ohdsi/oncologywg issues and pull requests

#100 - =: bug fixes for the time to treatment histogram plot

Pull Request - State: closed - Opened by meerapatelmd over 5 years ago

#100 - =: bug fixes for the time to treatment histogram plot

Pull Request - State: closed - Opened by meerapatelmd over 5 years ago

#99 - +: process cancer types to a cleaner substring in input data before p…

Pull Request - State: closed - Opened by meerapatelmd over 5 years ago

#99 - +: process cancer types to a cleaner substring in input data before p…

Pull Request - State: closed - Opened by meerapatelmd over 5 years ago

#98 - R survival v5

Pull Request - State: closed - Opened by meerapatelmd over 5 years ago

#98 - R survival v5

Pull Request - State: closed - Opened by meerapatelmd over 5 years ago

#97 - =: fix plot_functions.R bugs and aligning naming conventions between …

Pull Request - State: closed - Opened by meerapatelmd over 5 years ago

#97 - =: fix plot_functions.R bugs and aligning naming conventions between …

Pull Request - State: closed - Opened by meerapatelmd over 5 years ago

#96 - Bring in the ICDO3 Topography Classes into the OMOP vocabulary.

Issue - State: closed - Opened by mgurley over 5 years ago - 2 comments
Labels: CDM/Vocabulary Subgroup

#96 - Bring in the ICDO3 Topography Classes into the OMOP vocabulary.

Issue - State: closed - Opened by mgurley over 5 years ago - 2 comments
Labels: CDM/Vocabulary Subgroup

#95 - R survival v3

Pull Request - State: closed - Opened by meerapatelmd over 5 years ago

#94 - NAACCR Variable 1117 'METS AT DX-OTHER' missing missing NAACCR Values.

Issue - State: closed - Opened by mgurley over 5 years ago
Labels: CDM/Vocabulary Subgroup, NAACCR, Fix

#94 - NAACCR Variable 1117 'METS AT DX-OTHER' missing missing NAACCR Values.

Issue - State: closed - Opened by mgurley over 5 years ago
Labels: CDM/Vocabulary Subgroup, NAACCR, Fix

#93 - R time to treatment v2

Pull Request - State: closed - Opened by meerapatelmd over 5 years ago

#93 - R time to treatment v2

Pull Request - State: closed - Opened by meerapatelmd over 5 years ago

#92 - R scripts that take OMOP or other input data and produce survival and time to treatment plots

Pull Request - State: closed - Opened by meerapatelmd over 5 years ago

#92 - R scripts that take OMOP or other input data and produce survival and time to treatment plots

Pull Request - State: closed - Opened by meerapatelmd over 5 years ago

#91 - Filter out invalid dates from input format before inputing them into the CDM table.

Issue - State: closed - Opened by mgurley over 5 years ago
Labels: ETL

#91 - Filter out invalid dates from input format before inputing them into the CDM table.

Issue - State: closed - Opened by mgurley over 5 years ago
Labels: ETL

#90 - R time to treatment

Pull Request - State: closed - Opened by meerapatelmd over 5 years ago

#90 - R time to treatment

Pull Request - State: closed - Opened by meerapatelmd over 5 years ago

#89 - Remove extra drop/create for measurement_temp temporary table.

Issue - State: closed - Opened by mgurley over 5 years ago
Labels: ETL

#89 - Remove extra drop/create for measurement_temp temporary table.

Issue - State: closed - Opened by mgurley over 5 years ago
Labels: ETL

#88 - Fix duplicated NAACCR treatment modifiers.

Issue - State: closed - Opened by mgurley over 5 years ago
Labels: ETL

#88 - Fix duplicated NAACCR treatment modifiers.

Issue - State: closed - Opened by mgurley over 5 years ago
Labels: ETL

#87 - NAACCR Variable 1517 'Phase II Total Dose' has the wrong 'Has parent item' relationship.

Issue - State: closed - Opened by mgurley over 5 years ago
Labels: CDM/Vocabulary Subgroup, NAACCR, Fix

#87 - NAACCR Variable 1517 'Phase II Total Dose' has the wrong 'Has parent item' relationship.

