The Cistrome Search API is a dedicated API for users to query the latest CistromeDC database conveniently. You can use it to construct request URLs that will work in your browser, on the command line, and in your code easily.
The Cistrome Search API presents its result in standard XML format. You can view the structured result in most browsers, or use a parser to extract the information.
Note
If you encountered some bugs or problems, please commit it to cisapi issues to get help.
Following is a quick overview of the design of the interface, to help us understand the some important concept that will be used in the documents.
A Sample record describes a sequenced sample about what type of cell, which factor(Trancscript Factor or Histone Modification) was ChIPed. Each Sample record is assigned a unique and stable UniqueID. For example, if the data of a Sample is downloaded from GEO, its UniqueID will be GSMXXX. It also has a SampleID, which is increased automatically when new Samples added.
Serveral Sample may be included in a Dataset.
A Dataset record describes a set of sequenced samples about which samples are used as treatment/control, which samples are replicates to each other. Each Dataset is the result of a run of the pipeline and will be assigned a unique and stable DatasetID, which is increased automatically when new Datasets added.
The Dataset is different from the concept of GEO Series, or GSE. The Samples contained by a Dataset must be replicates of the same factor, which is not necessary to GEO Series. Dataset is also different from the concept of GEO Dataset.
June 11, stylesheet for the output of d2 and s2 so that it looks a little better.
June 4, add the FAQ section.
May 31, make some changes in the Search a Dataset section to be consistent with the newDC structure
May 13, add pmid parameter description in Search a Sample literally section.
All the codes of CistromeAPI locates at https://bitbucket.org/hanfeisun/cisapi/