HCLSIG/PharmaOntology/Publications/BIOONT-TMO-reviews

Paper: 16

Title: The Translational Medicine Ontology: Driving personalized medicine by bridging the gap from bedside to bench

REVIEW 1

OVERALL RATING: 3 (strong accept)

REVIEWER'S CONFIDENCE: 3 (high)

This paper describes a translational medicine ontology developed as part of the HCLS activities. This is a nice piece of community work involving a significant number of authors. The paper is well written. The work is well motivated. An AD use case is provided to concretely demonstrate how the ontology is designed and used. Efforts are also geared towards mapping TMO to other existing biomedical ontologies as well as linking it existing open linked datasets. Some example queries are provided. Overall the quality of the work is high. One minor typo is found. The title of section 3.4 should be "Translational Medicine Knowledge Base". Finally, a diagram showing (at a high level) the core entities and their relationships would help the reader get a quick understanding of the ontology structure.

REVIEW 2

OVERALL RATING: 2 (accept)

REVIEWER'S CONFIDENCE: 3 (high)

This paper introduces the Translational Medicine Ontology, including ontology design, data sources, data mapping, knowledge bases and its use for question answering. It is a very well-written paper, and the topic is important to the field. Below are a few comments:

1. It would be very interesting if the authors could briefly introduce how the participants have been involved in this efforts, how they collaborates with each other and how they reach agreement. How long has TMO taken since it was launched?

2. Do the authors have plans to evaluate and validate the ontology? What is its coverage?

3. Page 2, in Table 1, what are the "clinical decision support" users? Could you provide examples?

actionable items:

1. a high level diagram showing the core entities and their relationships.

2. a discussion on the HCLS & TMO structure and activities.

3. Ontology evaluation (+coverage)

4. Elaborate on "clinical decision support"