From 57a916e664954e45fb9bf80718100dfdb8e2921b Mon Sep 17 00:00:00 2001 From: Miller Date: Tue, 17 Oct 2023 23:18:02 -0400 Subject: [PATCH] docs continued... Remaining items: - Project Views - Project Walkthrough cleanup - Updated site map --- docs/background.html | 78 +++++++++-------- docs/development.html | 171 ++++++++++++++++++++++---------------- docs/gettingInvolved.html | 30 ++++++- docs/githubProject.html | 3 + docs/index.html | 22 ++--- docs/progressMap.html | 23 +++-- rmd/background.Rmd | 107 +++++++++++++----------- rmd/development.rmd | 114 +++++++++++++++---------- rmd/gettingInvolved.rmd | 16 +++- rmd/githubProject.rmd | 5 ++ rmd/index.Rmd | 1 - rmd/progressMap.rmd | 24 ++++-- 12 files changed, 360 insertions(+), 234 deletions(-) diff --git a/docs/background.html b/docs/background.html index dca86e0..bb6390e 100644 --- a/docs/background.html +++ b/docs/background.html @@ -464,72 +464,78 @@

Problem Space

-

Goals

+

Goals

The overarching goals of the OHDSI Oncology Working Group:


-

Oncology research

+

1) Oncology research

  • Enabling
    • +
  • Conducting
  • Promoting
    • -
  • Building +
+
+
+

2) Maturing oncology standards

    -
  • Innovation
    • -
  • A focused community
    • -
+
  • Data model, ontologies and conventions
    • +
  • A shared, international oncology data standard
    • +
  • Support of observational, claims and curated data sources
    • -
    -

    Harmonization

    +
    +

    3) Community growth

      -
    • Data standards
      • -
    • Ontologies
      • -
    • Community
      • -
    • Contributions
      • +
    • Model adoption and growth of network
      • +
    • Data holders, developers, and subject matter experts
      • +
    • Research use cases and applications
    -

    Transparency

    -
      -
    • Effort/ Processes
      • -
    • Documentation +

      4) Transparency

        -
      • Conventions
        • -
      • Approaches
        • -
      • -
    • Dynamic inventory of maturity effort
      • +
    • Clear processes and mechanisms for collaboration
      • +
    • Thorough documentation of conventions and approaches
      • +
    • Open-source development and project management


    -
    -

    Challenges

    +
    +

    Notable Challenges


    -
    -

    Data Variation

    -

    …in source data representations

    +
    +

    1) Oncology data in OMOP

      -
    • Goal of maximum accommodation +
    • OMOP typically a person-centric model
        -
      • while FAIR
        • -
      • Accelerating
        • -
      • Necessity of extensibility
        • +
      • Oncology data often requires additional levels of detail
        • +
      • e.g., “Observations about observations”
      • -
    • Curated & Observational data
      • +
    • Novel entity relationships in source data
    +


    -
    -

    Data Complexity

    +
    +

    2) Source data representations

      -
    • Representation in OMOP +
    • Differing granularity and detail between data sources
      • +
    • Goal of maximum accommodation while maintaing FAIR principles
      • +
    • Sources include observational, claims and curated data
        -
      • OMOP otherwise (exceptions?) person-centric model
        • -
      • Expanding level of detail
        • +
      • Sources often overlap and can provide complementary data for same +patient population
      • -
    • Novel entity relationships


    +
    +

    Condition Map

    +
    +Diagram illustrating condition modifier representation +
    +
    +


    diff --git a/docs/development.html b/docs/development.html index fbfebc3..261d122 100644 --- a/docs/development.html +++ b/docs/development.html @@ -425,113 +425,142 @@

    -
    -

    Overview

    -
    -

    Approach

    +
    +

    Purpose and Goals

    +


    +
    +

    “Collaboratively mature and expand the +representation of oncology data in OMOP by establishing +standard and transparent conventions”

    +
    +


    +

    Collaboration

      -
    • Estabishing “standard conventions” +
    • Encourage a diverse community to contribute towards global, +comprehensive standards
      • +
    • Leverage asynchronous mechanisms of collaboration for greater +international interoperability
      • +
    +

