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. 2020 Aug 26;16(8):e9235. doi: 10.15252/msb.20199235
Model

  • Recognized naming convention

    • o

      historical approach: i + authors initials + number of genes in model, e.g., iJE660 for the E. coli model constructed by Jeremy Edwards with 660 genes

    • o

      recommended approach: i + species indicator + iteration identifier, e.g., iPfal17 for P. falciparum published in 2017

  • Machine‐readable reference to organism embedded via MIRIAM annotation

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      full species name, including relevant identifiers if available (e.g., NCBI reference genome)

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      taxonomy ID

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      strain ID, if necessary

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      tissue type, if necessary

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      URL to obtain genome

  • Reference information

    • o

      DOI

    • o

      Author(s) names and contact information embedded

  • Consistent namespace for all model identifiers

Metabolite

  • Human‐readable, descriptive name (e.g., D‐Glucose)

  • Charge (e.g., 0)

  • Chemical formula (e.g., C6H12O6)

  • Structural identifiers

    • o

      InChI strings (if pH is known, pH‐relevant InChI ID for each metabolite)

    • o

      SMILES (optional)

  • At least one database identifier from a reliable resource, such as

    • o

      MetaNetX

    • o

      BiGG

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      KEGG Compound

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      ChEBI

    • o

      ModelSEED

    • o

      HMDb

    • o

      MetaCyc

Biochemical reaction

  • Human‐readable, descriptive name (e.g., phosphofructokinase)

  • Reaction formula (e.g., ATP + L‐glutamate + ammonium ⇌ ADP + L‐glutamine + H+ + phosphate)

  • At least one database identifier from a reliable resource, such as

    • o

      MetaNetX

    • o

      Rhea

    • o

      BiGG

    • o

      KEGG Reaction

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      ModelSEED

    • o

      MetaCyc

  • EC Number

  • Associated genes (gene‐protein‐reaction rule, or GPR)

  • Recommended: systems biology ontology (SBO) terms

Biochemical reaction

  • Human‐readable, descriptive name (e.g., phosphofructokinase)

  • Reaction formula (e.g., ATP + L‐glutamate + ammonium ⇌ ADP + L‐glutamine + H+ + phosphate)

  • At least one database identifier from a reliable resource, such as

    • o

      MetaNetX

    • o

      Rhea

    • o

      BiGG

    • o

      KEGG Reaction

    • o

      ModelSEED

    • o

      MetaCyc

  • EC Number

  • Associated genes (gene‐protein‐reaction rule, or GPR)

  • Recommended: systems biology ontology (SBO) terms

Gene

  • Name or gene symbol

  • DNA and/or Protein sequence ID (i.e., a mechanism for mapping this information to a sequence)

    • o

      Entrez

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      Ensembl

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      UniProt

    • o

      Other field‐specific database identifier

  • Position (including chromosome, if applicable)