNAL Science 340 (6138) , 1234192 (2013)
PUBMED 23766330
AUTHORS Signore ,A.V. , Campbell ,K. L . and Poinar ,H.N.
TITLE D i r e c t Submission
JOURNAL Submitted (09−JAN−2013) B i o l o g i c a l Sciences , U n i v e r s i t y of
Manitoba , 50 S i f t o n Road , Winnipeg , Manitoba R3T2N2 , Canada
COMMENT ##Assembly−Data−START##
Sequencing Technology : : Sanger dideoxy sequencing
##Assembly−Data−END##
source 1 . . 9 0 4 2
/ organism=”Mammuthus p r i m i g e n i u s ”Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/cour

EFetch
Using the WebEnv parameter.
Web environment string returned from a previous ESearch, EPost
or ELink call. When provided, ESearch will post the results of the
search operation to this pre-existing WebEnv.

EFetch
Searching extinct species in the NCBI taxonomy (’extinct[PROP]’)
c u r l ” h t t p s :// e u t i l s . ncbi . nlm . nih . 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”
<Count>145</Count>
<RetMax>20</RetMax>
<QueryKey>1</QueryKey>
<WebEnv>NCID 1 75550312 130.14.18.34 9001 1375948145 325582538</WebEnv>

<Id>1225531</ Id>
<Id>1225530</ Id>
<Id>1211276</ Id>
<Id>1211275</ Id>
<Id>1027716</ Id>
<Id>948961</ Id>
<Id>943952</ Id>
<Id>867394</ Id>
<Id>867393</ Id>
<Id>748142</ Id>
<Id>748141</ Id>
<Id>741158</ Id>
<Id>703576</ Id>
<Id>703571</ Id>
<Id>703559</ Id>
<Id>693865</ Id>
<Id>686441</ Id>
<Id>665113</ Id>
<Id>659069</ Id>
<Id>656807</ Id>Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/cour

EFetch
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 . ncbi . nlm . nih . 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>
<S c i e n t i f i c N a m e>Equus ovodovi</ S c i e n t i f i c N a m e>
<OtherNames>
<Synonym>Equus ( Sussemionus ) ovodovi</Synonym>
<Name>
<ClassCDE>a u t h o r i t y</ClassCDE>
<DispName>Equus ovodovi Eisenmann &amp ; Sergej , 2011</DispName>
</Name>
</OtherNames>
<ParentTaxId>1225530</ ParentTaxId>
<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>
<GeneticCode>
<GCId>1</GCId>
<GCName>Standard</GCName>
</ GeneticCode>
<MitoGeneticCode>
( . . . . )

EPOST

EPost
Uploads a list of UIDs to the Entrez History server
Appends a list of UIDs to an existing set of UID lists attached
to a Web Environment

EPost
Post gi to epost
Get a list of gis of extincts animals:
wget −O − ’ h t t p s :// e u t i l s . ncbi . nlm . nih . 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’ |
x m l l i n t −format − |
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

EPost
Post gi to epost
wget −O − ’ h t t p s :// e u t i l s . ncbi . nlm . nih . gov/ e n t r e z / e u t i l s / epost . f c g i ?db=taxonomy&
WebEnd=NCID 1 15435144 130 . 1 4 . 2 2 . 2 1 5
9001 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 ePostResult PUBLIC ”−//NLM//DTD ePostResult , 11 May 2002//EN” ” h t t p : //
www. ncbi . nlm . nih . gov/ e n t r e z / query /DTD/ ePost 020511 . dtd ”>
<ePostResult>
<WebEnv>NCID 1 15467192 130 . 1 4 . 2 2 . 2 1 5
9001 1474637456 570452194 0MetA0 S MegaStore F 1</WebEnv>
</ ePostResult>

EPost
Searching in the WebEnv
Search Homo Sapiens in WebEnv ?
c u r l −s ” h t t p s :// e u t i l s . ncbi . nlm . nih . 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 4
9001 1375948145 325582538&query key=1”
<Count>0</Count>
<RetMax>0</RetMax>
<WebEnv>NCID 1 75550312 130 . 1 4 . 1 8 . 3 4 9001 1375948145 325582538</WebEnv>