    Expand

      -
    • Adequately documented
      • -
    • Singular representation in OMOP
      • -
    • Favoring extensible over ad hoc solutions
      • -
    +
  • Create and expand conventions to accommodate the various +representations of oncology data in the OHDSI community
    • +
  • Supporting both observational and curated data sources
    • +
  • Source EMR and nation agnostic
    • -
    -
    -

    Goals

    +

    Standard

    +
      +
    • Unambiguous, standardized conventions
      • +
    • For a specific type of source data, there is a single standard +representation for it
      • +
    +

    Transparent

      -
    • Collaboratively mature the oncology standards in OMOP
      • -
    • Enable asynchronous mechanisms of collaboration for greater -international interoperability
      • -
    • Establish conventions that apply to the various representations of -oncology data
    • Thoroughly document all conventions from both an ETL and analysis -perspective to facilitate standardized representation
      • +perspective to facilitate standardized adoption and +interoperability +
    • Clearly and publicly describe the processes and outcomes of this +effort
    +


    +
    -
    -

    Scope / Timeline

    +
    +

    Context

    • An extensive and international outreach effort has been conducted to aggregate the gaps and pain points of implementing oncology data in -OMOP, which is the starting point of this project
      • -
    • Complete as much as we can, prioritized by use cases, in preparation -for a new stable release at the beginning of 2024. After that milestone -is reached, we will continue to iterate and improve while adhering to a -stable release schedule TBD.
      -
      • -
    • The majority of the outlined work is either investigating or -modifying the vocabularies. These have been and/or will be broken down -into smaller more easily tackled chunks such as “investigating an issue” -or “complete outstanding vocabulary changes that have content provided”, -or “documentation of _”. This is to help enable lots of small -contributions from a larger community.
      • +OMOP, which is the starting point of this project. All of that feedback +has been ingested and organized within a Github Project. That said, we +know what we know now but that list is always expanding, for the +better.
    • We are moving at a faster pace than the official OHDSI vocabulary releases and consequently will be maintaining a “delta”, or “development”, version of the vocabularies. At the end of this effort we plan to have these changes folded back into the standards. Additionally we will consult with the vocabulary team when applicable.
      • +
    • A global oncology standard cannot be static. It must be iteratively +expanding and maturing and requires an active community and extensible +solutions.
    +


    +
    -
    -

    Core Values

    +
    +

    Scope

      -
    • Enabling studies as determining factor for prioritization of -effort
      • -
    • Inclusion of as diverse of data as possible +
    • The majority of the outlined work is either falls into one of four +buckets: +
        +
      1. Deciding on a convention
        2. +
      2. Investigating vocabularies
        3. +
      3. Modifying the vocabularies
        4. +
      4. Creating documentation
        5. +
      • +
    • The tasks have been broken down into smaller more easily tackled +chunks such as “investigating an issue” or “complete outstanding +vocabulary changes that have content provided”, or “documentation of _”. +The intent is to enable many small contributions rather than few large +ones.
      • +
    • The plan is to complete as much as we can, prioritized by use cases, +in preparation for a new stable release. After that milestone is +reached, we will continue to iterate and improve while adhering to a +stable release schedule.
      • +
    +


    +
    +
    +
    +

    What we need

      -
    • International applicability
      • -
    • Clinical, registry, and other specialized data sources
      • -
    • Source EMR agnostic
      • +
    • Diverse community feedback +
        +
      • Feedback on decision points - Will this solution work for your +data?
        • +
      • Any experienced issues, hurdles or ambiguities
        • +
      • Use cases, studies, ambitions
      • -
    • Enabling interoperability and standardized analytics +
    • Community contributions +
        +
      • Vocabulary:
          -
        • Non-ambiguous, Standardized representation within OMOP; For a -specific type of source data, there is a single standard representation -for it
          • -
        • Improving and sometimes inventing new vocabulary relation mechanisms -to enable reliable and reusable phenotyping and analysis
          • -
        • Encourage a diverse community to contribute towards a universal -representation
          • +
        • Investigations - e.g., are there duplicate standard concepts for +laterality?
          +
          • +
        • Modifications - e.g., provide the modifications to +de-standardize duplicate laterality concepts
        • -
      -
    -
    -

