Introduction

Different data sources and files sometimes use different names to mean the same thing.  To ensure that data reference to the same thing can be displayed together, IGB supports the concept of genome version and chromosome name synonyms.

IGB supports two synonym file types:

• synonyms.txt - lists synonyms for genome version names
• chromosome.txt - lists synonyms for sequence names

Synonym files are tab-delimited. Each row of the file reports a list of synonyms for the same thing, with synonyms separated by tabs. A row can contain two or more columns of data. Synonyms can contain spaces or any other character except a tab.

The value listed first in each row is typically what IGB will display.

Note: If you create your own custom QuickLoad site, you can add chromosome.txt and synonyms.txt synonym files to your QuickLoad root directory (same level as contents.txt) and IGB will read them and adds the synonyms to its internal list of synonyms. Including one or both files is optional.

For more information about creating a QuickLoad site, see: Sharing data using QuickLoad sites.

How to make a chromosome.txt file

Do this if you have an alignment file or other data file that made with a reference genome sequence that used different names for chromosomes than what you see when you load that genome into IGB.

Create a tab-delimited file that uses the IGB preferred name in the first column and the synonym in the second column. You can add more synonyms in subsequent columns if you like.

To create a chromosome.txt synonym file:

1. Open a new file in a plain text editor (such as Notepad or TextEdit).
2. Enter the preferred IGB name (the display name) in column 1.
3. Press TAB to insert a tab character.
4. Enter the next synonym.
5. Repeat step 3 and 4 until all synonyms are entered.
6.  Save file as chromosome.txt 

How to make a synonyms.txt file

A synonyms.txt file lists synonyms for genome versions. IGB uses this file to integrate data from multiple sources when those sources use different names for the same genome. For information about how to create a synonyms.txt file, see: Use synonyms.txt to link genome version names to each other.

Loading synonym files

After you create your synonym file, you need to load it into IGB.

To load a synonym file into IGB:

1. Select File > Preferences > Data Sources.
2. Under Personal Synonyms, select the file you want to add.
   
   1. Select Version Synonyms to add synonyms.txt
   2. Select Chromosome Synonyms to add chromosomes.txt
3. Choose and open file.
4. Restart IGB.

Note: If you clear your preferences or install a new version of IGB, you may need to reload your synonym files.