Code

For comparison only: DEV branch#61

Code

Merged

matentzn merged 152 commits intomasterobophenotype/upheno-dev:masterfrom devobophenotype/upheno-dev:devCopy head branch name to clipboardSep 3, 2024

+3,401,682-271,515

Commits

Commits on Dec 13, 2023

• add obsolete classes due to renamed patterns

  jamesamcl

  committed
  fa49f0f

  Copy full SHA for fa49f0f

• add sssom mapping generation

  jamesamcl

  committed
  690f708

  Copy full SHA for 690f708

• Add obsoletion module

  matentzn

  committed
  28cfef2

  Copy full SHA for 28cfef2

• inheres_in_part_of

  jamesamcl

  committed
  9027175

  Copy full SHA for 9027175

• Add method to to postprocess modified patterns after matching

  matentzn

  committed
  2fedb71

  Copy full SHA for 2fedb71

• Merge branch 'dev' of https://github.com/obophenotype/upheno-dev into dev

  matentzn

  committed
  7fbee3e

  Copy full SHA for 7fbee3e

• Update upheno_prepare.py

  matentzn

  committed
  add9688

  Copy full SHA for add9688

• fix inheres_in pattern generation

  jamesamcl

  committed
  4ad5740

  Copy full SHA for 4ad5740

• add missing method to lib.py

  jamesamcl

  committed
  78965b9

  Copy full SHA for 78965b9

Commits on Jan 31, 2024

• add out path for sssom

  jamesamcl

  committed
  f07a464

  Copy full SHA for f07a464

• add mappings file wip

  jamesamcl

  committed
  9b6d25e

  Copy full SHA for 9b6d25e

• remove exit from prepare

  jamesamcl

  committed
  4193f75

  Copy full SHA for 4193f75

• remove missing bridges

  jamesamcl

  committed
  fe43954

  Copy full SHA for fe43954

• Merge branch 'master' into dev

  matentzn

  committed
  2e6c4ca

  Copy full SHA for 2e6c4ca

• reinstate excluded patterns with comment

  jamesamcl

  committed
  3b309d9

  Copy full SHA for 3b309d9

• Merge branch 'dev' of github.com:obophenotype/upheno-dev into dev

  jamesamcl

  committed
  71a03c5

  Copy full SHA for 71a03c5

Commits on Mar 6, 2024

• Updated patterns

  matentzn

  committed
  35015cf

  Copy full SHA for 35015cf

• Create upheno-pattern-deriver.ipynb

  matentzn

  committed
  0c329bb

  Copy full SHA for 0c329bb

Commits on Mar 8, 2024

• Updated patterns

  matentzn

  committed
  0432c8a

  Copy full SHA for 0432c8a

• add +x to upheno_pipeline.sh

  jamesamcl

  committed
  ee9af35

  Copy full SHA for ee9af35

• Add changed patterns generation step

  matentzn

  committed
  e7b0d8a

  Copy full SHA for e7b0d8a

• Merge branch 'dev' of https://github.com/obophenotype/upheno-dev into dev

  matentzn

  committed
  1966b9a

  Copy full SHA for 1966b9a

Commits on Mar 11, 2024

• fix variable same name as function

  jamesamcl

  committed
  0e0fa3c

  Copy full SHA for 0e0fa3c

Commits on Apr 10, 2024

• Update upheno_create_profiles.py

  matentzn

  committed
  41e06f1

  Copy full SHA for 41e06f1

• Update upheno_create_profiles.py

  matentzn

  committed
  3f4cb53

  Copy full SHA for 3f4cb53

Commits on Apr 11, 2024

• Update upheno_create_profiles.py

  Show description for 7456884
  matentzn

  committed
  7456884

  Copy full SHA for 7456884

Commits on Apr 18, 2024

• Review changed patterns

  matentzn

  committed
  e4b323b

  Copy full SHA for e4b323b

• Updating remaining classes

  matentzn

  committed
  e783292

  Copy full SHA for e783292

• Updated some more patterns

  matentzn

  committed
  e0b3ba9

  Copy full SHA for e0b3ba9

• Add a few more rewrite rules

  matentzn

  committed
  a84ad08

  Copy full SHA for a84ad08

• Update upheno-pattern-deriver.ipynb

  matentzn

  committed
  4d10c56

  Copy full SHA for 4d10c56

Commits on Apr 24, 2024

• Update upheno-config.yaml

  jamesamcl

  authored
  de437e3

  Copy full SHA for de437e3

• Update upheno_create_profiles.py

  matentzn

  committed
  157cfea

  Copy full SHA for 157cfea

• Merge branch 'dev' of https://github.com/obophenotype/upheno-dev into dev

