WORKFLOWS LIST

Get TP53 Mutation Function Entries and TP53 Cell Line Entries by Mutated Aminoacid and Codon Number
This workflow retrieves from two different databases two distinct set of entries starting from the same inputs data (i.e. the Mutated Aminoacid encoded at the codon in which the mutation occurred, and the Codon Number where the mutation occurs). Here follows a short description of the workflow itself: Input data: Mutant Amino Acid encoded at the codon in which the mutation occurred and Codon Number where the mutation is located Main workflow steps: - Retrieval of the complete list of ids of tp53 cell line status database which present mutations for the specified Mutant Amino Acid (done with a call to the 'Getp53CellLineIdsByMutAa' web service) - Retrieval of the complete list of ids of tp53 cell line status database which present mutations for the specified Codon Number (done with a call to the 'Getp53CellLineIdsByCodonNumber' web service) - Arrangement of the two above lists and identification/extraction of the Ids numeric values (done after local elaborations of both outputs; i.e. IDs are returned in two strings which must be transformed in lists (done by two specific 'SplitStringIntoStringListByRegularExpression' processors , then from the lists the numeric values of the identifiers are retrieved by means of two specific 'ExtractIdsFromCellLines' processors) - Specific comparison of the two above outputs and identification of the common subset (done by the 'Tp53CellLineFieldsIntersection' processor) - Retrieval of tp53 cell line status database records using as input the common subset identified (done with a call to the 'getP53CellLinesStatusEntryById' web service) - Retrieval of the complete list of ids of p53 mutant function database which present mutations for the specified Mutant Amino Acid (done with a call to the 'getMutantFunctionIdsByMutAa' web service) - Retrieval of the complete list of ids of p53 mutant function which present mutations for the specified Codon Number (done with a call to the 'getMutantFunctionIdsByCodonNumber' web service) - Arrangement of the two above lists and identification/extraction of the Ids numeric values (done after local elaborations of both outputs; i.e. IDs are returned in two strings which must be transformed in lists (done by two specific 'SplitStringIntoStringListByRegularExpression' processors , then from the lists the numeric values of the identifiers are retrieved by means of two specific 'ExtractIdsFromMutationFunction' processors) - Specific comparison of the two above outputs and identification of the common subset (done by the 'Tp53MutationFunctionFieldsIntersection' processor) - Retrieval of p53 mutant function database records using as input the common subset identified (done with a call to the 'getP53mutationFunctionEntryById' web service) Output: Two distinct records sets: one set of tp53 cell line status entries and another of p53 mutant function entries that have in common the same Mutated Amino Acid on the same Codon Number All these web services are available at the soaplab system at http://www.o2i.it:8080/axis/services Special requirements on input data are: - the MutAA (Mutated Amino Acid) in three letters code (Gly, Ala, Trp, Phe etc.) - the Codon Number range is 1-393, - other values may lead to errors, - when specifying more than one MutAA or Codon Number, they must be in a unique input string but on distinct text lines Get the workflow code in XML or, if you prefer, in TXT

Get TP53 Mutation Function Entries and TP53 Cell Line Entries by Mutated Aminoacid and Codon Number

