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  1. .gitattributes +4 -0
  2. .gitignore +8 -0
  3. MANIFEST.tsv +19 -0
  4. README.md +101 -0
  5. data/codiesp/evidence_relocations_full_exact.jsonl +3 -0
  6. data/codiesp/facts_test_full_exact.jsonl +3 -0
  7. data/codiesp/spotcheck_50_full_exact.tsv +0 -0
  8. data/codiesp/stats_full_exact.json +19 -0
  9. data/codiesp/test_docs_full_exact.txt +250 -0
  10. index/icd10cm_fy2018/code_metadata.jsonl +3 -0
  11. index/icd10cm_fy2018/icd10cm_fy2018_retrieval.jsonl +3 -0
  12. index/icd10cm_fy2018/inventory_manifest.json +12 -0
  13. index/icd10cm_fy2018/self_retrieval_probe.json +44 -0
  14. schema/icd10cm/normalization_map.json +274 -0
  15. schema/icd10cm/vocab_family.json +65 -0
  16. schema/icd10cm/vocab_qualifier.json +72 -0
  17. schema/icd10cm/vocab_role.json +47 -0
  18. schema/icd10cm/vocab_scope.json +29 -0
  19. schema/icd10cm/vocab_temporal.json +85 -0
  20. schema/icd10cm/vocab_temporal_raw.json +234 -0
.gitattributes CHANGED
@@ -58,3 +58,7 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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  # Video files - compressed
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  *.mp4 filter=lfs diff=lfs merge=lfs -text
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  *.webm filter=lfs diff=lfs merge=lfs -text
 
 
 
 
 
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  # Video files - compressed
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  *.mp4 filter=lfs diff=lfs merge=lfs -text
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  *.webm filter=lfs diff=lfs merge=lfs -text
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+ data/codiesp/evidence_relocations_full_exact.jsonl filter=lfs diff=lfs merge=lfs -text
62
+ data/codiesp/facts_test_full_exact.jsonl filter=lfs diff=lfs merge=lfs -text
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+ index/icd10cm_fy2018/code_metadata.jsonl filter=lfs diff=lfs merge=lfs -text
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+ index/icd10cm_fy2018/icd10cm_fy2018_retrieval.jsonl filter=lfs diff=lfs merge=lfs -text
.gitignore ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
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+ runs_codiesp_grounding_baseline/
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+ logs/
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+ raw/
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+ **/__pycache__/
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+ *.pyc
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+ *.out
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+ *.err
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+ slurm-*.out
MANIFEST.tsv ADDED
@@ -0,0 +1,19 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ 90 .gitignore
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+ 0 MANIFEST.tsv
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+ 2575 README.md
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+ 26979681 data/codiesp/evidence_relocations_full_exact.jsonl
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+ 49765580 data/codiesp/facts_test_full_exact.jsonl
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+ 104866 data/codiesp/spotcheck_50_full_exact.tsv
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+ 512 data/codiesp/stats_full_exact.json
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+ 6501 data/codiesp/test_docs_full_exact.txt
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+ 16854241 index/icd10cm_fy2018/code_metadata.jsonl
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+ 74477616 index/icd10cm_fy2018/icd10cm_fy2018_retrieval.jsonl
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+ 487 index/icd10cm_fy2018/inventory_manifest.json
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+ 1379 index/icd10cm_fy2018/self_retrieval_probe.json
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+ 7480 schema/icd10cm/normalization_map.json
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+ 1828 schema/icd10cm/vocab_family.json
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+ 938 schema/icd10cm/vocab_qualifier.json
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+ 883 schema/icd10cm/vocab_role.json
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+ 424 schema/icd10cm/vocab_scope.json
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+ 2782 schema/icd10cm/vocab_temporal.json
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README.md ADDED
@@ -0,0 +1,101 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # CodiEsp Diagnosis Grounding Data
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+
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+ This repository contains the prepared data files needed to reproduce the
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+ CodiEsp-D diagnosis grounding experiments. It is a data artifact only: it does
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+ not include experiment code, Slurm scripts, model outputs, logs, or raw source
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+ archives.
