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InterPro BioMart Help Page - the MartView Interface Introduction BioMart is developed jointly by the Ontario Institute for Cancer Research (OiCR) and the European Bioinformatics Institute (EBI). For quick help with the BioMart interface, linked both from here and directly from the InterPro BioMart page itself, you will find a short help page (linked from the Help button at the top of the BioMart MartView interface). BioMart allows you to retrieve public InterPro data from a query-optimised data warehouse that is synchronised with the main InterPro database shortly after each InterPro release. The BioMart interface allows you to build simple or complex queries, with total control over both how the data is filtered (to restrict which records are included) and also which attributes (equivalent to columns in a spreadsheet) are included in the results. This allows you to avoid the need to search through a massive table of results, much of which may be irrelevant to you, and focus specifically on the information that is important. You can specify the format of the results with options such as: HTML table in your browser comma separated values (plain text format) tab separated values (plain text format) Microsoft Excel spreadsheet You can also have the results returned to you as a compressed file if the number of results is expected to be large. This page describes the details of the InterPro BioMart.

Page Contents Selecting a Database Selecting a Dataset Building Filters InterPro Entries Protein Matches Specifying Attributes InterPro Entries Protein Matches Formatting Results

Selecting a BioMart Database

BioMart allows data to be queried and joined from separate BioMart databases. This is under the control of the BioMart developer. At the time of writing, the InterPro BioMart includes links to both the Reactome curated database of biological pathways and the PRIDE Proteomics Identifications Database, which is a repository of protein and peptide identifications arising from mass spectrometry. It is likely that additional BioMart databases will be linked to from the InterPro BioMart as they become available.

The links from the InterPro BioMart to both the Reactome and the PRIDE BioMart are based upon common UniProt protein accession, for example if you build a query against the InterPro BioMart, perhaps for the proteins that match a particular InterPro Entry, you can then additionally select to see data from Reactome describing the metabolic pathways that these proteins are part of, or alternatively find details of identifications of these proteins in the PRIDE database. More details are given at the foot of this page.

Both the InterPro BioMart itself and the linked BioMart databases appear in the "- CHOOSE DATABASE -" pull down list on the InterPro BioMart "MartView" interface.

You can start by querying any of these databases. The following instructions on this page focus on the "InterPro BioMart", so to follow through the page you should start by selecting this option.

Selecting a Data Set

Assuming that you have selected the InterPro BioMart database in the step above, you now have a choice of two 'Datasets' to choose from, as illustrated below.

You should select one dataset depending on how you are building your filters. (See Building Filters below). If you are querying by protein, select the "Protein Matches" dataset. If your filter is focused on InterPro entries, or member database signatures, select the "InterPro Entries" dataset.

If on the other hand, you cannot distinguish based upon the filter, (e.g. you wish to build a complex filter based on both proteins and entries / signatures), you are advised to select the "InterPro Entries" dataset that provides the largest range of attributes for inclusion in the results.

If you wish to build a filter based upon protein taxonomy you should use the "Protein Matches" dataset.

Building Filters

You can build simple or complex filters to restrict the records that are returned to you from the BioMart. It is possible to specify several different criteria for the records returned, all of which must be met for each record returned to you in the results.

To build your filter, click on the "Filters" heading in the left panel of the BioMart interface. You can then define your filter on the right hand panel.

You will see several expandable sections from which you can select filter criteria (you can select any number and combination of filters from all the sections). To open a section, click on the .

Filters That Accept Multiple Values

Each filter item is described in the tables below, one table for each dataset. Note that for some of the filters it is possible to specify more than one item. When this is used, the filter returns all records that match any of the items specified (using OR logic). Filters that accept multiple values are indicated below. To select multiple items, follow the following instructions:

• For fields that accept a typed, pasted or uploaded list, you can separate values using either white space or commas as illustrated in the two figures below:
  
  
  
  You may also upload a text file from your computer containing information formatted in the same way by clicking on the browse button.
  
  
• For fields that contain a list of possible values, you can select multiple values by holding the CTRL key (Microsoft Windows & Linux) or Apple & Shift key (Apple Mac) while clicking on the values that you wish to select as illustrated below:
  

Filters for the "InterPro Entries" Dataset

Filters for the "Protein Matches" Dataset

Specifying Attributes

The InterPro BioMart, in common with all BioMart interfaces, allows you to specify precisely which data items are included in the results. Data items are called "Attributes" in BioMart, being equivalent to a column of data in a spreadsheet.

To select attributes, click on "Attributes" in the left panel of the BioMart window. You can then check the check-boxes adjacent to each attribute that you wish to include in the results.

The InterPro BioMart attributes selection page is very simple, consisting of a single page of attributes split into four sections. You can select any number of attributes from any of the sections. The following table describes these four sections and lists each attribute.

Attributes for the "InterPro Entries" Dataset

Attributes for the "Protein Matches" Dataset

Formatting Results

When you have completed selecting attributes to display and filtering the data to include only the required results, you are then ready to preview and return the results for your query.

If you click on the 'Count' button at the top of the BioMart interface, you will be presented with a count of the number of InterPro entries or matching proteins, depending upon the dataset that you are querying. This is not necessarily the same as the number of results (rows of data) that will be returned. Depending upon the attributes that you have selected, the number of results may be several orders of magnitude greater than the stated count.

Clicking on the 'Results' button will return the first ten result rows in HTML format. You can then specify the format for your data set, as illustrated in the image below.

Click on the select pull down. This will allow you to select from a number of options as described below.

When you have selected the most appropriate format, you can then export the results as a file, for viewing in your internet browser (HTML, CSV or TSV only) or as a compressed file if you suspect that the number of results will be large.

For very large results sets, you can request an email to be sent to you with a link to the results set. Click on the "File" select pull-down and select the "Compressed web file (notify by email)" item. Finally enter your email address in the "Email notification to" text box and click on "Go"