cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.24373/pdsp-389
title: Oncology, Facility

description: This concept set contains codes intended to identify oncology or hematology/oncology visits (in combination with the oncology provider concept set). This concept set was generated by restricting the PCORnet CDM value set to facility types that mention "oncology". This value set is PCORnet-specific and is based on PCORnet CDM v6.0 2021-04. This concept set has some overlap with the Oncology, Facility concept set.
description: Concept set intended to assess the frequency with which patients sought care with specialties involved in patient care for and related to oncology.
description: This concept set was developed for the Preserving Kidney Function in Children with Chronic Kidney Disease (PRESERVE) study. Hematology/oncology visits are a covariate of interest across the PRESERVE study because treatments for malignancies may be associated with kidney function decline.
DOI: 10.24373/pdsp-362
title: Electrocardiogram

description: The concept set contains procedure codes for electrocardiograms. It was created by searching for the terms "ECG" or "EKG" or "electrocardiogra" and excluding the search terms "refer," "positron," "pet follow," "fetal," "sleep," "SAECG," "external patient," "radionuclide," "monitoring of ECG," "ecgonine," "cardiomemo," "stress test," "carotid pulse," "continuous," "electronic analysis," "assembly" "removal," "gated," "insertion of," "mitrale," "pulmonale," "database," "blood pressure," "biofeedback," "implantation," and "programming" in the measurement and procedure domains. It was created to assess diagnostic imaging and testing for patients with primary hyperoxaluria (PH) both before and after diagnosis of PH. The variable was intended to capture non-kidney stone-related utilization of health services for known organs involved in PH. This concept set is limited to ICD10PCS, HCPCS, ICD9Proc, CPT4, SNOMED, OPCS4 vocabularies in the measurement and procedure domains.
description: Concept set intended to identify patients having undergone an electrocardiographic procedure.
description: A Study to Evaluate DCR-PHXC in Children and Adults With Primary Hyperoxaluria Type 1 and Primary Hyperoxaluria Type 2 (PHYOX2) (Dicerna)
DOI: 10.24373/pdsp-155
title: Lactose Intolerance

description: This concept set is one of a set which was created en masse to evaluate Asthma as part of a study. ICD-10 and ICD-10-CM codes were requested specifically by the study PI and mapped to SNOMED by the developer.
description: Concept set intended to map lactose intolerance diagnoses concepts between SNOMED and ICD codes.
description: This concept set was developed for the study "Neighborhood Greenspace as a Protective Factor Against Childhood Asthma."
DOI: 10.24373/pdsp-358
title: Chronic Dialysis

description: This condition concept set for chronic & broad dialysis procedures. Limited to CPT4, HCPCS, ICD9Proc, ICD9ProcCN, ICD10PCS, and SNOMED diagnosis codes. ICD codes are included with and without decimal points, indicated by `cc_decimal_removal`. This code set is neither more specific nor more sensitive in picking up chronic dialysis patients compared to this alternative Kidney Dialysis code set, also developed as part of the PRESERVE study. However, it has the most optimal performance in term of overall accuracy. Some codes might seem redundant with the same `concept_id`; however, they have different `pcornet_vocabulary_id`s which is required to query all relevant data.
description: Concept set intended to identify patients who have initiated maintenance dialysis. This concept set was validated against United States Renal Data System (USRDS) data.
description: Preserving Kidney Function in Children with Chronic Kidney Disease (PRESERVE)
DOI: 10.24373/pdsp-347
title: Head Circumference, Measurement

description: This concept set contains the PEDSnet-specified LOINC code used to identify head circumference as listed in the PEDSnet Data Model specifications. It has been used in the PEDSnet Network Data Quality program. to evaluate the population of head circumference measurements across the network.
description: This concept set is intended to identify head circumference measurements.
DOI: 10.24373/pdsp-140
title: Eosinophilia

description: This concept set is one of a set which was created en masse to evaluate Asthma as part of a study. ICD-10 and ICD-10-CM codes were requested specifically by the study PI and mapped to SNOMED by the developer.
description: Concept set intended to map eosinophilia diagnoses concepts between SNOMED and ICD codes.
description: This concept set was developed for the study "Neighborhood Greenspace as a Protective Factor Against Childhood Asthma."
DOI: 10.24373/pdsp-167.2
title: Glomerular Disease

