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rtmill committed Oct 18, 2023
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78 changes: 42 additions & 36 deletions docs/background.html
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Expand Up @@ -464,72 +464,78 @@ <h1><strong>Problem Space</strong></h1>
<hr />
</div>
<div id="goals" class="section level1">
<h1>Goals</h1>
<h1><strong>Goals</strong></h1>
<p>The overarching goals of the OHDSI Oncology Working Group:</p>
<p><br></p>
<div id="oncology-research" class="section level3">
<h3><strong>Oncology research</strong></h3>
<h3>1) Oncology research</h3>
<ul>
<li>Enabling</li>
<li>Conducting</li>
<li>Promoting</li>
<li>Building
</ul>
</div>
<div id="maturing-oncology-standards" class="section level3">
<h3>2) Maturing oncology standards</h3>
<ul>
<li>Innovation</li>
<li>A focused community</li>
</ul></li>
<li>Data model, ontologies and conventions</li>
<li>A shared, international oncology data standard</li>
<li>Support of observational, claims and curated data sources</li>
</ul>
</div>
<div id="harmonization" class="section level3">
<h3><strong>Harmonization </strong></h3>
<div id="community-growth" class="section level3">
<h3>3) Community growth</h3>
<ul>
<li>Data standards</li>
<li>Ontologies</li>
<li>Community</li>
<li>Contributions</li>
<li>Model adoption and growth of network</li>
<li>Data holders, developers, and subject matter experts</li>
<li>Research use cases and applications</li>
</ul>
</div>
<div id="transparency" class="section level3">
<h3><strong>Transparency</strong></h3>
<ul>
<li>Effort/ Processes</li>
<li>Documentation
<h3>4) Transparency</h3>
<ul>
<li>Conventions</li>
<li>Approaches</li>
</ul></li>
<li>Dynamic inventory of maturity effort</li>
<li>Clear processes and mechanisms for collaboration</li>
<li>Thorough documentation of conventions and approaches</li>
<li>Open-source development and project management</li>
</ul>
<p><br></p>
<hr />
</div>
</div>
<div id="challenges" class="section level1">
<h1>Challenges</h1>
<div id="notable-challenges" class="section level1">
<h1><strong>Notable Challenges</strong></h1>
<p><br></p>
<div id="data-variation" class="section level3">
<h3><strong>Data Variation</strong></h3>
<p>…in source data representations</p>
<div id="oncology-data-in-omop" class="section level3">
<h3>1) Oncology data in OMOP</h3>
<ul>
<li>Goal of maximum accommodation
<li>OMOP typically a person-centric model
<ul>
<li>while FAIR</li>
<li>Accelerating</li>
<li>Necessity of extensibility</li>
<li>Oncology data often requires additional levels of detail</li>
<li>e.g., “Observations about observations”</li>
</ul></li>
<li>Curated &amp; Observational data</li>
<li>Novel entity relationships in source data</li>
</ul>
<p><br></p>
</div>
<div id="data-complexity" class="section level3">
<h3><strong>Data Complexity</strong></h3>
<div id="source-data-representations" class="section level3">
<h3>2) Source data representations</h3>
<ul>
<li>Representation in OMOP
<li>Differing granularity and detail between data sources</li>
<li>Goal of maximum accommodation while maintaing FAIR principles</li>
<li>Sources include observational, claims and curated data
<ul>
<li>OMOP otherwise (exceptions?) person-centric model</li>
<li>Expanding level of detail</li>
<li>Sources often overlap and can provide complementary data for same
patient population</li>
</ul></li>
<li>Novel entity relationships</li>
</ul>
<p><br></p>
<figure>
<p><img src="https://user-images.githubusercontent.com/57408355/76053847-9c1c5380-5f3c-11ea-8ac2-4efbcc4ee66e.png" alt="Condition Map"/></p>
<figcaption>
Diagram illustrating condition modifier representation
</figcaption>
</figure>
<p><br></p>
<hr />
</div>
</div>
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171 changes: 100 additions & 71 deletions docs/development.html
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Expand Up @@ -425,113 +425,142 @@ <h1 class="title toc-ignore"><img src="images/ohdsi40x40.png"></img>
</div>


