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1995 lines (1911 loc) · 75.3 KB
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<body class="article">
<div id="header">
<h1>OpenFurther Reference Documentation</h1>
</div>
<div id="content">
<div class="sect1">
<h2 id="_about">About</h2>
<div class="sectionbody">
<div class="paragraph"><p>The following documentation applies to <strong>OpenFurther version 1.4.0-SNAPSHOT</strong></p></div>
<div class="sect2">
<h3 id="_conventions">Conventions</h3>
<div class="admonitionblock">
<table><tr>
<td class="icon">
<div class="title">Note</div>
</td>
<td class="content">A note</td>
</tr></table>
</div>
<div class="admonitionblock">
<table><tr>
<td class="icon">
<div class="title">Important</div>
</td>
<td class="content">An important point</td>
</tr></table>
</div>
<div class="admonitionblock">
<table><tr>
<td class="icon">
<div class="title">Tip</div>
</td>
<td class="content">A tip</td>
</tr></table>
</div>
<div class="admonitionblock">
<table><tr>
<td class="icon">
<div class="title">Warning</div>
</td>
<td class="content">A warning</td>
</tr></table>
</div>
<div class="admonitionblock">
<table><tr>
<td class="icon">
<div class="title">Caution</div>
</td>
<td class="content">A point of caution</td>
</tr></table>
</div>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_introduction">Introduction</h2>
<div class="sectionbody">
<div class="paragraph"><p>OpenFurther is an informatics platform that supports federation and integration of data from heterogeneous and disparate data sources.</p></div>
<div class="paragraph"><p>It has been deployed at the University of Utah (UU) as the Federated Utah Research and Translational Health e-Repository (FURTHeR) since August 2011 and is available for use by all U of U employees and students. OpenFurther links heterogeneous data types, including clinical, public health, biospecimen and patient-generated data; empowering researchers with the ability to assess feasibility of particular clinical research studies, export biomedical datasets for analysis, and create aggregate databases for comparative effectiveness research. With the ability to link unique individuals from these sources, OpenFurther is able to identify cohorts for clinical research.</p></div>
<div class="paragraph"><p>It provides semantic and syntactic interoperability as it federates health information on-the-fly and in real-time and requires neither data extraction nor homogenization by data source partners, facilitating integration by retaining data in their native format and in their originating systems.</p></div>
<div class="paragraph"><p>OpenFurther is built upon Maven, Spring, Hibernate, ServiceMix, and other open source frameworks that promote OpenFurther’s code reusability and interoperability.</p></div>
</div>
</div>
<div class="sect1">
<h2 id="_architecture">Architecture</h2>
<div class="sectionbody">
<div class="paragraph"><p>Loosely, OpenFurther runs as a multi-tier application. The presentation layer or front end/user-interface is served (currently) through the i2b2 web client. The logic layer is served through the ServiceMix ESB, and the database layer is served using Oracle 11g, although it can be configured for other databases as well.</p></div>
<div class="sect2">
<h3 id="_user_interface">User Interface</h3>
<div class="paragraph"><p>OpenFurther utilizes the i2b2 web client as a front-end for querying data. The user interface has been modified to support federated querying.</p></div>
<div class="imageblock">
<div class="content">
<img src="images/figures/i2b2_ui_query_results.png" alt="images/figures/i2b2_ui_query_results.png" />
</div>
<div class="title">Figure 1. Customized i2b2 User Interface</div>
</div>
</div>
<div class="sect2">
<h3 id="_hooking_openfurther_into_i2b2">Hooking OpenFurther into i2b2</h3>
<div class="paragraph"><p>OpenFurther utilizes a Java Servlet Filter to divert query requests to the OpenFurther backend system. The Servlet filter looks for XML messages from i2b2 that indicate a query is being run. Those XML messages are then diverted to OpenFurther where OpenFurther converts them into a OpenFurther query and runs them. All other XML messages are ignored and i2b2 is allowed to run as normal.</p></div>
<div class="admonitionblock">
<table><tr>
<td class="icon">
<div class="title">Note</div>
</td>
<td class="content"><strong>No data is stored within i2b2, all data resides within its original location</strong></td>
</tr></table>
</div>
</div>
<div class="sect2">
<h3 id="_the_federated_query_engine_fqe">The Federated Query Engine (FQE)</h3>
<div class="paragraph"><p>In OpenFurther, the term "FQE" (Federated Query Engine) is broadly referred to as the set of software modules involved in the execution of a federated query.</p></div>
<div class="imageblock">
<div class="content">
<img src="images/figures/fqe.png" alt="images/figures/fqe.png" />
</div>
<div class="title">Figure 2. Federated Query Engine</div>
</div>
<div class="ulist"><ul>
<li>
<p>
A federated query written in FQL (an XML based query language) or an i2b2 query is submitted at <strong>1</strong>.
