https://wiki.transvar.org/display/ITD/Synonyms

Please add directions to the synonyms sub systems section.

I have added section for testing Chromosome synonyms.

Ann,
I could use some help with the genome version synonyms.
It would be nice if there was some existing use case we could use as a test.

Also I'm a little unclear on how they are supposed to work, so a short talk with you might help a lot.

re-assigning to Ann so she can think on this; either add to the test module give me some notes and assign it to me again.

Sorry for the delay on this, but I can help explain my understanding of the synonyms system.

There are 2 types of synonyms:

1) Chromosome Synonyms - makes it so that IGB treats "Chr1" and "ChrOne" as the same chromosome so users can see data on the same chromosome. 2 files are of interest in this case and answer the following questions:
1. chromosome.txt = "which chromosomes should we treat as the same chromsome?""
2. genome.txt = "what do you want the chromosome to display as in IGB?"

2) Version Synonyms - makes it so that IGB treats "Human Genome" and "Home Sapien" as the same genome. This is controlled by the species.txt and answers the questions, "what genomes should we treat as the same genome?"

***Testing Instructions:

*Chromosome Synonyms:
IGB uses the chromosome synonyms file to display data from Chr1 on the same chromosome as a file that has data from "ChrOne" for example. To see what I mean, you can follow these quick steps and also use these steps for testing (I have attached the files mentioned to this story):

1) Open IGB, select the A. thaliana genome, and drag the file ChromosomeTest.bed (attached) onto IGB to open it.
*Note: This is a file that has data for "ChrOne" instead of "Chr1", but we want to visualize this data with another file that has Chr1 data.
*Observe: Now that you have opened ChromosomeTest.bed in IGB, you can look at the Current Genome tab on the right-side of IGB and will notice an extra chromosome, "ChrOne", has been added to the list of chromosomes.

2) Now press Load Data on Chr1 to load data
*Observe: The new file contains no data for Chr1, but if you select the "ChrOne" chromosome and Load Data, you will see the file's data. This is a problem though because you cannot compare this data with the data already loaded in Chr1 without switching back and forth between chromsomes in IGB.

3) We need to add the Chromosome synonyms file so IGB can treat "Chr1" and "ChrOne" as the same chromosome, so open the Data Sources tab of IGB Preferences and add the chromsome.txt file (attached) using the Chromosome Synonyms file chooser.

4) Restart IGB, select the A. thaliana genome again, and drag the file ChromosomeTest.bed onto IGB again to open it.
*Observe: This time when you open the file, you will not see the extra "ChrOne" entry listed in the Current Genome tab with the other chromosomes. This is because we have added the Chromosome.txt file.

5) Now press Load Data on Chr1 to load data
Observe: You will see the data from the new file on Chr1, as desired, so you can compare it with the other data much more easily.

*Version Synonyms:

The Version Synonyms feature works differently. My understanding is that it allows IGB to recognize when one genome is the same as another so the data can all be displayed on the same genome version, for example, if someone added a Quickload site with an "A_thaliana_June_2009" folder and a "Arabidopsis9" folder, you could tell IGB to display these files on the same genome. To see what I mean, you can also follow these steps and use them for testing:

1) Start IGB and add the Quickload directory "SmallQuickload" (attached) within the Data Sources tab of IGB Preferences.
*Note: This Quickload contains a folder called "Arabidopsis9" which I made up and is not currently a synonym for any other genome in IGB.

2) Click the Species drop-down menu in the Current Genome tab on the right-side of IGB and scroll to find an entry called "Arabidopsis9". This should be right underneath "Arabidopsis thaliana" and this helps illustrate the problem because imagine that the user just wanted to add his "Arabidopsis9" data to the "Arabidopsis thaliana" genome in IGB, since he knows the genome's are actually the same.
*Observe: If you select the "Arabidopsis9" species and then select "A-thaliana_Jun_2009" as the genome version you will notice two files under Available Data, "Test1" and "Test2". If you switch to the "Arabidopsis thaliana" species and choose "A-thaliana_Jun_2009" as the genome version, you will not see the files mentioned.

3) We need to add the Version synonyms file so IGB can treat these genomes as the same genome, so open the Data Sources tab of IGB Preferences and add the synonyms.txt file (attached) using the Version Synonyms file chooser.

4) Restart IGB, and now click Species drop-down menu in the Current Genome tab on the right-side of IGB
*Observe: You will not see the "Arabidopsis9" entry listed and if you select the "Arabidopsis thaliana" genome and then select "A-thaliana_Jun_2009" as the genome version you will notice that the files Test1 and Test2 are seen under Available Data, indicating that IGB is recognizing "Arabidopsis9" as a synonym.

I hope this helps clear up any confusion on these features. Please let me know if you have any questions about this.

• Note new comment with explanations, instructions from MM.
• Add to release documentation.

Awesome!
I made some edits to the test page:
https://wiki.transvar.org/display/ITD/Synonyms
I opted to keep the existing test files.