aimedicalcoding 0.3.7__tar.gz → 0.3.9__tar.gz

{aimedicalcoding-0.3.7/aimedicalcoding.egg-info → aimedicalcoding-0.3.9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aimedicalcoding
-Version: 0.3.7
+Version: 0.3.9
 Summary: Detect missing/broken clinical codes (LOINC / SNOMED CT / RxNorm / ICD-10-CM / CVX) in CCDA and FHIR documents, with recovery evidence
 Author: Aakash Kag, Vinay Shankar Miryala, Siva Karthik, Mohammed Rayaan
 License: MIT

{aimedicalcoding-0.3.7 → aimedicalcoding-0.3.9}/aimedicalcoding/systems/cvx/patterns.py

@@ -73,13 +73,14 @@ def classify(stmt: ClinicalStatement) -> Optional[CvxGapPattern]:
     if cc and cc.code and cc.system not in STRUCTURAL:
         return CvxGapPattern.LOCAL_CODE_ONLY
 
+    # no usable code + no vaccine name -> nothing to recover -> not a gap
+    if not stmt.raw_text:
+        return None
     if _has_nullflavor(stmt):
         return CvxGapPattern.NULLFLAVOR
-    if stmt.raw_text:
-        if "/text" in (stmt.source_ref or ""):
-            return CvxGapPattern.NARRATIVE_ONLY
-        return CvxGapPattern.DISPLAY_ONLY
-    return None
+    if "/text" in (stmt.source_ref or ""):
+        return CvxGapPattern.NARRATIVE_ONLY
+    return CvxGapPattern.DISPLAY_ONLY
 
 
 # --------------------------------------------------------------------------
@@ -109,17 +110,20 @@ def parse_gap(stmt: ClinicalStatement, pattern: CvxGapPattern) -> Gap:
 
     if pattern == CvxGapPattern.RXNORM_ONLY and cc:
         gap.evidence["rxnorm_code"] = cc.code
-        gap.evidence["rxnorm_system"] = cc.raw_system
+        gap.evidence["rxnorm_system"] = cc.system.value if cc.system else None
+        gap.evidence["rxnorm_system_raw"] = cc.raw_system
         gap.note = ("Use the CDC/NLM CVX↔RxNorm crosswalk — deterministic; "
                     "LLM only if a generic RxCUI maps to multiple CVX valences.")
     elif pattern == CvxGapPattern.NDC_ONLY and cc:
         gap.evidence["ndc_code"] = cc.code
-        gap.evidence["ndc_system"] = cc.raw_system
+        gap.evidence["ndc_system"] = cc.system.value if cc.system else None
+        gap.evidence["ndc_system_raw"] = cc.raw_system
         gap.note = ("Use the CDC vaccine NDC↔CVX table (published, free) — "
                     "deterministic mapping from the dispensed NDC to CVX.")
     elif pattern == CvxGapPattern.LOCAL_CODE_ONLY and cc:
         gap.evidence["local_code"] = cc.code
-        gap.evidence["local_system"] = cc.raw_system
+        gap.evidence["local_system"] = cc.system.value if cc.system else None
+        gap.evidence["local_system_raw"] = cc.raw_system
         gap.note = ("Crosswalk local immunization code → CVX first; else search "
                     "by normalized vaccine concept (+ valence) → CVX.")
     elif pattern == CvxGapPattern.BAD_CODE and cc:

{aimedicalcoding-0.3.7 → aimedicalcoding-0.3.9}/aimedicalcoding/systems/icd10cm/patterns.py

@@ -67,13 +67,16 @@ def classify(stmt: ClinicalStatement) -> Optional[Icd10cmGapPattern]:
     if other:                                   # ICD-9 / local / anything else
         return Icd10cmGapPattern.LOCAL_CODE_ONLY
 