Issue - State: closed - Opened by mgurley over 5 years ago
Labels: CDM/Vocabulary Subgroup, NAACCR, Fix

#86 - R survival analysis

Pull Request - State: closed - Opened by meerapatelmd over 5 years ago - 2 comments

#86 - R survival analysis

Pull Request - State: closed - Opened by meerapatelmd over 5 years ago - 2 comments

#85 - Some surgery NAACCR values might have been accidentally placed in the 'Observation' domain.

Issue - State: closed - Opened by mgurley over 5 years ago
Labels: CDM/Vocabulary Subgroup, NAACCR, Fix

#85 - Some surgery NAACCR values might have been accidentally placed in the 'Observation' domain.

Issue - State: closed - Opened by mgurley over 5 years ago
Labels: CDM/Vocabulary Subgroup, NAACCR, Fix

#84 - Ingest ICDO 3.2 into the OMOP vocabulary tables.

Issue - State: open - Opened by mgurley over 5 years ago - 14 comments
Labels: CDM/Vocabulary Subgroup, ICDO3

#83 - Add missing ICDO Site/Histology combinations.

Issue - State: open - Opened by mgurley over 5 years ago - 2 comments
Labels: CDM/Vocabulary Subgroup, ICDO3, Fix

#83 - Add missing ICDO Site/Histology combinations.

Issue - State: open - Opened by mgurley over 5 years ago - 2 comments
Labels: CDM/Vocabulary Subgroup, ICDO3, Fix

#82 - Missing NAACCR Variable 790 'EOD--EXTENSION'

Issue - State: closed - Opened by mgurley over 5 years ago - 1 comment
Labels: CDM/Vocabulary Subgroup, NAACCR, Fix

#82 - Missing NAACCR Variable 790 'EOD--EXTENSION'

Issue - State: closed - Opened by mgurley over 5 years ago - 1 comment
Labels: CDM/Vocabulary Subgroup, NAACCR, Fix

#81 - Some more NAACCR Variables missing NAACCR Values.

Issue - State: closed - Opened by mgurley over 5 years ago - 4 comments
Labels: CDM/Vocabulary Subgroup, NAACCR, Fix

#81 - Some more NAACCR Variables missing NAACCR Values.

Issue - State: closed - Opened by mgurley over 5 years ago - 4 comments
Labels: CDM/Vocabulary Subgroup, NAACCR, Fix

#80 - Do not insert non-standard concepts into MEASUREMENT.value_as_concept_id for Numeric concepts.

Issue - State: closed - Opened by mgurley over 5 years ago - 1 comment
Labels: ETL

#80 - Do not insert non-standard concepts into MEASUREMENT.value_as_concept_id for Numeric concepts.

Issue - State: closed - Opened by mgurley over 5 years ago - 1 comment
Labels: ETL

#79 - NAACCR Variable 1117 'METS AT DX-OTHER' is missing NAACCR Values

Issue - State: closed - Opened by mgurley over 5 years ago - 1 comment
Labels: CDM/Vocabulary Subgroup, NAACCR, Fix

#79 - NAACCR Variable 1117 'METS AT DX-OTHER' is missing NAACCR Values

Issue - State: closed - Opened by mgurley over 5 years ago - 1 comment
Labels: CDM/Vocabulary Subgroup, NAACCR, Fix

#78 - NAACCR Variable 1060 'TNM EDITION NUMBER' is missing NAACCR Values.

Issue - State: closed - Opened by mgurley over 5 years ago - 1 comment
Labels: CDM/Vocabulary Subgroup, NAACCR, Fix

#78 - NAACCR Variable 1060 'TNM EDITION NUMBER' is missing NAACCR Values.

Issue - State: closed - Opened by mgurley over 5 years ago - 1 comment
Labels: CDM/Vocabulary Subgroup, NAACCR, Fix

#77 - Filter out ambigous NAACCR schemas with ambigious site/histology combinations from the ETL logic.

Issue - State: closed - Opened by mgurley over 5 years ago
Labels: Symposium, ETL

#77 - Filter out ambigous NAACCR schemas with ambigious site/histology combinations from the ETL logic.

