Details
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Type:
Improvement
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Status: To-Do (View Workflow)
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Priority:
Major
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Resolution: Unresolved
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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:2
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Epic Link:
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Sprint:Spring 6 2021 May 31 - June 11
Description
Situation: The Synonym Lookup module includes several files that are used to compare the species names found in IGB. This includes comparing the contents.txt, species.txt, and synonyms.txt. Genomes can come from Quickloads such as IGB Quickload and also from other services, such as UCSC DAS.
IGB friendly genome names follow the pattern of G_species_MMM_YYYY. In addition, a variety can be included - G_species_variety_MMM_YYYY.
While updating genomes for IGBF-781 an edge case was discovered. The opossum genome provided by UCSC DAS has an IGB friendly name of M_domestica. This is very similar to the IGB provided genome for apple, which is M_domestica_Borkh. However, IGB appears to ignore the variety and is just comparing the M_domestica, which is incorrect. As a workaround, a variety was added to the opossum genome to keep them separated.
Task: Identify why IGB considers the two M_domestica genomes to be the same. This should not be occurring, with or without the variety included.
Attachments
Issue Links
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Sprint | Spring 6 2021 May 31 - June 11 [ 122 ] | Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25 [ 122, 123 ] |
| Rank | Ranked higher |
| Sprint | Spring 6 2021 May 31 - June 11, Summer 1 2021 Jun 14 - Jun 25 [ 122, 123 ] | Spring 6 2021 May 31 - June 11 [ 122 ] |