Updated concepts to UMLS 2023AA (#235)

nlpie · Oct 31, 2023 · 9bf55b1 · 9bf55b1
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Showing 3 changed files with 68 additions and 2 deletions.
diff --git a/docs/test_results/3.2-full-data.yml b/docs/test_results/3.2-full-data.yml
@@ -0,0 +1,33 @@
+Concepts:
+  Precision: 0.5459940652818991
+  Process Method Duration: '0:00:00.011171'
+  Recall: 0.6938032670454546
+  Remote Call Duration: '0:00:00.013845'
+TnT Pos Tagger:
+  Accuracy: 0.9349333907344957
+  Process Method Duration: '0:00:00.006570'
+  Remote Call Duration: '0:00:00.008739'
+biomedicus-deepen:
+  F1: 0.9104573759931286
+  Gold Standard: 2010 i2b2-VA
+  Per-Document Mean Pipeline Duration: '0:00:00.108384'
+  Precision: 0.8800332088003321
+  Recall: 0.9430604982206405
+biomedicus-dependencies:
+  Corpus: MiPACQ converted to UD from PTB test set
+  LAS: 0.5475739822742978
+  Process Method Duration: '0:00:00.093425'
+  Remote Call Duration: '0:00:00.094957'
+  UAS: 0.683340844224125
+biomedicus-modification:
+  F1: 0.7100757788380578
+  Gold Standard: 2010 i2b2-VA
+  Per-Document Mean Pipeline Duration: '0:00:00.012159'
+  Precision: 0.9619771863117871
+  Recall: 0.5627224199288257
+biomedicus-negex:
+  F1: 0.8706162076481078
+  Gold Standard: 2010 i2b2-VA
+  Per-Document Mean Pipeline Duration: '0:00:00.009396'
+  Precision: 0.7849231868524473
+  Recall: 0.9773131672597865
diff --git a/docs/test_results/3.2-open-data.yml b/docs/test_results/3.2-open-data.yml
@@ -0,0 +1,33 @@
+Concepts:
+  Precision: 0.5283087018029679
+  Process Method Duration: '0:00:00.010522'
+  Recall: 0.6764026988636364
+  Remote Call Duration: '0:00:00.013096'
+TnT Pos Tagger:
+  Accuracy: 0.9349333907344957
+  Process Method Duration: '0:00:00.006520'
+  Remote Call Duration: '0:00:00.008676'
+biomedicus-deepen:
+  F1: 0.9104573759931286
+  Gold Standard: 2010 i2b2-VA
+  Per-Document Mean Pipeline Duration: '0:00:00.114825'
+  Precision: 0.8800332088003321
+  Recall: 0.9430604982206405
+biomedicus-dependencies:
+  Corpus: MiPACQ converted to UD from PTB test set
+  LAS: 0.5475739822742978
+  Process Method Duration: '0:00:00.094168'
+  Remote Call Duration: '0:00:00.095740'
+  UAS: 0.683340844224125
+biomedicus-modification:
+  F1: 0.7100757788380578
+  Gold Standard: 2010 i2b2-VA
+  Per-Document Mean Pipeline Duration: '0:00:00.012124'
+  Precision: 0.9619771863117871
+  Recall: 0.5627224199288257
+biomedicus-negex:
+  F1: 0.8706162076481078
+  Gold Standard: 2010 i2b2-VA
+  Per-Document Mean Pipeline Duration: '0:00:00.009357'
+  Precision: 0.7849231868524473
+  Recall: 0.9773131672597865
diff --git a/python/biomedicus/data_version.py b/python/biomedicus/data_version.py
@@ -13,5 +13,5 @@
 #  limitations under the License.
 """The expected data version and url to download data."""
 
-DATA_VERSION = "3.0"
-DATA_URL = "https://athena.ahc.umn.edu/downloads/open/biomedicus-3.0-standard-data.zip"
+DATA_VERSION = "2023-10-31"
+DATA_URL = "https://athena.ahc.umn.edu/downloads/open/biomedicus-open-data-2023-10-31.zip"