This workflow retrieves from two different databases two distinct set of entries starting from the same inputs data (i.e. the Mutated Aminoacid encoded at the codon in which the mutation occurred, and the Codon Number where the mutation occurs). Here follows a short description of the workflow itself:
Input data: Mutant Amino Acid encoded at the codon in which the mutation occurred and Codon Number where the mutation is located Main workflow steps:
- Retrieval of the complete list of ids of tp53 cell line status database which present mutations for the specified Mutant Amino Acid (done with a call to the 'Getp53CellLineIdsByMutAa' web service)
- Retrieval of the complete list of ids of tp53 cell line status database which present mutations for the specified Codon Number (done with a call to the 'Getp53CellLineIdsByCodonNumber' web service)
- Arrangement of the two above lists and identification/extraction of the Ids numeric values (done after local elaborations of both outputs; i.e. IDs are returned in two strings which must be transformed in lists (done by two specific 'SplitStringIntoStringListByRegularExpression' processors , then from the lists the numeric values of the identifiers are retrieved by means of two specific 'ExtractIdsFromCellLines' processors)
- Specific comparison of the two above outputs and identification of the common subset (done by the 'Tp53CellLineFieldsIntersection' processor)
- Retrieval of tp53 cell line status database records using as input the common subset identified (done with a call to the 'getP53CellLinesStatusEntryById' web service)
- Retrieval of the complete list of ids of p53 mutant function database which present mutations for the specified Mutant Amino Acid (done with a call to the 'getMutantFunctionIdsByMutAa' web service)
- Retrieval of the complete list of ids of p53 mutant function which present mutations for the specified Codon Number (done with a call to the 'getMutantFunctionIdsByCodonNumber' web service)
- Arrangement of the two above lists and identification/extraction of the Ids numeric values (done after local elaborations of both outputs; i.e. IDs are returned in two strings which must be transformed in lists (done by two specific 'SplitStringIntoStringListByRegularExpression' processors , then from the lists the numeric values of the identifiers are retrieved by means of two specific 'ExtractIdsFromMutationFunction' processors)
- Specific comparison of the two above outputs and identification of the common subset (done by the 'Tp53MutationFunctionFieldsIntersection' processor) - Retrieval of p53 mutant function database records using as input the common subset identified (done with a call to the 'getP53mutationFunctionEntryById' web service)
Output: Two distinct records sets: one set of tp53 cell line status entries and another of p53 mutant function entries that have in common the same Mutated Amino Acid on the same Codon Number
All these web services are available at the soaplab system at http://www.o2i.it:8080/axis/services
Special requirements on input data are:
- the MutAA (Mutated Amino Acid) in three letters code (Gly, Ala, Trp, Phe etc.)
- the Codon Number range is 1-393,
- other values may lead to errors,
- when specifying more than one MutAA or Codon Number, they must be in a unique input string but on distinct text lines

Get the workflow code in XML or, if you prefer, in TXT

Get TP53 Mutations by Exon
This workflow takes the exon and the TP53 somatic mutation database as input and retrieve the full TP53 somatic mutation description(s) by first retrieving the TP53 somatic mutation database unique IDs associated with the input (done via a call to the getP53MutationIdsByExon web service) and then using IDs for retrieving the full TP53 somatic mutations descriptions (done via a call to the getP53MutationsByIds web service). Both these web services are available at the soaplab system at http://www.o2i.it:8080/axis/services A number of string or string list local elaborations 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, that is implemented by using a Split_string_into_string_list_by_regular_expression 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, - when specifying more than one exon, they must be in a unique input string but on distinct text lines Get the workflow code in XML or, if you prefer, in TXT

Get TP53 Mutations by Exon

This workflow takes the exon and the TP53 somatic mutation database as input and retrieve the full TP53 somatic mutation description(s) by first retrieving the TP53 somatic mutation database unique IDs associated with the input (done via a call to the getP53MutationIdsByExon web service) and then using IDs for retrieving the full TP53 somatic mutations descriptions (done via a call to the getP53MutationsByIds web service). Both these web services are available at the soaplab system at http://www.o2i.it:8080/axis/services
A number of string or string list local elaborations 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, that is implemented by using a Split_string_into_string_list_by_regular_expression 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,
- when specifying more than one exon, they must be in a unique input string but on distinct text lines

