Retrieve TP53 mutations for CABRI cell-lines

Created: 2010-01-12 13:58:46

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This workflow retrieve information on known TP53 mutations (from IARC TP53 Mutation Database as implemented in SRS at IST, Genoa) for all cell lines included in a given CABRI collection of human and animal cel lines. The result consists in the list of all cell lines' descriptions each of which is followed by the related information on mutations.

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Workflow Components

Inputs (1)

Name	Description
cell_line_lib

Processors (25)

Name	Type	Description
token_position	stringconstant
label_identifier_regex	stringconstant
split_list_regex	stringconstant
tp53_somatic_database	stringconstant
wild_card	stringconstant
tp53_iarc_label_separator	stringconstant
Remove_any_blank_space	beanshell
Remove_any_minus_character	beanshell
String_Constant	stringconstant
Filter_list_of_strings_extracting_match_to_a_regex_for_tp53	local
Split_string_into_string_list_by_regular_expression	local
String_list_intersection	local
Filter_list_of_strings_extracting_match_to_a_regex	local
Filter_list_of_strings_extracting_match_to_a_regex1	local
Split_string_into_string_list_by_regular_expression_for_tp53	local
Filter_list_of_strings_extracting_match_to_a_regex2	local
Get_pubmed_xml_by_pmid	local
Concatenate_two_strings	local
getP53MutationIdsBySampleName	soaplabwsdl	Get tp53 gene mutation ids by sample (cell line) name from IARC TP53 Database catalogue (see srs.o2i.it/srs71/)
getP53SampleNames	soaplabwsdl	Get tp53 gene mutation sample (cell line) names from IARC TP53 Database catalogue (see srs.o2i.it/srs71/)
getCellLineByName	soaplabwsdl	Get cell lines by name from CABRI human and animal cell lines catalogues (see www.cabri.org)
getP53PubMedIdByIds	soaplabwsdl	Get PubMed id by tp53 mutation ids from IARC TP53 Database catalogue (see srs.o2i.it/srs71/)
Retrieve_all_cell_line_names	soaplabwsdl	Get cell lines names from CABRI human and animal cell lines catalogues (see www.cabri.org)
getP53MutationsBySampleName	soaplabwsdl	Get tp53 mutations by sample (cell line) name from IARC TP53 Database catalogue (see srs.o2i.it/srs71/)
Concatenate_two_strings1	local

Beanshells (2)

Name	Description	Inputs	Outputs
Remove_any_blank_space		input_str	output_str
Remove_any_minus_character		input_str	output_str

Outputs (1)

Name	Description
result

Links (37)

Source	Sink
cell_line_lib	Retrieve_all_cell_line_names:libs
Retrieve_all_cell_line_names:result	Split_string_into_string_list_by_regular_expression:string
split_list_regex:value	Split_string_into_string_list_by_regular_expression:regex
Split_string_into_string_list_by_regular_expression:split	Filter_list_of_strings_extracting_match_to_a_regex:stringlist
token_position:value	Filter_list_of_strings_extracting_match_to_a_regex:group
label_identifier_regex:value	Filter_list_of_strings_extracting_match_to_a_regex:regex
wild_card:value	Retrieve_all_cell_line_names:id
wild_card:value	getP53SampleNames:id
tp53_somatic_database:value	getP53SampleNames:libs
getP53SampleNames:result	Split_string_into_string_list_by_regular_expression_for_tp53:string
split_list_regex:value	Split_string_into_string_list_by_regular_expression_for_tp53:regex
token_position:value	Filter_list_of_strings_extracting_match_to_a_regex_for_tp53:group
tp53_iarc_label_separator:value	Filter_list_of_strings_extracting_match_to_a_regex_for_tp53:regex
Split_string_into_string_list_by_regular_expression_for_tp53:split	Filter_list_of_strings_extracting_match_to_a_regex_for_tp53:stringlist
Filter_list_of_strings_extracting_match_to_a_regex:filteredlist	String_list_intersection:list1
Filter_list_of_strings_extracting_match_to_a_regex_for_tp53:filteredlist	String_list_intersection:list2
tp53_somatic_database:value	getP53MutationsBySampleName:libs
String_list_intersection:intersection	Remove_any_blank_space:input_str
Remove_any_blank_space:output_str	Remove_any_minus_character:input_str
Remove_any_minus_character:output_str	getP53MutationsBySampleName:sample
cell_line_lib	getCellLineByName:libs
Remove_any_minus_character:output_str	getCellLineByName:sample
getCellLineByName:result	Concatenate_two_strings:string1
getP53MutationsBySampleName:result	Concatenate_two_strings:string2
tp53_somatic_database:value	getP53MutationIdsBySampleName:libs
Remove_any_minus_character:output_str	getP53MutationIdsBySampleName:sample
getP53MutationIdsBySampleName:result	Filter_list_of_strings_extracting_match_to_a_regex1:stringlist
token_position:value	Filter_list_of_strings_extracting_match_to_a_regex1:group
Filter_list_of_strings_extracting_match_to_a_regex1:filteredlist	getP53PubMedIdByIds:id
String_Constant:value	Filter_list_of_strings_extracting_match_to_a_regex1:regex
String_Constant:value	Filter_list_of_strings_extracting_match_to_a_regex2:regex
token_position:value	Filter_list_of_strings_extracting_match_to_a_regex2:group
Filter_list_of_strings_extracting_match_to_a_regex2:filteredlist	Get_pubmed_xml_by_pmid:id
getP53PubMedIdByIds:result	Filter_list_of_strings_extracting_match_to_a_regex2:stringlist
Concatenate_two_strings:output	Concatenate_two_strings1:string1
Get_pubmed_xml_by_pmid:outputText	Concatenate_two_strings1:string2
Concatenate_two_strings1:output	result

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Information Workflow Type

Taverna 1

Information Uploader

Paolo Romano

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Information Statistics

2994 viewings

2255 downloads

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Version History

In chronological order:

untitled

Created by Paolo Romano on Wednesday 03 October 2007 18:36:20 (UTC)
Retrieve TP53 mutations for CABRI cell lines

Created by Paolo Romano on Wednesday 03 October 2007 18:36:20 (UTC)

Last edited by Paolo Romano on Wednesday 03 October 2007 18:36:21 (UTC)
Retrieve TP53 mutations for CABRI cell-lines

Created by Paolo Romano on Tuesday 12 January 2010 13:58:46 (UTC)

Revision comment:

The workflow has been adapted to the revised structure of the IARC TP53 Mutation database (release 14, Nov. 2009), as implemented in SRS in Jan 2010.

Moreover, the following refinements were implemented:

- a new beanshell script removes possible "/" characters from cell line names, as in "PLC/PRF/5"

- the getP53PubMedIdByIds processor has been substituted with the new getP53PubMedIdByRefId (Get PubMed Id by Reference Id from IARC TP53 Database catalogue) Web Service,also due to the new structure,

- the processor Filter_list_of_strings_extracting_match_to_a_regex2<x-tab> was modified and renamed.</x-tab>