UTSW has Diagnosis and Procedures mapped to the GPC standard, they are just under a different project. We also have the majority of the PCORI terminology useable in i2b2. Due to different requirements of different project, ACT, GPC, PCORI, Local, it’s often necessary, or easier, to deploy multiple versions of the same terminology.
I really think that SHRINE would give people a reason to map and use the shared terminologies, especially if it can save them time in reproducing queries. Phillip From: <[email protected]<mailto:[email protected]>> on behalf of Dan Connolly <[email protected]<mailto:[email protected]>> Date: Monday, August 8, 2016 at 10:14 AM To: "<[email protected]<mailto:[email protected]>>" <[email protected]<mailto:[email protected]>> Subject: struggles with alignment on diagnoses, labs in PI-CONNECT federated query I have aggregated data from 8 of 10 sites. Despite the fact that we agreed on our diagnosis ontology March 2014 (#63<https://informatics.gpcnetwork.org/trac/Project/ticket/63>) and labs Nov 2015 (#158<https://informatics.gpcnetwork.org/trac/Project/ticket/158>), terms were different enough that I had to scrape codes from various parts of paths and labels. We are not in a position to use SHRINE for queries with these terms. UTSW is the only site whose IgG lab term path matches the GPC standard: ... IgG Levels In [54]: igg_term = summary[summary.variable.str.contains(r'\bIgG\b|IMMUNOGLOBULIN G', case=False)].copy() igg_path_72 = r'\GPC\Laboratory Tests\LP31388-9\LP15838-3\LP31769-0\LP14672-7\ '[4:-1] igg_path_65 = r'\GPC\Laboratory Tests\LP31388-9\LP15838-3\LP31769-0\LP14672-7\LP43122-8\2465-3\ '[4:-1] igg_term['aligned'] = igg_term.concept_path.apply(lambda p: p.endswith(igg_path_72) or p.endswith(igg_path_65)) per_site(igg_term)[['variable', 'concept_path', 'aligned']] Out[54]: variable concept_path aligned site IU 0 0 0 KUMC IgG (LP14672-7) \i2b2\Laboratory Tests\Chemistry\Protein\Immun... False MCRF 2465-3: Igg \i2b2\LP29693-6\LP29697-7\LP7834-7\55121-8\246... False MCW 0 0 0 MU IgG (LP14672-7) \i2b2\Laboratory Tests\Chemistry\Protein\Immun... False UIOWA IgG SerPl-mCnc \i2b2\Labtests\LP31388-9\LP15838-3\LP31769-0\L... False UNMC IgG \UNMC\Laboratory Results\Blood and body fluids... False UTHSCSA IgG SerPl-mCnc (2465-3) \i2b2\Laboratory Tests\Chemistry\Protein\Immun... False UTSW IgG (LP14672-7) \i2b2\Laboratory Tests\LP31388-9\LP15838-3\LP3... True WISC IMMUNOGLOBULIN G \lab_information\lab_standard\igg\immunoglobul... False ... We're doing better on diagnoses, though 4 of 10 sites is still a minority: ... Normalizing diagnosis codes In [27]: import re def icd9_from_label(label): return [g1 for (g1, g2) in re.findall(r'(\d+(\.\d+)?)', label)] icd9_from_label(u'283 Acquired hemolytic anemias') Out[27]: [u'283'] In [28]: dx_term = summary[~ summary.variable.isin(igg_term.variable)].copy() def find_icd9(x): name_code = icd9_from_label(x.variable) return ''.join(name_code if name_code else x.concept_path.split('\\')[-2:]) dx_term['code'] = [find_icd9(row) for (ix, row) in dx_term.iterrows()] In [29]: pneumonia = dx_term[dx_term.code == '486'].copy() gpc_486 = r'\i2b2\Diagnoses\ICD9\A18090800\A8359006\A8354357\A12966666\486\ '[20:-1] pneumonia['aligned'] = pneumonia.concept_path.apply(lambda p: p.endswith(gpc_486)) per_site(pneumonia)[['variable', 'concept_path', 'code', 'aligned']] Out[29]: variable concept_path code aligned site IU 0 0 0 0 KUMC 486 Pneumonia, organism unspecified \i2b2\Diagnoses\ICD9\A18090800\A8359006\A83543... 486 True MCRF 486 Pneumonia, organism unspecified \i2b2\Diagnoses\A18090800\A8359006\A8354357\A1... 486 True MCW 0 0 0 0 MU Pneumonia, organism unspecified (486) \i2b2\Diagnoses\Diseases of the Respiratory Sy... 486 False UIOWA Pneumonia, organism unspecified \i2b2\Diagnoses\460-519\480-488\486\ 486 False UNMC 486 Pneumonia, organism unspecified \i2b2\Diagnoses\A18090800\A8359006\A8354357\A1... 486 True UTHSCSA 486 Pneumonia, organism unspecified \i2b2\Diagnoses\A18090800\A8359006\A8354357\A1... 486 True UTSW (486)Pneumonia, organism unspecified \i2b2\Diagnoses(ICD9CM)\DISEASES AND INJURIES\... 486 False WISC 486: Pneumonia, organism unspecified \diagnosis_information\icd\icd09\001-999.99\46... 486 False ... -- Dan ________________________________ UT Southwestern Medical Center The future of medicine, today.
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