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Annotation Format

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Peter Robinson edited this page Jan 12, 2020 · 2 revisions

MAxO Annotation Format

Item Example
  1. Disease ID
 MONDO:0014586
  1. Disease label
 congenital myasthenic syndrome 4B
  1. MAxO ID
 MAXO:0000214
  1. MAxO label
 serotonin-norepinephrine reuptake inhibitor agent therapy
  1. HPO ID
 HP:0001324
  1. HPO label
 Muscle weakness
  1. Evidence
 ECO:0006016
  1. Extension id
 CHEBI:5118
  1. Extension label
 fluoxetine
  1. Relation
 is substance that treats
  1. Source
 PMID:29395675
  1. Biocuration
 HPO:lcarmody[YYYY-MM-DD]
  1. Comment
 Optional free text

Explanations

1./2. MAxO annotations use Mondo terms to denote diseases. Some MAxO annotations will use specific diseases, e.g., congenital myasthenic syndrome 4B, but others might refer to groups of diseases (e.g., treatment of limbs with hydration and lipid-based unguents is indicated for all forms of hereditary sensory and autonomic neuropathy, irregardless of the genetic subform).

3./4. The columns contain the MAxO id and label

5./6. In many cases, treatment of a disease is targeted at a particular manifestation of complication of that disease. In this case, the approproate Human Phenotype Ontology (HPO) should be indicated.

  1. Evidence. Terms from the Evidence & Conclusion Ontology (ECO) should be used. In many cases, author statement from published clinical study (ECO:0006016) is the appropriate term.

8./9. The Extension id/label is intended to be used analogously to the extensions in the Gene Ontology annotation format: They contain cross references to other ontologies that can be used to qualify or enhance the annotation. In this case, we annotate the disease to the class of action of the medication (serotonin-norepinephrine reuptake inhibitor agent therapy), but use the term fluoxetine from ChEBI to indicate the specific agent.

  1. Relation. We will endeavour to use terms from the Relation Ontology to describe how the treatment or item in MAxO is related to the disease. For instance, is substance that treats is RO:0002606. We anticipate that new relations will be required and we will allow temporary MAxO Ids in this case, while we request terms from RO.
  2. Source. MAxO annotations prefer to use PubMed ids.
  3. Biocuration. We will indicate the name/identifier of the curator. CURIEs or ORCID ids are accepted. We plan to introduce functionality to indicate attribution to a group.
  4. Comment. This is a free text field that can be used to record additional information about the annotation. In the present case, the comment field is: "Fluoxetine is a serotonin-norepinephrine reuptake inhibitor. 3 patients had decremental responses to repetitive nerve stimulation (RNS) and repetitive compound muscle action potentials (CMAPs), with the second component of each CMAPs decrementing faster than the first component. All 3 initially responded to pyridostigmine, but then became weaker. All 3 benefited from fluoxetine (40-60 mg/day) and improved further with the additional use of salbutamol (12 mg/day)."

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