Get the workflow code in XML or, if you prefer, in TXT

Get TP53 Mutations by Intron
This workflow takes the intron and the TP53 somatic mutation database as input and retrieve the full TP53 somatic mutation description(s) by first retrieving the TP53 somatic mutation database unique IDs associated with the input (done via a call to the getP53MutationIdsByIntron web service) and then using IDs for retrieving the full TP53 somatic mutations descriptions (done via a call to the getP53MutationsByIds web service). Both these web services are available at the soaplab system at http://www.o2i.it:8080/axis/services A number of string or string list local elaborations 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, that is implemented by using a Split_string_into_string_list_by_regular_expression 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 intron range of numbers is 2-11, - when specifying more than one intron, they must be in a unique input string but on distinct text lines Get the workflow code in XML or, if you prefer, in TXT

Get TP53 Mutations by Intron

This workflow takes the intron and the TP53 somatic mutation database as input and retrieve the full TP53 somatic mutation description(s) by first retrieving the TP53 somatic mutation database unique IDs associated with the input (done via a call to the getP53MutationIdsByIntron web service) and then using IDs for retrieving the full TP53 somatic mutations descriptions (done via a call to the getP53MutationsByIds web service). Both these web services are available at the soaplab system at http://www.o2i.it:8080/axis/services
A number of string or string list local elaborations 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, that is implemented by using a Split_string_into_string_list_by_regular_expression 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 intron range of numbers is 2-11,
- when specifying more than one intron, they must be in a unique input string but on distinct text lines

Get the workflow code in XML or, if you prefer, in TXT

Get TP53 Mutations by Exon and Effect
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://www.o2i.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 Get the workflow code in XML or, if you prefer, in TXT

Get TP53 Mutations by Exon and Effect

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://www.o2i.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

Get the workflow code in XML or, if you prefer, in TXT

Get TP53 Mutations by Exon and Effect Arranged According to Different Boolean Combinations
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 http://www.o2i.it:8080/axis/services 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 Get the workflow code in XML or, if you prefer, in TXT

Get TP53 Mutations by Exon and Effect Arranged According to Different Boolean Combinations

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 http://www.o2i.it:8080/axis/services
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

Get the workflow code in XML or, if you prefer, in TXT

Get TP53 Mutations by Intron and Effect
This workflow takes the intron, 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 intron (done via a call to the getP53MutationIdsByIntron web service) - second otput: 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://www.o2i.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 intron 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 intron or effect, they must be in a unique input string but on distinct text lines Get the workflow code in XML or, if you prefer, in TXT

Get TP53 Mutations by Intron and Effect

This workflow takes the intron, 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 intron (done via a call to the getP53MutationIdsByIntron web service)
- second otput: 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://www.o2i.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 intron 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 intron or effect, they must be in a unique input string but on distinct text lines

Get the workflow code in XML or, if you prefer, in TXT

Get TP53 Mutations by Intron and Effect Arranged According to Different Boolean Combinations
This workflow takes the intron, 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 'intron' (done via a call to the getP53MutationIdsByIntron 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://www.o2i.it:8080/axis/services 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 intron 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 intron or effect, they must be in a unique input string but on distinct text lines Get the workflow code in XML or, if you prefer, in TXT

Get TP53 Mutations by Intron and Effect Arranged According to Different Boolean Combinations

This workflow takes the intron, 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 'intron' (done via a call to the getP53MutationIdsByIntron 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://www.o2i.it:8080/axis/services
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 intron 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 intron or effect, they must be in a unique input string but on distinct text lines