Issue - State: closed - Opened by mgurley over 5 years ago
Labels: Symposium, ETL

#76 - HemOnc regimens that are ambiguous

Issue - State: open - Opened by jeremywarner over 5 years ago
Labels: Hemonc.org, CDM/Vocabulary Subgroup, Fix

#76 - HemOnc regimens that are ambiguous

Issue - State: open - Opened by jeremywarner over 5 years ago
Labels: Hemonc.org, CDM/Vocabulary Subgroup, Fix

#75 - HemOnc regimens that have discrepancy between "Has antineopl Rx" and "Has antineoplastic"

Issue - State: open - Opened by jeremywarner over 5 years ago - 3 comments
Labels: Hemonc.org, CDM/Vocabulary Subgroup, Fix

#75 - HemOnc regimens that have discrepancy between "Has antineopl Rx" and "Has antineoplastic"

Issue - State: open - Opened by jeremywarner over 5 years ago - 3 comments
Labels: Hemonc.org, CDM/Vocabulary Subgroup, Fix

#74 - Populate EPISODE.episode_parent_id for 'Treatment Episode' entries in the EPISODE table.

Issue - State: closed - Opened by mgurley over 5 years ago - 1 comment
Labels: Symposium, ETL

#73 - Insert Treatment 'did not happen' concepts into the OBSERVATION table.

Issue - State: closed - Opened by mgurley over 5 years ago - 11 comments
Labels: NAACCR, Symposium, ETL, Development Subgroup

#72 - Insert NAACCR treatments into PROCEDURE_OCCURRENCE and DRUG_EXPOSURE as well as EPISODE.

Issue - State: closed - Opened by mgurley over 5 years ago - 1 comment
Labels: Symposium, ETL

#72 - Insert NAACCR treatments into PROCEDURE_OCCURRENCE and DRUG_EXPOSURE as well as EPISODE.

Issue - State: closed - Opened by mgurley over 5 years ago - 1 comment
Labels: Symposium, ETL

#71 - For NAACCR radiation therapy treatment variables, add a 'Variable has end date' relationship.

Issue - State: closed - Opened by mgurley over 5 years ago - 8 comments
Labels: CDM/Vocabulary Subgroup, NAACCR, Fix

#71 - For NAACCR radiation therapy treatment variables, add a 'Variable has end date' relationship.

Issue - State: closed - Opened by mgurley over 5 years ago - 8 comments
Labels: CDM/Vocabulary Subgroup, NAACCR, Fix

#70 - Disambiguate the Hemonc.org “OR” regimens into multiple regimens.

Issue - State: open - Opened by mgurley over 5 years ago - 3 comments
Labels: Hemonc.org, CDM/Vocabulary Subgroup, Symposium

#70 - Disambiguate the Hemonc.org “OR” regimens into multiple regimens.

Issue - State: open - Opened by mgurley over 5 years ago - 3 comments
Labels: Hemonc.org, CDM/Vocabulary Subgroup, Symposium

#69 - Create new 'Regimen' domain, move all the Hemonc.org regimens into the new domain, create entries in the new domain for NAACCR high-level drug concepts and non-standardize existing drug NAACCR item codes.

Issue - State: closed - Opened by mgurley over 5 years ago - 8 comments
Labels: CDM/Vocabulary Subgroup, Symposium

#69 - Create new 'Regimen' domain, move all the Hemonc.org regimens into the new domain, create entries in the new domain for NAACCR high-level drug concepts and non-standardize existing drug NAACCR item codes.

Issue - State: closed - Opened by mgurley over 5 years ago - 8 comments
Labels: CDM/Vocabulary Subgroup, Symposium

#68 - Move NAACCR Treatment 'did not happen' concepts into the Observation domain.

Issue - State: closed - Opened by mgurley over 5 years ago
Labels: CDM/Vocabulary Subgroup, NAACCR, Symposium

#68 - Move NAACCR Treatment 'did not happen' concepts into the Observation domain.

Issue - State: closed - Opened by mgurley over 5 years ago
Labels: CDM/Vocabulary Subgroup, NAACCR, Symposium

#67 - Create ICDO concept for 'Unknown Histology' and precoordinate with all ICDO sites.

Issue - State: closed - Opened by mgurley over 5 years ago - 18 comments
Labels: CDM/Vocabulary Subgroup, ICDO3, Fix

#67 - Create ICDO concept for 'Unknown Histology' and precoordinate with all ICDO sites.

