Compatibility and translators
The BioRECIPE format is compatible with a range of representation formats, databases, and tools, either directly, or through translation.
Attribute compatibility
Here we provide an overview of which attributes that BioRECIPE considers are included in other representation formats, output by several tools, including LLMs, or input in models by human curators. Note: additional standards, databaes, and tools are listed in the following section.
Translators
The tables below list example formats, databases, and tools and links to translators. The translator repositories provide further instructions for the use of translators.
Standard |
Format |
To BioRECIPE |
From BioRECIPE |
Description |
|---|---|---|---|---|
SBML |
RDF/XML |
✓ |
✓ |
Translation to BioRECIPE Executable Model and from BioRECIPE Interaction List |
SBML-qual |
RDF/XML |
✓ |
✓ |
Translation to and from BioRECIPE Executable Model |
SIF |
TXT |
✓ |
✓ |
Translation to and from BioRECIPE Interaction List and from BioRECIPE Executable Model |
BioPAX |
RDF/OWL, SBML |
✓ |
✓ |
Translation from and to BioPAX files can be done through SBML translation to and from BioRECIPE |
BEL |
TXT (INDRA) |
✓ |
✓ |
Translation from and to BEL statements through INDRA statements |
PySB |
SBML |
✓ |
✓ |
Translation from and to PySB files can be done through the SBML translation to and from BioRECIPE |
REACH |
CMU format |
✓ |
N/A |
Translation from REACH CMU format to BioRECIPE interaction List |
TRIPS |
XML |
✓ |
N/A |
Translation from TRIPS output to BioRECIPE Interaction List |
Database |
Format |
To BioRECIPE |
From BioRECIPE |
Description |
|---|---|---|---|---|
KGML, SBML |
✓ |
✓ |
Translation from and to KGML files through the SBML translation to and from BioRECIPE |
|
SBML, BioPAX |
✓ |
✓ |
See SBML and BioPAX translation |
|
SIF, BioPAX |
✓ |
✓ |
See SIF and BioPAX translation |
|
SIF, BEL(INDRA), BioPAX |
✓ |
✓ |
See SIF BEL and BioPAX translation |
|
SBML, SBML-qual |
✓ |
✓ |
Tool (external) |
Format |
To BioRECIPE |
From BioRECIPE |
Description |
|---|---|---|---|---|
SIF, CX(INDRA) |
✓ |
✓ |
See SIF translation or INDRA translation and CX assembler |
|
SBML-qual |
✓ |
✓ |
||
SBML |
✓ |
✓ |
See SBML translation |
|
SBML |
✓ |
✓ |
See SBML translation |
|
JSON |
✓ |
✓ |
Translation to and from BioRECIPE Interaction List |
|
JSON |
✓ |
N/A |
Translation to BioRECIPE Interaction List directly or through INDRA |
|
XML |
✓ |
N/A |
Translation to BioRECIPE Interaction List directly or through INDRA |
Tool |
Description |
|---|---|
Uses BioRECIPE Executable Model format at input |
|
Uses BioRECIPE Interaction List format at input and output |
|
VIOLIN |
Uses BioRECIPE Interaction List and Executable Model formats at input and output |
Uses BioRECIPE Interaction List and Executable Model formats at input and output |
|
Uses BioRECIPE Interaction List and Executable Model formats at input and output |
|
PIANO |
Uses BioRECIPE Executable Model format at input |
Uses BioRECIPE Interaction List and Executable Model formats at input |
|
MINUET |
Uses BioRECIPE Interaction List format at input and output |