+    # diagnosis is value-slot: require a value-slot label to recover from.
+    # No code AND no value label (e.g. dataAbsentReason, no text) -> not a gap.
+    val_label = stmt.value and (stmt.value.original_text or stmt.value.raw)
+    if not val_label:
+        return None
     if _has_nullflavor(stmt):
         return Icd10cmGapPattern.NULLFLAVOR
-    if stmt.raw_text or (stmt.value and (stmt.value.original_text or stmt.value.raw)):
-        if "/text" in (stmt.source_ref or ""):
-            return Icd10cmGapPattern.NARRATIVE_ONLY
-        return Icd10cmGapPattern.DISPLAY_ONLY
-    return None
+    if "/text" in (stmt.source_ref or ""):
+        return Icd10cmGapPattern.NARRATIVE_ONLY
+    return Icd10cmGapPattern.DISPLAY_ONLY
 
 
 # --------------------------------------------------------------------------
@@ -117,7 +120,8 @@ def parse_gap(stmt: ClinicalStatement, pattern: Icd10cmGapPattern) -> Gap:
                     "deterministic; LLM to pick among targets / add specificity.")
     elif pattern == Icd10cmGapPattern.LOCAL_CODE_ONLY and cc:
         gap.evidence["local_code"] = cc.code
-        gap.evidence["local_system"] = (cc.system.value if cc.system else cc.raw_system)
+        gap.evidence["local_system"] = (cc.system.value if cc.system else None)
+        gap.evidence["local_system_raw"] = cc.raw_system
         gap.note = ("Crosswalk the source code → ICD-10-CM (ICD-9 → use CMS GEMs); "
                     "else text + qualifier search.")
     elif pattern == Icd10cmGapPattern.BAD_CODE and cc:

{aimedicalcoding-0.3.7 → aimedicalcoding-0.3.9}/aimedicalcoding/systems/loinc/patterns.py

@@ -77,6 +77,11 @@ def classify(stmt: ClinicalStatement) -> Optional[GapPattern]:
     if clinical_codes:
         return GapPattern.LOCAL_CODE_ONLY
 
+    # No usable code: a gap is only actionable if a concept label exists to
+    # search with. No code AND no label (e.g. dataAbsentReason with no text)
+    # -> nothing to fill -> not a gap.
+    if not stmt.raw_text:
+        return None
     has_nullflavor = any(c.system == System.NULLFLAVOR for c in stmt.codings)
     if has_nullflavor:
         return GapPattern.NULLFLAVOR
@@ -94,7 +99,10 @@ def parse_local_code_only(stmt: ClinicalStatement, expand_abbrev: bool = False)
     local = next((c for c in stmt.codings if c.code and c.system != System.LOINC), None)
     ev = axes.evidence_packet(stmt, expand_abbrev)
     ev["local_code"] = local.code if local else None
-    ev["local_system"] = (local.raw_system if local else None)
+    # canonical system (format-independent: "CPT" whether from a CCDA OID or a
+    # FHIR URI) drives the crosswalk; raw is kept for provenance.
+    ev["local_system"] = (local.system.value if local and local.system else None)
+    ev["local_system_raw"] = (local.raw_system if local else None)
     return Gap(
         type=GapPattern.LOCAL_CODE_ONLY.value,
         match_key=axes.build_match_key(stmt, expand_abbrev),

{aimedicalcoding-0.3.7 → aimedicalcoding-0.3.9}/aimedicalcoding/systems/rxnorm/patterns.py

@@ -68,13 +68,14 @@ def classify(stmt: ClinicalStatement) -> Optional[RxnormGapPattern]:
     if cc and cc.code and cc.system not in STRUCTURAL:
         return RxnormGapPattern.LOCAL_CODE_ONLY   # local/formulary/other
 
+    # no usable code + no drug name -> nothing to recover -> not a gap
+    if not stmt.raw_text:
+        return None
     if _has_nullflavor(stmt):
         return RxnormGapPattern.NULLFLAVOR
-    if stmt.raw_text:
-        if "/text" in (stmt.source_ref or ""):
-            return RxnormGapPattern.NARRATIVE_ONLY
-        return RxnormGapPattern.DISPLAY_ONLY
-    return None
+    if "/text" in (stmt.source_ref or ""):
+        return RxnormGapPattern.NARRATIVE_ONLY
+    return RxnormGapPattern.DISPLAY_ONLY
 
