Code

Merging KG2.10.1 build code#411

Code

Merged

ecwood merged 126 commits intomasterRTXteam/RTX-KG2:masterfrom midjuly24workRTXteam/RTX-KG2:midjuly24workCopy head branch name to clipboardSep 8, 2024

+2,423-1,234

Commits

Commits on Jul 11, 2024

• #390 first attempt at reducing dependencies

  ecwood

  committed
  42d1a43

  Copy full SHA for 42d1a43

• #390 hopefully these can go as well

  ecwood

  committed
  20eeff6

  Copy full SHA for 20eeff6

Commits on Jul 16, 2024

• #398 first pass at clinical trials kg

  ecwood

  committed
  281bf43

  Copy full SHA for 281bf43

• #398 forgot the url map entry

  ecwood

  committed
  4f338f5

  Copy full SHA for 4f338f5

• #399 to avoid confusion

  ecwood

  committed
  cfd305e

  Copy full SHA for cfd305e

• #398 updating the Snakemake pipeline

  ecwood

  committed
  42d9872

  Copy full SHA for 42d9872

• #398 correcting a typo

  ecwood

  committed
  134f5ec

  Copy full SHA for 134f5ec

• #398 correcting another typo

  ecwood

  committed
  a61d098

  Copy full SHA for a61d098

• #398 correcting typo in extract

  ecwood

  committed
  93168e7

  Copy full SHA for 93168e7

• #398 correcting typo in conversion

  ecwood

  committed
  dd73e65

  Copy full SHA for dd73e65

• #398 correcting to standardize in kg2_util

  ecwood

  committed
  0c16ea3

  Copy full SHA for 0c16ea3

• #398 versioning attempt

  ecwood

  committed
  4a13131

  Copy full SHA for 4a13131

• #398 clean up the versioning

  ecwood

  committed
  974ed5c

  Copy full SHA for 974ed5c

• #398 add an entry into KL/AT map

  ecwood

  committed
  9d65fd9

  Copy full SHA for 9d65fd9

• #398 reworking update date

  ecwood

  committed
  bdf1ad1

  Copy full SHA for bdf1ad1

• #398 revising some access patterns

  ecwood

  committed
  f0f73fd

  Copy full SHA for f0f73fd

• #398 changing data type for datetime

  ecwood

  committed
  73c085f

  Copy full SHA for 73c085f

• #398 have to save as a string afterwards

  ecwood

  committed
  6bdee23

  Copy full SHA for 6bdee23

• #398 handling an edge case

  ecwood

  committed
  00d53f4

  Copy full SHA for 00d53f4

• #398 some debugging code

  ecwood

  committed
  98b6ad5

  Copy full SHA for 98b6ad5

• #398 more debugging code

  ecwood

  committed
  a6049fc

  Copy full SHA for a6049fc

• #398 another (very strange) edge case

  ecwood

  committed
  0cc5805

  Copy full SHA for 0cc5805

• #393

  ecwood

  committed
  a163ae3

  Copy full SHA for a163ae3

• #398 remove debugging info

  ecwood

  committed
  65543c9

  Copy full SHA for 65543c9

• #140 architecture for versioning files

  ecwood

  committed
  e5544dc

  Copy full SHA for e5544dc

• #140 comment out s3 command for ci

  ecwood

  committed
  2796ecd

  Copy full SHA for 2796ecd

• #140 a lot more changes to log file names and tsv output

  ecwood

  committed
  1270624

  Copy full SHA for 1270624

Commits on Jul 17, 2024

• #140 on the neo4j side

  ecwood

  committed
  f0aee45

  Copy full SHA for f0aee45

• #140 adding the name to the name of other build artifacts as well

  ecwood

  committed
  07c8549

  Copy full SHA for 07c8549

• #140 made sure its only defined once

  ecwood

  committed
  184fa6e

  Copy full SHA for 184fa6e

• #393 remove RepoDB from the build system

  ecwood

  committed
  49d75ed

  Copy full SHA for 49d75ed

• #393 have to remove info from kg2_util as well

  ecwood

  committed
  ce8d8de

  Copy full SHA for ce8d8de

• #400 first pass at this

  ecwood

  committed
  6bdb5a6

  Copy full SHA for 6bdb5a6

• #400 try this instead

  ecwood

  committed
  31cb00a

  Copy full SHA for 31cb00a

• #400 handling the expansion map (hopefully)

