Search TP53 Somatic Mutation catalogue by exon and effect and retrieve full somatic mutation descriptions

Created: 2010-01-15 16:23:23

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: - 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 http://bioinformatics.istge.it:8080/axis/services
A number or string list local elaborations (for both outputs) are 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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