About The Molecular Oncology Almanac

Purpose

The Molecular Oncology Almanac attempts to capture the current body of knowledge on how genetic alterations affect clinical actionability. As the field of precision medicine grows, the quantity of research on how specific alterations affect therapeutic response and patient prognosis expands at an increasing rate. The Molecular Oncology Almanac seeks to curate this information from the literature, increasing the abilities of clinicians and researchers alike to rapidly assess the importance of an alteration.

Data access

The contents of the Molecular Oncology Almanac may be downloaded here. Each feature represented in the almanac (e.g., "somatic variant," "knockdown," etc.) is represented in a separate tab-separated value (TSV) file. The collection of TSV files representing the entire Almanac database is provided in a single ZIP file. The knowledge base can also be programmatically interfaced with through our API endpoints.

Please consider suggesting relationships through our web form or our Google Chrome extension.

Predictive implication levels

The Molecular Oncology Almanac categorizes each curated assertion by the strength of evidence asserting the relationship between a given molecular feature and clinical action. The levels used are:

LevelDescription
FDA-Approved The Food and Drug Association (FDA) recognizes an association between the alteration and recommended clinical action.
Guideline This relationship is catalogued as a guideline for standard of care treatment.
Clinical trial The alteration is or has been used as an eligibility criterion for a clinical trial.
Clinical evidence The relationship is reported in a clinical study that did not directly involve a clinical trial.
Preclinical evidence This relationship is reported in a study involving mice, cell lines, or patient derived models.
Inferential evidence The relationship is inferred as a result of mathematical modeling or an association between molecular features.

Literature curation

The Molecular Oncology Almanac draws primarily from primary research articles, review articles, and the NCCN guidelines. Data is curated through both expert review and using a Natural Language Processing (NLP) approach to select potentially informative articles from PubMed.

The Molecular Oncology Almanac is co-developed with the PHIAL (Precision Heuristics for Interpreting the Alteration Landscape) algorithm, which draws from Molecular Oncology Almanac and other alterations databases to classify patient tumor data.

Terms

The Molecular Oncology Almanac is made available under the Open Database License (ODbL). A "plain-language" summary of the ODbL is available here.

You are free to share and modify the contents of The Molecular Oncology Almanac under the following restrictions:

  1. All public use of the data (either in its entirety or in part) must be attributed.
  2. Any works produced using the data must also be licensed under the ODbL.
  3. Any works produced using the data must be open; if you distribute a version encumbered by technological restrictions (e.g., DRM), another version without such restrictions must be made available.
  4. All other terms of the ODbL must be followed.

DIAGNOSTIC AND CLINICAL USE PROHIBITED. THE BROAD INSTITUTE and DFCI MAKE NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT OR VALIDITY OF ANY INTELLECTUAL PROPERTY RIGHTS OR CLAIMS, WHETHER ISSUED OR PENDING, AND THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE.

In no event shall Broad or DFCI or their Trustees, Directors, Officers, Employees, Students, Affiliates, Core Faculty, Associate Faculty and Contractors, be liable for incidental, punitive, consequential or special damages, including economic damages or injury to persons or property or lost profits, regardless of whether the party was advised, had other reason to know or in fact knew of the possibility of the foregoing, regardless of fault, and regardless of legal theory or basis. You may not download or use any portion of this program for any use not expressly authorized by the Broad. You further agree that the program shall not be used as the basis of a commercial product and that the program shall not be rewritten or otherwise adapted to circumvent the need for obtaining permission for use of the program other than as specified herein.

Illustration by Eric Kofman