Get Started with Cistrome Search API

Search a Sample

Return a sample record that matches a speciefied query.

Resource URL

http://cistrome.org/cisapi/get/s

Warning

It’s better NOT to open the above URL in browser as it’ll cost huge memory space to render them in browser. Use wget or curl instead.

Parameters

id	The ID of the Sample (SampleID) Example Values: 100
fid	The ID of the Factor ChIPed in the Sample. Example Values: 7
uid	The unique ID of the Sample (Fuzzy Search) Example Values: SRX, ESM000328

Examples

Fetch all (use wget or curl to fetch):

http://cistrome.org/cisapi/get/s

Query the Samples with GSM58857 as the UniqueID.

http://cistrome.org/cisapi/get/s?uid=GSM58857

Query all Samples whose source is ENCODE and use 41 as the ID of Factor.

http://cistrome.org/cisapi/get/s?uid=ESM&fid=41

Output Structure

<?xml version="1.0" encoding="utf-8" ?>
<samples >
  <sample id='1463' mode='id'>
    <factor>12</factor>
    <unique>GSM588576</unique>
    <cellLine>104</cellLine>
    <cellType>1</cellType>
    <cellPop>None</cellPop>
    <species>1</species>
    <tissue>7</tissue>
    <diseaseState>5</diseaseState>
    <paper>139</paper>
    <url>ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX038/SRX038747</url>
  </sample>
</sample>
</samples>

Search a Sample literally

Return a sample record that matches a speciefied query literally.

Note

This function is different from the function above because it will output the actual names of each entity such as Factor and CellLine instead of IDs.

Resource URL

http://cistrome.org/cisapi/get/s2

Warning

It’s better NOT to open the above URL in browser as it’ll cost huge memory space to render them in browser. Use wget or curl instead.

Parameters

id	The ID of the Sample (Sample ID) Example Values: 5
uid	The Unique ID of the Sample (Fuzzy Search) Example Values: GSM588574
fname	The Factor name of the Sample Example Values: ctcf
dname	The DiseaseState name of the Sample Example Values: Ductal Carcinoma
clname	The CellLine name of the Sample Example Values: MCF-7
ctname	The CellType name of the Sample Example Values: Epithelial
cpname	The CellPop name of the Sample Example Values: HCF, CD4
tname	The Tissue name of the Sample Example Values: Blood
sname	The Species name of the Sample Example Values: Homo sapiens
pid	The PaperID of the Sample Example Values: 1
pmid	The Pubmed ID of the Paper for the Sample Example Values: 22237151
aname	One of the authors’ names of the Sample Example Values: Young RA, Ren B

Warning

If you want to search CD4+ Cell Population, please use cd4 instead of cd4+ to search. The reason is that + will be escaped in the URL call.

Example

Query the Samples done by Shirley’s lab

http://cistrome.org/cisapi/get/s2?aname=liu%20xs

Query the H3K4me3 Samples in cells related to embryo with Normal state

http://cistrome.org/cisapi/get/s2?fname=h3k4me3&sname=mus&dname=normal&ctname=embryo

Query the samples whose Pubmed ID is 22237151 and use CD4+ as Cell Population

http://cistrome.org/cisapi/get/s2?cpname=cd4&pmid=22237151

Output Structure

<?xml version="1.0" encoding="utf-8" ?>
<?xml-stylesheet type="text/xsl" href="/cisapi_static/sample2.xsl" ?>
<samples >
  <sample id='435' mode='verbose'>
    <factor>H3K27me3</factor>
    <cellLine>nil</cellLine>
    <cellType>T Lymphocyte</cellType>
    <cellPop>CD4+ / CD8+</cellPop>
    <species>Mus musculus</species>
    <tissue>Blood</tissue>
    <diseaseState>nil</diseaseState>
    <paper>Genetic inactivation of the polycomb repressive complex 2 in T cell acute lymphoblastic leukemia</paper>
    <pmid>22237151</pmid>
    <authors>Ntziachristos P, Tsirigos A, Vlierberghe PV, Nedjic J, Trimarchi T, Flaherty MS, Ferres-Marco D, da Ros V, Tang Z, Siegle J, Asp P, Hadler M, Rigo I, Keersmaecker KD, Patel J, Huynh T, Utro F, Poglio S, Samon JB, Paietta E, Racevskis J, Rowe JM, Rabadan R</authors>
    <uniqueID>GSM859496</uniqueID>
    <url>None</url>
  </sample>
</samples>

Search a Dataset

Return a Dataset record that match a specified query.

Resource URL

http://cistrome.org/cisapi/get/d

Parameters

id	The ID of the Dataset Example Values: 1, 1456
uid	The sample ID of the Samples that a Dataset contains Example Values: 890, ``

Warning

The meaning of uid here has changed. It now uses Sample ID instead of unique ID to search.

Examples

Fetch all:

http://cistrome.org/cisapi/get/d

Query Dataset 5512:

http://cistrome.org/cisapi/get/d?id=5512

Search a Dataset Literally

Return a Dataset record that match a specified query literally.

Resource URL

http://cistrome.org/cisapi/get/d2

Parameters

id	The ID of the Dataset Example Values: 1, 1456

Examples

Query Dataset 5092:

http://cistrome.org/cisapi/get/d2?id=5092

Output Structure

<?xml version="1.0" encoding="utf-8" ?>
<?xml-stylesheet type="text/xsl" href="/cisapi_static/dataset2.xsl" ?>
<dataset id='5099'>
<treatment >
 <sample id='921' mode='verbose'>
  <factor>HNF4G</factor>
  <cellLine>HepG2</cellLine>
  <cellType>Epithelial</cellType>
  <cellPop>nil</cellPop>
  <species>Homo sapiens</species>
  <tissue>Liver</tissue>
  <diseaseState>Hepatocellular Carcinoma</diseaseState>
  <paper>Proteomic analysis of native hepatocyte nuclear factor-4? (HNF4?) isoforms, phosphorylation status, and interactive cofactors.</paper>
  <pmid>21047794</pmid>
  <authors>Daigo K,Kawamura T,Ohta Y,Ohashi R,Katayose S,Tanaka T,Aburatani H,Naito M,Kodama T,Ihara S,Hamakubo T</authors>
  <uniqueID>GSM469865</uniqueID>
  <url>ftp://ftp-trace.ncbi.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX018/SRX018627</url>
 </sample>
</treatment>
<control >
</control>
</dataset>