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+
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+ ## Directory Layout
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+
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+ ```text
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+ data/codiesp/
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+ facts_test_full_exact.jsonl
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+ evidence_relocations_full_exact.jsonl
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+ stats_full_exact.json
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+ test_docs_full_exact.txt
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+ spotcheck_50_full_exact.tsv
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+
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+ index/icd10cm_fy2018/
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+ icd10cm_fy2018_retrieval.jsonl
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+ code_metadata.jsonl
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+ inventory_manifest.json
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+ self_retrieval_probe.json
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+
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+ schema/icd10cm/
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+ normalization_map.json
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+ vocab_family.json
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+ vocab_role.json
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+ vocab_qualifier.json
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+ vocab_scope.json
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+ vocab_temporal.json
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+ vocab_temporal_raw.json
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+ ```
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+
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+ ## Main Evaluation File
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+
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+ ```text
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+ data/codiesp/facts_test_full_exact.jsonl
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+ ```
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+
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+ This is the prepared CodiEsp-D test set used by the second-domain experiments.
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+ It contains the exact-English-relocation slice of the official CodiEsp test
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+ split.
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+
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+ Summary from `data/codiesp/stats_full_exact.json`:
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+
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+ - Source documents: 250
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+ - Target facts: 3,144
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+ - Unique gold diagnosis codes: 958
49
+ - Exact relocation parse rate: 1.0
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+ - Exact substring rate: 1.0
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+
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+ Each JSONL row contains the clinical mention, English context fields, document
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+ identifier, one gold diagnosis code, and relocation metadata.
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+
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+ ## Relocation Files
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+
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+ ```text
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+ data/codiesp/evidence_relocations_full_exact.jsonl
59
+ data/codiesp/spotcheck_50_full_exact.tsv
60
+ ```
61
+
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+ These files document how Spanish CodiEsp diagnosis spans were relocated into
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+ the English context used for retrieval. The evaluation JSONL keeps only facts
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+ with exact English substring relocation.
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+
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+ ## Retrieval Inventory
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+
68
+ ```text
69
+ index/icd10cm_fy2018/icd10cm_fy2018_retrieval.jsonl
70
+ ```
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+
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+ This is the candidate label inventory used by retrieval. It contains 71,344
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+ candidate diagnosis-code entries. Each entry contains a code identifier,
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+ canonical English label, retrieval/documentation text, and structural metadata.
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+
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+ Inventory construction metadata is in:
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+
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+ ```text
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+ index/icd10cm_fy2018/inventory_manifest.json
80
+ ```
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+
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+ ## Schema Files
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+
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+ ```text
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+ schema/icd10cm/
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+ ```
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+
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+ This directory contains the controlled vocabularies and normalization map used
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+ by the CodiEsp structured grounding schema.
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+
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+ ## Not Included
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+
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+ The following are intentionally excluded:
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+
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+ - Experiment code and Slurm scripts.
96
+ - Model outputs and intermediate run files.
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+ - Slurm logs.
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+ - Raw downloaded CodiEsp or diagnosis-code archives.
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+ - Python bytecode caches.
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+
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+ `MANIFEST.tsv` lists the files in this data artifact with byte sizes.
