List Upload

InterMine has a sophisticated list import system. The page aims to describe how it works.

Users can paste any identifier into the list upload form; it can be an identifier, symbol or name. The list upload form runs a series of queries to try to match the identifier to an object in the database.

This is also how the LOOKUP constraint works.

Queries

1 default query

First, we query for the value in key fields. For example:

select * from gene 
where name = 'adh' OR 
      symbol = 'adh' or 
      primaryIdentifier = 'adh' or 
      secondaryIdentifier = 'adh';

If this query returned results, that object is added to our list and we are done.

If this query didn't return any results, we move on to step 2.

2 bag queries

Next we run queries listed in bag-queries.xml (see below)

1. looks for cross references
2. looks for synonyms

Matches returned from this query are not added to the list, they are displayed under the synonyms matched heading. Users can optionally add them to their list.

If this query didn't return any results, we move on to step 3.

See bag-queries.xml

3 converters

Next we run appropriate converter template, which are templates tagged with im:converter. See: Tagging

Matches returned from this query are not added to the list, they are displayed under the converted type heading. Users can optionally add them to their list.

Configuration

example list: The example list is set in "bag.example.identifiers" property in WebProperties.
types: See ClassKeys
organisms: All organisms in your database will be displayed here. You can set the default in WebProperties.
valid delimiters: The default valid delimiters are comma, space, tab or new line. You can change this value by setting the "list.upload.delimiters" property in WebProperties.