 
 # --------------------------------------------------------------------------
@@ -115,7 +116,8 @@ def parse_gap(stmt: ClinicalStatement, pattern: RxnormGapPattern) -> Gap:
 
     if pattern == RxnormGapPattern.NDC_ONLY and cc:
         gap.evidence["ndc_code"] = cc.code
-        gap.evidence["ndc_system"] = cc.raw_system
+        gap.evidence["ndc_system"] = cc.system.value if cc.system else None
+        gap.evidence["ndc_system_raw"] = cc.raw_system
         gap.note = ("Use the NDC↔RxNorm crosswalk (RxNorm release / REST API) — "
                     "deterministic; LLM only if multiple RxCUIs map.")
     elif pattern in _SOURCE_VOCAB_PATTERN.values() and cc:
@@ -123,15 +125,18 @@ def parse_gap(stmt: ClinicalStatement, pattern: RxnormGapPattern) -> Gap:
         gap.evidence["source_code"] = cc.code
         gap.evidence["source_vocab"] = vocab
         gap.evidence["source_system"] = cc.raw_system
-        # serialize.py builds a crosswalk hint from local_code/local_system
+        # serialize.py builds a crosswalk hint from local_code/local_system.
+        # local_system is the canonical vocab (format-independent); raw kept too.
         gap.evidence["local_code"] = cc.code
         gap.evidence["local_system"] = vocab
+        gap.evidence["local_system_raw"] = cc.raw_system
         gap.note = (f"Crosswalk {vocab} → RxNorm via the UMLS Metathesaurus "
                     f"(shared CUI) or the vendor's RxNorm map — deterministic; "
                     f"LLM only if the mapping is ambiguous or 1→many.")
     elif pattern == RxnormGapPattern.LOCAL_CODE_ONLY and cc:
         gap.evidence["local_code"] = cc.code
-        gap.evidence["local_system"] = cc.raw_system
+        gap.evidence["local_system"] = cc.system.value if cc.system else None
+        gap.evidence["local_system_raw"] = cc.raw_system
         gap.note = ("Crosswalk local/formulary code → RxNorm first; else search by "
                     "ingredient + strength + dose form → SCD/SBD.")
     elif pattern == RxnormGapPattern.NULLFLAVOR:

{aimedicalcoding-0.3.7 → aimedicalcoding-0.3.9}/aimedicalcoding/systems/snomed/patterns.py

@@ -113,16 +113,17 @@ def classify(stmt: ClinicalStatement) -> Optional[SnomedGapPattern]:
     if cc and cc.code and cc.system not in STRUCTURAL:
         return SnomedGapPattern.LOCAL_CODE_ONLY   # CPT / local / other
 
-    # no usable concept code. The label must come from the CONCEPT's slot
-    # (value display/originalText for value-slot contexts) — raw_text alone
-    # misses e.g. reaction observations whose code tag is a bare ASSERTION.
+    # no usable concept code. A gap is only actionable if a recoverable label
+    # exists for the concept's slot (value display/originalText for value-slot
+    # contexts). If there is neither a code NOR a label (e.g. dataAbsentReason
+    # with no value text/note), there is nothing to fill -> not a gap.
+    if not concept_term(stmt):
+        return None
     if _has_nullflavor(stmt):
         return SnomedGapPattern.NULLFLAVOR
-    if concept_term(stmt):
-        if "/text" in (stmt.source_ref or ""):
-            return SnomedGapPattern.NARRATIVE_ONLY
-        return SnomedGapPattern.DISPLAY_ONLY
-    return None
+    if "/text" in (stmt.source_ref or ""):
+        return SnomedGapPattern.NARRATIVE_ONLY
+    return SnomedGapPattern.DISPLAY_ONLY
 