<T r a n s l a t i o n S e t />
<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>
<Explode>N</ Explode>
</TermSet>
<OP>AND</OP>
<QueryTranslation>(#2) AND homo s a p i e n s [ A l l Names ]</ QueryTranslation>

EPost
Searching in the WebEnv
Search Tyranosaurus in WebEnv ?
$ c u r l −s ” h t t p s :// e u t i l s . ncbi . nlm . nih . 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 4
9001 1375948145 325582538&query key=1”
<Count>1</Count>
<RetMax>1</RetMax>
<WebEnv>NCID 1 75550312 130 . 1 4 . 1 8 . 3 4 9001 1375948145 325582538</WebEnv>

<Id>436494</ Id>

<T r a n s l a t i o n S e t />
<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>
<Explode>N</ Explode>
</TermSet>
<OP>AND</OP>
<QueryTranslation>(#2) AND Tyrannosaurus [ A l l Names ]</ QueryTranslation>

EDirect: combining tools

Piping Edirect
esearch −db taxonomy −query ” Tyrannosaurus ” |
e f e t c h −format xml

Piping Edirect
esearch −db pubmed −query ” Tyrannosaurus ” |
e f i l t e r −mindate 2005 |
e f e t c h −format docsum |
x t r a c t −pattern DocumentSummary
−element MedlineCitation /PMID
−element Id 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 the
same or a diﬀerent Entrez database
Returns UIDs linked to other UIDs in the same Entrez
database that match an Entrez query
Checks for the existence of Entrez links for a set of UIDs
within 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 single
UID

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

ELink
Searching the pubmed records associated to sequence gi:507866428
h t t p s :// e u t i l s . ncbi . nlm . nih . gov/ e n t r e z / e u t i l s / e l i n k . f c g i ? dbfrom=n u 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
<e L i n k R e s u l t>
<LinkSet>
<DbFrom>nuccore</DbFrom>

<Id>507866428</ Id>

<LinkSetDb>
<DbTo>pubmed</DbTo>
<LinkName>nuccore pubmed</LinkName>
<Link>
<Id>23766330</ Id>
<Score>0</ Score>
</ Link>
</ LinkSetDb>
</ LinkSet>
</ e L i n k R e s u l t>
$ c u r l −s ” h t t p s :// e u t i l s . ncbi . nlm . nih . 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=medline&retmode=t e x t ”
PMID− 23766330
TI − E v o l u t i o n of mammalian d i v i n g c a p a c i t y t r a c e d by myoglobin net s u r f a c e
charge .
PG − 1234192
LID − 10.1126/ s c i e n c e .1234192 [ doi ]

Transformations

Efetch
Transforming to SVG
Using the stylesheet
https://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 . github . 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
/ bio / ncbi / gb2svg . x s l ” )
” h t t p s ://www. ncbi . nlm . nih . gov/ e n t r e z / e u t i l s / e f e t c h . f c g i ?db=n u c l e o t i d e&i d
=14971102& retmode=xml&r e t t y p e=gbc”

Efetch
Transforming to SVG
1 <?xml v e r s i o n=” 1.0 ” encoding=”UTF−8”?>
2 <s v g : s v g xmlns:svg=” h t t p : //www. w3 . org /2000/ svg ” h e i g h t=”121” width=”920” s t y l e=”
stroke−width: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=” black ”/>
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=” black ”/>
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=” white ”/>
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 transform=” 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=” black ”/>
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 0 7 4 ”/>
22 <s v g : t e x t y=”54” x=”460” text−anchor=” middle ”><s v g : t s p a n s t y l e=” font−
w e i g h t : b o l d ; ”>source</ s v g : t s p a n><s v g : t s p a n x m l n s : x s i=” h t t p : //www. w3
. org /2001/XMLSchema−i n s t a n c e ” x m l n s : x l i n k=” h t t p : //www. w3 . org /1999/
x l i n k ” font−weight=” bold ”>organism</ 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 x m l n s : x s i=” h t t p : //www. w3 . org /2001/XMLSchema−i n s t a n c e ”
x m l n s : x l i n k=” h t t p : //www. w3 . org /1999/ x l i n k ” font−weight=” bold ”>
mol type</ s v g : t s p a n>:genomic RNA <s v g : t s p a n x m l n s : x s i=” h t t p : //www.Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/cour