    What we need

    +
  • Documentation
      -
    • Diverse community contribution
      • -
    • Feedback on decision points from oncology data holders and SME
      • -
    • Experienced issues & hurdles
      • -
    • Use cases
      • -
    • Development/vocabulary effort
      • +
    • Identifying gaps
      • +
    • Populating content
      • +
    • + +


    -

    Project Management

    -
    -

    Collaborative approach

      -
    • Everyone is welcome and encouraged to join the effort
      • -
    • To enable international contributions and rapid progress, we are -facilitating communication both within meetings and asynchronously -through Github and Teams. Any decision points discussed during the calls -will also be represented in Teams for further discussion before final -decisions are made
      • +
    • Enabling studies is the primary determining factor for +prioritization of effort
    • The Github Project will be the main resource for tracking the project deliverables, progress, and avenues for contribution
      • -
    • Discussions around items will be held off-line within MS Teams -environment
      • +
    • To enable international contributions and rapid progress, we are +facilitating communication both within meetings and asynchronously +through Github and the OHDSI Oncology MS Teams. Any decision points +discussed during the calls will also be represented in Github/Teams for +further discussion before final decisions are made
    -
    +


    +

    Github Project

      -
    • While discussions will be had in Teams, the project will be tracked -and managed through Github.
      • +
    • This development effort will be tracked and managed through +Github.
    • The link to the project can be found here: https://github.com/orgs/OHDSI/projects/13
      • diff --git a/docs/gettingInvolved.html b/docs/gettingInvolved.html index dccea9c..8d27b6c 100644 --- a/docs/gettingInvolved.html +++ b/docs/gettingInvolved.html @@ -490,9 +490,33 @@

      Review Project Documentation


    -
    -

    Onboarding Form

    -

    (TODO)

    +
    +

    Contributing

    +
      +

    1. Submitting use cases, questions, documentation gaps, etc.:

      +
        +
      • (preferred) Submit an issue on the OncologyWG repository +
          +
        • Ticket will be triaged accordingly
          • +
        • +
      • (alternate) If Github is a barrier, send a message in the OHDSI +Oncology WG MS Teams channel +
          +
        • If applicable, someone will create a ticket for you
          • +
        • +
      2. +
    +


    +
      +

    1. Volunteering to contribute to a specific task

      +
        +
      • If you are already a contributor to the OncologyWG Github +repository, assign yourself to that ticket
        • +
      • Otherwise, make a comment on the Github ticket for that task stating +your intent and you will be invited to the repository and assigned +accordingly
        • +
      2. +
    diff --git a/docs/githubProject.html b/docs/githubProject.html index f69aaea..d78a2ec 100644 --- a/docs/githubProject.html +++ b/docs/githubProject.html @@ -635,6 +635,9 @@

    Complete outstanding work

    Validate and ingest

    +

    // https://github.com/OHDSI/OncologyWG/tree/master/vocabTools#tools-used-to-assist-with-developing-omop-vocabulary

    You will need the vocabTools directory and its contents downloaded to your computer to make use of the tools in the following steps. The easiest way to download vocabTools (and subsequently push Oncology diff --git a/docs/index.html b/docs/index.html index f07de39..909749d 100644 --- a/docs/index.html +++ b/docs/index.html @@ -534,50 +534,46 @@

    Site Map

    -Prioritization -Overview of current development effort - - Miro Map Overview of current development effort - + Roadmap Overview of current development effort - + Github Project Orientation - + Approach Overview of current development effort - + Architecture Overview of current development effort - + Project Views Overview of current development effort - + Example Walkthrough Overview of current development effort - + Getting Involved - + Collaboration Channels Overview of current development effort - + Review Project Documentation Overview of current development effort diff --git a/docs/progressMap.html b/docs/progressMap.html index ccfc56e..04607cf 100644 --- a/docs/progressMap.html +++ b/docs/progressMap.html @@ -427,20 +427,29 @@


    -
    -

    Prioritization

    -

    (TODO)

    -

    Miro Map

    +

    The Miro Map below is an alternate way to view the progress of the +development effort at the task group level.

