Implementing CTAnn model and processing pipeline #38

johardi · 2025-02-20T22:59:06Z

Highlights:

Upgraded LinkML to 1.8.7.
Modified the original SSSOM schema to meet data processing needs.
Introduced a new schema for the ctann digital object.
Added new normalization and enrichment processes for ctann data.
Improved logging in setup-schema.sh for clearer execution progress and easier error debugging.
Fixed incorrect term dct:reference and replaced it with dct:references.
Made various minor fixes, including typo corrections and removal of unused variables.

Refer to linkml/linkml#1855 ticket to learn more about the bug.

… generation.

Thanks to Andi who pointed this out.

sonarqubecloud · 2025-02-21T18:19:03Z

Quality Gate failed

Failed conditions
4.2% Duplication on New Code (required ≤ 3%)

johardi added 15 commits February 11, 2025 16:49

Commit the sssom schema

681a2b9

Convert the attributes to first class slots

3d88a2b

Removing 'equals_string' expression due to known LinkML bug

3d69479

Refer to linkml/linkml#1855 ticket to learn more about the bug.

Improve execution logging to debug better

ce16bde

Remove unnecessary prefixes

6e4de5e

Explicitly declare slot_uri and class_uri to avoid mix-ups during OWL…

ccdcc75

… generation.

Fix info logging should use the name variable

9d1b5f9

Exclude Eukaryota organism hierarchy

437f8ac

Remove unused variables

d8fa04d

Fix typo

24bce78

Thanks to Andi who pointed this out.

Commit schema for ctann DO

b7bc8b1

Initial commit for ctann data normalization

d867b08

Initial commit for CTAnn data enrichment.

211ef18

Update LinkML versions

0bc0d42

Replace with full IRI

722cd69