  ecwood

  committed
  4750665

  Copy full SHA for 4750665

Commits on Jul 22, 2024

• #392 initial edge blocklist (no synonyms yet)

  ecwood

  committed
  89591c3

  Copy full SHA for 89591c3

• #387 grouping together xml blocks

  ecwood

  committed
  e33b320

  Copy full SHA for e33b320

• #392 autism synonyms

  ecwood

  committed
  d7743bb

  Copy full SHA for d7743bb

• #392 full edge blocklist

  ecwood

  committed
  7c53a60

  Copy full SHA for 7c53a60

Commits on Jul 25, 2024

• #387 parses it into little dictionaries (generically)

  ecwood

  committed
  f5c7274

  Copy full SHA for f5c7274

Commits on Jul 27, 2024

• #387 corrected some bugs with the XML parsing

  ecwood

  committed
  6db935f

  Copy full SHA for 6db935f

• #387 handling case where something is just one line and not in another nest

  ecwood

  committed
  7b4ac97

  Copy full SHA for 7b4ac97

Commits on Aug 1, 2024

• #404, testing it out on CI first

  ecwood

  committed
  31b4779

  Copy full SHA for 31b4779

• #404 predicate remapping for biolink 4.2.1

  ecwood

  committed
  b7597b9

  Copy full SHA for b7597b9

• Merge branch 'dependencypruning' of github.com:RTXteam/RTX-KG2 into midjuly24work