<div id="overview" class="section level1">
<h1><strong>Overview</strong></h1>
<hr />
<div id="approach" class="section level2">
<h2>Approach</h2>
<div id="purpose-and-goals" class="section level1">
<h1><strong>Purpose and Goals</strong></h1>
<p><br></p>
<blockquote>
<p><strong>“<ins>Collaboratively</ins> mature and <ins>expand</ins> the
representation of oncology data in OMOP by establishing
<ins>standard</ins> and <ins>transparent</ins> conventions”</strong></p>
</blockquote>
<p><br></p>
<p><strong>Collaboration</strong></p>
<ul>
<li>Estabishing “standard conventions”
<li>Encourage a diverse community to contribute towards global,
comprehensive standards</li>
<li>Leverage asynchronous mechanisms of collaboration for greater
international interoperability</li>
</ul>
<p><strong>Expand</strong></p>
<ul>
<li>Adequately documented</li>
<li>Singular representation in OMOP</li>
<li>Favoring extensible over ad hoc solutions</li>
</ul></li>
<li>Create and expand conventions to accommodate the various
representations of oncology data in the OHDSI community</li>
<li>Supporting both observational and curated data sources</li>
<li>Source EMR and nation agnostic</li>
</ul>
</div>
<div id="goals" class="section level2">
<h2>Goals</h2>
<p><strong>Standard</strong></p>
<ul>
<li>Unambiguous, standardized conventions</li>
<li>For a specific type of source data, there is a single standard
representation for it</li>
</ul>
<p><strong>Transparent</strong></p>
<ul>
<li>Collaboratively mature the oncology standards in OMOP</li>
<li>Enable asynchronous mechanisms of collaboration for greater
international interoperability</li>
<li>Establish conventions that apply to the various representations of
oncology data</li>
<li>Thoroughly document all conventions from both an ETL and analysis
perspective to facilitate standardized representation</li>
perspective to facilitate standardized adoption and
interoperability</li>
<li>Clearly and publicly describe the processes and outcomes of this
effort</li>
</ul>
<p><br></p>
<hr />
</div>
<div id="scope-timeline" class="section level2">
<h2>Scope / Timeline</h2>
<div id="context" class="section level1">
<h1><strong>Context</strong></h1>
<ul>
<li>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</li>
<li>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.<br />
</li>
<li>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.</li>
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.</li>
<li>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.</li>
<li>A global oncology standard cannot be static. It must be iteratively
expanding and maturing and requires an active community and extensible
solutions.</li>
</ul>
<p><br></p>
<hr />
</div>
<div id="core-values" class="section level2">
<h2>Core Values</h2>
<div id="scope" class="section level1">
<h1><strong>Scope</strong></h1>
<ul>
<li>Enabling studies as determining factor for prioritization of
effort</li>
<li>Inclusion of as diverse of data as possible
<li>The majority of the outlined work is either falls into one of four
buckets:
<ol style="list-style-type: decimal">
<li>Deciding on a convention</li>
<li>Investigating vocabularies</li>
<li>Modifying the vocabularies</li>
<li>Creating documentation</li>
</ol></li>
<li>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.</li>
<li>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.</li>
</ul>
<p><br></p>
<hr />
</div>
<div id="what-we-need" class="section level1">
<h1><strong>What we need</strong></h1>
<ul>
<li>International applicability</li>
<li>Clinical, registry, and other specialized data sources</li>
<li>Source EMR agnostic</li>
<li>Diverse community feedback
<ul>
<li>Feedback on decision points - <em>Will this solution work for your
data?</em></li>
<li>Any experienced issues, hurdles or ambiguities</li>
<li>Use cases, studies, ambitions</li>
</ul></li>
<li>Enabling interoperability and standardized analytics
<li>Community contributions
<ul>
<li>Vocabulary:
<ul>
<li>Non-ambiguous, Standardized representation within OMOP; For a