Efetch
Transforming to SVG

Efetch
Transforming to R
$ c u r l −s ” h t t p s :// e u t i l s . ncbi . nlm . nih . 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 ” | x m l l i n t −−format −
$ c u r l −s ” h t t p s :// e u t i l s . ncbi . nlm . nih . 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 5
9001 1375957034 1619786167&query key=1&retmode=xml”

Efetch
Transforming to R
1 <?xml v e r s i o n=’ 1.0 ’ encoding=”UTF−8” ?>
2 <x s l : s t y l e s h e e t x m 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 ”/>
4
5
6 <x s l : t e m p l a t e match=”/”>
7 date2count &l t ;− l i s t ()
8 <x s l : a p p l y −templates s e l e c t=”/ PubmedArticleSet / PubmedArticle [ M e d l i n e C i t a t i o n /
DateCreated / Year ] ”/>
9 df &l t ;− data . frame (
10 Year=as . i n t e g e r ( names ( date2count ) ) ,
11 Count=u n l i s t ( date2count )
12 )
13 png ( ’ jeterpubmed . png ’ )
14 p l o t ( df )
15 t i t l e ( ’ pubmed: count ( a r t i c l e s )=f ( year ) ’ )
16 dev . o f f ()
17 </ x s l : t e m p l a t e>
18
19 <x s l : t e m p l a t e match=” PubmedArticle ”>
20 <x s l : v a r i a b l e name=” year ” s e l e c t=” M e d l i n e C i t a t i o n / DateCreated / Year ”/>
21 date2count [ [ ”<x s l : v a l u e −of s e l e c t=”$ year ”/>” ] ] &l t ;− i f e l s e ( i s . n u l l ( date2count [ [
”<x s l : v a l u e −of s e l e c t=”$ year ”/>” ] ] ) ,1 ,1+ date2count [ [ ”<x s l : v a l u e −of s e l e c t=”
$ year ”/>” ] ] )
22 </ x s l : t e m p l a t e>
23
24 </ x s l : s t y l e s h e e t>

Efetch
Transforming to R
$ c u r l ” h t t p s :// e u t i l s . ncbi . nlm . nih . 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&
9001 1375957034 1619786167&query key=1&retmode=xml” |
x s l t p r o c pubmed2rstats . x s l −
date2count <− l i s t ()
date2count [ [ ”2013” ] ] <− i f e l s e ( i s . n u l l ( date2count [ [ ”2013” ] ] ) ,1 ,1+ date2count [ [ ”
2013” ] ] )
2012” ] ] )
2012” ] ] )
2011” ] ] )
2011” ] ] )
( . . )
df <− data . frame (
Year=as . i n t e g e r ( names ( date2count ) ) ,
Count=u n l i s t ( date2count )
)
png ( ’ jeterpubmed . png ’ )
p l o t ( df )
t i t l e ( ’ pubmed : count ( a r t i c l e s )=f ( year ) ’ )
dev . o f f ()

Efetch
Transforming to R
$ c u r l ” h t t p s :// e u t i l s . ncbi . nlm . nih . 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&
9001 1375957034 1619786167&query key=1&retmode=xml” |
x s l t p r o c pubmed2rstats . x s l − |
R −−no−save