 
 # --------------------------------------------------------------------------
@@ -149,7 +150,8 @@ def parse_gap(stmt: ClinicalStatement, pattern: SnomedGapPattern) -> Gap:
 
     if pattern == SnomedGapPattern.LOCAL_CODE_ONLY and cc:
         gap.evidence["local_code"] = cc.code
-        gap.evidence["local_system"] = cc.raw_system
+        gap.evidence["local_system"] = cc.system.value if cc.system else None
+        gap.evidence["local_system_raw"] = cc.raw_system
         gap.note = ("Crosswalk (system, code) → SNOMED first (e.g. CPT/local map); "
                     "else hierarchy-constrained text search, then LLM.")
     elif pattern == SnomedGapPattern.ICD_ONLY and cc:
@@ -159,7 +161,8 @@ def parse_gap(stmt: ClinicalStatement, pattern: SnomedGapPattern) -> Gap:
                     "LLM only to choose among multiple map targets.")
     elif pattern == SnomedGapPattern.RXNORM_ONLY and cc:
         gap.evidence["rxnorm_code"] = cc.code
-        gap.evidence["rxnorm_system"] = cc.raw_system
+        gap.evidence["rxnorm_system"] = cc.system.value if cc.system else None
+        gap.evidence["rxnorm_system_raw"] = cc.raw_system
         gap.note = ("RxNorm-coded allergen (drug allergy) — crosswalk RxNorm → "
                     "SNOMED substance/product via UMLS CUI; LLM only if the "
                     "ingredient maps ambiguously.")

{aimedicalcoding-0.3.7 → aimedicalcoding-0.3.9/aimedicalcoding.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aimedicalcoding
-Version: 0.3.7
+Version: 0.3.9
 Summary: Detect missing/broken clinical codes (LOINC / SNOMED CT / RxNorm / ICD-10-CM / CVX) in CCDA and FHIR documents, with recovery evidence
 Author: Aakash Kag, Vinay Shankar Miryala, Siva Karthik, Mohammed Rayaan
 License: MIT

{aimedicalcoding-0.3.7 → aimedicalcoding-0.3.9}/docs/GAP_SCHEMA.md

@@ -80,7 +80,7 @@ Each record separates four concerns:
   "search_terms": ["BUN", "Blood Urea Nitrogen"],   // text to query (raw + normalized)
   "filters": { "specimen": "...", "property": "...", "scale": "..." },  // LOINC axis filters
   "ecl": "< 404684003",                              // SNOMED: the candidate constraint
-  "crosswalk": { "from_system": "LOCAL", "from_code": "BUN" },   // try first (local/ICD → target)
+  "crosswalk": { "from_system": "CPT", "from_code": "80061" },   // try first (local/ICD/NDC → target). from_system is the CANONICAL system (e.g. "CPT","NDC","ICD-10-CM"), identical for CCDA and FHIR; the raw OID/URI is in evidence as *_system_raw
   "checkdigit_correction": "2160-0",                 // BAD_CODE only
   "match_key": "…",                                  // human summary (do NOT query verbatim)
   "suggested_action": "…"
@@ -132,7 +132,7 @@ CODE tag's — the other slot's labels are not mixed in.
   "recovery": {
     "search_terms": ["BUN", "Blood Urea Nitrogen"],
     "filters": { "specimen": "Ser/Plas", "property": "MCnc", "scale": "Qn" },
-    "crosswalk": { "from_system": "2.16.840.1.113883.19.5.99999.1", "from_code": "BUN" },
+    "crosswalk": { "from_system": "LOCAL", "from_code": "BUN" },
     "match_key": "component:BUN | specimen:Ser/Plas | property:MCnc | scale:Qn | method:-",
     "suggested_action": "crosswalk local code → target; else text + filter search"
   },

{aimedicalcoding-0.3.7 → aimedicalcoding-0.3.9}/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name="aimedicalcoding",
-    version="0.3.7",
+    version="0.3.9",
     author="Aakash Kag, Vinay Shankar Miryala, Siva Karthik, Mohammed Rayaan",
     description=(
         "Detect missing/broken clinical codes (LOINC / SNOMED CT / RxNorm / "