    +
      +
    • Green indicates the task group is +complete and should contain a link to the +documentation
      • +
    • Orange indicates the task group is still in +progress and should contain a link to the Github +ticket
      • +
    +


    -

    TODO: Explanation of intent and links

    +


    +

    Roadmap

    -

    Our goal is to create an interoperable OMOP extension that enables -application of all OMOP analysis tools to rich oncology data.

    +

    Our goal is to create an comprehensive, interoperable representation +for oncology data in OMOP and consequently leverage the full suite of +OMOP analysis tools.

    For more information see:

    • Development Effort documentation
      • diff --git a/rmd/background.Rmd b/rmd/background.Rmd index 5ae26b4..e4106dd 100644 --- a/rmd/background.Rmd +++ b/rmd/background.Rmd @@ -10,89 +10,98 @@ output:
      - # **Problem Space** In a typical observational study, the definition of the study population (cohort), exposures and outcomes are usually based on diagnostic codes in addition to drug exposures, procedure occurrences or lab measurements. For cancer studies, this information is typically not sufficient, as more details are required for the proper identification of the study population, treatment and subsequent outcomes. -Appropriate characterization of cancer requires details such as anatomical site, morphology, local penetration, affected lymph nodes, metastatic spread, biomarkers, and disease staging and grading. In typical observational data sources, this necessary level of detail is not regularly present. Patient results from diagnostic procedures are collected but may not be available within the given data source or what is collected cannot appropriately serve as a surrogate for the above attributes. Correct identification of cancer treatment regimens also tends to be more complex compared to other disease modalities within observational data. Most cancer treatments are administered in chemotherapy regimens with complex dosing and scheduling in multiple cycles and are often combined with targeted therapies, immunotherapies, surgery or radiotherapy. None of these attributes follow standard definition to be applied to observational data, as most regimens are personalized to the individual patient need, making a priori standardized definitions more complex. Additionally, clinically relevant information on disease, treatment and outcomes that appropriately reflects a patient’s journey including information on the time of diagnosis, response to treatments, time to treatment failure, disease progression, recurrence and (disease-free and overall) survival requires data abstraction and is rarely available in the source data and has not been traditionally supported in OMOP CDM. +Appropriate characterization of cancer requires details such as anatomical site, morphology, local penetration, affected lymph nodes, metastatic spread, biomarkers, and disease staging and grading. In typical observational data sources, this necessary level of detail is not regularly present. Patient results from diagnostic procedures are collected but may not be available within the given data source or what is collected cannot appropriately serve as a surrogate for the above attributes. Correct identification of cancer treatment regimens also tends to be more complex compared to other disease modalities within observational data. Most cancer treatments are administered in chemotherapy regimens with complex dosing and scheduling in multiple cycles and are often combined with targeted therapies, immunotherapies, surgery or radiotherapy. None of these attributes follow standard definition to be applied to observational data, as most regimens are personalized to the individual patient need, making a priori standardized definitions more complex. Additionally, clinically relevant information on disease, treatment and outcomes that appropriately reflects a patient's journey including information on the time of diagnosis, response to treatments, time to treatment failure, disease progression, recurrence and (disease-free and overall) survival requires data abstraction and is rarely available in the source data and has not been traditionally supported in OMOP CDM. The Oncology CDM Extension of the OMOP CDM aims to provide a foundation for representing cancer data at the levels of granularity and abstraction required to support observational cancer research. The extension has been tested in EHR and Cancer Registry data against a number of typical use cases. ---- +------------------------------------------------------------------------ -# Goals +# **Goals** The overarching goals of the OHDSI Oncology Working Group: -
      +
      + +### 1) Oncology research + +- Enabling +- Conducting +- Promoting -### **Oncology research** - - - Enabling - - Promoting - - Building - - Innovation - - A focused community - - -### **Harmonization ** - - - Data standards - - Ontologies - - Community - - Contributions - -### **Transparency** - - Effort/ Processes - - Documentation - - Conventions - - Approaches - - Dynamic inventory of maturity effort +### 2) Maturing oncology standards + +- Data model, ontologies and conventions +- A shared, international oncology data standard +- Support of observational, claims and curated data sources + +### 3) Community growth + +- Model adoption and growth of network +- Data holders, developers, and subject matter experts +- Research use cases and applications + +### 4) Transparency + +- Clear processes and mechanisms for collaboration +- Thorough documentation of conventions and approaches +- Open-source development and project management
      ---- +------------------------------------------------------------------------ + +# **Notable Challenges** + +
      + +### 1) Oncology data in OMOP + +- OMOP typically a person-centric model + - Oncology data often requires additional levels of detail + - e.g., "Observations about observations" +- Novel entity relationships in source data - -# Challenges
      -### **Data Variation** -...in source data representations - - Goal of maximum accommodation - - while FAIR - - Accelerating - - Necessity of extensibility - - Curated & Observational data - -### **Data Complexity** +### 2) Source data representations + +- Differing granularity and detail between data sources +- Goal of maximum accommodation while maintaing FAIR principles +- Sources include observational, claims and curated data + - Sources often overlap and can provide complementary data for same patient population +
      + + +
      - - Representation in OMOP - - OMOP otherwise (exceptions?) person-centric model - - Expanding level of detail - - Novel entity relationships +Condition Map +
      Diagram illustrating condition modifier representation
      + +