Get the workflow code in XML or, if you prefer, in TXT

Retrieve Cell Lines Descriptions By Name
This workflow takes the cell line name and the catalogue(s) name(s) as input and retrieve the full cell line description(s) by first retrieving the cell lines' unique IDs associated with the input (done via a call to the getCellLineIdsByName web service) and then using IDs for retrieving the full cell lines descriptions (done via a call to the getCellLinesByIds web service). Both these web services are available at the soaplab system at http://www.o2i.it:8080/axis/services A number of string or string list local elaborations are required: - returned IDs are in a string and this must be transformed in a list (done by the 'Separate_cell_line_ids' processor, that is implemented by using a Split_string_into_string_list_by_regular_expression local processor) - returned IDs include catalogues' names and this must be removed before their utilization for further processing (done by the 'Extract_ids_by_removing_catalogues_names' processor, that is implemented by using a Filter_list_of_strings_extracting_match_to_a_regex local processor) - returned IDs include a blank character and this must be substituteb by a '_SP_' characters string before submissing the data to the 'getCellLinesByIds' web service (done by a trivial beanshell script). Special requirements on input data are: - one or more of the following catalogues names can be specified: 'iclc', 'ecacc_cell', 'dsmz_mutz'. Other names may lead to errors, - when specifying more than one catalogue names, they must be in a unique input string but on distinct text lines, - cell lines names can only be made by a single word, excluding special characters as '/','-' and '*', - cell lines names are case insensitive. Example of valid cell lines names are: - vero - hela - a172 - calu6 Get the workflow code in XML or, if you prefer, in TXT

Retrieve Cell Lines Descriptions By Name

This workflow takes the cell line name and the catalogue(s) name(s) as input and retrieve the full cell line description(s) by first retrieving the cell lines' unique IDs associated with the input (done via a call to the getCellLineIdsByName web service) and then using IDs for retrieving the full cell lines descriptions (done via a call to the getCellLinesByIds web service). Both these web services are available at the soaplab system at http://www.o2i.it:8080/axis/services
A number of string or string list local elaborations are required: - returned IDs are in a string and this must be transformed in a list (done by the 'Separate_cell_line_ids' processor, that is implemented by using a Split_string_into_string_list_by_regular_expression local processor) - returned IDs include catalogues' names and this must be removed before their utilization for further processing (done by the 'Extract_ids_by_removing_catalogues_names' processor, that is implemented by using a Filter_list_of_strings_extracting_match_to_a_regex local processor) - returned IDs include a blank character and this must be substituteb by a '_SP_' characters string before submissing the data to the 'getCellLinesByIds' web service (done by a trivial beanshell script).
Special requirements on input data are: - one or more of the following catalogues names can be specified: 'iclc', 'ecacc_cell', 'dsmz_mutz'. Other names may lead to errors, - when specifying more than one catalogue names, they must be in a unique input string but on distinct text lines, - cell lines names can only be made by a single word, excluding special characters as '/','-' and '*', - cell lines names are case insensitive.
Example of valid cell lines names are: - vero - hela - a172 - calu6

Get the workflow code in XML or, if you prefer, in TXT

Retrieve Descriptions of Bacteria Strains
Retrieve full descriptions of bacteria strains from CABRI catalogues (see CABRI site) by their scientific name (genus and species only). Inputs of the workflow are the name of the involved CABRI catalogues (text/plain string with one catalogue name per line) and the scientific name of the desired bacteria strain (a text/plain string including genus and species separated by a blank space). Data is retrieved from CABRI Web Services in two steps. First, all bacteria strains IDs are retrieved by using the getBacteriaIdsByName method, and after descriptions are retrieved by using the getBacteriaById method. Some list/text elaboration is required to remove catalogue names from returned IDs and to substitute blank spaces with the '_SP_' string in the search terms. Get the workflow code in XML or, if you prefer, in TXT

Retrieve Descriptions of Bacteria Strains

Retrieve full descriptions of bacteria strains from CABRI catalogues (see CABRI site) by their scientific name (genus and species only).
Inputs of the workflow are the name of the involved CABRI catalogues (text/plain string with one catalogue name per line) and the scientific name of the desired bacteria strain (a text/plain string including genus and species separated by a blank space).
Data is retrieved from CABRI Web Services in two steps. First, all bacteria strains IDs are retrieved by using the getBacteriaIdsByName method, and after descriptions are retrieved by using the getBacteriaById method.
Some list/text elaboration is required to remove catalogue names from returned IDs and to substitute blank spaces with the '_SP_' string in the search terms.

Get the workflow code in XML or, if you prefer, in TXT