Cellular Phenotype Database

Download

There are several ways to download results from the Cellular Phenotypes database.

The results of a phenotype search and of phenotype browsing can be downloaded using the functionality «export search results» located on the top right hand side of a search results page. Here (FTP) the raw export from our repository are available for download:

• The genes to phenotypes raw mappings can be downloaded from our FTP site (link). This data is available in JSON format and CSV format, containing the following information: «phenotypes array» ensGID (Ensembl Gene ID);
  The «phenotypes array» has the following structure:

          "phenolist" : [
                  {
                          "phenodata" : [
                                  {
                                          "bestgenes" : number of the genes with loss-of-function phenotype(s) observed, see phenotypes object below,
                                          "ScrID" : Study's screen ID,
                                          "howgood" : 1 (means that no less than the half of replicas have shown this phenotype(s)),
                                          "phcluster" : cluster here is the sorted list of phenotype's IDs observed simultaneously,
                                          "phenotypes" : [
                                                  {
                                                          "ScrID" : Study's screen ID,
                                                          "phWEIGHT" : the phenotype's evidence,
                                                          "phNAME" : Phenotype given name,
                                                          "phID" : Phenotype ID (within a given Study)
                                                  }
                                          ]
                                  },
                                  ...
                          ],
                          "rgID" : Cellular Phenotype DB reagent's ID,
                          "probeID" : Supplier reagent's ID,
                          "goodmatch" : 1 for unique mapping of this reagent to the gene, 0 for non-unique mapping
                  }
          ]
  

• Reagents information can be downloaded in CSV format. This files contains the following information: reagent's supplier ID as probeID, our internal ID for reagent as rgID, seq_1, seq_2, supplier prefix.

We are currently working on providing data export for any gene set of interest to the user.