  matentzn

  committed
  fed7de1

  Copy full SHA for fed7de1

• filter out bfo

  jamesamcl

  committed
  fe758e2

  Copy full SHA for fe758e2

Commits on Jun 19, 2024

• Update scripts and files

  Show description for 4dfb83f
  matentzn

  committed
  4dfb83f

  Copy full SHA for 4dfb83f

• Update components and add new top level classes

  matentzn

  committed
  67cccc5

  Copy full SHA for 67cccc5

• Remove three patterns for matches

  matentzn

  committed
  9e31002

  Copy full SHA for 9e31002

Commits on Jun 20, 2024

• Update some phenotype patterns

  matentzn

  committed
  98878a5

  Copy full SHA for 98878a5

• Huge refactor

  Show description for 62c1905
  matentzn

  committed
  62c1905

  Copy full SHA for 62c1905

Commits on Jun 21, 2024

• Update some data files

  matentzn

  committed
  682fd5d

  Copy full SHA for 682fd5d

• Update upheno_prepare.py

  matentzn

  committed
  c8c94d7

  Copy full SHA for c8c94d7

• Update lexical_mapping.py

  matentzn

  committed
  92ac6d9

  Copy full SHA for 92ac6d9

• Update lib.py

  matentzn

  committed
  f14488a

  Copy full SHA for f14488a

• Update upheno-config.yaml

  matentzn

  committed
  55680e9

  Copy full SHA for 55680e9

• Update upheno.Makefile

  matentzn

  committed
  420f775

  Copy full SHA for 420f775

• Update upheno_pipeline.sh

  matentzn

  committed
  793cb2f

  Copy full SHA for 793cb2f

Commits on Jun 22, 2024

• Huge refactor, no words

  matentzn

  committed
  06a63f9

  Copy full SHA for 06a63f9

• Updated files during release

  matentzn

  committed
  a95da92

  Copy full SHA for a95da92

• Merge branch 'master' into dev

  matentzn

  committed
  67299a9

  Copy full SHA for 67299a9

• Refactor uPheno makefile continued

  matentzn

  committed
  47ba698

  Copy full SHA for 47ba698

• Update catalog-v001.xml

  matentzn

  committed
  c922bf2

  Copy full SHA for c922bf2

• Update import

  matentzn

  committed
  a9788c1

  Copy full SHA for a9788c1

• Update merged_import.owl

  matentzn

  committed
  986d849

  Copy full SHA for 986d849

Commits on Jun 23, 2024

• State of latest fixed version of uPheno

  matentzn

  committed
  35dcb4c

  Copy full SHA for 35dcb4c

• Update upheno_id_map.txt

  Show description for 89df4e2
  matentzn

  committed
  89df4e2

  Copy full SHA for 89df4e2

• Create upheno_id_map_december_2023.txt

  matentzn

  committed
  941c9dd

  Copy full SHA for 941c9dd

• set SOT for upheno_id_map to github agaimn

  matentzn

  committed
  8102d97

  Copy full SHA for 8102d97

• Update upheno-config.yaml

  matentzn

  committed
  443378c

  Copy full SHA for 443378c

• Add uPheno fillers to version control

  matentzn

  committed
  8f56da2

  Copy full SHA for 8f56da2

• More huge refactors

  matentzn

  committed
  abf8127

  Copy full SHA for abf8127

• Update python depedencies

  matentzn

  committed
  4817c7b

  Copy full SHA for 4817c7b

• More refactoring

  matentzn

  committed
  a30df2d

  Copy full SHA for a30df2d

• Update upheno.Makefile

  matentzn

  committed
  597d5ea

  Copy full SHA for 597d5ea

• Update patterns

  matentzn

  committed
  4a36bf2

  Copy full SHA for 4a36bf2

• Update upheno_build.py

  matentzn

  committed
  7b8a55a

  Copy full SHA for 7b8a55a

• refactor

  matentzn

  committed
  0a54e3b

  Copy full SHA for 0a54e3b

• Update fillers

  matentzn

  committed
  c6cb03a

  Copy full SHA for c6cb03a

• Fix fillers pipeline

  matentzn

  committed
  fe24d2e

  Copy full SHA for fe24d2e

• Update upheno.Makefile

  matentzn

  committed
  b6eb68e

  Copy full SHA for b6eb68e

• Update upheno fillers

  matentzn

  committed
  72fcd69

  Copy full SHA for 72fcd69

• Update fillers

  matentzn

  committed
  4fd297e

  Copy full SHA for 4fd297e

• Update upheno_id_map.txt

  matentzn

  committed
  47e7217

  Copy full SHA for 47e7217

• Make sure upheno map is updated correctly