  ecwood

  committed
  26f551b

  Copy full SHA for 26f551b

Commits on Aug 8, 2024

• #387 handle doctype special case from foodon

  ecwood

  committed
  2e62525

  Copy full SHA for 2e62525

Commits on Aug 9, 2024

• #387 handle doctype special case from foodon

  ecwood

  committed
  38634dd

  Copy full SHA for 38634dd

Commits on Aug 11, 2024

• #387 refactored for clarity

  ecwood

  committed
  23ff6ea

  Copy full SHA for 23ff6ea

• #387 more refactoring, but pre-sorting into classes

  ecwood

  committed
  9b8dfc4

  Copy full SHA for 9b8dfc4

Commits on Aug 12, 2024

• #387 refactored into class form

  ecwood

  committed
  bab707c

  Copy full SHA for bab707c

Commits on Aug 13, 2024

• #387 added in output filing

  ecwood

  committed
  a55212c

  Copy full SHA for a55212c

• #387 moving bc of kg2_util

  ecwood

  committed
  e8d9e88

  Copy full SHA for e8d9e88

• #387 slightly more efficient

  ecwood

  committed
  8d6668f

  Copy full SHA for 8d6668f

Commits on Aug 15, 2024

• #387 loads multiple files now

  ecwood

  committed
  b377ae9

  Copy full SHA for b377ae9

Commits on Aug 17, 2024

• #387 save the name of the output file as well

  ecwood

  committed
  e735855

  Copy full SHA for e735855

Commits on Aug 23, 2024

• #387 start of processing the ontologies JSON Lines file

  ecwood

  committed
  462c0bf

  Copy full SHA for 462c0bf

Commits on Aug 27, 2024

• #387 additional weird sources due to FOODON

  ecwood

  committed
  b12e984

  Copy full SHA for b12e984

• #387 more additional weird source links due to FOODON

  ecwood

  committed
  e9d6d68

  Copy full SHA for e9d6d68

• #387 even more additional weird source links due to FOODON

  ecwood

  committed
  61c3f06

  Copy full SHA for 61c3f06

• #387 final additional weird source links due to FOODON

  ecwood

  committed
  da66493

  Copy full SHA for da66493

• #387 patch to get around weird ids showing up when trying to prefix match

  ecwood

  committed
  0d40be8

  Copy full SHA for 0d40be8

• #387 more weird prefixes

  ecwood

  committed
  0a22964

  Copy full SHA for 0a22964

• #387 today's work on the ontologies ETL

  ecwood

  committed
  919d3b8

  Copy full SHA for 919d3b8

• #387 finishing up the different edge types

  ecwood

  committed
  6613470

  Copy full SHA for 6613470

Commits on Aug 29, 2024

• #387 for testing purposes

  ecwood

  committed
  0750062

  Copy full SHA for 0750062

• #387 don't need that print statement anymore

  ecwood

  committed
  7ed39cb

  Copy full SHA for 7ed39cb

• #387 looks like we're not using this anymore

  ecwood

  committed
  7d18400

  Copy full SHA for 7d18400

• #387 try out the new validate kg2 util

  ecwood

  committed
  2eb8b00

  Copy full SHA for 2eb8b00

• #387 drastic changes: REMOVAL OF ONTOBIO from kg2_util and validation

  ecwood

  committed
  2375994

  Copy full SHA for 2375994

• #387 the ACTUAL removal of ontobio

  ecwood

  committed
  5508b9b

  Copy full SHA for 5508b9b

• #387 addressing a name change

  ecwood

  committed
  a890695

  Copy full SHA for a890695

• #387 format adjustment

  ecwood

  committed
  86492f5

  Copy full SHA for 86492f5

• #387 adjustments to the mapping file to go along with new comparison system

  ecwood

  committed
  86d431f

  Copy full SHA for 86d431f

• #387 apparently these have to be different to match biolink

  ecwood

  committed
  e63311b

  Copy full SHA for e63311b

• #387 kg2_util didn't previously commit correctly

  ecwood

  committed
  9d7213b

  Copy full SHA for 9d7213b

• #387 the recursive category picker is workingpython3 ontologies_jsonl_to_kg_jsonl.py ontologies.json maps/curies-to-categories.yaml null > ontology_nodes.json python3 ontologies_jsonl_to_kg_jsonl.p…

  Show description for e191988
  ecwood

  committed
  e191988

  Copy full SHA for e191988

Commits on Sep 2, 2024

• #387 some date restructuring, ontology node versioning, and changes to handle ORDO

