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For comparison only: DEV branch #61

Merged
merged 152 commits into from
Sep 3, 2024
Merged

For comparison only: DEV branch #61

merged 152 commits into from
Sep 3, 2024

Commits on Dec 13, 2023

  1. add obsolete classes due to renamed patterns

    @jamesamcl
    jamesamcl committed Dec 13, 2023
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  2. add sssom mapping generation

    @jamesamcl
    jamesamcl committed Dec 13, 2023
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  3. Add obsoletion module

    @matentzn
    matentzn committed Dec 13, 2023
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  4. inheres_in_part_of

    @jamesamcl
    jamesamcl committed Dec 13, 2023
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  5. Add method to to postprocess modified patterns after matching

    @matentzn
    matentzn committed Dec 13, 2023
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  6. Merge branch 'dev' of https://github.com/obophenotype/upheno-dev into… 

    … dev
    @matentzn
    matentzn committed Dec 13, 2023
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  7. Update upheno_prepare.py

    @matentzn
    matentzn committed Dec 13, 2023
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  8. fix inheres_in pattern generation

    @jamesamcl
    jamesamcl committed Dec 13, 2023
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  9. add missing method to lib.py

    @jamesamcl
    jamesamcl committed Dec 13, 2023
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Commits on Jan 31, 2024

  1. add out path for sssom

    @jamesamcl
    jamesamcl committed Jan 31, 2024
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  2. add mappings file wip

    @jamesamcl
    jamesamcl committed Jan 31, 2024
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  3. remove exit from prepare

    @jamesamcl
    jamesamcl committed Jan 31, 2024
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  4. remove missing bridges

    @jamesamcl
    jamesamcl committed Jan 31, 2024
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  5. Merge branch 'master' into dev

    @matentzn
    matentzn committed Jan 31, 2024
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  6. reinstate excluded patterns with comment

    @jamesamcl
    jamesamcl committed Jan 31, 2024
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  7. Merge branch 'dev' of github.com:obophenotype/upheno-dev into dev

    @jamesamcl
    jamesamcl committed Jan 31, 2024
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Commits on Mar 6, 2024

  1. Updated patterns

    @matentzn
    matentzn committed Mar 6, 2024
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  2. Create upheno-pattern-deriver.ipynb

    @matentzn
    matentzn committed Mar 6, 2024
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Commits on Mar 8, 2024

  1. Updated patterns

    @matentzn
    matentzn committed Mar 8, 2024
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  2. add +x to upheno_pipeline.sh

    @jamesamcl
    jamesamcl committed Mar 8, 2024
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  3. Add changed patterns generation step

    @matentzn
    matentzn committed Mar 8, 2024
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  4. Merge branch 'dev' of https://github.com/obophenotype/upheno-dev into… 

    … dev
    @matentzn
    matentzn committed Mar 8, 2024
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Commits on Mar 11, 2024

  1. fix variable same name as function

    @jamesamcl
    jamesamcl committed Mar 11, 2024
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Commits on Apr 10, 2024

  1. Update upheno_create_profiles.py

    @matentzn
    matentzn committed Apr 10, 2024
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  2. Update upheno_create_profiles.py

    @matentzn
    matentzn committed Apr 10, 2024
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Commits on Apr 11, 2024

  1. Update upheno_create_profiles.py 

    cc @jamesamcl
    @matentzn
    matentzn committed Apr 11, 2024
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Commits on Apr 18, 2024

  1. Review changed patterns

    @matentzn
    matentzn committed Apr 18, 2024
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  2. Updating remaining classes

    @matentzn
    matentzn committed Apr 18, 2024
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  3. Updated some more patterns

    @matentzn
    matentzn committed Apr 18, 2024
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  4. Add a few more rewrite rules

    @matentzn
    matentzn committed Apr 18, 2024
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  5. Update upheno-pattern-deriver.ipynb

    @matentzn
    matentzn committed Apr 18, 2024
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Commits on Apr 24, 2024

  1. Update upheno-config.yaml

    @jamesamcl
    jamesamcl authored Apr 24, 2024
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  2. Update upheno_create_profiles.py