      ---- +------------------------------------------------------------------------ # **Publications/Presentation** -- [2020 OHDSI Symposium - Oncology Tutorial](https://github.com/OHDSI/OncologyWG/wiki/Oncology-Tutorial) +- [2020 OHDSI Symposium - Oncology Tutorial](https://github.com/OHDSI/OncologyWG/wiki/Oncology-Tutorial) -- [2020 OHDSI Symposium - Genomic Variant Harmonization Poster Presentation](https://github.com/OHDSI/OncologyWG/wiki/Genomic-Variant-Harmonization) +- [2020 OHDSI Symposium - Genomic Variant Harmonization Poster Presentation](https://github.com/OHDSI/OncologyWG/wiki/Genomic-Variant-Harmonization) -- [Bladder Cancer Study](https://github.com/OHDSI/OncologyWG/wiki/Bladder-Cancer-Study) +- [Bladder Cancer Study](https://github.com/OHDSI/OncologyWG/wiki/Bladder-Cancer-Study) -- [JCO Clinical Cancer Informatics](https://ascopubs.org/doi/10.1200/CCI.20.00079) +- [JCO Clinical Cancer Informatics](https://ascopubs.org/doi/10.1200/CCI.20.00079)
      - diff --git a/rmd/development.rmd b/rmd/development.rmd index 2fb0ae8..1257113 100644 --- a/rmd/development.rmd +++ b/rmd/development.rmd @@ -8,76 +8,104 @@ output: collapsed: false --- -# **Overview** - --- -## Approach +# **Purpose and Goals** + +
      - - Estabishing "standard conventions" - - Adequately documented - - Singular representation in OMOP - - Favoring extensible over ad hoc solutions +> **"Collaboratively mature and expand the representation of oncology data in OMOP by establishing standard and transparent conventions"** -## Goals +
      - - Collaboratively mature the oncology standards in OMOP - - Enable asynchronous mechanisms of collaboration for greater international interoperability - - Establish conventions that apply to the various representations of oncology data - - Thoroughly document all conventions from both an ETL and analysis perspective to facilitate standardized representation +**Collaboration** + - Encourage a diverse community to contribute towards global, comprehensive standards + - Leverage asynchronous mechanisms of collaboration for greater international interoperability -## Scope / Timeline - - An extensive and international outreach effort has been conducted to aggregate the gaps and pain points of implementing oncology data in OMOP, which is the starting point of this project - - Complete as much as we can, prioritized by use cases, in preparation for a new stable release at the beginning of 2024. After that milestone is reached, we will continue to iterate and improve while adhering to a stable release schedule TBD. - - The majority of the outlined work is either investigating or modifying the vocabularies. These have been and/or will be broken down into smaller more easily tackled chunks such as “investigating an issue” or “complete outstanding vocabulary changes that have content provided”, or “documentation of _”. This is to help enable lots of small contributions from a larger community. - - We are moving at a faster pace than the official OHDSI vocabulary releases and consequently will be maintaining a “delta”, or “development”, version of the vocabularies. At the end of this effort we plan to have these changes folded back into the standards. Additionally we will consult with the vocabulary team when applicable. -## Core Values +**Expand** + - Create and expand conventions to accommodate the various representations of oncology data in the OHDSI community + - Supporting both observational and curated data sources + - Source EMR and nation agnostic + +**Standard** - - Enabling studies as determining factor for prioritization of effort - - Inclusion of as diverse of data as possible - - International applicability - - Clinical, registry, and other specialized data sources - - Source EMR agnostic - - Enabling interoperability and standardized analytics - - Non-ambiguous, Standardized representation within OMOP; For a specific type of source data, there is a single standard representation for it - - Improving and sometimes inventing new vocabulary relation mechanisms to enable reliable and reusable phenotyping and analysis - - Encourage a diverse community to contribute towards a universal representation + - Unambiguous, standardized conventions + - For a specific type of source data, there is a single standard representation for it -## What we need +**Transparent** - - Diverse community contribution - - Feedback on decision points from oncology data holders and SME - - Experienced issues & hurdles - - Use cases - - Development/vocabulary effort + - Thoroughly document all conventions from both an ETL and analysis perspective to facilitate standardized adoption and interoperability + - Clearly and publicly describe the processes and outcomes of this effort +
