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  1. IGB
  2. IGBF-4006

Update IGB's species and synonyms files

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: 10.2.0
        • Labels:
          None

          Description

          Situation: I've prepared four new genomes to be added to IGB Quickload via svn. Now, IGB's species and synonym's files need to be updated so that these genomes can be included in a future IGB release.

          Task: Add the following to IGB's species.txt and synonyms.txt files:

          species.txt

          Aedes albopictus	Asian tiger mosquito	A_albopictus
Capitella teleta	Capitella teleta	C_teleta
Dama dama	Fallow deer	D_dama
Hydra vulgaris	Swiftwater hydra	H_vulgaris
Oryzias latipes	Japanese medaka	O_latipes
Vanessa cardui	Painted lady	V_cardui

          synonyms.txt

          A_albopictus_Jan_2024	AalbF5
C_teleta_Jan_2013	Capca1
D_dama_Nov_2023	ASM3311817v1
H_vulgaris_Feb_2022	HydraT2T_AEP
O_latipes_Jul_2017	ASM223467v1
V_cardui_Feb_2021	ilVanCard2.1

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              pkulzer Paige Kulzer (Inactive) created issue -
              pkulzer Paige Kulzer (Inactive) made changes -
              Field Original Value New Value
              Epic Link IGBF-3823 [ 23122 ]
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              nfreese Nowlan Freese added a comment -

              Need to update the species.txt for O latipes:
              Oryzias latipes Japanese rice fish (Medaka) O_latipes oryLat Oryzias_latipes oryzias_latipes

              Show
              nfreese Nowlan Freese added a comment - Need to update the species.txt for O latipes: Oryzias latipes Japanese rice fish (Medaka) O_latipes oryLat Oryzias_latipes oryzias_latipes
              ann.loraine Ann Loraine made changes -
              Sprint Winter 1 [ 209 ] Winter 1, Spring 1 [ 209, 210 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              nfreese Nowlan Freese made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
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              nfreese Nowlan Freese added a comment -

              dama dama

              Show
              nfreese Nowlan Freese added a comment - dama dama
              nfreese Nowlan Freese made changes -
              Status In Progress [ 3 ] To-Do [ 10305 ]
              ann.loraine Ann Loraine made changes -
              Sprint Winter 1, Spring 1 [ 209, 210 ] Winter 1, Spring 1, Spring 2 [ 209, 210, 211 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              ann.loraine Ann Loraine made changes -
              Sprint Winter 1, Spring 1, Spring 2 [ 209, 210, 211 ] Winter 1, Spring 1, Spring 2, Spring 3 [ 209, 210, 211, 212 ]
              ann.loraine Ann Loraine made changes -
              Rank Ranked higher
              nfreese Nowlan Freese made changes -
              Description *Situation*: I've prepared four new genomes to be added to IGB Quickload via svn. Now, IGB's species and synonym's files need to be updated so that these genomes can be included in a future IGB release.

              *Task*: Add the following to IGB's species.txt and synonyms.txt files:

              +species.txt+
              {noformat}
              Capitella teleta Capitella teleta C_teleta
              Hydra vulgaris Fresh-water polyp H_vulgaris
              Oryzias latipes Japanese rice fish O_latipes
              Vanessa cardui Painted lady V_cardui
              {noformat}

              +synonyms.txt+
              {noformat}
              C_teleta_Jan_2013 Capitella teleta Capca1
              H_vulgaris_Feb_2022 Hydra vulgaris HydraT2T_AEP
              O_latipes_Jul_2017 Oryzias latipes ASM223467v1
              V_cardui_Feb_2021 Vanessa cardui ilVanCard2.1
              {noformat}
              		*Situation*: I've prepared four new genomes to be added to IGB Quickload via svn. Now, IGB's species and synonym's files need to be updated so that these genomes can be included in a future IGB release.

              *Task*: Add the following to IGB's species.txt and synonyms.txt files:

              +species.txt+
              {noformat}
              Aedes albopictus Asian tiger mosquito A_albopictus
              Capitella teleta Capitella teleta C_teleta
              Dama dama Fallow deer D_dama
              Hydra vulgaris Fresh-water polyp H_vulgaris
              Oryzias latipes Japanese rice fish O_latipes
              Vanessa cardui Painted lady V_cardui
              {noformat}

              +synonyms.txt+
              {noformat}
              A_albopictus_Jan_2024 Aedes albopictus AalbF5
              C_teleta_Jan_2013 Capitella teleta Capca1
              D_dama_Nov_2023 Dama dama ASM3311817v1
              H_vulgaris_Feb_2022 Hydra vulgaris HydraT2T_AEP
              O_latipes_Jul_2017 Oryzias latipes ASM223467v1
              V_cardui_Feb_2021 Vanessa cardui ilVanCard2.1
              {noformat}
              nfreese Nowlan Freese made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              nfreese Nowlan Freese made changes -
              Description *Situation*: I've prepared four new genomes to be added to IGB Quickload via svn. Now, IGB's species and synonym's files need to be updated so that these genomes can be included in a future IGB release.

              *Task*: Add the following to IGB's species.txt and synonyms.txt files:

              +species.txt+
              {noformat}
              Aedes albopictus Asian tiger mosquito A_albopictus
              Capitella teleta Capitella teleta C_teleta
              Dama dama Fallow deer D_dama
              Hydra vulgaris Fresh-water polyp H_vulgaris
              Oryzias latipes Japanese rice fish O_latipes
              Vanessa cardui Painted lady V_cardui
              {noformat}

              +synonyms.txt+
              {noformat}
              A_albopictus_Jan_2024 Aedes albopictus AalbF5
              C_teleta_Jan_2013 Capitella teleta Capca1
              D_dama_Nov_2023 Dama dama ASM3311817v1
              H_vulgaris_Feb_2022 Hydra vulgaris HydraT2T_AEP
              O_latipes_Jul_2017 Oryzias latipes ASM223467v1
              V_cardui_Feb_2021 Vanessa cardui ilVanCard2.1
              {noformat}
              		*Situation*: I've prepared four new genomes to be added to IGB Quickload via svn. Now, IGB's species and synonym's files need to be updated so that these genomes can be included in a future IGB release.

              *Task*: Add the following to IGB's species.txt and synonyms.txt files:

              +species.txt+
              {noformat}
              Aedes albopictus Asian tiger mosquito A_albopictus
              Capitella teleta Capitella teleta C_teleta
              Dama dama Fallow deer D_dama
              Hydra vulgaris Fresh-water polyp H_vulgaris
              Oryzias latipes Japanese rice fish O_latipes
              Vanessa cardui Painted lady V_cardui
              {noformat}

              +synonyms.txt+
              {noformat}
              A_albopictus_Jan_2024 AalbF5
              C_teleta_Jan_2013 Capca1
              D_dama_Nov_2023 ASM3311817v1
              H_vulgaris_Feb_2022 HydraT2T_AEP
              O_latipes_Jul_2017 ASM223467v1
              V_cardui_Feb_2021 ilVanCard2.1
              {noformat}
              Hide
              Permalink
              nfreese Nowlan Freese added a comment - - edited

              Commit: https://bitbucket.org/nfreese/nowlanfork-igb/commits/3374785b8199efff271b80abc20edfdbfff58fce

              To test using my branch:

              1. Build and run IGB
              2. Check each of the above mentioned genomes such that the species and synonyms appear correctly.
              Show
              nfreese Nowlan Freese added a comment - - edited Commit: https://bitbucket.org/nfreese/nowlanfork-igb/commits/3374785b8199efff271b80abc20edfdbfff58fce To test using my branch : Build and run IGB Check each of the above mentioned genomes such that the species and synonyms appear correctly.
              nfreese Nowlan Freese made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
              nfreese Nowlan Freese made changes -
              Assignee Nowlan Freese [ nfreese ]
              pkulzer Paige Kulzer (Inactive) made changes -
              Assignee Paige Kulzer [ pkulzer ]
              pkulzer Paige Kulzer (Inactive) made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
              Hide
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              pkulzer Paige Kulzer (Inactive) added a comment - - edited

              Cloned and fetched Nowlan's branch for testing on Mac, here's what I found:

              • Aedes albopictus - OK
              • Capitella teleta - OK
              • Dama dama - OK
              • Hydra vulgaris - You've listed "Fresh-water polyp" as an alternative name for this species in the Description of this ticket, but in IGB I'm seeing "Swiftwater hydra". Which is correct?
              • Oryzias latipes - The two O_latipes subspecies have "Japanese medaka" as their alternative name. For consistency, maybe we should update "Medaka" to "Japanese medaka" for this species.
              • Vanessa cardui - OK

              Moving this back to do, please review the notes I've left here and make changes accordingly.

              Show
              pkulzer Paige Kulzer (Inactive) added a comment - - edited Cloned and fetched Nowlan's branch for testing on Mac, here's what I found: Aedes albopictus - OK Capitella teleta - OK Dama dama - OK Hydra vulgaris - You've listed "Fresh-water polyp" as an alternative name for this species in the Description of this ticket, but in IGB I'm seeing "Swiftwater hydra". Which is correct? Oryzias latipes - The two O_latipes subspecies have "Japanese medaka" as their alternative name. For consistency, maybe we should update "Medaka" to "Japanese medaka" for this species. Vanessa cardui - OK Moving this back to do, please review the notes I've left here and make changes accordingly.
              pkulzer Paige Kulzer (Inactive) made changes -
              Status First Level Review in Progress [ 10301 ] To-Do [ 10305 ]
              pkulzer Paige Kulzer (Inactive) made changes -
              Assignee Paige Kulzer [ pkulzer ] Nowlan Freese [ nfreese ]
              nfreese Nowlan Freese made changes -
              Description *Situation*: I've prepared four new genomes to be added to IGB Quickload via svn. Now, IGB's species and synonym's files need to be updated so that these genomes can be included in a future IGB release.

              *Task*: Add the following to IGB's species.txt and synonyms.txt files:

              +species.txt+
              {noformat}
              Aedes albopictus Asian tiger mosquito A_albopictus
              Capitella teleta Capitella teleta C_teleta
              Dama dama Fallow deer D_dama
              Hydra vulgaris Fresh-water polyp H_vulgaris
              Oryzias latipes Japanese rice fish O_latipes
              Vanessa cardui Painted lady V_cardui
              {noformat}

              +synonyms.txt+
              {noformat}
              A_albopictus_Jan_2024 AalbF5
              C_teleta_Jan_2013 Capca1
              D_dama_Nov_2023 ASM3311817v1
              H_vulgaris_Feb_2022 HydraT2T_AEP
              O_latipes_Jul_2017 ASM223467v1
              V_cardui_Feb_2021 ilVanCard2.1
              {noformat}
              		*Situation*: I've prepared four new genomes to be added to IGB Quickload via svn. Now, IGB's species and synonym's files need to be updated so that these genomes can be included in a future IGB release.

              *Task*: Add the following to IGB's species.txt and synonyms.txt files:

              +species.txt+
              {noformat}
              Aedes albopictus Asian tiger mosquito A_albopictus
              Capitella teleta Capitella teleta C_teleta
              Dama dama Fallow deer D_dama
              Hydra vulgaris Swiftwater hydra H_vulgaris
              Oryzias latipes Japanese rice fish O_latipes
              Vanessa cardui Painted lady V_cardui
              {noformat}

              +synonyms.txt+
              {noformat}
              A_albopictus_Jan_2024 AalbF5
              C_teleta_Jan_2013 Capca1
              D_dama_Nov_2023 ASM3311817v1
              H_vulgaris_Feb_2022 HydraT2T_AEP
              O_latipes_Jul_2017 ASM223467v1
              V_cardui_Feb_2021 ilVanCard2.1
              {noformat}
              nfreese Nowlan Freese made changes -
              Description *Situation*: I've prepared four new genomes to be added to IGB Quickload via svn. Now, IGB's species and synonym's files need to be updated so that these genomes can be included in a future IGB release.

              *Task*: Add the following to IGB's species.txt and synonyms.txt files:

              +species.txt+
              {noformat}
              Aedes albopictus Asian tiger mosquito A_albopictus
              Capitella teleta Capitella teleta C_teleta
              Dama dama Fallow deer D_dama
              Hydra vulgaris Swiftwater hydra H_vulgaris
              Oryzias latipes Japanese rice fish O_latipes
              Vanessa cardui Painted lady V_cardui
              {noformat}

              +synonyms.txt+
              {noformat}
              A_albopictus_Jan_2024 AalbF5
              C_teleta_Jan_2013 Capca1
              D_dama_Nov_2023 ASM3311817v1
              H_vulgaris_Feb_2022 HydraT2T_AEP
              O_latipes_Jul_2017 ASM223467v1
              V_cardui_Feb_2021 ilVanCard2.1
              {noformat}
              		*Situation*: I've prepared four new genomes to be added to IGB Quickload via svn. Now, IGB's species and synonym's files need to be updated so that these genomes can be included in a future IGB release.

              *Task*: Add the following to IGB's species.txt and synonyms.txt files:

              +species.txt+
              {noformat}
              Aedes albopictus Asian tiger mosquito A_albopictus
              Capitella teleta Capitella teleta C_teleta
              Dama dama Fallow deer D_dama
              Hydra vulgaris Swiftwater hydra H_vulgaris
              Oryzias latipes Japanese medaka O_latipes
              Vanessa cardui Painted lady V_cardui
              {noformat}

              +synonyms.txt+
              {noformat}
              A_albopictus_Jan_2024 AalbF5
              C_teleta_Jan_2013 Capca1
              D_dama_Nov_2023 ASM3311817v1
              H_vulgaris_Feb_2022 HydraT2T_AEP
              O_latipes_Jul_2017 ASM223467v1
              V_cardui_Feb_2021 ilVanCard2.1
              {noformat}
              nfreese Nowlan Freese made changes -
              Status To-Do [ 10305 ] In Progress [ 3 ]
              Hide
              Permalink
              nfreese Nowlan Freese added a comment -

              Updated branch: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-4006

              Show
              nfreese Nowlan Freese added a comment - Updated branch: https://bitbucket.org/nfreese/nowlanfork-igb/branch/IGBF-4006
              nfreese Nowlan Freese made changes -
              Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
              nfreese Nowlan Freese made changes -
              Assignee Nowlan Freese [ nfreese ] Paige Kulzer [ pkulzer ]
              pkulzer Paige Kulzer (Inactive) made changes -
              Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
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              pkulzer Paige Kulzer (Inactive) added a comment -

              Tested again on Mac, my notes for the Hydra vulgaris and Oryzias latipes genomes have been addressed. I'm now seeing the correct species and genome names for each of the six species. Ready for PR!

              Show
              pkulzer Paige Kulzer (Inactive) added a comment - Tested again on Mac, my notes for the Hydra vulgaris and Oryzias latipes genomes have been addressed. I'm now seeing the correct species and genome names for each of the six species. Ready for PR!
              pkulzer Paige Kulzer (Inactive) made changes -
              Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
              pkulzer Paige Kulzer (Inactive) made changes -
              Assignee Paige Kulzer [ pkulzer ] Nowlan Freese [ nfreese ]
              Hide
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              nfreese Nowlan Freese added a comment -

              PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1062

              Show
              nfreese Nowlan Freese added a comment - PR: https://bitbucket.org/lorainelab/integrated-genome-browser/pull-requests/1062
              nfreese Nowlan Freese made changes -
              Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
              nfreese Nowlan Freese made changes -
              Assignee Nowlan Freese [ nfreese ]
              nfreese Nowlan Freese made changes -
              Assignee Ann Loraine [ aloraine ]
              Hide
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              ann.loraine Ann Loraine added a comment - - edited

              PR is merged, new installers are built and deployed to early access section on bioviz.org.
              Ready for testing.

              Show
              ann.loraine Ann Loraine added a comment - - edited PR is merged, new installers are built and deployed to early access section on bioviz.org. Ready for testing.
              ann.loraine Ann Loraine made changes -
              Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
              ann.loraine Ann Loraine made changes -
              Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
              ann.loraine Ann Loraine made changes -
              Assignee Ann Loraine [ aloraine ]
              nfreese Nowlan Freese made changes -
              Assignee Paige Kulzer [ pkulzer ]
              pkulzer Paige Kulzer (Inactive) made changes -
              Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
              Hide
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              pkulzer Paige Kulzer (Inactive) added a comment -

              Downloaded the early access version of IGB from BioViz.org and tested on Mac. All species and synonyms are displaying when hovering over these genomes in the Species and Genome Version drop-down menus. Reference sequences loaded when I zoomed into a location on each of these genomes and clicked Load Sequence. No errors in the Log.

              Closing this ticket!

              Show
              pkulzer Paige Kulzer (Inactive) added a comment - Downloaded the early access version of IGB from BioViz.org and tested on Mac. All species and synonyms are displaying when hovering over these genomes in the Species and Genome Version drop-down menus. Reference sequences loaded when I zoomed into a location on each of these genomes and clicked Load Sequence. No errors in the Log. Closing this ticket!
              pkulzer Paige Kulzer (Inactive) made changes -
              Resolution Done [ 10000 ]
              Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]
              pkulzer Paige Kulzer (Inactive) made changes -
              Assignee Paige Kulzer [ pkulzer ] Nowlan Freese [ nfreese ]
              pkulzer Paige Kulzer (Inactive) made changes -
              Fix Version/s 10.2.0 [ 11100 ]

                People

                • Assignee:
                  nfreese Nowlan Freese
                  Reporter:
                  pkulzer Paige Kulzer (Inactive)
                • Votes:
                  0 Vote for this issue
                  Watchers:
                  3 Start watching this issue

                  Dates

                  • Created:
                    Updated:
                    Resolved: