Compatibility and translators

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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.

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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