      --- -# **Project Management** +# **Context** + - An extensive and international outreach effort has been conducted to aggregate the gaps and pain points of implementing oncology data in OMOP, which is the starting point of this project. All of that feedback has been ingested and organized within a Github Project. That said, we know what we know now but that list is always expanding, for the better. + - We are moving at a faster pace than the official OHDSI vocabulary releases and consequently will be maintaining a “delta”, or “development”, version of the vocabularies. At the end of this effort we plan to have these changes folded back into the standards. Additionally we will consult with the vocabulary team when applicable. + - A global oncology standard cannot be static. It must be iteratively expanding and maturing and requires an active community and extensible solutions. + +
      +--- + +# **Scope** -## Collaborative approach + - The majority of the outlined work is either falls into one of four buckets: + 1) Deciding on a convention + 2) Investigating vocabularies + 3) Modifying the vocabularies + 4) Creating documentation + - The tasks have been broken down into smaller more easily tackled chunks such as “investigating an issue” or “complete outstanding vocabulary changes that have content provided”, or “documentation of _”. The intent is to enable many small contributions rather than few large ones. + - The plan is to complete as much as we can, prioritized by use cases, in preparation for a new stable release. After that milestone is reached, we will continue to iterate and improve while adhering to a stable release schedule. - - Everyone is welcome and encouraged to join the effort - - To enable international contributions and rapid progress, we are facilitating communication both within meetings and asynchronously through Github and Teams. Any decision points discussed during the calls will also be represented in Teams for further discussion before final decisions are made - - The Github Project will be the main resource for tracking the project deliverables, progress, and avenues for contribution - - Discussions around items will be held off-line within MS Teams environment +
      + +--- + + +# **What we need** + + - Diverse community feedback + - Feedback on decision points - *Will this solution work for your data?* + - Any experienced issues, hurdles or ambiguities + - Use cases, studies, ambitions + - Community contributions + - Vocabulary: + - Investigations - *e.g., are there duplicate standard concepts for laterality?* + - Modifications - *e.g., provide the modifications to de-standardize duplicate laterality concepts* + - Documentation + - Identifying gaps + - Populating content +
      +--- + + +# **Project Management** + + - Enabling studies is the primary determining factor for prioritization of effort + - The Github Project will be the main resource for tracking the project deliverables, progress, and avenues for contribution + - To enable international contributions and rapid progress, we are facilitating communication both within meetings and asynchronously through Github and the OHDSI Oncology MS Teams. Any decision points discussed during the calls will also be represented in Github/Teams for further discussion before final decisions are made + +
      + +--- ## Github Project - - While discussions will be had in Teams, the project will be tracked and managed through Github. - - The link to the project can be found here: https://github.com/orgs/OHDSI/projects/13 - - Please review the Github Project Orientation materials: [Github Project Documentation](githubProject.html) - - To learn how to best get involved, please also visit: [Getting Involved](gettingInvolved.html) +- This development effort will be tracked and managed through Github. +- The link to the project can be found here: +- Please review the Github Project Orientation materials: [Github Project Documentation](githubProject.html) +- To learn how to best get involved, please also visit: [Getting Involved](gettingInvolved.html) diff --git a/rmd/gettingInvolved.rmd b/rmd/gettingInvolved.rmd index 726497e..902698c 100644 --- a/rmd/gettingInvolved.rmd +++ b/rmd/gettingInvolved.rmd @@ -49,6 +49,18 @@ And the Github 'Project' where we manage our work can be found here: https://git --- -# **Onboarding Form** +# **Contributing** -(TODO) \ No newline at end of file +1) Submitting use cases, questions, documentation gaps, etc.: + + - (preferred) Submit an issue on the OncologyWG repository + - Ticket will be triaged accordingly + - (alternate) If Github is a barrier, send a message in the OHDSI Oncology WG MS Teams channel + - If applicable, someone will create a ticket for you + +
      + +2) Volunteering to contribute to a specific task + + - If you are already a contributor to the OncologyWG Github repository, assign yourself to that ticket + - Otherwise, make a comment on the Github ticket for that task stating your intent and you will be invited to the repository and assigned accordingly \ No newline at end of file diff --git a/rmd/githubProject.rmd b/rmd/githubProject.rmd index f0b3dee..8a8a0ef 100644 --- a/rmd/githubProject.rmd +++ b/rmd/githubProject.rmd @@ -138,6 +138,9 @@ Closing the tickets will automatically check the boxes in the Task issue. Once a ### Validate and ingest +// https://github.com/OHDSI/OncologyWG/tree/master/vocabTools#tools-used-to-assist-with-developing-omop-vocabulary + + You will need the vocabTools directory and its contents downloaded to your computer to make use of the tools in the following steps. The easiest way to download vocabTools (and subsequently push Oncology Development Vocabulary changes back to GitHub) is by cloning the OncologyWG: `git clone https://github.com/OHDSI/OncologyWG.git` @@ -150,6 +153,8 @@ After your database is set up with a prod and a dev schema, update the config.tx #### Validate + + In the last task, you created concept and concept_relationship table fragments to complete the vocabulary work orders. In this step, we will validate these locally by integrating them into the dev schema of the database we have set up and comparing the augmented dev schema and prod schema. First, move all of the concept_*.csv and concept_relationship_*.csv files to the concept and concept_relationship directories in your local copy of vocabTools: diff --git a/rmd/index.Rmd b/rmd/index.Rmd index b0aa7d5..7891fdc 100644 --- a/rmd/index.Rmd +++ b/rmd/index.Rmd @@ -57,7 +57,6 @@ This site contains the following sections: | **[Development Overview](development.html)** | Overview of current development effort | | [Project Management](development.html#Project_Management) | Overview of current development effort | | **[Progress](progressMap.html)** | | -| [Prioritization](progressMap.html#Prioritization) | Overview of current development effort | | [Miro Map](progressMap.html#Miro_Map) | Overview of current development effort | | [Roadmap](progressMap.html#Roadmap) | Overview of current development effort | | **[Github Project Orientation](githubProject.html)** | | diff --git a/rmd/progressMap.rmd b/rmd/progressMap.rmd index 315afe5..05243a4 100644 --- a/rmd/progressMap.rmd +++ b/rmd/progressMap.rmd @@ -10,26 +10,32 @@ output:
      ---- +------------------------------------------------------------------------ -# **Prioritization** +# **Miro Map** - (TODO) +The Miro Map below is an alternate way to view the progress of the development effort at the task group level. +- **Green** indicates the task group is **complete** and should contain **a link to the documentation** +- **Orange** indicates the task group is still **in progress** and should contain **a link to the Github ticket** +
      -# **Miro Map** + + -TODO: Explanation of intent and links +
      + + +--- # **Roadmap** -Our goal is to create an interoperable OMOP extension that enables application of all OMOP analysis tools to rich oncology data. +Our goal is to create an comprehensive, interoperable representation for oncology data in OMOP and consequently leverage the full suite of OMOP analysis tools. For more information see: - - [Development Effort documentation](development.html) - - and [OHDSI Github - Oncology Release 2.0 Project](https://github.com/orgs/OHDSI/projects/13) +- [Development Effort documentation](development.html) +- and [OHDSI Github - Oncology Release 2.0 Project](https://github.com/orgs/OHDSI/projects/13)