Code

qualifiers / biolink3 update#106

Code

Merged

colleenXu merged 57 commits intomasterNCATS-Tangerine/translator-api-registry:masterfrom biolink3NCATS-Tangerine/translator-api-registry:biolink3Copy head branch name to clipboardMar 16, 2023

+7,898-2,208

Commits

Commits on Oct 11, 2022

• dgidb: agonist and agonist-rev operations using simplified predicate and added qualifiers section

  colleenXu

  committed
  59cd82c

• dgidb: add qualifier refactoring to some operations

  Show description for 98f22c7
  colleenXu

  committed
  98f22c7

Commits on Oct 13, 2022

• dgidb: for non-canonical directions, changing qualified_predicate to caused_by

  Show description for 56e857a
  colleenXu

  committed
  56e857a

Commits on Oct 27, 2022

• dgidb: update 1 set of commented-out operations

  Show description for b19b6ff
  colleenXu

  committed
  b19b6ff

• go bp: update process_regulates_process, process_positively_regulates_process, process_negatively_regulates_process predicates

  colleenXu

  committed
  06bd8ce

• dgidb / semmeddb: update entity_positively_regulat* predicates for qualifier-refactor

  colleenXu

  committed
  100dfff

• text-mining targeted: update entity_positively_regulat* predicates for qualifier-refactor

  colleenXu

  committed
  2864a60

• text-mining targeted: update entity_negatively_regulat* predicates for qualifier-refactor

  colleenXu

  committed
  fd34e03

• semmeddb: update entity_negatively_regulat* predicates for qualifier-refactor

  colleenXu

  committed
  f951fcd

• dgidb: fix comments, update directly_interacts_with predicate for qualifier refactor

  colleenXu

  committed
  923f5f8

• Merge branch 'master' into biolink3

  colleenXu

  committed
  e473543

Commits on Oct 28, 2022

• dgidb: refine predicates/qualifiers,comments. including interacts_with

  colleenXu

  committed
  f2c0443

• idisk, mychem: update causes_adverse_event predicate and its inverse for biolink 3.0.2

  colleenXu

  committed
  d24d07f

• semmeddb: change associated_with predicate to related_to, due to definition of associated_with in biolink 3.0.2

  colleenXu

  committed
  6747750

• dgidb: adjust commented-out operation inducer

  colleenXu

  committed
  7bd11ba

• biolink/monarch and idisk: update interacts_with predicate for biolink 3.0.2

  colleenXu

  committed
  65a7c80

• dgidb: update comments

  colleenXu

  committed
  32463d9

• idisk: keep interacts_with predicate

  colleenXu

  committed
  186faf3

• biolink/monarch: update comment

  colleenXu

  committed
  f34dffa

Commits on Oct 31, 2022

• semmeddb: fix accidental empty lines

  colleenXu

  committed
  6d8030a

• DISEASES,biolink/monarch,idisk,mychem: update source response-mapping

  colleenXu

  committed
  828d955

Commits on Nov 1, 2022

• biolink/monarch,mygene,quickgo: update relation -> biolink:original_predicate

  colleenXu

  committed
  e94ae27

• bindingdb,mychem,mygene,pfocr: update edge-attribute url keys

  Show description for 7860b47
  colleenXu

  committed
  7860b47

• pfocr: update a comment

  colleenXu

  committed
  f5dd3be

• EBIg2p: update response-mapping keys, comments

  colleenXu

  committed
  c8d665f

• mydisease,myvariant: update response-mapping keys (trying to use biolink terms for some), comments

  colleenXu

  committed
  7334b4e

Commits on Nov 2, 2022

• update biolink-version to 3.0.3, openapi to 3.0.3, and more

  Show description for 8d5e8b6
  colleenXu

  committed
  8d5e8b6

• fix indentation typo

  tokebe

  authored
  72bacb0

Commits on Nov 4, 2022

• text-mining targeted: rewind qualifier-refactor edits

  Show description for 8e1f0a0
  colleenXu

  committed
  8e1f0a0

• semmeddb: replace regulates/regulated_by with affects/affected_by

  Show description for adc41c4
  colleenXu

  committed
  adc41c4

• dgidb,semmeddb: use snake_case for qualifier-values

  Show description for 4e724af
  colleenXu

  committed
  4e724af

Commits on Nov 9, 2022

• Merge branch 'master' into biolink3

  colleenXu

  committed
  a2af5fe

• Merge branch 'master' into biolink3

  colleenXu

  committed
  bf4ea68

• Merge branch 'master' into biolink3

  colleenXu

  committed
  c1a4a02

Commits on Nov 11, 2022

• semmeddb notebook: update to use qualifiers, biolink 3.0.3

  Show description for ddf6c68
  colleenXu

  committed
  ddf6c68

• Merge branch 'master' into biolink3

  colleenXu

  committed
  5fe63d8

Commits on Nov 15, 2022

• service provider: add new SRI test-data file for qualifiers

  colleenXu

  committed
  f501fd0

Commits on Nov 22, 2022

• biolink/monarch,dgidb: revert to using interacts_with predicate

  Show description for 47f3054
  colleenXu

  committed
  47f3054

• service provider: add test-data url for qualifiers, change production test-data url to default

  colleenXu

  committed
  3d798b9

• service provider: fix dev test-data-url to development

  colleenXu

  committed
  75b9553

• Merge branch 'master' into biolink3

  colleenXu

  committed
  7eee1b9

Commits on Dec 5, 2022

• Merge branch 'master' into biolink3

  colleenXu

  committed
  3e449f3

Commits on Dec 8, 2022

• semmeddb notebook: update code for using biolink 3.1.1

  Show description for da2e91d
  colleenXu

  committed
  da2e91d

Commits on Dec 14, 2022

• Merge branch 'master' into biolink3

  colleenXu

  committed
  7838c86

• many apis: update biolink version to 3.1.1

  colleenXu

  committed
  fb46c57

Commits on Jan 25, 2023

• change subject/object to subject_id/object_id

  Show description for e5797fa
  colleenXu

  committed
  e5797fa

Commits on Jan 30, 2023

• Merge branch 'master' into biolink3

  colleenXu

  committed
  0bf4eeb

Commits on Jan 31, 2023

• multiple biothings apis: change api names

  Show description for ed1b1f2
  colleenXu

  committed
  ed1b1f2

• Merge branch 'master' into biolink3

  colleenXu

  committed
  ed9bfb5

Commits on Feb 6, 2023

• mychem: update drugcentral.bioactivity operations

  Show description for 5d4391a
  colleenXu

  committed
  5d4391a

Commits on Feb 24, 2023

• bioplanet,mygene,myvariant,biolink/monarch: update to add node label support

  Show description for e3930e3
  colleenXu

  committed
  e3930e3

Commits on Feb 27, 2023

• mychem: add chembl.drug_mechanisms general operations

  Show description for db32e89
  colleenXu

  committed
  db32e89

Commits on Mar 1, 2023

• mychem for biolink 3.1.1: merge 2 drugcentral bioactivity chem->gene operations

  colleenXu

  committed
  fc2a207

• mychem for biolink 3.1.1: add drugcentral-bioactivity allosteric mod and mod operation

  colleenXu

  committed
  c97da47

Commits on Mar 8, 2023

• biolink/monarch: add gene-disease and gene-pheno x-bte operations that automatically use gene-ortholog intermediate

  colleenXu

  committed
  7387523

Commits on Mar 9, 2023

• Merge branch 'master' into biolink3

  colleenXu

  committed
  004010b

• multiple apis: updating biolink-version annotation for biolink 3.1.1

  colleenXu

  committed
  ec1da25