Call for Participation: TREC 2019 Precision Medicine Track

[Kirk Roberts]

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TREC 2019 Precision Medicine Track

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Most work on precision medicine focuses on developing new treatments based on an individual's genetic, environmental, and lifestyle profile. The result is a data-driven approach investigating the best treatment for an individual patient. This promising approach has led to significant advances, including an explosion of scientific research, as embodied by the Precision Medicine Initiative (PMI). This presents an information problem for clinicians, however, as the vast literature available for precision medicine can make it difficult to find the most appropriate treatment for the clinician's current patient. The ability to quickly locate relevant information for a current patient using information retrieval (IR) has the potential to be an important tool for helping clinicians find the most up-to-date evidence-based treatment for their patients.

The 2019 TREC Precision Medicine track continues the prior 2017 and 2018 Precision Medicine tracks, which was a specialization of the previous TREC Clinical Decision Support track. Specifically, the 2019 Precision Medicine track focuses on the case of providing clinical decision support to cancer patients with genetic variations that might impact the choice of treatment. This year increased focus will be devoted to returning treatment-specific information.

The track uses synthetic patients developed by precision oncologists at the world-famous MD Anderson Cancer Center in Houston, TX. For each patient, participants are challenged with retrieving relevant scientific literature articles discussing potential treatments, as well as potential clinical trials for which the patient may be eligible.

--- Task Description ---

* Topics/Queries: Synthetic patients with cancer and one or more genetic variants

* Data Collection: (1) scientific abstracts, (2) clinical trials

* Website: http://www.trec-cds.org/2019.html [still under development, see previous year's website for more information: http://www.trec-cds.org/2018.html]

* Mailing List: http://groups.google.com/d/forum/trec-cds

We will be using synthetic cases created by precision oncologists at the University of Texas MD Anderson Cancer Center. Each case will describe the patient's disease (type of cancer), the relevant genetic variants (which genes), basic demographic information (age, sex), and other potential factors that may be relevant. The cases are semi-structured and require minimal natural language processing.

Participants of the track will be challenged with retrieving (1) biomedical articles, in the form of article abstracts (largely from MEDLINE/PubMed), addressing relevant treatments for the given patient, and (2) clinical trials (from ClinicalTrials.gov), addressing relevant clinical trials for which the patient is eligible. The first set of results represents the retrieval of existing knowledge in the scientific literature, while the second represents the potential for connecting patients with experimental treatments if existing treatments have been ineffective.

--- Important Dates ---

ASAP: TREC Registration: https://ir.nist.gov/trecsubmit.open/application.html

Early May 2019: Document collection available for download

Late May 2019: Topics available for download

July/August 2019: Results submission deadline

October 2019: Relevance judgements and individual evaluation scores released

Late October 2019: Initial system description papers due

November 13-15 2019: TREC 2019 conference at NIST

--- Organizing Committee ---

Kirk Roberts (UTHealth)

William Hersh, Steven Bedrick (OHSU)

Dina Demner-Fushman (NLM)

Ellen Voorhees (NIST)

Shubham Pant, Alexandar Lazar (UT MD Anderson Cancer Center)

--- Contact ---

Mailing List: http://groups.google.com/d/forum/trec-cds