kg2-versions.md

2.8.6

Date: 2023.09.09

Counts:

• Nodes: 8,493,096
• Edges: 56,911,675

Issues:

• Issue #316
• Issue #344
• Additional issues that arose during the build: #349 (Comment)

Build info:

• Biolink Model version: 3.5.2
• Build host: kg286build.rtx.ai
• Build directory: /home/ubuntu/kg2-build
• Build code branch: issue-316
• Neo4j endpoint CNAME:
• Neo4j endpoint hostname:
• Tracking issue for the build: Issue #349
• Major knowledge source versions:
  • SemMedDB: 43 (2023)
  • UMLS: 2023AA
  • ChEMBL: 33
  • DrugBank: 5.1.10
  • Ensembl: 106
  • GO annotations: 2023-6-11
  • UniProtKB: 2023_02
  • DrugCentral: 52
  • KEGG: 107.0

2.8.5

Date: 2023.08.05

Counts:

• Nodes: 8,437,312
• Edges: 54,274,882

Issues:

• Issue #321
• Issue #323
• Issue #336 - attempt failed though
• Issue #337
• Issue #339
• Additional issues that arose during the build: #343

Build info:

• Biolink Model version: 3.5.2
• Build host: kg285build.rtx.ai
• Build directory: /home/ubuntu/kg2-build
• Build code branch: jsonlines
• Neo4j endpoint CNAME:
• Neo4j endpoint hostname:
• Tracking issue for the build: Issue #312
• Major knowledge source versions:
  • SemMedDB: 43 (2023)
  • UMLS: 2023AA
  • ChEMBL: 33
  • DrugBank: 5.1.10
  • Ensembl: 106
  • GO annotations: 2023-6-11
  • UniProtKB: 2023_02
  • DrugCentral: 52
  • KEGG: 107.0

2.8.4

Date: 2023.07.20

Counts:

• Nodes: 8,436,874
• Edges: 54,363,492

Issues:

• Issue #216
• Issue #230
• Issue #232
• Issue #262
• Issue #276
• Issue #278
• Issue #279
• Issue #280
• Issue #281
• Issue #286
• Issue #287
• Issue #290
• Issue #291
• Issue #292
• Issue #293
• Issue #294
• Issue #295
• Issue #296
• Issue #297
• Issue #298
• Issue #299
• Issue #300
• Issue #301
• Issue #302
• Issue #303 - we are using a pickled copy of an old version of FOODON in this build
• Issue #304
• Issue #305
• Issue #307 – LOINC dropped from KG2
• Issue #310
• Issue #311
• Issue #315
• Issue #319
• Issue #320
• Issue #324
• Issue #325
• Additional issues that arose during the build: #294 (comment), #312 (comment), #327, #328, #329, #330

Build info:

• Biolink Model version: 3.5.2
• Build host: buildkg2.rtx.ai (new instance, old version was deprecated)
• Build directory: /home/ubuntu/kg2-build
• Build code branch: kg2.8.4prep
• Neo4j endpoint CNAME: kg2-8-4.rtx.ai
• Neo4j endpoint hostname: kg2endpoint4.rtx.ai
• Tracking issue for the build: Issue #312
• Major knowledge source versions:
  • SemMedDB: 43 (2023)
  • UMLS: 2023AA
  • ChEMBL: 33
  • DrugBank: 5.1.10
  • Ensembl: 106
  • GO annotations: 2023-6-11
  • UniProtKB: 2023_02
  • DrugCentral: 52
  • KEGG: 107.0

2.8.3

Date: 2023.XX.XX

Counts:

• Nodes: 10,370,747
• Edges: 54,078,936

Issues:

• Issue #265
• Issue #269
• Issue #273
• Additional issues that arose during the build: #

Build info:

• Biolink Model version: 3.1.2
• Build host: buildkg2.rtx.ai
• Build directory: /home/ubuntu/kg2-build
• Build code branch: issue-263
• Neo4j endpoint CNAME:
• Neo4j endpoint hostname:
• Tracking issue for the build: Issue #264
• Major knowledge source versions:
  • SemMedDB: 43 (2023)
  • UMLS: 2022AA
  • ChEMBL: 30
  • DrugBank: 5.1.9
  • Ensembl: 106
  • GO annotations: 2023-6-11
  • UniProtKB: 2023_02
  • DrugCentral: 52
  • KEGG: 105.0

2.8.2

Date: 2023.XX.XX

Counts:

• Nodes: 10,370,747
• Edges: 54,078,936

Issues:

• Issue #263
• Build abandoned due to nonsensical predicates [#269]
• Additional issues that arose during the build: #269

Build info:

• Biolink Model version: 3.1.2
• Build host: buildkg2.rtx.ai
• Build directory: /home/ubuntu/kg2-build
• Build code branch: issue-263
• Neo4j endpoint CNAME:
• Neo4j endpoint hostname:
• Tracking issue for the build: Issue #264
• Major knowledge source versions:
  • SemMedDB: 43 (2023)
  • UMLS: 2022AA
  • ChEMBL: 30
  • DrugBank: 5.1.9
  • Ensembl: 106
  • GO annotations: 2023-6-11
  • UniProtKB: 2023_02
  • DrugCentral: 52
  • KEGG: 105.0

2.8.1

Date: 2022.XX.XX

Counts:

• Nodes: 10,370,747
• Edges: 54,078,936

Issues:

• Issue #253
• Issue #251
• Issue #250
• Issue #246
• Additional issues that arose during the build:

Build info:

• Biolink Model version: 3.1.2
• Build host: buildkg2.rtx.ai
• Build directory: /home/ubuntu/kg2-build
• Build code branch: issue-252
• Neo4j endpoint CNAME: kg2-8-1.rtx.ai
• Neo4j endpoint hostname: kg2endpoint2.rtx.ai
• Tracking issue for the build: Issue #252
• Major knowledge source versions:
  • SemMedDB: 43 (2023)
  • UMLS: 2022AA
  • ChEMBL: 30
  • DrugBank: 5.1.9
  • Ensembl: 106
  • GO annotations: 2022-11-17
  • UniProtKB: 2022_03
  • UniChem: 385
  • DrugCentral: 48
  • KEGG: 105.0

2.8.0

Date: 2022.12.12

Counts:

• Nodes: 10,370,747
• Edges: 54,078,936

Issues:

• Issue #220
• Issue #221
• Issue #222
• Additional issues that arose during the build: #227, #228, #229, #230, #231, #232, #233, #234, #235, #236, #237, #238, #243, #244

Build info:

• Biolink Model version: 3.0.0
• Build host: buildkg2.rtx.ai
• Build directory: /home/ubuntu/kg2-build
• Build code branch: issue-226
• Neo4j endpoint CNAME: kg2-8-0.rtx.ai
• Neo4j endpoint hostname: kg2endpoint2.rtx.ai
• Tracking issue for the build: Issue #226
• Major knowledge source versions:
  • SemMedDB: 23 (2021)
  • UMLS: 2022AA
  • ChEMBL: 30
  • DrugBank: 5.1.9
  • Ensembl: 106
  • GO annotations: 2021-07-01
  • UniProtKB: 2022_02
  • UniChem: 385
  • DrugCentral: 48
  • KEGG: 103.0

2.7.6

Date: 2022.05.10

Counts:

• Nodes: 10,370,747
• Edges: 54,078,936

Issues:

• Issue #196
• Issue #201
• Additional issues that arose during the build: 203, 204, 205, 206

Build info:

• Biolink Model version: 2.2.11
• Build host: buildkg2.rtx.ai
• Build directory: /home/ubuntu/kg2-build
• Build code branch: master
• Neo4j endpoint CNAME: kg2-7-6.rtx.ai
• Neo4j endpoint hostname: kg2endpoint2.rtx.ai
• Tracking issue for the build: Issue #202
• Major knowledge source versions:
  • SemMedDB: 23 (2021)
  • UMLS: 2020AA
  • ChEMBL: 27
  • DrugBank: 5.1
  • Ensembl: 103
  • GO annotations: 2021-11-08
  • UniProtKB: 2021_04
  • UniChem: 385
  • DrugCentral: 48
  • KEGG: 101.0

2.7.5

Date: 2022.02.08

Counts:

• Nodes: 10,361,234
• Edges: 54,068,633

Issues:

• Issue #193
• Additional issues that arose during the build: In build ticket

Build info:

• Biolink Model version: 2.2.11
• Build host: buildkg2.rtx.ai
• Build directory: /home/ubuntu/kg2-build
• Build code branch: master
• Neo4j endpoint CNAME: kg2-7-5.rtx.ai
• Neo4j endpoint hostname: kg2endpoint4.rtx.ai
• Tracking issue for the build: Issue #193