</p>
</li>
<li>
<p>
Utilizing the publish-subscribe pattern, one or more data source adapters are subscribed to the Query Topic at <strong>2</strong>.
</p>
</li>
<li>
<p>
If the query is an i2b2 query, the FQE converts the i2b2 query to a federated query.
</p>
</li>
<li>
<p>
The FQE then posts the query to the Query Topic (<strong>2</strong>) and each listening data source adapter receives a copy of the query.
</p>
</li>
<li>
<p>
Each data source adapter runs through a number of steps to initialize, process, and translate a query for a given data source (Explained below).
</p>
</li>
<li>
<p>
Throughout the processing, status messages are sent to a Status Queue at <strong>3</strong>.
</p>
</li>
<li>
<p>
Once results are translated to a common model, they are persisted to the In-Memory database and result count is sent to <strong>4</strong>.
</p>
</li>
</ul></div>
</div>
<div class="sect2">
<h3 id="_data_source_adapters">Data Source Adapters</h3>
<div class="paragraph"><p>Data source adapters are facades around an existing data source. Data source adapters can be entirely custom for any given implementation or they can use a pre-written adapter if their data source is already in a well-known format such as OMOP, i2b2, OpenEMR, etc</p></div>
<div class="imageblock">
<div class="content">
<img src="images/figures/data_source_adapters.png" alt="images/figures/data_source_adapters.png" />
</div>
<div class="title">Figure 3. Data Source Adapters</div>
</div>
<div class="ulist"><ul>
<li>
<p>
Data source adapters follow the chain-of-responsibility pattern. The process of adapting a query is broken down into several small steps and each output is passed on to the next step. Data source adapters typically have 4 commons steps.
</p>
<div class="olist arabic"><ol class="arabic">
<li>
<p>
They are given an initialization step which allows them to determine whether or not the given data source can answer the given query. It also provides for any other initialization required throughout the process.
</p>
</li>
<li>
<p>
Query translation translates the logical FQL that is not specific to any data source into data source specific language. This will vary with data sources. Some data sources will utilize SQL, other’s might be a web service. It utilizes the Metadata Repository (MDR) for translating attributes and values (e.g. logical query uses Gender but actual data source uses Sex as the attribute). It also utilizes DTS (Terminology Server) to translate from a given code (e.g. ICD9 250) to the data source’s code (e.g. 12345)
</p>
</li>
<li>
<p>
The query is executed against the data source and results are returned in their native format (SQL ResultSet, XML, etc).
</p>
</li>
<li>
<p>
Result translations translates the results into a common model with standardized vocabulary/terminology utilizing the Metadata Repository (MDR) and DTS (Terminology Server).
</p>
</li>
</ol></div>
</li>
</ul></div>
</div>
<div class="sect2">
<h3 id="_terminology_server">Terminology Server</h3>
<div class="paragraph"><p>OpenFurther utilizes Apelon’s Distributed Terminology System version 3.5.2.203 (aka. DTS) for terminology related functionality. The OpenFurther instance of DTS contains concepts from the standard terminologies SNOMED-CT, ICD-9, RxNorm, and UCUM. There are also non-standard terminologies (aka Local) for each of the data sources as well as associated mappings. The use of standard terminologies and mappings make it possible for the software to resolve differences between concepts in various data sources and achieve a degree of semantic interoperability. Use of Apelon DTS is an assumption of agreement to the Apache Version 2 standard open source license agreement <a href="http://www.apache.org/licenses/LICENSE-2.0.html">http://www.apache.org/licenses/LICENSE-2.0.html</a>. For more information about Apelon DTS please see their website <a href="http://www.apelon.com">http://www.apelon.com</a>.</p></div>
<div class="sect3">
<h4 id="_features_of_apelon_dts">Features of Apelon DTS</h4>
<div class="paragraph"><p>The Apelon DTS (Distributed Terminology System) is an integrated set of open source components that provides comprehensive terminology services in distributed application environments.</p></div>
<div class="paragraph"><p>DTS Supports national and international data standards, which are a necessary foundation for comparable and interoperable health information, as well as local vocabularies.</p></div>
<div class="paragraph"><p>DTS consists of</p></div>
<div class="ulist"><ul>
<li>
<p>
DTS Core - the core system, database, api, etc
</p>
</li>
<li>
<p>
DTS Editor - a GUI interface for viewing, adding, and editing concepts
</p>
</li>
<li>
<p>
DTS Browser - a web interface for viewing concepts
</p>
</li>
<li>
<p>