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+ {
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+ "selected_documents": 250,
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+ "with macular edema",
36
+ "with retinal neovascularization",
37
+ "with tophus (tophi)",
38
+ "without tophus (tophi)"
39
+ ],
40
+ "sequela": [
41
+ "sequela",
42
+ "sequela of fracture"
43
+ ],
44
+ "stage": [
45
+ "early dry stage",
46
+ "indeterminate stage",
47
+ "intermediate dry stage",
48
+ "mild stage",
49
+ "moderate stage",
50
+ "severe stage"
51
+ ],
52
+ "subsequent-delayed-healing": [
53
+ "subsequent encounter for closed fracture with delayed healing",
54
+ "subsequent encounter for fracture with delayed healing",
55
+ "subsequent encounter for open fracture type I or II with delayed healing",
56
+ "subsequent encounter for open fracture type IIIA, IIIB, or IIIC with delayed healing"
57
+ ],
58
+ "subsequent-encounter": [
59
+ "subsequent encounter"
60
+ ],
61
+ "subsequent-malunion": [
62
+ "subsequent encounter for closed fracture with malunion",
63
+ "subsequent encounter for fracture with malunion",
64
+ "subsequent encounter for open fracture type I or II with malunion",
65
+ "subsequent encounter for open fracture type IIIA, IIIB, or IIIC with malunion"
66
+ ],
67
+ "subsequent-nonunion": [
68
+ "subsequent encounter for closed fracture with nonunion",
69
+ "subsequent encounter for fracture with nonunion",
70
+ "subsequent encounter for open fracture type I or II with nonunion",
71
+ "subsequent encounter for open fracture type IIIA, IIIB, or IIIC with nonunion"
72
+ ],
73
+ "subsequent-routine-healing": [
74
+ "subsequent encounter for closed fracture with routine healing",
75
+ "subsequent encounter for fracture with routine healing",
76
+ "subsequent encounter for open fracture type I or II with routine healing",
77
+ "subsequent encounter for open fracture type IIIA, IIIB, or IIIC with routine healing"
78
+ ],
79
+ "unspecified": [
80
+ "not applicable or unspecified",
81
+ "stage unspecified",
82
+ "unspecified eye",
83
+ "unspecified time"
84
+ ]
85
+ }
schema/icd10cm/vocab_temporal_raw.json ADDED
@@ -0,0 +1,234 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ [
2
+ {
3
+ "definition": "24 hours or more after hospital admission",
4
+ "count": 4
5
+ },
6
+ {
7
+ "definition": "advanced atrophic with subfoveal involvement",
8
+ "count": 1
9
+ },
10
+ {
11
+ "definition": "advanced atrophic without subfoveal involvement",
12
+ "count": 1
13
+ },
14
+ {
15
+ "definition": "at arrival to emergency department",
16
+ "count": 4
17
+ },
18
+ {
19
+ "definition": "at hospital admission",
20
+ "count": 4
21
+ },
22
+ {
23
+ "definition": "bilateral",
24
+ "count": 25
25
+ },
26
+ {
27
+ "definition": "early dry stage",
28
+ "count": 1
29
+ },
30
+ {
31
+ "definition": "fetus 1",
32
+ "count": 15
33
+ },
34
+ {
35
+ "definition": "fetus 2",
36
+ "count": 15
37
+ },
38
+ {
39
+ "definition": "fetus 3",
40
+ "count": 15
41
+ },
42
+ {
43
+ "definition": "fetus 4",
44
+ "count": 15
45
+ },
46
+ {
47
+ "definition": "fetus 5",
48
+ "count": 15
49
+ },
50
+ {
51
+ "definition": "in the field [EMT or ambulance]",
52
+ "count": 4
53
+ },
54
+ {
55
+ "definition": "indeterminate stage",
56
+ "count": 11
57
+ },
58
+ {
59
+ "definition": "initial encounter",
60
+ "count": 408
61
+ },
62
+ {
63
+ "definition": "initial encounter for closed fracture",
64
+ "count": 31
65
+ },
66
+ {
67
+ "definition": "initial encounter for fracture",
68
+ "count": 8
69
+ },
70
+ {
71
+ "definition": "initial encounter for open fracture",
72
+ "count": 10
73
+ },
74
+ {
75
+ "definition": "initial encounter for open fracture type I or II",
76
+ "count": 3
77
+ },
78
+ {
79