Generating a JAVA parser

Using the XML schema
XML 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 ” encoding=”UTF−8”?>
<xsd:schema xmlns:xsd=” h t t p : //www. w3 . org /2001/XMLSchema” xmlns=” h t t p : //www. ncbi . nlm . nih .
ementFormDefault=” q u a l i f i e d ” a t t r i b u t e F o r m D e f a u l t=” u n q u a l i f i e d ”>
<x s d : e l e m e n t name=” ExchangeSet ”>
<x s d : a n n o t a t i o n>
<xsd:documentation>Set of dbSNP refSNP docsums , v e r s i o n 3.4</ xsd:documentation>
</ x s d : a n n o t a t i o n>
<xsd:complexType>
<x s d : s e q u e n c e>
<x s d : e l e m e n 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 ”>
<xsd:documentation>NCBI taxonomy ID f o r v a r i a t i o n</ xsd:documentation>
</ 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=” organism ” type=” x s d : s t r i n g ” use=” r e q u i r e d ”>
<xsd:documentation>common name f o r s p e c i e s used as part of database name
<x s d : a t t r i b u t e name=”dbSnpOrgAbbr” type=” x s d : s t r i n g ”>
<xsd:documentation>organism a b b r e v i a t i o n used i n dbSNP . </ xsd:documentat
<x s d : a t t r i b u t e name=” gpipeOrgAbbr ” type=” x s d : s t r i n g ”>
<xsd:documentation>organism 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

Compiling the XML Schema for dbSNP with XJC
$ x j c −d . ” f t p :// f t p . ncbi . nlm . nih . gov/ snp / specs /docsum 3 . 4 . xsd ”
p a r s i n g a schema . . .
comp iling a schema . . .
h t t p s / www ncbi nlm nih gov / snp /docsum/ Assay . j a v a
h t t p s / www ncbi nlm nih gov / snp /docsum/ Assembly . j a v a
h t t p s / www ncbi nlm nih gov / snp /docsum/BaseURL . j a v a
h t t p s / www ncbi nlm nih gov / snp /docsum/Component . j a v a
h t t p s / www ncbi nlm nih gov / snp /docsum/ ExchangeSet . j a v a
h t t p s / www ncbi nlm nih gov / snp /docsum/ FxnSet . j a v a
h t t p s / www ncbi nlm nih gov / snp /docsum/MapLoc . j a v a
h t t p s / www ncbi nlm nih gov / snp /docsum/ ObjectFactory . j a v a
h t t p s / www ncbi nlm nih gov / snp /docsum/ PrimarySequence . j a v a
h t t p s / www ncbi nlm nih gov / snp /docsum/Rs . j a v a
h t t p s / www ncbi nlm nih gov / snp /docsum/ RsLinkout . j a v a
h t t p s / www ncbi nlm nih gov / snp /docsum/ RsStruct . j a v a
h t t p s / www ncbi nlm nih gov / snp /docsum/Ss . j a v a
h t t p s / www ncbi nlm nih 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 ncbi nlm nih gov . snp . docsum . ∗ ;
2 import j a va x . xml . bind . ∗ ;
3 import j a va x . xml . stream . ∗ ;
4 import j a va x . xml . stream . even ts . ∗ ;
5 c l a s s ParseDbSnp
6 {
7 p u b l i c s t a t i c void main ( S t r i n g [ ] args ) throws Exception
8 {
9 JAXBContext jaxbCtxt=JAXBContext . newInstance ( ” h t t p s . www ncbi nlm nih gov
. snp . docsum” ) ;
10 Unmarshaller u n m a r s h a l l e r=jaxbCtxt . c r e a t e U n m a r s h a l l e r () ;
11 XMLInputFactory i f a c t o r y = XMLInputFactory . newInstance () ;
12 XMLEventReader r= i f a c t o r y . createXMLEventReader ( System . i n ) ;
13 while ( r . hasNext () )
14 {
15 XMLEvent evt=r . peek () ;
16 i f ( ! ( evt . i s S t a r t E l e m e n t () && evt . asStartElement () . getName () .
g e t L o c a l P a r t () . e q u a l s ( ”Rs” ) ) )
17 {
18 evt=r . nextEvent () ;
19 continue ;
20 }
21
22 Rs r s=u n m a r s h a l l e r . unmarshal ( r , Rs . c l a s s ) . getValue () ;
23 i f ( ” genomic ” . e q u a l s ( r s . getMolType () ) ) continue ;
24 System . out . p r i n t l n ( ” r s ”+r s . getRsId ()+” ”+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 ncbi nlm nih gov / snp /docsum /∗. j a v a
and run...
$ c u r l −s ” f t p :// f t p . ncbi . nih . gov/ snp / organisms /human 9606/XML/ ds ch1 . xml . gz” |
gunzip −c |
j a v a ParseDbSnp
rs701 cDNA
rs860 cDNA
rs861 cDNA
rs862 cDNA
rs863 cDNA
rs864 cDNA
rs865 cDNA
rs866 cDNA
rs877 cDNA
rs878 cDNA
rs879 cDNA
rs880 cDNA
rs882 cDNA
rs883 cDNA
rs884 cDNA
rs885 cDNA
rs886 cDNA
rs913 cDNA
rs945 cDNA
rs946 cDNA
( . . . )