specific type of source data, there is a single standard representation
for it</li>
<li>Improving and sometimes inventing new vocabulary relation mechanisms
to enable reliable and reusable phenotyping and analysis</li>
<li>Encourage a diverse community to contribute towards a universal
representation</li>
<li>Investigations - <em>e.g., are there duplicate standard concepts for
laterality?</em><br />
</li>
<li>Modifications - <em>e.g., provide the modifications to
de-standardize duplicate laterality concepts</em></li>
</ul></li>
</ul>
</div>
<div id="what-we-need" class="section level2">
<h2>What we need</h2>
<li>Documentation
<ul>
<li>Diverse community contribution</li>
<li>Feedback on decision points from oncology data holders and SME</li>
<li>Experienced issues &amp; hurdles</li>
<li>Use cases</li>
<li>Development/vocabulary effort</li>
<li>Identifying gaps</li>
<li>Populating content</li>
</ul></li>
</ul></li>
</ul>
<p><br></p>
<hr />
</div>
</div>
<div id="project-management" class="section level1">
<h1><strong>Project Management</strong></h1>
<div id="collaborative-approach" class="section level2">
<h2>Collaborative approach</h2>
<ul>
<li>Everyone is welcome and encouraged to join the effort</li>
<li>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</li>
<li>Enabling studies is the primary determining factor for
prioritization of effort</li>
<li>The Github Project will be the main resource for tracking the
project deliverables, progress, and avenues for contribution</li>
<li>Discussions around items will be held off-line within MS Teams
environment</li>
<li>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</li>
</ul>
</div>
<p><br></p>
<hr />
<div id="github-project" class="section level2">
<h2>Github Project</h2>
<ul>
<li>While discussions will be had in Teams, the project will be tracked
and managed through Github.</li>
<li>This development effort will be tracked and managed through
Github.</li>
<li>The link to the project can be found here: <a
href="https://github.com/orgs/OHDSI/projects/13"
class="uri">https://github.com/orgs/OHDSI/projects/13</a></li>
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30 changes: 27 additions & 3 deletions docs/gettingInvolved.html
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Expand Up @@ -490,9 +490,33 @@ <h1><strong>Review Project Documentation</strong></h1>
<p><br></p>
<hr />
</div>
<div id="onboarding-form" class="section level1">
<h1><strong>Onboarding Form</strong></h1>
<p>(TODO)</p>
<div id="contributing" class="section level1">
<h1><strong>Contributing</strong></h1>
<ol style="list-style-type: decimal">
<li><p>Submitting use cases, questions, documentation gaps, etc.:</p>
<ul>
<li>(preferred) Submit an issue on the OncologyWG repository
<ul>
<li>Ticket will be triaged accordingly</li>
</ul></li>
<li>(alternate) If Github is a barrier, send a message in the OHDSI
Oncology WG MS Teams channel
<ul>
<li>If applicable, someone will create a ticket for you</li>
</ul></li>
</ul></li>
</ol>
<p><br></p>
<ol start="2" style="list-style-type: decimal">
<li><p>Volunteering to contribute to a specific task</p>
<ul>
<li>If you are already a contributor to the OncologyWG Github
repository, assign yourself to that ticket</li>
<li>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</li>
</ul></li>
</ol>
</div>


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3 changes: 3 additions & 0 deletions docs/githubProject.html
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Expand Up @@ -635,6 +635,9 @@ <h3>Complete outstanding work</h3>
</div>
<div id="validate-and-ingest" class="section level3">
<h3>Validate and ingest</h3>
<p>// <a
href="https://github.com/OHDSI/OncologyWG/tree/master/vocabTools#tools-used-to-assist-with-developing-omop-vocabulary"
class="uri">https://github.com/OHDSI/OncologyWG/tree/master/vocabTools#tools-used-to-assist-with-developing-omop-vocabulary</a></p>
<p>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
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