CLI

MainExtractor

  • entry point: de.unirostock.sems.masymos.main.MainExtractor
Arguments
Argument Type Required Default Description
-dbPath String true / pointsthepath of your database, if no DB exists one will be created
-directory String annoOnly==false / points to the directory containing SBML, CellML, Sed-ML files, also OWL files can be processed
-type String annoOnly==false SBML

specifies the expected type of input SBML|CELLML|SEDML|OWL|P2M

P2M is working in the intended usage if one wants to index Path2Models files
-ontology String type==OWL / is expected when -type is OWL, used to define the ontology namespace
-quiet boolean false false rewires the stdOut to dev0, faster but no debugging
-noAnno boolean false false creates only the model structures but does not resolve and index model annotations
-annoOnly boolean false false creates only the annotation index
  • The arguments -noAnno and -annoOnly can not be used together, obviously.
  • If -annoOnly is provided all other parameters except for -dbPath are ignored.

Creating the annotation index is time consuming, it spawns several Threads, uses MiriamWebService to resolve all annotations into URLs and subsequently downloads several hundred webpages for text extraction and index creation.

MainIndex

  • entry point: de.unirostock.sems.masymos.main.MainIndex
Arguments
Argument Type Required Default Description
-dbPath String true / pointsthepath of your database, if no DB exists one will be created
-deleteIndex bool false false if true, delete all created index structures

MainAnalyzer

  • entry point: de.unirostock.sems.masymos.main.MainAnalyzer

The MainAnalyzer allows to play around with some customized analysers, for more information go. This is handy if you want to check how text and queries are processed.

MainQuery

  • entry point: de.unirostock.sems.masymos.main.MainQuery
Arguments
Argument Type Required Default Description
-dbPath String true / points the path of your database, if no DB exists one will be created