Search TP53 Somatic Mutation catalogue by exon and by effect according to the boolean operators (�and�, �or� and �butnot�) and retrieve full somatic mutation descriptions

Created: 2010-01-15 16:22:15

This workflow takes the exon, the effect and the TP53 somatic mutation database as input and retrieves the full TP53 somatic mutation description(s) by first retrieving two different outputs and arranging them according to the boolean operators (�and�, �or� and �butnot�): - first output: a TP53 somatic mutation database unique IDs list associated with the input 'exon' (done via a call to the getP53MutationIdsByExon web service) - second output: a TP53 somatic mutation database unique IDs list associated with the input 'effect' (done via a call to the getP53MutationIdsByEffect web service)and then using IDs for retrieving the full TP53 somatic mutations descriptions (done via a call to the getP53MutationsByIds web service) All these web services are available at the soaplab system at
A number or string list local elaborations (for both outputs) are now required:

- returned IDs are in a string and this must be transformed in a list (done by the 'Split_string_into_string_list_by_regular_expression' processor and by the 'Split_string_into_string_list_by_regular_expression_2' processor, that are implemented by using a Split_string_into_string_list_by_regular_expression local processor) - comparison of the two above outputs and identification of the common subset (done by the 'String_list_intersection' processor, that is implemented by using a String_list_intersection local processor) - returned IDs include catalogues' names and this must be removed before their utilization for further processing (done by the 'Filter_list_of_strings_extracting_match_to_a_regex' processor, that is implemented by using a Filter_list_of_strings_extracting_match_to_a_regex local processor)
Special requirements on input data are:

- the exon range of numbers is 2-11, - one or more of the following effects can be specified: 'fs' (frameshift), 'missense', 'na' (not available), 'nonsense', 'other', 'silent', 'splice'. Other values may lead to errors, - when specifying more than one exon or effect, they must be in a unique input string but on distinct text lines

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