Modular Classifier - allows for extending standard ontologies
</p>
</li>
</ul></div>
</div>
</div>
</div>
</div>
<div class="sect1">
<h2 id="_terminology">Terminology</h2>
<div class="sectionbody">
<div class="sect2">
<h3 id="_getting_started">Getting Started</h3>
<div class="paragraph"><p>In order to utilize the OpenFurther software, it is necessary to have terminology mappings from your desired data sources to standard terminologies. These standard codes are then translated via the software, terminology server, and associated mappings to be able to resolve to a local data source’s codes/terms.</p></div>
<div class="admonitionblock">
<table><tr>
<td class="icon">
<div class="title">Important</div>
</td>
<td class="content">It is important to note that the content distributed with OpenFurther is for demonstration purposes only. The standard terminologies have been provided with permission via Apelon’s distribution of free subscription content available on their open source website <a href="http://apelon-dts.sourceforge.net/">http://apelon-dts.sourceforge.net/</a>. This standard content is several years out of date and would not be the most suitable for a real world instance.</td>
</tr></table>
</div>
<div class="admonitionblock">
<table><tr>
<td class="icon">
<div class="title">Tip</div>
</td>
<td class="content">It is recommended for organizations that desire to use the OpenFurther software to consider resourcing a dedicated terminologist or someone that has experience with controlled vocabularies and ontologies to work on managing/mapping local vocabularies/codes to their specific implementation of OpenFurther.</td>
</tr></table>
</div>
<div class="paragraph"><p>Apelon provides a content delivery subscription service at a reasonable cost. Standard terminologies can also be downloaded from the U.S. National Library of Medicine Unified Medical Language System (link: <a href="http://www.nlm.nih.gov/research/umls/">UMLS</a>) after meeting and accepting their requirements and license agreements.</p></div>
<div class="admonitionblock">
<table><tr>
<td class="icon">
<div class="title">Note</div>
</td>
<td class="content">The local vocabularies have been mapped to the best possible matches to the available standard terminologies. However, in some cases such as OpenMRS, local concepts had to be created to fit the OpenFurther demonstration scenario. Any creation of local concepts was done in best accordance of the specifications provided by the source.</td>
</tr></table>
</div>
<div class="paragraph"><p>OpenFurther’s i2b2 front end user interface contains an ontology based off of the recommendations of the Healthcare Information Technology Standards Panel (HITSP). For instance, HITSP recommends the use of ICD-9 codes for diagnosis and LOINC for laboratory data. Please note that because of licensing agreements, not all of the HITSP recommendations could be followed for OpenFurther. For example, HITSP recommends the use of CPT for procedures. In OpenFurther, procedures will be based off the SNOMED CT hierarchy for procedures.</p></div>
<div class="sect3">
<h4 id="_why_are_mappings_needed">Why are mappings needed?</h4>
<div class="paragraph"><p>Mappings are needed because of the variations in terminology used between disparate data sources. Mappings equate concepts that are intended to mean the same thing.</p></div>
<div class="admonitionblock">
<table><tr>
<td class="icon">
<div class="title">Tip</div>
</td>
<td class="content">Mapping can be a very human labor intensive task. Mappings must be verified and tested to ensure quality of results. Involving subject matter experts and collaborating effectively across datasources will be paramount to achieving a successful implementation of terminology.</td>
</tr></table>
</div>
<div class="imageblock">
<div class="content">
<img src="images/figures/mapping_terminology.png" alt="images/figures/mapping_terminology.png" />
</div>
<div class="title">Figure 4. Mapping Terminology</div>
</div>
</div>
<div class="sect3">
<h4 id="_initial_steps">Initial Steps</h4>
<div class="paragraph"><p>Apelon DTS provides excellent documentation and examples of how to use their terminology server software. All Apelon documentation can be found at: <a href="http://apelon-dts.sourceforge.net/documents.html">http://apelon-dts.sourceforge.net/documents.html</a></p></div>
<div class="admonitionblock">
<table><tr>
<td class="icon">
<div class="title">Important</div>
</td>
<td class="content">It is highly recommended that you familiarize yourself with the basic use of the Apelon DTS software. The instance included in OpenFurther can serve as an example of how the OpenFurther team has used Apelon DTS but the best instruction on how to use Apelon DTS is provided directly from Apelon.</td>
</tr></table>