Model level Annotations

This document describes the metadata that we would like to see TA-1 extracting from papers, code, and other artifacts that describe the model, in addition to the core dynamics.

In https://github.com/indralab/mira/pull/138, we implemented this data model so MIRA can extract these fields from SBML files in the BioModels database and more generally represent these data in a structured way.

Schema with Examples

Field	Field Description	Example (From Bertozzi 2020 SIR model)
Name	Human-readable label	SIR model of scenarios of COVID-19 spread in CA and NY
Description	Description of the model	We detail three regional scale models for forecasting and assessing the course of the pandemic ...
License	A string representing the model string, ideally from SPDX	CC0
Authors	A list of authors	Andrea L Bertozzi, Elisa Franco, George Mohler, Martin B Short, Daniel Sledge
References	A list of references given as CURIEs, ideally using PubMed, DOI, or PMC	pubmed:32616574
Time Start	The date and time of the beginning of the applicability of the model	March, 2020
Time End	The date and time of the end of the applicability of the model	August, 2020
Location(s)	The location(s) of applicability of the model given as CURIEs, ideally using GeoNames or Wikidata	geonames:5128581, geonames:5332921
Pathogen(s)	A list of pathogens present in the model given as CURIEs, ideally using NCBITaxon	ncbitaxon:2697049
Host(s)	A list of hosts present in the model given as CURIEs, ideally using NCBITaxon	ncbitaxon:9606
Model Type(s)	A list of model type annotations with the Mathematical Modeling Ontology (MAMO) vocabulary	mamo:0000028, mamo:0000046
Coordinate System	The coordinate system used in the model (e.g., spherical, cylindrical)

Example as JSON

The following is a concrete example of data in the JSON format from the Bertozzi 2020 SIR model (see also biomodels.db:BIOMD0000000956 for a structured SBML version of this data.

The JSON schema for this data is encoded in https://github.com/indralab/mira/blob/improve-sbml-annotation-processing/mira/metamodel/schema.json.

{
  "name": "SIR model of scenarios of COVID-19 spread in CA and NY",
  "description": "The coronavirus disease 2019 (COVID-19) pandemic has ..",
  "license": "CC0",
  "authors": [
    {"name": "Andrea L Bertozzi"},
    {"name": "Elisa Franco"},
    {"name": "George Mohler"},
    {"name": "Martin B Short"},
    {"name": "Daniel Sledge"}
  ],
  "references": ["pubmed:32616574"],
  "time_start": "2020-03-01T00:00:00",
  "time_end": "2020-08-01T00:00:00",
  "locations": ["geonames:5128581", "geonames:5332921"],
  "pathogens": ["ncbitaxon:2697049"],
  "diseases": ["doid:0080600"],
  "hosts": ["ncbitaxon:9606"],
  "model_types": ["mamo:0000028", "mamo:0000046"]
}