MAxO Annotation Guidelines

To understand the scope of MAxO annotations, it is important to first understand the scope of MAxO.

Scope of MAxO

Numerous computational resources exist to annotate and analyze pharmaceutical data, including DrugCentral, DrugBank, and the PharmGKB.` However, clinical management includes many other measures that collectively we refer to as medical actions. For instance, clinicians may prescribe a certain dietary intervention such as coenzyme Q10 supplementation for individuals with primary coenzyme Q10 deficiencies, or recommend the avoidance of a ketogenic diet, which although helpful for some individuals with epilepsy is contraindicated for individuals with certain diseases. Other medical actions include surgical procedures, ablations, treatment with biologics, behavioral and cognitive interventions, deep brain stimulation, and many others.

There are two main types of MAxO annotations.

Diagnostic annotations

The diagnostic annotations relate MAxO terms to individual phenotypic abnormalities represented by Human Phenotype Ontology terms. These MAxO annotations indicate how to ascertain a phenotypic abnormality. For instance, Rib fusion (HP:0000902) is_observable_through chest radiograph procedure (MAXO:0010356).

Diagnostic annotations are independent of the disease in the sense that the same diagnostic procedure can be used to ascertain the feature regardless of the underlying disease. For instance, rib fusion is a feature of multiple diseases including Congenital disorder of glycosylation, type IIg, Craniofacial dysmorphism, skeletal anomalies, and impaired intellectual development 1, and Escobar syndrome, but in each case the same diagnostic procedure, a chest radiograph, can be used to ascertain whether rib fusion is present.

Descriptions of clinical tests are included In contrast, purely research lab tests are not in scope. MAxO is not intended to be used for annotating results of clinical tests.

Therapeutic annotations

These annotations are made for each disease or disease group, annotating Mondo terms.

It is possible to annotate at a specific disease, e.g., Bardet-Biedl syndrome 5 (MONDO:0014434), or a group of related diseases, e.g., Bardet-Biedl syndrome (MONDO:0015229), which is a grouping class in Mondo that includes each of the 22 genetic subtypes of this disease.

Annotations can be made for that following items:

Therapeutic procedure:

  • Biologic therapy

  • Pharmacotherapy

  • Physical therapy

  • Radiation therapy

  • Surgical procedure

  • etc.

Palliative care:

  • end-of-life care

  • pain management

  • etc.

Preventative therapeutics:

  • smoking prevention

  • preventative immunization

  • prevention of abnormal physiologic state, i.e., hypertension prevention

  • ketosis prevention

  • etc.

Complementary and alternative therapies:

  • Acupuncture therapy

  • Chiropractic therapy

  • etc.

Medical action avoidance:

  • ketogenic diet intake avoidance

  • avoid CT scan

  • radiograph imaging avoidance

  • etc.

Supplementation or alternative therapies are only included if there are studies indicating their utility and have been recommended in the clinical literature. Examples: chiropractic therapy, amino acid/vitamin supplementation(yes), herbal supplementation(no)-*