aimedicalcoding 0.3.6__tar.gz → 0.3.8__tar.gz

{aimedicalcoding-0.3.6/aimedicalcoding.egg-info → aimedicalcoding-0.3.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aimedicalcoding
-Version: 0.3.6
+Version: 0.3.8
 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-0.3.6 → aimedicalcoding-0.3.8}/aimedicalcoding/adapters/fhir/codes.py

@@ -169,7 +169,9 @@ def extract_value(resource: dict) -> Optional[ValueInfo]:
 # --------------------------------------------------------------------------
 
 def extract_companion(resource: dict) -> dict:
-    """interpretation + reference range (Observation-shaped resources)."""
+    """interpretation + reference range + method + body site (Observation-shaped
+    resources). FHIR analog of the CCDA extractor: Observation.method and
+    Observation.bodySite are CodeableConcepts (the LOINC Method axis / site)."""
     out: dict[str, Any] = {}
     for interp in resource.get("interpretation") or []:
         code = next((clean(c.get("code")) for c in interp.get("coding") or []
@@ -189,6 +191,22 @@ def extract_companion(resource: dict) -> dict:
         if clean(rr.get("text")):
             out["reference_range"] = clean(rr.get("text"))
             break
+
+    # method: LOINC Method axis (Observation.method CodeableConcept)
+    m_codings, m_text = concept_codings(resource.get("method"))
+    method = best_label(m_codings, m_text)
+    if method:
+        out["method"] = method
+
+    # body site: Observation.bodySite CodeableConcept
+    b_codings, b_text = concept_codings(resource.get("bodySite"))
+    body_site = best_label(b_codings, b_text)
+    if body_site:
+        out["body_site"] = body_site
+        primary = next((c for c in b_codings if c.code), None)
+        if primary:
+            out["body_site_code"] = primary.code
+    return out
     return out
 
 

{aimedicalcoding-0.3.6 → aimedicalcoding-0.3.8}/aimedicalcoding/systems/cvx/patterns.py

@@ -109,17 +109,20 @@ 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-0.3.6 → aimedicalcoding-0.3.8}/aimedicalcoding/systems/icd10cm/patterns.py

@@ -117,7 +117,8 @@ 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-0.3.6 → aimedicalcoding-0.3.8}/aimedicalcoding/systems/loinc/patterns.py

@@ -94,7 +94,10 @@ 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-0.3.6 → aimedicalcoding-0.3.8}/aimedicalcoding/systems/rxnorm/patterns.py

@@ -115,7 +115,8 @@ 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 +124,18 @@ 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-0.3.6 → aimedicalcoding-0.3.8}/aimedicalcoding/systems/snomed/patterns.py

@@ -149,7 +149,8 @@ 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 +160,8 @@ 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-0.3.6 → aimedicalcoding-0.3.8/aimedicalcoding.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: aimedicalcoding
-Version: 0.3.6
+Version: 0.3.8
 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-0.3.6 → aimedicalcoding-0.3.8}/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-0.3.6 → aimedicalcoding-0.3.8}/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name="aimedicalcoding",
-    version="0.3.6",
+    version="0.3.8",
     author="Aakash Kag, Vinay Shankar Miryala, Siva Karthik, Mohammed Rayaan",
     description=(
         "Detect missing/broken clinical codes (LOINC / SNOMED CT / RxNorm / "