description: This concept set includes glomerular disease diagnosis codes. This code list was generated by including ICD codes that map to descendants of SNOMED code 197679002 "Glomerular disease" as well as including ICD10 range N00-N08 and ICD 9 range 580-583. ICD codes are included with and without decimal points, indicated by cc_decimal_removal.
description: This concept set was created to identify patients with a diagnosis of glomerular disease for implementation of a computational phenotype which was validated using the OMOP data model. The purpose was to identify glomerular disease etiologies of chronic kidney disease.
description: Preserving Kidney Function in Children with Chronic Kidney Disease (PRESERVE)
DOI: 10.24373/pdsp-67
title: Nephrotic Syndrome

description: This concept set is inteded to identify patients with a diagnosis of nephrotic syndrome.
description: This concept set was created for the Pediatric KIDney Stone (PKIDS) Care Improvement Network.
DOI: 10.24373/pdsp-68
title: Urinary Tract Infection for Individuals with Primary Hyperoxaluria Type 1

description: The concept set includes codes for urinary tract infection. The concept set is intentionally broad. The sponsor was interested in exploring common symptoms of patients with primary hyperoxaluria, type 1 (PH1). We assessed whether there was record of each symptom both before and after the patient was diagnosed with PH1. UTI was included in exploratory analyses but was ultimately not used as a covariate in the final analyses. The study PI, Greg Tasian, provided a list of ICD9 and ICD10 codes for UTI which were mapped to SNOMED codes and all descendants taken. The concept set is limited to SNOMED diagnosis codes.
description: This concept set is inteded to identify patients with a diagnosis of a urinary tract infection.
description: Health Services and Clinical Characteristics that Precede Diagnosis of Primary Hyperoxaluria Type 1 (Alnylam)
DOI: 10.24373/pdsp-166
title: Addison's Disease

description: The condition concept set was for terms related to primary adrenalocortical insufficiency (Addison's disease). The code list was generated by searching for all descendants of the SNOMED concept 'Primary adrenocortical insufficiency' and ICD codes related to G47.4. This concept set was limited to ICD-10 and SNOMED codes because the look-back was only to 2016.
description: This concept set is inteded to identify patients with a diagnosis of Addison's Disease.
description: This was developed as part of autoimmune/chronic conditions for a RECOVER study manuscript exploring features of children with PASC.
DOI: 10.24373/pdsp-79
title: Allergies, Non-Food, Drug, or Respiratory

description: This concept set is one of a set which was created en masse to evaluate Asthma as part of a study. ICD-10 and ICD-10-CM codes were requested specifically by the study PI and mapped to SNOMED by the developer.
description: Concept set intended to map lower respiratory infection diagnoses concepts between SNOMED and ICD codes.
description: This concept set was developed for the study "Neighborhood Greenspace as a Protective Factor Against Childhood Asthma."
DOI: 10.24373/pdsp-344.2
title: Diastolic Blood Pressure, Measurement

description: The PEDSnet CDM represents diastolic blood pressure measurements using LOINC codes. The codes which should be used are specified in the PEDSnet ETL guidelines. Because the concept set is small, the codes are often provided directly in the code rather than using a CSV. A PCORnet equivalent representation of systolic blood pressure measurement can be found in Version 1 below.
description: This field is used to represent diastolic blood pressure measurements in the PEDSnet CDM.
description: This concept set was developed to provide a PEDSnet data model equivalent to the PCORnet data model diastolic BP specifications.
DOI: 10.24373/pdsp-405
title: Urology, Provider

description: This concept set contains codes intended to identify urology visits (in combination with the urology facility concept set). This concept set was generated by restricting the PCORnet CDM value set to provider types that mention "urology". The value set uses the "Medicare Specialty" vocabulary, though the PEDSnet CDM also uses "ABMS", "NUCC", and "PEDSnet" vocabularies. The concept set is based on PCORnet CDM v6.0 2021-04. A PEDSnet equivalent concept set is linked below.
description: Concept set intended to assess the frequency with which patients sought care with specialties involved in patient care for and related to urology.
description: This concept set was developed for the Preserving Kidney Function in Children with Chronic Kidney Disease (PRESERVE) study. Urology visits are a covariate of interest across the PRESERVE study, given the relationship between kidney issues and the genitourinary system.
DOI: 10.24373/pdsp-104
title: Congenital Anorectal Anomalies