+ "definition": "initial encounter for open fracture type IIIA, IIIB, or IIIC",
80
+ "count": 3
81
+ },
82
+ {
83
+ "definition": "intermediate dry stage",
84
+ "count": 1
85
+ },
86
+ {
87
+ "definition": "left eye",
88
+ "count": 25
89
+ },
90
+ {
91
+ "definition": "mild stage",
92
+ "count": 11
93
+ },
94
+ {
95
+ "definition": "moderate stage",
96
+ "count": 11
97
+ },
98
+ {
99
+ "definition": "not applicable or unspecified",
100
+ "count": 15
101
+ },
102
+ {
103
+ "definition": "other fetus",
104
+ "count": 15
105
+ },
106
+ {
107
+ "definition": "right eye",
108
+ "count": 25
109
+ },
110
+ {
111
+ "definition": "sequela",
112
+ "count": 445
113
+ },
114
+ {
115
+ "definition": "sequela of fracture",
116
+ "count": 2
117
+ },
118
+ {
119
+ "definition": "severe stage",
120
+ "count": 11
121
+ },
122
+ {
123
+ "definition": "stable",
124
+ "count": 2
125
+ },
126
+ {
127
+ "definition": "stage unspecified",
128
+ "count": 13
129
+ },
130
+ {
131
+ "definition": "subsequent encounter",
132
+ "count": 408
133
+ },
134
+ {
135
+ "definition": "subsequent encounter for closed fracture with delayed healing",
136
+ "count": 3
137
+ },
138
+ {
139
+ "definition": "subsequent encounter for closed fracture with malunion",
140
+ "count": 3
141
+ },
142
+ {
143
+ "definition": "subsequent encounter for closed fracture with nonunion",
144
+ "count": 3
145
+ },
146
+ {
147
+ "definition": "subsequent encounter for closed fracture with routine healing",
148
+ "count": 3
149
+ },
150
+ {
151
+ "definition": "subsequent encounter for fracture with delayed healing",
152
+ "count": 36
153
+ },
154
+ {
155
+ "definition": "subsequent encounter for fracture with malunion",
156
+ "count": 30
157
+ },
158
+ {
159
+ "definition": "subsequent encounter for fracture with nonunion",
160
+ "count": 34
161
+ },
162
+ {
163
+ "definition": "subsequent encounter for fracture with routine healing",
164
+ "count": 36
165
+ },
166
+ {
167
+ "definition": "subsequent encounter for open fracture type I or II with delayed healing",
168
+ "count": 3
169
+ },
170
+ {
171
+ "definition": "subsequent encounter for open fracture type I or II with malunion",
172
+ "count": 3
173
+ },
174
+ {
175
+ "definition": "subsequent encounter for open fracture type I or II with nonunion",
176
+ "count": 3
177
+ },
178
+ {
179
+ "definition": "subsequent encounter for open fracture type I or II with routine healing",
180
+ "count": 3
181
+ },
182
+ {
183
+ "definition": "subsequent encounter for open fracture type IIIA, IIIB, or IIIC with delayed healing",
184
+ "count": 3
185
+ },
186
+ {
187
+ "definition": "subsequent encounter for open fracture type IIIA, IIIB, or IIIC with malunion",
188
+ "count": 3
189
+ },
190
+ {
191
+ "definition": "subsequent encounter for open fracture type IIIA, IIIB, or IIIC with nonunion",
192
+ "count": 3
193
+ },
194
+ {
195
+ "definition": "subsequent encounter for open fracture type IIIA, IIIB, or IIIC with routine healing",
196
+ "count": 3
197
+ },
198
+ {
199
+ "definition": "unspecified eye",
200
+ "count": 25
201
+ },
202
+ {
203
+ "definition": "unspecified time",
204
+ "count": 4
205
+ },
206
+ {
207
+ "definition": "with active choroidal neovascularization",
208
+ "count": 1
209
+ },
210
+ {
211
+ "definition": "with inactive choroidal neovascularization",
212
+ "count": 1
213
+ },
214
+ {
215
+ "definition": "with inactive scar",
216
+ "count": 1
217
+ },
218
+ {
219
+ "definition": "with macular edema",
220
+ "count": 2
221
+ },
222
+ {
223
+ "definition": "with retinal neovascularization",
224
+ "count": 2
225
+ },
226
+ {
227
+ "definition": "with tophus (tophi)",
228
+ "count": 1
229
+ },
230
+ {
231
+ "definition": "without tophus (tophi)",
232
+ "count": 1
233
+ }
234
+ ]