Category Model

Current Category Model

The categories that are currently included as targets for the document classification work:

General Aspects

• 0.1. Disease Nomenclature - a paper defining a new disease nomenclature.
• 0.2. Related Diseases - a paper where the focus is on relationships between diseases (comorbidity, etc).

Clinical Aspects

• 1.1. Clinical Characteristics, Disease Pathology, and Diagnosis - Text that describes (A) symptoms, signs, or ‘phenotype’ of a disease; (B) the effects of the disease on patient organs, tissues, or cells; (C) the results of clinical tests that reveal pathology (including biomarkers); (D) research that use this information to figure out a diagnosis.
• 1.2. Quality of Life (QOL) - A study describing patient experience or outcomes such as survival times, impact on mobility and other measures used to denote how the disease affects the patient’s quality of life. It is important to note we consider subjective measures that quantify the patient experience to be included in this category. If a paper measures a clinical characteristic or pathology and then states that this improves patients' quality of life, we would only include it if there is an explicit measurement that conforms to the above definition.
• 1.3. Therapeutics in the Clinic - A study describing how treatments work in the clinic (but not in a clinical trial).
• 1.4. Epidemiology - A study that describes (A) population-level incidence, distribution, and possible control of diseases and other factors relating to health. (B) We also place statements related to the socioeconomic or economic costs of the disease/disease burden into this category. (C) Studies focussed on developing registries or large-scale datasets that address this question should also be placed into this category. (D) Studies of geographic aspects of populations of patients suffering from the disease under study;
• 1.5. Influence of the Environment - A study that describes the influence of the physical environment on aspects of the disease (including transmission, risk factors, etc).

Basic Science Aspects

• 2.1. Disease Mechanisms - A study that describes either (A) mechanistic involvement of specific genes in disease (deletions, gain of function, etc); (B) how molecular signalling or metabolism (binding, activating, phosphorylation, concentration increase, etc.) are involved in the mechanism of a disease; or (C) the physiological mechanism of disease at the level of tissues, organs, and body systems.
• 2.2. Normal Biology - A paper that describes normal function of biological systems as the overall goal of a given study.
• 2.3. Non-in-vivo human or non-human Model System - A paper that describes basic-science experimental models that are not based on in-vivo studies of humans.
• 2.4. Basic Research Involving Human Subjects - Basic-science papers that are primarily focussed on developing new methods that are based on in-vivo studies of humans.
• 2.5. Computational Biology and Informatics research - A paper where the primary contribution is the development or application of computational methods.

Translational Aspects

• 3.1. Therapeutic Hypothesis - A study where a significant contribution of the paper is to put forward a new hypothesize for how basic science findings could lead to the development of therapeutic or diagnostic methods.
• 3.2. Drug Mechanism - A paper describing any drugs’ pharmaceutical activity - including sites of potential (or actual) pharmaceutical intervention, mechanisms of action, metabolism, etc.
• 3.3. Preclinical Therapeutics - Studies describing analysis of possible therapy in laboratory-based non-human subjects.
• 3.4. Patient-Driven Therapeutics - Studies describing the following scenarios involving human subjects (A) Clinical trials (studies of therapeutic measures being used on patients in a clinical trial); (B) Post Marketing Drug Surveillance (effects of a drug after approval in the general population or as part of ‘standard healthcare’); (C) Drug repurposing (how a drug that has been approved for one use is being applied to a new disease).

Categories of interest to be added in later iterations

• Patient Data - Studies that involve the creation of a new data resource
• Health Disparities - Studies that focus on unequal delivery of health care to different populations based on race, gender, or other categories.
• Natural Resistance to Disease - Studies highlighting natural resilience
• Prevention - The majority of rare diseases are genetic and cannot be 'prevented' (in the same way as infectious disease), but this category will be present in many diseases that do not have a genetic etiology.
• Health Care Disparities - Health care delivery can be uneven based on Race, SES, gender, and other factors. Highlighting these disparities forms an important part of our mission at CZI.