  ecwood

  committed
  314b54f

  Copy full SHA for 314b54f

• #387 need to have name for ontology node

  ecwood

  committed
  c36f46c

  Copy full SHA for c36f46c

• credits for me

  ecwood

  committed
  d4ffa05

  Copy full SHA for d4ffa05

• #387 removing unnecessary curies

  ecwood

  committed
  7860506

  Copy full SHA for 7860506

• #387 no longer want biolink as an ontology source due to the parsing hassle

  ecwood

  committed
  0f56540

  Copy full SHA for 0f56540

• #387 we have this predicate again

  ecwood

  committed
  b3c8cea

  Copy full SHA for b3c8cea

• #387 remove sed-ing from validation tests now that biolink is gone

  ecwood

  committed
  c36d3c3

  Copy full SHA for c36d3c3

• #387 #390

  ecwood

  committed
  9a3c22f

  Copy full SHA for 9a3c22f

• #387 ordo actually included in ETL

  ecwood

  committed
  e94e431

  Copy full SHA for e94e431

• #387 moving to its permanent home

  ecwood

  committed
  c8c63de

  Copy full SHA for c8c63de

• #387 moving owlparser to its permanent home

  ecwood

  committed
  2ec98bd

  Copy full SHA for 2ec98bd

• #387 don't need this one anymore

  ecwood

  committed
  82e6acb

  Copy full SHA for 82e6acb

• #387 #405 rethreading the pipeline for new ETL

  ecwood

  committed
  192039c

  Copy full SHA for 192039c

• #387 forgot to add the new extract

  ecwood

  committed
  d09ce05

  Copy full SHA for d09ce05

• #387 adjusting some of the variables for new pipelining

  ecwood

  committed
  76b996b

  Copy full SHA for 76b996b

• #387 adjusting for new pipelining syntax error

  ecwood

  committed
  168071e

  Copy full SHA for 168071e

• #387 adjusting for new pipelining naming error

  ecwood

  committed
  8baa763

  Copy full SHA for 8baa763

• #387 cleaning up the formatting of the new files

  ecwood

  committed
  58d1bdd

  Copy full SHA for 58d1bdd

• #387 comments about the inner workings of ontologies conversion

  ecwood

  committed
  59c6192

  Copy full SHA for 59c6192

• #387 archiving multi ont

  ecwood

  committed
  b085055

  Copy full SHA for b085055

• #387 archiving build multi ont

  ecwood

  committed
  321981c

  Copy full SHA for 321981c

• updating executability for newer files

  ecwood

  committed
  cea05b7

  Copy full SHA for cea05b7

• #387 comments through owlparser

  ecwood

  committed
  fd482ba

  Copy full SHA for fd482ba

• #387 adjusting for CHEBI issues

  ecwood

  committed
  7bd5e8f

  Copy full SHA for 7bd5e8f

• #387 want to remove old ontologies

  ecwood

  committed
  0804556

  Copy full SHA for 0804556

• #387 have to fully handle CHEBI

  ecwood

  committed
  a1a7c6e

  Copy full SHA for a1a7c6e

• #387 revising predicate remap for new ontology etl

  ecwood

  committed
  b0aee1c

  Copy full SHA for b0aee1c

• #387 updating provided by to infores for new ontologies etl

  ecwood

  committed
  139b1d5

  Copy full SHA for 139b1d5

• #387 adding biolink version node in and correcting source node category

  ecwood

  committed
  ee09f49

  Copy full SHA for ee09f49

• #392 edge blocklist logic implemented

  ecwood

  committed
  4f17e56

  Copy full SHA for 4f17e56

• #387 correcting the pipeline for new ontologies input

  ecwood

  committed
  e3f0f8e

  Copy full SHA for e3f0f8e

• #392 restringing pipeline for edge blocklist

  ecwood

  committed
  0e96110

  Copy full SHA for 0e96110

• #387 correcting biolink version number code

  ecwood

  committed
  c499f55

  Copy full SHA for c499f55

• #387 use correct dictionary to map IRI

  ecwood

  committed
  36c63c6

  Copy full SHA for 36c63c6

• #387 correct variable names

  ecwood

  committed
  d54a3d6

  Copy full SHA for d54a3d6

• #387 can use shortened link now that we don't actually have to download biolink

  ecwood

  committed
  59347ab

  Copy full SHA for 59347ab

• #387 actually just change the biolink link to the repo

  ecwood

  committed
  f718815

  Copy full SHA for f718815

• #140 correct the filename

  ecwood

  committed
  0699d84

  Copy full SHA for 0699d84

• #387 pipelining issue thwarted

  ecwood

  committed
  e104912

  Copy full SHA for e104912

• #405 umls cleanup issue

  ecwood

  committed
  bd93687

  Copy full SHA for bd93687

• #408 #398 curl problems

  ecwood

  committed
  3488401

  Copy full SHA for 3488401

• #408 issue with DisGeNET download

  ecwood

  committed
  848a24f

  Copy full SHA for 848a24f

• #408 typo for download

  ecwood

  committed
  e7d76d6

  Copy full SHA for e7d76d6

• #408 download SMPDB while link is failing

  ecwood

  committed
  7edd988

  Copy full SHA for 7edd988

Commits on Sep 3, 2024

• #408 cURL issue with HMDB

  ecwood

  committed
  5cef56a

  Copy full SHA for 5cef56a

Commits on Sep 4, 2024

• #408 build issue with knowledge_source node curies

  ecwood

  committed
  893fb71

  Copy full SHA for 893fb71

• #408 missing predicate

  ecwood

  committed
  b37ee73

  Copy full SHA for b37ee73

Commits on Sep 8, 2024

• #408 bucket problem

  ecwood

  committed
  2579972

  Copy full SHA for 2579972

• #408 kg2-versions entry for KG2.10.1

  ecwood

  committed
  08bd4c5

  Copy full SHA for 08bd4c5

• #408 rest of kg2-versions entry for KG2.10.1

  ecwood

  committed
  b158cc5

  Copy full SHA for b158cc5