User Guide, 21 May 2009 © Copyright ISAteam 1 ISAconfigurator for ISAcreator User Guide Alpha version: May 2009 Contact: Download:

User Guide, 21 May 2009 © Copyright ISAteam 2 ISAconfigurator INTRODUCTION A standalone Java application to regulate ISA-Tab fields in the ISAcreator, editor tool –The ISAconfigurator is not intended for the experimentalists/data producers but for those supporting them in the collection, annotation and storage process, i.e. curators and developers –A configuration should be defined by the last group of users and saved into the ISAcreator tool package to be distributed to the experimentalists ISAconfigurator allows you to –Restrict a field for taking values and limit the search to one of any of the ontologies served by the Ontology Lookup Service and BioPortal or allow to search all Ontology Lookup ServiceBioPortal Note that due to the limitation of this alpha release, you cannot yet limit the search to two, or a subset of ontologies –Enforce a particular data type validation using regular expressions –Mandate certain fields to comply with minimum reporting guidelines –Enforce a particular range of values using predefined lists –Specify the type of the following ISA-Tab elements: Characteristic[ ], Factor[ ], Parameter [ ] and Comment[ ] Note that due to the limitation of this alpha release, you cannot yet specify Parameter[ ] –Note that due to the limitation of this alpha release, the tool allows you to remove ISA-Tab elements; this, however, should not be done as it produces invalid configuration files that will not load into ISAcreator and consequently fail to meet the the ISAvalidator requirements

User Guide, 21 May 2009 © Copyright ISAteam 3 The ISAconfigurator is distributed with an example of configuration file: >. You can open it or edit it or create your specific one, following the ISA-Tab specification.ISA-Tab specification ISAconfigurator MAIN MENU

User Guide, 21 May 2009 © Copyright ISAteam 4 ISAconfigurator FUNCTIONALITIES (1) The field definition screen is divided in 3 sections: the left most section, ‘tables’, lists the various tables implementing the ISA-Tab specifications; the middle section, ‘elements’, lists all the fields defining a table (here the element and up/down buttons enable adding and ordering field within a table); and the right most section, ‘field definition’, allow you to regulate a given field.

User Guide, 21 May 2009 © Copyright ISAteam 5 ISAconfigurator FUNCTIONALITIES (2) ‘Field definition’ section. You can regulate a field by specifying the type in its name, for the following ISA-Tab elements only: Characteristic[ ], Factor[ ], Comment[ ] and Parameter [ ] the latter not yet available in this alpha release). For example Characteristic[specie], Characteristic[cell type], Characteristic[provider] etc, and Factor[compound], Factor[dose], Factor[unit], etc. Comment [ ] accommodates fields that are neither Characteristic, nor Parameter nor Factor, for example Comment [compound class]; refer to the ISA-Tab specification for more information. You can also regulate a field by specifying the data type (i.e. string, list, ontology term) and it behavioral attributes (i.e. whether it is required to comply with minimum reporting guidelines). Also depending on the data type selected, additional restrictions may be defined (see next slide).ISA-Tab specification

User Guide, 21 May 2009 © Copyright ISAteam 6 ISAconfigurator FUNCTIONALITIES (3) ‘String’ as data type. By ticking the box ‘is the input formatted’ you display the ‘input format’ field which can be used to define a regular expression and test it with the ‘CheckRegex’ widget before saving the configuration.

User Guide, 21 May 2009 © Copyright ISAteam 7 ISAconfigurator FUNCTIONALITIES (4) ‘OntologyEntry’ as data type. By default the search of terms is open to all the ontologies served by the Ontology Lookup Service and BioPortal. To limit the search to one ontology only, you tick the ‘use of recommended ontology source’ box and select the one of interest.Ontology Lookup Service BioPortal

User Guide, 21 May 2009 © Copyright ISAteam 8 ISAconfigurator SAVE/EXPORT When your configuration is complete, you (1) save the.tco file in the ISAconfigurator folder or elsewhere, for your reference and future editing, and (2) export the table configuration files in a folder to be named >. To use this new configuration in the ISAcreator, you have manually replace the existing > folder (distributed as default example with the ISAcreator) with the one you have created. This is due to the limitation of this alpha release, but it will be solved in the next version.