  matentzn

  committed
  248cd20

  Copy full SHA for 248cd20

• Update upheno.Makefile

  matentzn

  committed
  0d278fe

  Copy full SHA for 0d278fe

• Update lib.py

  matentzn

  committed
  3526c62

  Copy full SHA for 3526c62

• Update upheno_create_profiles.py

  matentzn

  committed
  0ae1bf9

  Copy full SHA for 0ae1bf9

Commits on Jun 24, 2024

• Add all uPheno patterns to patterns dir

  matentzn

  committed
  8dc82f1

  Copy full SHA for 8dc82f1

• Add automatic from upheno map

  matentzn

  committed
  518ca35

  Copy full SHA for 518ca35

• Add all changed patterns to pattern directory

  matentzn

  committed
  4317b81

  Copy full SHA for 4317b81

• Update a few pattern names

  matentzn

  committed
  89184ab

  Copy full SHA for 89184ab

• Update pattern names

  matentzn

  committed
  2abbfd5

  Copy full SHA for 2abbfd5

• Remove modified patterns

  matentzn

  committed
  2a85058

  Copy full SHA for 2a85058

• Remove modified patterns

  matentzn

  committed
  40b540b

  Copy full SHA for 40b540b

• Update pipelines

  matentzn

  committed
  af1cca6

  Copy full SHA for af1cca6

• Add missing cols to obsolete tsv

  matentzn

  committed
  8dd05cd

  Copy full SHA for 8dd05cd

• Remove obsolete classes form set

  matentzn

  committed
  46bd970

  Copy full SHA for 46bd970

• Update DOSDP

  matentzn

  committed
  a52c40c

  Copy full SHA for a52c40c

• More refactoring

  matentzn

  committed
  69f7882

  Copy full SHA for 69f7882

Commits on Jun 25, 2024

• Get rid of some patterns we dont need anymore

  matentzn

  committed
  29c0f7c

  Copy full SHA for 29c0f7c

• Another huge refactor

  matentzn

  committed
  bdfe3c2

  Copy full SHA for bdfe3c2

• Add obsoletion pipeline

  matentzn

  committed
  e378993

  Copy full SHA for e378993

• Update merged.owl goal

  matentzn

  committed
  16a9cd5

  Copy full SHA for 16a9cd5

• Update definitions.owl

  matentzn

  committed
  ace925f

  Copy full SHA for ace925f

Commits on Jun 27, 2024

• Update obsolete.tsv

  matentzn

  committed
  189e4ee

  Copy full SHA for 189e4ee

• Update upheno-odk.yaml

  matentzn

  committed
  1c1e2a2

  Copy full SHA for 1c1e2a2

• Update abnormalAnatomicalEntity.tsv

  matentzn

  committed
  165ae54

  Copy full SHA for 165ae54

• Updated patterns

  matentzn

  committed
  48a8c1c

  Copy full SHA for 48a8c1c

• Update upheno-deprecated.owl

  matentzn

  committed
  cfe807d

  Copy full SHA for cfe807d

• Create upheno_qc.ipynb

  matentzn

  committed
  6140e9f

  Copy full SHA for 6140e9f

• Obsolete all of the gocc_anatomical_entity cases

  matentzn

  committed
  a0512de

  Copy full SHA for a0512de

• Apply all cc_cl removals

  matentzn

  committed
  3668ff5

  Copy full SHA for 3668ff5

• Get rid of resistence_to_entity_chebi case in uPheno

  matentzn

  committed
  296573d

  Copy full SHA for 296573d

• Dealt with bp_and_mf

  matentzn

  committed
  f3d50db

  Copy full SHA for f3d50db

• Update obsolete.tsv

  matentzn

  committed
  18f4132

  Copy full SHA for 18f4132

Commits on Aug 4, 2024

• Remove some obsoleted classes from patterns

  matentzn

  committed
  b0bfdee

  Copy full SHA for b0bfdee

• Deleting a lot of redundant class definitions

  matentzn

  committed
  c96d7bb

  Copy full SHA for c96d7bb

• Updated release files

  matentzn

  committed
  8cfae0b

  Copy full SHA for 8cfae0b

• Update imports and components

  matentzn

  committed
  cecfc2a

  Copy full SHA for cecfc2a

• Update ODK

  matentzn

  committed
  5442cde

  Copy full SHA for 5442cde

• ODK 1.5.2 update

  matentzn

  committed
  b0af5e3

  Copy full SHA for b0af5e3

• Update upheno-edit.owl

  matentzn

  committed
  43be67d

  Copy full SHA for 43be67d

• Remove all NBO phenotypes from abnormalBiologicalProcess pattern

  matentzn

  committed
  67d6e7b

  Copy full SHA for 67d6e7b