NCBI EBot

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

NCBI EBot
Sample output
#!/ usr / bin / p e r l
( . . . )
# PUBLIC DOMAIN NOTICE
# N a t i o n a l Center f o r Biotechnology I n f o r m a t i o n
use LWP: : Simple ;
use LWP: : UserAgent ;
use Net : : FTP;
my $delay = 0;
my $maxdelay = 3;
my $base = ” h t t p s :// e u t i l s . ncbi . nlm . nih . gov/ e n t r e z / e u t i l s /” ;
$params{email} = ”nobody@nowhere . com” ;
$params{db} = ” nuccore ” ;
$params{ t o o l } = ” ebot ” ;
$params{term} = ”Mammuthus+p r i m 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 } = ” n a t i v e ” ;
e f e t c h b a t c h (%params ) ;

BLAST

Standalone Blast
Downloading
Standalone tools are available at ftp://ftp.ncbi.nlm.nih.gov/
blast/executables/blast+/LATEST/
#add BLAST to your path
export PATH=${PATH}:/ path / to / ncbi−blast −2.2.28+/ bin

Standalone Blast
Download a sample
apis mellifera proteins
c u r l −o p r o t e i n . fa . gz
” f t p :// f t p . ncbi . nih . 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 . fa . gz”
gunzip p r o t e i n . fa . gz

Standalone Blast
Create a Blast database with makeblastdb
Getting help...
$ makeblastdb −help
( . . . )
−dbtype <String , ‘ nucl ’ , ‘ prot ’>
Molecule type of t a r g e t db
−in <F i l e I n >
Input f i l e / database name
Default = ‘−’
−i n p u t t y p e <String , ‘ asn1 bin ’ , ‘ asn1 txt ’ , ‘ blast
Type of the data s p e c i f i e d in i n p u t f i l e
Default = ‘ fasta ’
( . . )

Standalone Blast
Create a Blast database with makeblastdb
Create the BLAST database:
$ makeblastdb −in p r o t e i n . fa −dbtype prot
B u i l d i n g a new DB, c u r r e n t time : 09/02/2013 18:29:38
New DB name : p r o t e i n . fa
New DB t i t l e : p r o t e i n . fa
Sequence type : Protein
Keep Linkouts : T
Keep MBits : T
Maximum f i l e s i z e : 1000000000B
Adding sequences from FASTA; added 10570 sequences

Standalone Blast
Query a Blast database with blastp
Get help:
$ b l a s t p −help
( . . . )
−query <F i l e I n >
Input f i l e name
Default = ‘−’
−db <String >
BLAST database name
( . . . )