2.7.4

Date: 2021.11.12

Counts:

• Nodes: 10,346,321
• Edges: 54,828,529

Issues:

• Issue #167
• Issue #165
• Issue #164
• Issue #157
• Issue #156
• Issue #155
• Additional issues that arose during the build: 180, 178, 177, 175, 174, 173, 168, 164

Build info:

• Biolink Model version: 2.2.6
• Build host: buildkg2.rtx.ai
• Build directory: /home/ubuntu/kg2-build
• Build code branch: issue165
• Neo4j endpoint CNAME: kg2-7-4.rtx.ai
• Neo4j endpoint hostname: kg2endpoint3.rtx.ai
• Tracking issue for the build: Issue #166

2.7.3

Date: 2021.09.17

Counts:

• Nodes: 10,238,961
• Edges: 54,041,267

Issues:

• Issue #145
• Issue #142
• Issue #141
• Issue #136
• Issue #131
• Additional issues that arose during the build: 150, 149, 148, 147, 146, 145, 144

Build info:

• Biolink Model version: 2.1.0
• Build host: buildkg2.rtx.ai
• Build directory: /home/ubuntu/kg2-build
• Build code branch: master
• Neo4j endpoint CNAME: kg2-7-3.rtx.ai
• Neo4j endpoint hostname: kg2endpoint4.rtx.ai
• Tracking issue for the build: Issue #138

2.7.2

Date: 2021.08.19

Counts:

• Nodes: 10,237,436
• Edges: 54,036,959

Issues:

• Issue #95
• Issue #105
• Issue #120
• Additional issues that arose during the build: 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119

Build info:

• Biolink Model version: 2.1.0
• Build host: buildkg2.rtx.ai
• Build directory: /home/ubuntu/kg2-build
• Build code branch: issue95
• Neo4j endpoint CNAME: kg2-7-2.rtx.ai
• Tracking issue for the build: Issue #104

2.7.1

Date: 2021.07.13

Counts:

• Nodes: 9,738,008
• Edges: 48,781,064

Note:

• Building on kg2steve.rtx.ai inadvertantly pulled in old versions of ontologies (from Sept. 2020)

Issues:

• Issue #97

Build info:

• Biolink Model Version: 2.1.0
• Build host: kg2steve.rtx.ai
• Build directory: /home/ubuntu/kg2-build/
• Build code branch: biolink-2.0
• Neo4j endpoint CNAME: kg2endpoint-kg2-7-1.rtx.ai

2.7.0

Date: 2021.07.08

Biolink Model Version: 2.1.0

Nodes: 9,738,008 Edges: 48,781,064

Notes:

• Reactome released a new version which resulted in a failure of the compartment related queries, which are now commented out in the code.

Issues:

• Issue #77
• Issue #64

Build host: kg2steve.rtx.ai Build directory: /home/ubuntu/kg2-build/ Build code branch: biolink-2.0

2.6.7

Date: 2021.06.23

Biolink Model Version: 1.8.1

Nodes: 9,781,698

Edges: 46,296,048

Notes:

• Only edited edges.tsv file from KG2.6.6 (and nodes.tsv to increase version)

Issues:

• Issue #81

Build host: kg2lindsey.rtx.ai Build directory: /home/ubuntu/kg2-build/ Build code branch: master Neo4j endpoint CNAME: kg2endpoint-kg2-6-7.rtx.ai

2.6.6

Date: 2021.06.22

Biolink Model Version: 1.8.1

Nodes: 9,781,698

Edges: 46,296,048

Notes:

• Only edited edges.tsv file from KG2.6.5 (and nodes.tsv to increase version)

Issues:

• Issue #78

Build host: kg2lindsey.rtx.ai /home/ubuntu/kg2-build/

2.6.5

Date: 2021.6.20

Biolink Model Version: 1.8.1

Nodes: 9,781,698

Edges: 46,296,048

Notes:

• Of the source JSON files, only regenerated kg2-ont.json to minimize build time (to get build out quicker)

Issues:

• Issue #56
• Issue #49
• Issue #55
• Issue #47
• Issue #68
• Issue #9
• Issue #62
• Issue #14
• Issue #19

Build host: kg2lindsey.rtx.ai /home/ubuntu/kg2-build/

2.6.3

Date: 2021.5.7

Biolink Model Version: 1.8.1

Nodes: 10,694,772

Edges: 51,687,002

Notes:

• Built by modifying edges.tsv to address 1432 speedily. changes then incorporated into the whole build process.