description: Concept set to identify patients with congenital anorectal anomalies. This concept set is intended to be used in conjunction with several other concept sets identifying patients with rare congenital diseases (linked below).
description: Concept set to identify patients with congenital anorectal anomalies.
description: This concept set was developed for a PEDSnet feasibility query investigating readily identifiable rare congenital anomalies.
DOI: 10.24373/pdsp-259
title: Urine Creatinine, Lab Results

description: The measurement concept set includes all urine creatinine labs. This code list was generated by searching all mentions of 'creatinine' with 'urine' in the concept_name. Limited to the LOINC vocabulary_id. Filtered out labs that have ratios with creatinine.
description: A concept set indicating that a patient received a laboratory measurement for urine creatinine.
description: Developed for the Preserving Kidney Function in Children with Chronic Kidney Disease (PRESERVE) study for urine creatinine lab values.
DOI: 10.24373/pdsp-316
title: Injectable Antibiotic, Drug Exposure

description: This broad concept set was developed to identify injectable antibiotic exposures for a cohort of neonates. The medication codes were compiled using RxNorm at the Clinical Dose Form Group level containing the injectable version of specific antibiotic ingredients, including: amikacin Injectable Product cilastatin / imipenem Injectable Product cefamandole Injectable Product cefazolin Injectable Product cefoperazone Injectable Product cefotaxime Injectable Product cefotetan Injectable Product cefoxitin Injectable Product ceftazidime Injectable Product ceftizoxime Injectable Product ceftriaxone Injectable Product cefuroxime Injectable Product ampicillin / sulbactam Injectable Product ampicillin Injectable Product azithromycin Injectable Product aztreonam Injectable Product tobramycin Injectable Product piperacillin / tazobactam Injectable Product piperacillin Injectable Product itraconazole Injectable Product vancomycin Injectable Product cefepime Injectable Product doripenem Injectable Product ertapenem Injectable Product erythromycin Injectable Product penicillin G Injectable Product meropenem Injectable Product ceftolozane / tazobactam Injectable Product avibactam / ceftazidime Injectable Product ceftaroline fosamil Injectable Product gentamicin Injectable Product
description: Concept set intended to identify neonatal patients with an exposure to an injectable antibiotic medication.
description: This concept set was developed as support of the study "Natural History of Enteroviral Sepsis Using Real World Data."
DOI: 10.24373/pdsp-306
title: Loop Diuretic, Drug Exposure

description: This medication concept set includes the following ingredients: Furosemide, Bumetanide, Ethacrynic acid and Torsemide. It also includes combinations of these ingredients with other antihypertensive medications. This code list was generated by taking the descendants of all the loop diuretic ingredients of interest and string matching on the concept_name of the ingredient. This broad concept set was intended to identify patients who received loop diuretics. Limited to NDC, RxNorm, and RxNorm Extension codes. Meds were expected to be only oral/enteral/IV, not topical or buccal. Note: This concept set was created when ingredients were required for some sites. It could be enhanced by using SCDF drug levels and taking descendants, making this easier to refresh.
description: Concept set intended to identify patients with an exposure to a loop diuretic medication.
description: Preserving Kidney Function in Children with Chronic Kidney Disease (PRESERVE)
DOI: 10.24373/pdsp-366
title: MRI Scan

description: Concept set intended to identify patients having undergone a magnetic resonance imaging (MRI) procedure.
description: SPARK Registry- PEDSnet Linkage Pilot
DOI: 10.24373/pdsp-202
title: Abnormal Weight Gain

description: This concept set contains diagnoses related to abnormal weight gain. This codeset was developed by finding the concept_ids for a subset of the AHRQ CCSR clusters (https://hcup-us.ahrq.gov/toolssoftware/ccsr/dxccsr.jsp#overview) related to weight gain. This concept set alone was not reviewed by a clinician, but it was a component of a larger codeset that was reviewed by Chris Forrest. This concept set contains only ICD10 and ICD10CM codes. It does not contain versions of the concept_code with the decimal removed.
description: This concept set is inteded to identify patients with a diagnosis of abnormal weight gain.
description: Concept set developed as part of syndromic conditions for a RECOVER study manuscript exploring features of PASC in children.
DOI: 10.24373/pdsp-131
title: Cystitis

