SBGN output (indra.assemblers.sbgn.assembler
)
- class indra.assemblers.sbgn.assembler.SBGNAssembler(statements=None)[source]
This class assembles an SBGN model from a set of INDRA Statements.
The Systems Biology Graphical Notation (SBGN) is a widely used graphical notation standard for systems biology models. This assembler creates SBGN models following the Process Desctiption (PD) standard, documented at: https://github.com/sbgn/process-descriptions/blob/master/UserManual/sbgn_PD-level1-user-public.pdf. For more information on SBGN, see: http://sbgn.github.io/sbgn/
- Parameters
stmts (Optional[list[indra.statements.Statement]]) – A list of INDRA Statements to be assembled.
- sbgn
The structure of the SBGN model that is assembled, represented as an XML ElementTree.
- Type
lxml.etree.ElementTree
- add_statements(stmts)[source]
Add INDRA Statements to the assembler’s list of statements.
- Parameters
stmts (list[indra.statements.Statement]) – A list of
indra.statements.Statement
to be added to the statement list of the assembler.
- make_model()[source]
Assemble the SBGN model from the collected INDRA Statements.
This method assembles an SBGN model from the set of INDRA Statements. The assembled model is set as the assembler’s sbgn attribute (it is represented as an XML ElementTree internally). The model is returned as a serialized XML string.
- Returns
sbgn_str – The XML serialized SBGN model.
- Return type