Issue - State: closed - Opened by mgurley over 5 years ago - 18 comments
Labels: CDM/Vocabulary Subgroup, ICDO3, Fix

#66 - Add 'Metatdata' 'Table' and 'Field' entries for EPISODE and EPISODE_EVENT and new columns in MEASUREMENT.

Issue - State: closed - Opened by mgurley over 5 years ago - 14 comments
Labels: CDM/Vocabulary Subgroup, Symposium

#66 - Add 'Metatdata' 'Table' and 'Field' entries for EPISODE and EPISODE_EVENT and new columns in MEASUREMENT.

Issue - State: closed - Opened by mgurley over 5 years ago - 14 comments
Labels: CDM/Vocabulary Subgroup, Symposium

#65 - Make non-standard NAACCR treatment 'did not happen' concepts.

Issue - State: closed - Opened by mgurley over 5 years ago - 1 comment
Labels: CDM/Vocabulary Subgroup

#65 - Make non-standard NAACCR treatment 'did not happen' concepts.

Issue - State: closed - Opened by mgurley over 5 years ago - 1 comment
Labels: CDM/Vocabulary Subgroup

#64 - The 'NAACCR Proc Schema' entries do not have all the necessary relationships to ICDO codes via 'Proc Schema to ICDO'

Issue - State: closed - Opened by mgurley over 5 years ago - 3 comments
Labels: CDM/Vocabulary Subgroup, Symposium

#64 - The 'NAACCR Proc Schema' entries do not have all the necessary relationships to ICDO codes via 'Proc Schema to ICDO'

Issue - State: closed - Opened by mgurley over 5 years ago - 3 comments
Labels: CDM/Vocabulary Subgroup, Symposium

#63 - Make EPISODE.episode_end_datetime nullable.

Issue - State: closed - Opened by mgurley over 5 years ago - 2 comments

#63 - Make EPISODE.episode_end_datetime nullable.

Issue - State: closed - Opened by mgurley over 5 years ago - 2 comments

#62 - Add index on concept_id for CONCEPT_NUMERIC.

Issue - State: closed - Opened by mgurley over 5 years ago

#62 - Add index on concept_id for CONCEPT_NUMERIC.

Issue - State: closed - Opened by mgurley over 5 years ago

#61 - The concept_codes to Surgery NAACCR item codes use NAACCR schema concept_names instead of NAACCR schemaconcept_codes.

Issue - State: closed - Opened by mgurley over 5 years ago - 3 comments

#61 - The concept_codes to Surgery NAACCR item codes use NAACCR schema concept_names instead of NAACCR schemaconcept_codes.

Issue - State: closed - Opened by mgurley over 5 years ago - 3 comments

#60 - Fix missing leading zeros in the concept_codes for Treatment NAACCR item codes.

Issue - State: closed - Opened by mgurley over 5 years ago - 3 comments
Labels: CDM/Vocabulary Subgroup, Symposium

#60 - Fix missing leading zeros in the concept_codes for Treatment NAACCR item codes.

Issue - State: closed - Opened by mgurley over 5 years ago - 3 comments
Labels: CDM/Vocabulary Subgroup, Symposium

#59 - Create a mapping table to be used for handling ambiguous ICDO site/histology combinations present in multiple schemas.

Issue - State: closed - Opened by mgurley over 5 years ago - 1 comment
Labels: CDM/Vocabulary Subgroup, NAACCR, Fix

#59 - Create a mapping table to be used for handling ambiguous ICDO site/histology combinations present in multiple schemas.

Issue - State: closed - Opened by mgurley over 5 years ago - 1 comment
Labels: CDM/Vocabulary Subgroup, NAACCR, Fix

#58 - Note of presentation in implementing Oncology CDM in EHR based CDM

Pull Request - State: closed - Opened by neal1202 over 5 years ago

#58 - Note of presentation in implementing Oncology CDM in EHR based CDM

Pull Request - State: closed - Opened by neal1202 over 5 years ago

#57 - Udate DDL documentaiton to reflect decision to link 'Disease First Occurrence' and subsequent 'Disease Episode' entries via EPISODE.episode_parent_id.

Issue - State: closed - Opened by mgurley over 5 years ago - 1 comment

GitHub / ohdsi/oncologywg issues and pull requests