Please see the commit below:
https://bitbucket.org/pbadzuh/genome-dashboard_pbdev/commits/49a3da31a713d9da614d0e48a8e8619df8ef934d?at=IGBF-2451

The changes made above:

• ensure genomes have proper common names
• ensure genomes have full scientific names

I have a doubt:

It seems like the code is getting the scientific name for each organism from the Quickload "contents.txt" files. If so, this needs to be changed. The "species.txt" file provides the scientific name.

See: https://wiki.transvar.org/display/igbman/Use+species.txt+to+link+species+names+to+IGB+genome+names for details.

Thanks for the explanation today during the daily meeting.
Please submit PR when ready.
cc: Philip Badzuh

No problem!

Please see PR below:
https://bitbucket.org/lorainelab/genome-dashboard/pull-requests/23/igbf-2451-fix-genome-scientific-and-common/diff

Post merge testing:

• The scientific name and the common name for the organism Oryza sativa japonica appear correctly.
• The common name now appears as "Rice (japonica)" and the scientific name appears as "Oryza sativa japonica"
• The scientific name for other species with a name longer than two words appear correctly as well
• Some common names are still displayed incorrectly however (more info below)

Steps taken to confirm this:
1. Loaded https://test.bioviz.org/genome-dashboard
2. Scrolled down to "Rice (japonica)"
3. Confirmed that the scientific name and common name appear correctly
4. Confirmed that other long scientific names appear correctly such as "Musa acuminata DH Pahang", "Malus domestica Borkh", and "Thermococcus kodakaraensis KOD1"

Philip Badzuh Organisms such as Maize B73, Yarrowia lipolytica CLIB122, Yarrowia lipolytica PO1f, and Yarrowia lipolytica WSH-Z06 do not have the proper common name.

Since multiple common names appear incorrectly, I am moving this ticket back to "To-Do" and re-assigning it to Philip Badzuh

Thanks for noticing this, Jay Chamma. It seems that some common names are defined incorrectly in the data source itself. See:
https://bitbucket.org/lorainelab/integrated-genome-browser/raw/master/core/synonym-lookup/src/main/resources/species.txt

• The second tab-delimited column represents common names

[~aloraine], would it be safe to update the file mentioned above with the correct common names?

Thanks for the comment. The code is indeed behaving correctly. I think it is OK to use the common names as shown, even though they seem a bit weird. I think that researchers working with these organisms would recognize these names.

So I think for now we can leave it as is.

Moving this to closed.