    @matentzn
    matentzn committed Apr 24, 2024
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  3. Merge branch 'dev' of https://github.com/obophenotype/upheno-dev into… 

    … dev
    @matentzn
    matentzn committed Apr 24, 2024
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  4. filter out bfo

    @jamesamcl
    jamesamcl committed Apr 24, 2024
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Commits on Jun 19, 2024

  1. Update scripts and files 

    This commit messages will be rewritten before this branch is merged
    @matentzn
    matentzn committed Jun 19, 2024
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  2. Update components and add new top level classes

    @matentzn
    matentzn committed Jun 19, 2024
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  3. Remove three patterns for matches

    @matentzn
    matentzn committed Jun 19, 2024
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Commits on Jun 20, 2024

  1. Update some phenotype patterns

    @matentzn
    matentzn committed Jun 20, 2024
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  2. Huge refactor 

    Will break down into smaller commits later
    @matentzn
    matentzn committed Jun 20, 2024
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Commits on Jun 21, 2024

  1. Update some data files

    @matentzn
    matentzn committed Jun 21, 2024
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  2. Update upheno_prepare.py

    @matentzn
    matentzn committed Jun 21, 2024
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  3. Update lexical_mapping.py

    @matentzn
    matentzn committed Jun 21, 2024
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  4. Update lib.py

    @matentzn
    matentzn committed Jun 21, 2024
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  5. Update upheno-config.yaml

    @matentzn
    matentzn committed Jun 21, 2024
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  6. Update upheno.Makefile

    @matentzn
    matentzn committed Jun 21, 2024
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  7. Update upheno_pipeline.sh

    @matentzn
    matentzn committed Jun 21, 2024
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Commits on Jun 22, 2024

  1. Huge refactor, no words

    @matentzn
    matentzn committed Jun 22, 2024
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  2. Updated files during release

    @matentzn
    matentzn committed Jun 22, 2024
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  3. Merge branch 'master' into dev

    @matentzn
    matentzn committed Jun 22, 2024
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  4. Refactor uPheno makefile continued

    @matentzn
    matentzn committed Jun 22, 2024
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  5. Update catalog-v001.xml

    @matentzn
    matentzn committed Jun 22, 2024
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  6. Update import

    @matentzn
    matentzn committed Jun 22, 2024
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  7. Update merged_import.owl

    @matentzn
    matentzn committed Jun 22, 2024
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Commits on Jun 23, 2024

  1. State of latest fixed version of uPheno

    @matentzn
    matentzn committed Jun 23, 2024
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  2. Update upheno_id_map.txt 

    Set to @jamesamcl version of december 2023
    @matentzn
    matentzn committed Jun 23, 2024
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  3. Create upheno_id_map_december_2023.txt

    @matentzn
    matentzn committed Jun 23, 2024
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  4. set SOT for upheno_id_map to github agaimn

    @matentzn
    matentzn committed Jun 23, 2024
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  5. Update upheno-config.yaml

    @matentzn
    matentzn committed Jun 23, 2024
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  6. Add uPheno fillers to version control

    @matentzn
    matentzn committed Jun 23, 2024
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  7. More huge refactors

    @matentzn
    matentzn committed Jun 23, 2024
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  8. Update python depedencies

    @matentzn
    matentzn committed Jun 23, 2024
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  9. More refactoring

    @matentzn
    matentzn committed Jun 23, 2024
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  10. Update upheno.Makefile

    @matentzn
    matentzn committed Jun 23, 2024
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  11. Update patterns

    @matentzn
    matentzn committed Jun 23, 2024
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  12. Update upheno_build.py

    @matentzn
    matentzn committed Jun 23, 2024
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  13. refactor

    @matentzn
    matentzn committed Jun 23, 2024
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  14. Update fillers

    @matentzn
    matentzn committed Jun 23, 2024
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  15. Fix fillers pipeline

    @matentzn
    matentzn committed Jun 23, 2024
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  16. Update upheno.Makefile

    @matentzn
    matentzn committed Jun 23, 2024
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  17. Update upheno fillers

    @matentzn
    matentzn committed Jun 23, 2024
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  18. Update fillers

    @matentzn
    matentzn committed Jun 23, 2024
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  19. Update upheno_id_map.txt

