Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:0.75
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Epic Link:
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Sprint:Summer 2: 22 Jun - 3 Jul
Description
Several organisms have scientific names that are longer than two words, such as Oryza sativa japonica.
In this case, "japonica" is a cultivar or variety name.
There is a bug in Genome Dashboard that causes it to not display the full scientific name for this and other species that have scientific names containing more than two words. Also, the common name is not being displayed.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Description |
Several organisms have scientific names that are longer than two words, such as Oryza sativa japonica.
In this case, "japonica" is a cultivar or variety name. There is a bug in Genome Dashboard that causes it to not display the full scientific name for this and other species with more than two words. Also, the common name is not being displayed. |
Several organisms have scientific names that are longer than two words, such as Oryza sativa japonica.
In this case, "japonica" is a cultivar or variety name. There is a bug in Genome Dashboard that causes it to not display the full scientific name for this and other species that have scientific names containing more than two words. Also, the common name is not being displayed. |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Story Points | 0.5 | 0.75 |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Assignee | Ann Loraine [ aloraine ] | Philip Badzuh [ pbadzuh ] |
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.
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
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
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Jay Chamma [ gchamma ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
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
| Status | Post-merge Testing In Progress [ 10003 ] | To-Do [ 10305 ] |
| Assignee | Jay Chamma [ gchamma ] | Philip Badzuh [ pbadzuh ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
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?
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Philip Badzuh [ pbadzuh ] |
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.
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Please see the commit below:
https://bitbucket.org/pbadzuh/genome-dashboard_pbdev/commits/49a3da31a713d9da614d0e48a8e8619df8ef934d?at=IGBF-2451
The changes made above: