missing zebrafish lines

[sbello]

@claude what zebrafish breeds are missing from the ontology?

[claude]

Claude finished @sbello's task —— View job

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Analysis: Missing Zebrafish Lines from VBO

Current VBO Zebrafish Lines (3 total)

VBO currently contains only 3 zebrafish lines:

1. AB (VBO:0017495) - ZFIN:ZDB-GENO-960809-7 ✓
2. GloFish (VBO:0017496) - Commercial variant
3. SJD (VBO:0017497) - ZFIN:ZDB-GENO-990308-9 ✓

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Missing Wild-Type Lines from ZFIN

ZFIN documents 32 wild-type zebrafish lines, but VBO only includes 2 of them (AB and SJD). The following 29 wild-type lines are missing:

Major Research Lines (High Priority)

These are the most commonly used lines in zebrafish research:

1. TU (Tübingen) - ZDB-GENO-990623-3

   • One of the three most popular laboratory strains
   • Used for the Zebrafish Sequencing Project
   • Originated from pet shops in Tübingen, Germany (1994)

2. WIK (Wild India Kolkata) - ZDB-GENO-010531-2

   • One of the three most popular laboratory strains
   • Derived from wild-caught fish (1997)
   • Higher genetic diversity than AB and TU

3. TL (Tupfel Long Fin) - ZDB-GENO-990623-2

   • Commonly used laboratory strain
   • Derived from AB × TU cross

4. EKW - ZDB-GENO-990520-2

   • Frequently used in research
   • Referenced in genomic studies

Hybrid/Derived Lines

5. AB/TU - ZDB-GENO-010924-10
6. AB/TL - ZDB-GENO-031202-1
7. AB/C32 - ZDB-GENO-070425-3
8. AB/EKW - ZDB-GENO-091223-1
9. HK/AB - ZDB-GENO-980210-40
10. HK/SING - ZDB-GENO-980210-38
11. SJD/C32 - ZDB-GENO-070425-2
12. WIK/AB - ZDB-GENO-050511-1

Other Wild-Type Lines

13. ABO - ZDB-GENO-181106-1
14. C32 - ZDB-GENO-030501-1
15. CB - ZDB-GENO-180717-1
16. DAR - ZDB-GENO-960809-13
17. HK - ZDB-GENO-980210-34
18. IND - ZDB-GENO-980210-28
19. INDO - ZDB-GENO-980210-32
20. KOLN - ZDB-GENO-010725-1
21. NA - ZDB-GENO-030115-2
22. NHGRI-1 - ZDB-GENO-150204-3
23. RW - ZDB-GENO-070802-4
24. SAT - ZDB-GENO-100413-1
25. SING - ZDB-GENO-980210-24
26. SJA - ZDB-GENO-061206-2
27. SPF 5-D - ZDB-GENO-120309-3
28. SPF AB - ZDB-GENO-120309-2
29. TLN - ZDB-GENO-080307-1
30. WT - ZDB-GENO-030619-2

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Missing Mutant/Variant Lines

Based on research literature, these notable mutant or variant lines are also missing:

31. Casper - Transparent strain (nacre × roy orbison mutant)

• Widely used for imaging studies
• Developed at Boston Children's Hospital (2008)

32. Golden - Pigmentation mutant (SLC24A5 mutation)

• Used in pigmentation research

33. Leopard - Spotted color morph

• Available in pet trade and research

34. Longfin - Long-finned variant

• Available in pet trade and research

35. Nacre - Melanophore-deficient mutant

• Used for imaging

36. Roy Orbison (roy) - Iridophore-deficient mutant

• Used for imaging

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Summary

Total Missing Lines: ~33+

• 29 ZFIN wild-type lines with official ZFIN IDs
• 4+ mutant/variant lines commonly used in research or pet trade

Priority Recommendations:
The highest priority additions would be the "big four" wild-type laboratory strains:

1. TU (Tübingen)
2. WIK (Wild India Kolkata)
3. TL (Tupfel Long Fin)
4. EKW

These four, along with AB and SJD (already in VBO), represent the most commonly used wild-type zebrafish lines in biomedical research.

Additional Consideration:
The Casper strain should also be high priority as it's one of the most important transgenic/mutant lines for imaging research.

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References:

• ZFIN Wild-Type Lines: https://zfin.org/action/feature/wildtype-list
• ZIRC Catalog: https://zebrafish.org/fish/lineAll.php
• Recent research: Comparative study of AB, SJD, TU, WIK lines (2024)

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[sbello]

@claude create a PR to add the missing strains that have ZFIN IDs to the ontology.

[claude]

Claude finished @sbello's task —— View job • claude/issue-60-20251118-1728 • Create PR ➔

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Adding Missing Zebrafish Strains to VBO

Task List

• Gather context and understand VBO editing workflow
• Check available VBO:777xxxx IDs for new terms
• Create term definitions for 29 ZFIN wild-type zebrafish lines
• Validate OBO format
• Commit and push changes
• Provide PR creation link

Summary

Successfully added 29 missing ZFIN wild-type zebrafish lines to VBO with IDs VBO:7770001-VBO:7770030.

Added Strains

High-Priority Research Lines:

• TU (Tübingen) - VBO:7770001 - ZFIN:ZDB-GENO-990623-3
• WIK (Wild India Kolkata) - VBO:7770002 - ZFIN:ZDB-GENO-010531-2
• TL (Tupfel Long Fin) - VBO:7770003 - ZFIN:ZDB-GENO-990623-2
• EKW - VBO:7770004 - ZFIN:ZDB-GENO-990520-2

Hybrid/Derived Lines (8):
AB/TU, AB/TL, AB/C32, AB/EKW, HK/AB, HK/SING, SJD/C32, WIK/AB

Other Wild-Type Lines (17):
ABO, C32, CB, DAR, HK, IND, INDO, KOLN, NA, NHGRI-1, RW, SAT, SING, SJA, SPF 5-D, SPF AB, TLN, WT

Term Format

Each term includes:

• VBO identifier (VBO:777xxxx range for new terms)
• Name format: [Line Code] (Zebrafish)
• Synonym with most_common_name tag
• ZFIN identifier as source
• Taxonomy parent: NCBITaxon:7955 (Danio rerio)
• Parent class: VBO:0400000 (Vertebrate breed)
• Contributor: Sue Bello (ORCID: 0000-0003-4606-0597)
• Link to this issue (missing zebrafish lines #60)

Changes

• Modified: src/ontology/vbo-edit.obo (+333 lines)
• Added 30 new [Term] stanzas with complete metadata

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[sbello]

Note in the PR it made the parent 'vertebrate breed' not zebrafish breed

[sbello]

@claude modify the PR to use Zebrafish breed (VBO:0400043) as the parent class for the new terms

[claude]

Claude finished @sbello's task —— View job • Create PR ➔

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Modifying Parent Class for Zebrafish Strains

Task List

• Verify VBO:0400043 (Zebrafish breed) exists
• Found all 30 zebrafish terms in the previous PR branch
• Update parent class from VBO:0400000 to VBO:0400043 (30 terms updated)
• Validate changes via git diff
• Commit and push changes
• Update PR link

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Summary

Successfully updated the parent class for all 30 newly added zebrafish strains from VBO:0400000 (Vertebrate breed) to VBO:0400043 (Zebrafish breed).

Changes Made

• Modified src/ontology/vbo-edit.obo
• Updated 30 zebrafish terms (VBO:7770001 through VBO:7770030)
• Changed parent class from generic "Vertebrate breed" to specific "Zebrafish breed"
• All terms now properly inherit from VBO:0400043

Updated Terms

All 30 ZFIN wild-type zebrafish lines including:

• TU (Tübingen) - VBO:7770001
• WIK (Wild India Kolkata) - VBO:7770002
• TL (Tupfel Long Fin) - VBO:7770003
• EKW - VBO:7770004
• Plus 26 additional hybrid and wild-type lines

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• claude/issue-60-20251118-1728