Compatibility and translators

The BioRECIPE format is compatible with a range of representation formats, databases, and tools, either directly, or through translation. Some examples are listed in the figure above.

Attribute compatibility

Here we provide a summary of attributes that BioRECIPE considers and indicate whether they are included in other representation formats, output by several tools, including large alnguage models (LLMs), or added to models by human curators.

Additional standards, databases, and tools and their compatibilities with BioRECIPE are listed in the following sections.

Translators summary

All translators with ReadMe files are available in the translators folder in the BioRECIPE GitHub repository. All example input and output files and the two Jupyter notebooks are available in the examples folder in the repository. The interactive Jupyter notebooks demonstrate:

• an example workflow where BioRECIPE format is used with several modeling, curation, and simulation tools (filtering interaction lists, classifying and clustering them, examining the possible extensions and simulating and verifying against golden properties)

• the use of translators, including input and output examples, before and after translation,respectively

Individual links to formats, databases, and tools, and links to corresponding translators are provided in the tables below.

Table 12 Formats compatible with BioRECIPE

Standard	Format	To BioRECIPE	From BioRECIPE	Description
SBML	RDF/XML	✓	✓	Direct translation to and from BioRECIPE
SBML-qual	RDF/XML	✓	✓	Direct translation to and from BioRECIPE
SIF	TXT	✓	✓	Direct translation to and from BioRECIPE
BioPAX	RDF/OWL, SBML	✓	✓	Translation from and to BioPAX files can be done via SBML translation to and from BioRECIPE
BEL	Structured TXT (BEL statements)	✓	✓	Translation from and to BEL statements via INDRA engine translation
PySB	SBML	✓	✓	Translation from and to PySB files can be done via SBML translation to and from BioRECIPE
REACH	Tabular (e.g., tsv)	✓	N/A	Direct translation from REACH tabular format to BioRECIPE interaction list
TRIPS	XML	✓	N/A	Translation from TRIPS output to BioRECIPE interaction list

Table 13 Databases compatible with BioRECIPE

Database	Format	To BioRECIPE	From BioRECIPE	Description
KEGG	KGML, SBML	✓	✓	Translation from and to KGML files through the SBML translation to and from BioRECIPE
REACTOME	SBML, BioPAX	✓	✓	See SBML and BioPAX translation
Pathway Commons	SIF, BioPAX	✓	✓	See SIF and BioPAX translation
NDEx	SIF, BEL(INDRA), BioPAX	✓	✓	See SIF BEL and BioPAX translation
BioModels	SBML, SBML-qual	✓	✓	See SBML and SBML-qual translation

Table 14 External tools compatible with BioRECIPE

Tool (external)	Format	To BioRECIPE	From BioRECIPE	Description
Cytoscape	SIF, CX(INDRA)	✓	✓	See SIF translation or INDRA translation and CX assembler
Cell Collective	SBML-qual	✓	✓	See SBML-qual translation
CellNetAnalyzer	SBML	✓	✓	See SBML translation
CellDesigner	SBML	✓	✓	See SBML translation
INDRA	JSON	✓	✓	Translation to and from BioRECIPE Interaction List
REACH	JSON	✓	N/A	Translation to BioRECIPE Interaction List directly or through INDRA
TRIPS	XML	✓	N/A	Translation to BioRECIPE Interaction List directly or through INDRA

Table 15 MeLoDy Lab tools compatible with BioRECIPE

Tool	Description
DiSH	Uses BioRECIPE Executable Model format at input
FLUTE	Uses BioRECIPE Interaction List format at input and output
VIOLIN	Uses BioRECIPE Interaction List and Executable Model formats at input and output
CLARINET	Uses BioRECIPE Interaction List and Executable Model formats at input and output
ACCORDION	Uses BioRECIPE Interaction List and Executable Model formats at input and output
PIANO	Uses BioRECIPE Executable Model format at input
FIDDLE	Uses BioRECIPE Interaction List and Executable Model formats at input
MINUET	Uses BioRECIPE Interaction List format at input and output