• Update definitions.owl

  matentzn

  committed
  cdeef4e

  Copy full SHA for cdeef4e

• Remove some more classes

  matentzn

  committed
  f361dfb

  Copy full SHA for f361dfb

• Remove some redundant classes from patterns

  matentzn

  committed
  2bc12f1

  Copy full SHA for 2bc12f1

Commits on Aug 25, 2024

• Update component files

  matentzn

  committed
  c5c5958

  Copy full SHA for c5c5958

• Update scripts

  matentzn

  committed
  52fa451

  Copy full SHA for 52fa451

Commits on Aug 26, 2024

• Update MISC

  matentzn

  committed
  5b3c3c6

  Copy full SHA for 5b3c3c6

Commits on Aug 27, 2024

• Update scripts

  matentzn

  committed
  8744032

  Copy full SHA for 8744032

• Update patterns (mainly removals)

  matentzn

  committed
  6094b5b

  Copy full SHA for 6094b5b

• Update imports files

  matentzn

  committed
  ffd42b3

  Copy full SHA for ffd42b3

• Remove merged import which has become to large to be handled

  matentzn

  committed
  495c35a

  Copy full SHA for 495c35a

• Adding remaining SSPOs to imports

  matentzn

  committed
  680213c

  Copy full SHA for 680213c

• Update bridge files

  matentzn

  committed
  535ed65

  Copy full SHA for 535ed65

• Obsolete 8 redundant classes

  matentzn

  committed
  beca8b3

  Copy full SHA for beca8b3

Commits on Aug 28, 2024

• Update components and mappings

  matentzn

  committed
  ba2d541

  Copy full SHA for ba2d541

• Update templates

  matentzn

  committed
  8f93933

  Copy full SHA for 8f93933

• Update pipelines

  matentzn

  committed
  0bf5b98

  Copy full SHA for 0bf5b98

• Update remove duplicative classes from pattern files

  matentzn

  committed
  f45150c

  Copy full SHA for f45150c

• ODK config fixes

  matentzn

  committed
  5dcfd61

  Copy full SHA for 5dcfd61

• Update upheno.Makefile

  matentzn

  committed
  d437b65

  Copy full SHA for d437b65

Commits on Aug 30, 2024

• Add anatomy mappings into upheno pattern matching process

  matentzn

  committed
  e84feaa

  Copy full SHA for e84feaa

• Add Uberon sssom file to uPheno

  matentzn

  committed
  cce685c

  Copy full SHA for cce685c

• Update components and mappings

  matentzn

  committed
  eae3bf1

  Copy full SHA for eae3bf1

• Add a few more mapping sets to upheno odk config

  matentzn

  committed
  c9c7e40

  Copy full SHA for c9c7e40

Commits on Aug 31, 2024

• Update COmponents and mappings

  matentzn

  committed
  7b47abe

  Copy full SHA for 7b47abe

• Update obsolete.tsv

  matentzn

  committed
  e62ee96

  Copy full SHA for e62ee96

• Update uPheno deprecated

  matentzn

  committed
  7c39ab3

  Copy full SHA for 7c39ab3

• Remove a few obsolete c-s matches

  matentzn

  committed
  c41d47a

  Copy full SHA for c41d47a

• Providing some last tweaks to the ontology

  matentzn

  committed
  60ffca9

  Copy full SHA for 60ffca9

• Update upheno.Makefile

  matentzn

  committed
  2a5cf80

  Copy full SHA for 2a5cf80

• Update upheno.Makefile

  matentzn

  committed
  8c0a9ca

  Copy full SHA for 8c0a9ca

Commits on Sep 1, 2024

• Add root alignments

  matentzn

  committed
  3e0f60a

  Copy full SHA for 3e0f60a

• Various updates

  matentzn

  committed
  aa78439

  Copy full SHA for aa78439

Commits on Sep 3, 2024

• Update uPheno release files

  matentzn

  committed
  cf2ab7c

  Copy full SHA for cf2ab7c

• Remove upheno.owl

  matentzn

  committed
  49e8e82

  Copy full SHA for 49e8e82

• Delete upheno-base.owl

  matentzn

  committed
  abe17c5

  Copy full SHA for abe17c5

• Update makefile

  matentzn

  committed
  a7a9069

  Copy full SHA for a7a9069

• MISC custom makefile updates

  matentzn

  committed
  0413f08

  Copy full SHA for 0413f08

• Add lexical matching command to CLI

  matentzn

  committed
  c858992

  Copy full SHA for c858992

• Update release files

  matentzn

  committed
  75726f0

  Copy full SHA for 75726f0