Help & Documentation

Non-programmatic data access

Quick links in this section

For addtional information about these services, please scroll down.

If you would like to access IMPC data programmatically, please see the section on Programmatic data access.

Please note, IMPC data is freely availabe to use and distribute under specific terms and conditions (see our FAQ Is IMPC data freely available). IMPC data can be downloaded for independent analysis or use the analysed data as is. Several channels are available, each tailored to specific needs — individual items, small sets, or in bulk.

Data access through the web portal

Data on individual items – such as genes or experiments – are summarized on dedicated pages in the web portal (gene or chart pages, respectively). Tables and charts have export links. Those export links create files, such as a TXT or XLS files, that can be opened in a spreadsheet. Similarly, images and charts can also be downloaded and saved to your computer.

Data access using the batch query tool

For summary data for small subsets of genes, the batch query tool provides a convenient interface that can be customized using a web form. This can be used to download phenotyping status, significant phenotypes, and other fields.

Please note, our batch query tool is currently under construction and will be substituted for an improved version soon.

Reports and data in bulk (FTP)

Snapshots of the entire dataset captured at the time of each data release are available for bulk download via FTP (ftp://ftp.ebi.ac.uk/pub/databases/impc/). Starting with DR12, we have changed the structure of the FTP site in order to accommodate requests made by our users.

To go to the latest data release, please navigate to all-data-releases, then select the latest data relase. These are ordered from older to most recent. Alternatively, go to all-data-releases/latest, which will take you to the latest data release directly. To find the latest data and reports, please navigate to all-data-releases/latest/results.

The mapping of the old reports to the new reports is indicated in the README file within all-data-releases/latest/results. Additionally, we have added or updated README files at various levels throughout the FTP directory. If you can open README.md files, these are more nicely formatted, otherwise use README.txt. Their content is identical.

The reports in the results folder are purpose-built reports intended for general use. The genotype-phenotype-assertions reports contain all the genotype to phenotype significant associations ascribed to Mammalian Phenotype (MP) ontology terms, based on the statistical analysis performed (using the OpenStat R package starting with DR12, previously the PhenStat R package was used). “ALL”, “IMPC”, “EuroPhenome”, “MGP” and “3I” in the file names indicate different projects. “ALL” encompasses all data in the “IMPC”, “EuroPhenome”, “MGP” and “3I” files.

For programmatic data access, see next section.

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