Issues:

• Issue #1432

Build host: kg2lindsey.rtx.ai /home/ubuntu/kg2-build/

2.6.2

Date: 2021.5.1

Biolink Model Version: 1.8.1

Nodes: 10,694,772

Edges: 51,687,002

Notes:

• Partial rebuild from Simplify on branch Ontobio507TempFix

Issues:

• Issue #1423

Build host: kg2lindsey.rtx.ai /home/ubuntu/kg2-build/

2.6.1

Date: 2021.4.28

Biolink Model Version: 1.8.1

Nodes: 10,694,772

Edges: 51,687,002

Notes:

• this build was done from the branch Ontobio507TempFix, with an uncommitted workaround to add some of the KEGG nodes back in

Issues:

• Issue #1400

Build host: kg2lindsey.rtx.ai /home/ubuntu/kg2-build/

2.6.0

Date: 2021.4.23

Biolink Model Version: 1.8.1

Nodes: 10,675,990

Edges: 49,342,413

Notes:

• KG1 was dropped from this build, and with it KEGG
• this build was done from the branch Ontobio507TempFix

Issues:

• Issue #1381
• Issue #1374
• Issue #1362
• Issue #1362
• Issue #1358
• Issue #1345
• Issue #1343
• Issue #1335
• Issue #1332
• Issue #1322
• Issue #1311
• Issue #1292
• Issue #1286
• Issue #1278
• Issue #1273
• Issue #1247
• Issue #1246
• Issue #1245
• Issue #1220
• Issue #1213
• Issue #1199
• Issue #1189
• Issue #1170
• Issue #1125
• Issue #1078
• Issue #1027
• Issue #636
• Issue #550
• Issue #545

Build host: kg2lindsey.rtx.ai /home/ubuntu/kg2-build/ Json file(s) stored on same host, /home/ubuntu/kg2-build/KG2-6-0/

2.5.2

Date: 2021.3.6

Nodes: 10,546,338 Edges: 53,739,675

• Issue #1283
• Issue #1271
• Issue #1270
• Issue #1267
• Issue #1266
• Issue #1264
• Issue #1263
• Issue #1259
• Issue #1253
• Issue #1249
• Issue #1243
• Issue #1230
• Issue #1219
• Issue #1216
• Issue #1214
• Issue #1175
• Issue #1171
• Issue #1160
• Issue #1128
• Issue #1114
• Issue #1050
• Issue #1025
• Issue #964
• Issue #762

Build host: kg2steve.rtx.ai /home/ubuntu/kg2-build/

2.5.1

Date: 2021.1.24

Nodes: 10,533,862

Edges: 53,474,162

• Issue #1185
• Issue #1171 (tentative)
• Issue #1122
• Issue #1200
• Issue #1079

Build host: kg2lindsey.rtx.ai /home/ubuntu/kg2-build/

2.5.0

Date: 2021.1.14

Nodes: 10,533,862

Edges: 53,416,143

• Issue #1173
• Issue #1180
• Issue #1155
• Issue #1083

Build host: kg2lindsey.rtx.ai /home/ubuntu/kg2-build/

2.4.0

Date: 2020.12.11

Nodes: 10,533,792

Edges: 53,415,986

• Issue #1161
• Issue #1126
• Issue #1123
• Issue #1142

Build host: kg2lindsey.rtx.ai /home/ubuntu/kg2-build/

2.3.5

Date: 2020.10.26

Nodes: 10,543,712

Edges: 53,456,505

• Issue #1091
• Issue #1103
• Issue #1102
• Issue #1107
• Issue #1115
• Issue #1053
• Issue #1076
• Issue #981
• Issue #1098
• Issue #931
• Issue #891

Build host: kg2lindsey.rtx.ai /home/ubuntu/kg2-build-3.5/

2.3.4

Date: 2020.09.04

Nodes: 10,527,134

Edges: 53,589,306

• Issue #1051
• Issue #1045(?)
• Issue #1027(?)
• Issue #931
• Issue #999
• Issue #762

Build host: kg2steve.rtx.ai.

2.3.1

Date: 2020.08.21

Nodes: 9,633,671

Edges: 52,537,504

• Issue #1031
• Issue #1033
• Issue #1019
• Issue #1024
• Issue #1016
• Issue #1000
• Issue #1006
• Issue #1007
• Issue #988

Build host: kg2dev.rtx.ai.