Standalone Blast
Blast human EIF4G1 gi:187956781
$ c u r l ” h t t p s :// e u t i l s . ncbi . nlm . nih . 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 . fa
Query= g i |187956781| gb | AAI40897 . 1 | EIF4G1 p r o t e i n [Homo s a p i e n s ]
( . . . )
Score E
Sequences producing s i g n i f i c a n t alignments : ( 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−49
g 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 0.017
g 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 n
i n i t i a t i o n f a c t o r 4 gamma 2− l i k e [ Apis m e l l i f e r a ]
Length=899
Score = 189 b i t s (479) , Expect = 4e−49, Method : Compositional matrix 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
S b j c t 22 RKPSETTVGLVIKDDIRSLSTEQRWIPPSTLRRDALTPE−−−−−−−−SRNNFIFRKVRGI 73
Query 775 LNKLTPQMFQQLMKQVTQLAIDTEERLKGVIDLIFEKAISEPNFSVAYANMCRCL−−−−− 829
LNKLTP+ F +L + + ++++ LKGVI LIFEKA+ EP +S YA +C+ L
S b j c t 74 LNKLTPEKFAKLSNDLLNVELNSDVILKGVIFLIFEKALDEPKYSSMYAQLCKRLSDEAA 133
Query 830 −MALKVPTTEKPTVTVNFRKLLLNRCQKEFEKDKDDDEVFEKKQKEMDEAATAEERGRLK 888
K E F LLL++C+ EFE E FE + DE EE
S b j c t 134 NFEPKKALIESQKGQSTFTFLLLSKCRDEFENRSKASEAFENQ−−−−DELGPEEE−−−−− 184Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/cour

Standalone Blast
Blast human EIF4G1 gi:187956781 , ouput XML
$ c u r l ” h t t p s :// e u t i l s . ncbi . nlm . nih . 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 . fa −outfmt 5
( . . . )
<H i t h s p s>
<Hsp>
<Hsp num>1</Hsp num>
<Hsp bit−s c o r e>189.119</ Hsp bit−s c o r e>
<Hsp score>479</ Hsp score>
<Hsp evalue>3.78314 e−49</ Hsp evalue>
<Hsp query−from>717</ Hsp query−from>
<Hsp query−to>1017</ Hsp query−to>
<Hsp hit−from>22</ Hsp hit−from>
<Hsp hit−to>319</ Hsp hit−to>
<Hsp query−frame>0</ Hsp query−frame>
<Hsp hit−frame>0</ Hsp hit−frame>
<H s p i d e n t i t y>115</ H s p i d e n t i t y>
<H s 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 align−l e n>319</ Hsp align−l e n>
<Hsp qseq>KEPRKIIATVLMTEDIKLNKAEKAWKPSS−−KRTAADKDRGEEDADGSKTQDLFRRVRSILNKLTPQMFQQ
IARRRSLGNIKFIGELFKLKMLTEAIMHDCVVKLL−−−−−−−−KNHDEESLECLCRLLTTIGKDLDFEKAKPRMDQYFNQMEKIIKEKK
<Hsp hseq>RKPSETTVGLVIKDDIRSLSTEQRWIPPSTLRRDALTPE−−−−−−−−SRNNFIFRKVRGILNKLTPEKFAKLS
VAKRKMLGNIKFIGELGKLGIVSETILHRCILQLLEKKRRRRSRGDTAEDIECLCQIMRTCGRILDSDKGRGLMDQYFKRMNSLAESRD
<Hsp midline>++P + +++ +DI+ E+ W P S +R A + S+ +FR+VR ILNKLTP+ F
+ + ++++ LKGVI LIFEKA+ EP +S YA +C+ L K E F LLL++C+ EFE
E FE + DE EE E
R +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 midline>
</Hsp>
( . . . )Pierre Lindenbaum@yokofakun pierre.lindenbaum@univ-nantes.fr http://plindenbaum.blogspot.comAdvanced NCBI.The Entrez APIhttps://github.com/lindenb/cour

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. ncbi . nlm . nih . 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”
( . . . )
<!−−QBlastInfoBegin
RID = 1NRYGX9K014
RTOE = 29
QBlastInfoEnd
−−>
( . . . )

The End

NCBI Entrez API Guide for Advanced Bioinformatics

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NCBI Entrez API Guide for Advanced Bioinformatics