description: This diagnosis concept set includes codes for cystitis and complications of cystitis. The set was developed as part of a study to assess whether patients had a record of anemia or associated symptoms before and after a diagnosis of primary hyperoxaluria, type 1 (PH1). As very few patients with diagnosed cystitis were found, anemia was ultimately not included as a covariate in the analyses. This concept was developed from a list of ICD-10 codes provided by the requestor which had been used for anemia for another (non-PEDSnet) study. All of the ICD-10 codes started with N30*. Those codes were mapped to SNOMED and supplemented with basic string searching (e.g. "cystitis"). This concept set contains only SNOMED codes present in the OMOP vocabulary and the domain is limited to condition_occurrence.
description: This concept set is inteded to identify patients with a diagnosis of cystitis.
description: Developed for exploratory use in the study "Health Services and Clinical Characteristics that Precede Diagnosis of Primary Hyperoxaluria Type 1", but ultimately not used in the final research.
DOI: 10.24373/pdsp-58
title: Sjogren's Syndrome

description: This concept set contains diagnosis codes for Sj�gren's syndrome. This was developed as part of autoimmune/chronic conditions for a RECOVER study manuscript exploring features of children with PASC. The code list was generated by searching for all descendants of the SNOMED code 83901003 (Sj�gren's syndrome) plus all ICD10 or ICD10CM codes mapping to those SNOMED descendants. String matching was also performed looking for the string "sjogren" or "sicca syndrome" in domains excluding the measurement domain and excluding the terms "family history" or "not specified as sjogren". The concept set was limited to ICD10, ICD10CM, and SNOMED vocabularies.
description: This concept set is inteded to identify patients with a diagnosis of Sjogren's Syndrome.
description: The original concept set was developed for the initial RECOVER work exploring clinical features of PASC in children. This codeset was a part of the autoimmune conditions subset of features.
DOI: 10.24373/pdsp-32
title: Dermatitis Herpertiformis

description: This condition concept set contains terms for and related to dermatitis herpetiformis. The code list was generated by searching for all descendants of the SNOMED code 111196000 (Dermatitis herpetiformis) plus all ICD10 or ICD10CM codes mapping to those SNOMED descendants. String matching was also performed looking for the string "ermatitis herpetiformis" in the condition domain and excluding the term "family history".
description: This concept set is inteded to identify patients with a diagnosis of dermatitis herpertiformis.
description: This was developed as part of autoimmune/chronic conditions for a RECOVER study manuscript exploring features of children with PASC.
DOI: 10.24373/pdsp-325
title: COVID-19 Medications, Drug Exposure

description: Concept set intended to identify patients with an exposure to any medication used to treat SARS-CoV-2.
description: The Researching COVID to Enhance Recovery (RECOVER) Post-Acute Sequelae of SARS-CoV-2 (PASC) Electronic Health Record (EHR) Cohort Study
DOI: 10.24373/pdsp-399
title: Inpatient Visits

description: This concept set contains encounter types which are inpatient admissions in the PCORnet data model. It was created by limiting the PCORnet value set for the ENC_TYPE field in the ENCOUNTER table to inpatient and emergency department to inpatient admissions. This concept set was not reviewed, but it is a generally accepted subset of the PCORnet value sets that does not contain clinical terms. It was created to identify inpatient visits in the PCORnet data model. All concepts are expected to appear in the ENC_TYPE field in the PCORnet CDM ENCOUNTER table. This concept set contains the term for emergency department to inpatient admission in addition to inpatient admission, so if the frequency of admission is of interest, caution should be taken in not double-counting an inpatient admission + an emergency department admit that led to an inpatient admission.
description: Concept set intended to assess the frequency with which patients received care at an inpatient care facility.
description: Preserving Kidney Function in Children with Chronic Kidney Disease (PRESERVE)
DOI: 10.24373/pdsp-369
title: Bone Marrow Transplant

description: Procedure concept set that includes transplant of both autogenic and allogenic bone marrow, stem cells. It was developed by searching for terms such as "bone marrow", "hematopoietic stem cell", and "Blood Stem Cells & Transfusion", followed by selective removal of the false positive. It was developed by the collaborating PI Sarah Dain, MD who used Atlas to build the codeset. Chart review were not performed formally, however this study involves tying back to the EHR data at CHOP. Hence a dual approach was used where patients identified using this codeset and the bone marrow registry/dataset that PI had were used together to create the study variable. The intention of this concept set was to identify a list of patients receiving bone marrow transplant. For our study use case, bone marrow transplant was a variable (covariate). The codeset was developed to be as broad as possible. Elimination of vocabularies such as Nebraska Lexicon, MedDRA, and NAACCR was performed. The concept set includes some vocabularies not typically found in procedures; these were not used in variable construction.
description: Concept set intended to identify patients having undergone a bone marrow transplantation procedure.
description: Impact of Early and Universal Hydroxyurea on Cerebrovascular Outcomes in Sickle Cell Disease
DOI: 10.24373/pdsp-375
title: Kidney Biopsy