    @matentzn
    matentzn committed Jun 23, 2024
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  20. Make sure upheno map is updated correctly

    @matentzn
    matentzn committed Jun 23, 2024
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  21. Update upheno.Makefile

    @matentzn
    matentzn committed Jun 23, 2024
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  22. Update lib.py

    @matentzn
    matentzn committed Jun 23, 2024
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  23. Update upheno_create_profiles.py

    @matentzn
    matentzn committed Jun 23, 2024
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Commits on Jun 24, 2024

  1. Add all uPheno patterns to patterns dir

    @matentzn
    matentzn committed Jun 24, 2024
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  2. Add automatic from upheno map

    @matentzn
    matentzn committed Jun 24, 2024
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  3. Add all changed patterns to pattern directory

    @matentzn
    matentzn committed Jun 24, 2024
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  4. Update a few pattern names

    @matentzn
    matentzn committed Jun 24, 2024
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  5. Update pattern names

    @matentzn
    matentzn committed Jun 24, 2024
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  6. Remove modified patterns

    @matentzn
    matentzn committed Jun 24, 2024
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  7. Remove modified patterns

    @matentzn
    matentzn committed Jun 24, 2024
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  8. Update pipelines

    @matentzn
    matentzn committed Jun 24, 2024
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  9. Add missing cols to obsolete tsv

    @matentzn
    matentzn committed Jun 24, 2024
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  10. Remove obsolete classes form set

    @matentzn
    matentzn committed Jun 24, 2024
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  11. Update DOSDP

    @matentzn
    matentzn committed Jun 24, 2024
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  12. More refactoring

    @matentzn
    matentzn committed Jun 24, 2024
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Commits on Jun 25, 2024

  1. Get rid of some patterns we dont need anymore

    @matentzn
    matentzn committed Jun 25, 2024
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  2. Another huge refactor

    @matentzn
    matentzn committed Jun 25, 2024
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  3. Add obsoletion pipeline

    @matentzn
    matentzn committed Jun 25, 2024
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  4. Update merged.owl goal

    @matentzn
    matentzn committed Jun 25, 2024
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  5. Update definitions.owl

    @matentzn
    matentzn committed Jun 25, 2024
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Commits on Jun 27, 2024

  1. Update obsolete.tsv

    @matentzn
    matentzn committed Jun 27, 2024
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  2. Update upheno-odk.yaml

    @matentzn
    matentzn committed Jun 27, 2024
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  3. Update abnormalAnatomicalEntity.tsv

    @matentzn
    matentzn committed Jun 27, 2024
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  4. Updated patterns

    @matentzn
    matentzn committed Jun 27, 2024
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  5. Update upheno-deprecated.owl

    @matentzn
    matentzn committed Jun 27, 2024
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  6. Create upheno_qc.ipynb

    @matentzn
    matentzn committed Jun 27, 2024
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  7. Obsolete all of the gocc_anatomical_entity cases

    @matentzn
    matentzn committed Jun 27, 2024
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  8. Apply all cc_cl removals

    @matentzn
    matentzn committed Jun 27, 2024
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  9. Get rid of resistence_to_entity_chebi case in uPheno

    @matentzn
    matentzn committed Jun 27, 2024
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  10. Dealt with bp_and_mf

    @matentzn
    matentzn committed Jun 27, 2024
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  11. Update obsolete.tsv

    @matentzn
    matentzn committed Jun 27, 2024
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Commits on Aug 4, 2024

  1. Remove some obsoleted classes from patterns

    @matentzn
    matentzn committed Aug 4, 2024
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  2. Deleting a lot of redundant class definitions

    @matentzn
    matentzn committed Aug 4, 2024
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  3. Updated release files

    @matentzn
    matentzn committed Aug 4, 2024
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  4. Update imports and components

    @matentzn
    matentzn committed Aug 4, 2024
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  5. Update ODK

    @matentzn
    matentzn committed Aug 4, 2024
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  6. ODK 1.5.2 update

    @matentzn
    matentzn committed Aug 4, 2024
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  7. Update upheno-edit.owl

    @matentzn
    matentzn committed Aug 4, 2024
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  8. Remove all NBO phenotypes from abnormalBiologicalProcess pattern

    @matentzn
    matentzn committed Aug 4, 2024
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  9. Update definitions.owl

    @matentzn
    matentzn committed Aug 4, 2024
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  10. Remove some more classes

    @matentzn
    matentzn committed Aug 4, 2024
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  11. Remove some redundant classes from patterns

    @matentzn
    matentzn committed Aug 4, 2024
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Commits on Aug 25, 2024

  1. Update component files

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    matentzn committed Aug 25, 2024
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  2. Update scripts

    @matentzn
    matentzn committed Aug 25, 2024
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Commits on Aug 26, 2024

  1. Update MISC

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    matentzn committed Aug 26, 2024
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Commits on Aug 27, 2024

  1. Update scripts

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    matentzn committed Aug 27, 2024
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  2. Update patterns (mainly removals)

    @matentzn
    matentzn committed Aug 27, 2024
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  3. Update imports files

    @matentzn
    matentzn committed Aug 27, 2024
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  4. Remove merged import which has become to large to be handled

    @matentzn
    matentzn committed Aug 27, 2024
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  5. Adding remaining SSPOs to imports

    @matentzn
    matentzn committed Aug 27, 2024
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  6. Update bridge files

    @matentzn
    matentzn committed Aug 27, 2024
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  7. Obsolete 8 redundant classes

    @matentzn
    matentzn committed Aug 27, 2024
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Commits on Aug 28, 2024

  1. Update components and mappings

    @matentzn
    matentzn committed Aug 28, 2024
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  2. Update templates

    @matentzn
    matentzn committed Aug 28, 2024
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  3. Update pipelines

    @matentzn
    matentzn committed Aug 28, 2024
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  4. Update remove duplicative classes from pattern files

    @matentzn
    matentzn committed Aug 28, 2024
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  5. ODK config fixes

    @matentzn
    matentzn committed Aug 28, 2024
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  6. Update upheno.Makefile

    @matentzn
    matentzn committed Aug 28, 2024
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Commits on Aug 30, 2024

  1. Add anatomy mappings into upheno pattern matching process

    @matentzn
    matentzn committed Aug 30, 2024
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  2. Add Uberon sssom file to uPheno

    @matentzn
    matentzn committed Aug 30, 2024
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  3. Update components and mappings

    @matentzn
    matentzn committed Aug 30, 2024
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  4. Add a few more mapping sets to upheno odk config

    @matentzn
    matentzn committed Aug 30, 2024
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Commits on Aug 31, 2024

  1. Update COmponents and mappings

    @matentzn
    matentzn committed Aug 31, 2024
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  2. Update obsolete.tsv

    @matentzn
    matentzn committed Aug 31, 2024
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  3. Update uPheno deprecated

    @matentzn
    matentzn committed Aug 31, 2024
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  4. Remove a few obsolete c-s matches

    @matentzn
    matentzn committed Aug 31, 2024
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  5. Providing some last tweaks to the ontology

    @matentzn
    matentzn committed Aug 31, 2024
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  6. Update upheno.Makefile

    @matentzn
    matentzn committed Aug 31, 2024
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  7. Update upheno.Makefile

    @matentzn
    matentzn committed Aug 31, 2024
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Commits on Sep 1, 2024

  1. Add root alignments

    @matentzn
    matentzn committed Sep 1, 2024
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  2. Various updates

    @matentzn
    matentzn committed Sep 1, 2024
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Commits on Sep 3, 2024

  1. Update uPheno release files

    @matentzn
    matentzn committed Sep 3, 2024
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  2. Remove upheno.owl

    @matentzn
    matentzn committed Sep 3, 2024
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  3. Delete upheno-base.owl

    @matentzn
    matentzn committed Sep 3, 2024
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  4. Update makefile

    @matentzn
    matentzn committed Sep 3, 2024
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  5. MISC custom makefile updates

    @matentzn
    matentzn committed Sep 3, 2024
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  6. Add lexical matching command to CLI

    @matentzn
    matentzn committed Sep 3, 2024
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  7. Update release files

    @matentzn
    matentzn committed Sep 3, 2024
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