description: This concept set contains codes pertaining to kidney biopsy procedures. It was developed by taking the union of (a) procedures which include the string "kidney"/"renal" AND "biopsy" and (b) procedures which include the strings "excision"/"extraction"/"drainage" AND "kidney" AND "diagnostic". (b) captured ICD-10-PCS codes. Levon Utidjian (clinician/informaticist) noted that "excision"/"extraction"/"drainage" codes were limited to those with "diagnostic" qualifiers since those are most appropriate for biopsy per CMS guidance. ICD codes are included with and without decimal points, indicated by cc_decimal_removal, indicated by cc_decimal_removal.
description: Concept set intended to identify patients having undergone a kidney biopsy procedure.
description: This concept set was developed for the Preserving Kidney Function in Children with Chronic Kidney Disease (PRESERVE) study. Glomerular Disease is one of the etiology groups of interest for the PRESERVE study. This concept was used to define kidney biopsy in the PCORnet adaptation of the glomerular disease phenotype, which is used across multiple analyses for the project.
DOI: 10.24373/pdsp-211
title: Allergic Conjunctivitis

description: This concept set is one of a set which was created en masse to evaluate Asthma as part of a study. ICD-10 and ICD-10-CM codes were requested specifically by the study PI and mapped to SNOMED by the developer.
description: Concept set intended to map allergic conjunctuvitis diagnoses concepts between SNOMED and ICD codes.
description: This concept set was developed for the study "Neighborhood Greenspace as a Protective Factor Against Childhood Asthma."
DOI: 10.24373/pdsp-398
title: Urology, Facility

description: This concept set contains codes intended to identify urology visits (in combination with the urology provider concept set). This concept set was generated by restricting the PCORnet CDM value set to facility types that mention "urology". This value set is PCORnet-specific and is based on PCORnet CDM v6.0 2021-04. A PEDSnet-equivalent concept set is linked below.
description: Concept set intended to assess the frequency with which patients sought care with specialties involved in patient care for and related to urology.
description: This concept set was developed for the Preserving Kidney Function in Children with Chronic Kidney Disease (PRESERVE) study. Urology visits are a covariate of interest across the PRESERVE study, given the relationship between kidney issues and the genitourinary system.
DOI: 10.24373/pdsp-262
title: Fetal Hemoglobin, Lab Results

description: The concept set was generated by searching for terms "Hemoglobin" and restricting to labs that obtain fetal hemoglobin in the vocabulary table. Limited to LOINC codes for the Laboratory domain.
description: A concept set indicating that a patient received a laboratory measurement for fetal hemoglobin.
description: This concept set was used for Impact of the 2014 NHLBI Guidelines on Cerebrovascular Events in Sickle Cell Disease to identify sickle cell patients with at least one lab record of Fetal Hemoglobin.
DOI: 10.24373/pdsp-266
title: Factor VIII, Lab Results

description: The concept set was generated by searching for terms Factor VIII in the vocabulary table limiting to LOINC code for Lab domain.
description: A concept set indicating that a patient received a laboratory measurement for Factor VIII.
description: This concept set was used for the "Impact of the 2014 NHLBI Guidelines on Cerebrovascular Events in Sickle Cell Disease" study to identify sickle cell patients with at least one lab record of Factor VIII.
DOI: 10.24373/pdsp-139
title: Non-Respiratory Sequelae of COVID-19

description: This concept set is inteded to identify patients with a diagnosis of non-respiratory sequelae of COVID-19.
description: The Researching COVID to Enhance Recovery (RECOVER) Post-Acute Sequelae of SARS-CoV-2 (PASC) Electronic Health Record (EHR) Cohort Study
DOI: 10.6084/m9.figshare.29483972
title: SF1 Repliseq RT Various Resolutions

description: Repli-seq various resolutions file (9 files zipped)