complete_2_text_mining.xml

Created: 2008-07-12 09:33:56 Last updated: 2008-07-12 09:35:15

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Workflow Components

Inputs (0)

Processors (29)

Name	Type	Description
end	stringconstant
regex1	stringconstant
split_by_regex_2	local
comma	stringconstant
split_by_regex_3	local
array_name	stringconstant
chromosome	stringconstant
comma_separated	stringconstant
split_by_regex_4	local
start	stringconstant
getcurrentdatabase	soaplabwsdl	Retrieves the current databases from ENSEMBL for a species
Remove_duplicates	workflow
Parse_swiss_ids	workflow
split_by_regex	local
merge_list_2	local
regex_2	stringconstant
species	stringconstant
merge_string_list	local
merge_list_3	local
Remove_gene_nulls	workflow
Probesets_to_genes	workflow
Remove_swiss_nulls	workflow
Ensembl_gene_info	workflow
Uniprot_record_search	workflow
getgenesbyspecies	soaplabwsdl	Retrieves a list of Ensembl genes for a given species, chromosome and position
Probeset_in_QTL	workflow
Text_mining	workflow
Parse_gene_name	workflow
remove_genes_from_probesets	beanshell

Beanshells (5)

Name	Inputs	Outputs
parse_swiss	input	output
remove_Nulls	input	output
remove_Nulls	input	output
parse_gene_info	input	output
remove_genes_from_probesets	input	output

Outputs (9)

Name	Description
current_database
genes_in_region
gene_info
probesets_in_qtl
genes_from_probesets
swiss_prot
gene_name
uniprot_records
text_mining_url

Links (47)

Source	Sink
Ensembl_gene_info:gene_info	Parse_gene_name:gene_info
Ensembl_gene_info:gene_info	Parse_swiss_ids:gene_info
Parse_gene_name:gene_name	Remove_gene_nulls:input_string
Parse_swiss_ids:swiss_ids	Remove_swiss_nulls:input_string
Probeset_in_QTL:probesets_in_qtl	split_by_regex:string
Probesets_to_genes:genes_from_probeset	remove_genes_from_probesets:input
Remove_duplicates:unique_list	split_by_regex_3:string
Remove_swiss_nulls:removed_nulls	split_by_regex_2:string
Uniprot_record_search:uniprot_record	merge_list_2:stringlist
array_name:value	Probeset_in_QTL:array_name
chromosome:value	Probeset_in_QTL:chromosome
chromosome:value	Probesets_to_genes:chromosome
chromosome:value	getgenesbyspecies:chromo
comma:value	merge_string_list:seperator
comma_separated:value	merge_list_3:seperator
end:value	Probeset_in_QTL:end
end:value	Probesets_to_genes:end
end:value	getgenesbyspecies:end
getcurrentdatabase:output	Probeset_in_QTL:database
getcurrentdatabase:output	Probesets_to_genes:database
getcurrentdatabase:output	getgenesbyspecies:database
getgenesbyspecies:output	Remove_duplicates:input_list_2
merge_list_3:concatenated	Text_mining:terms
merge_string_list:concatenated	Probesets_to_genes:probeset_list
remove_genes_from_probesets:output	Remove_duplicates:input_list_1
Ensembl_gene_info:gene_info	gene_info
Parse_swiss_ids:swiss_ids	swiss_prot
Probeset_in_QTL:probesets_in_qtl	probesets_in_qtl
Probesets_to_genes:genes_from_probeset	genes_from_probesets
Remove_gene_nulls:removed_nulls	gene_name
Remove_gene_nulls:removed_nulls	split_by_regex_4:string
Text_mining:output	text_mining_url
merge_list_2:concatenated	uniprot_records
regex1:value	split_by_regex:regex
regex_2:value	split_by_regex_2:regex
regex_2:value	split_by_regex_3:regex
regex_2:value	split_by_regex_4:regex
species:value	getcurrentdatabase:species
split_by_regex:split	merge_string_list:stringlist
split_by_regex_2:split	Uniprot_record_search:swissprot_id
split_by_regex_3:split	Ensembl_gene_info:genes_in_region
split_by_regex_4:split	merge_list_3:stringlist
start:value	Probeset_in_QTL:start
start:value	Probesets_to_genes:start
start:value	getgenesbyspecies:start
getcurrentdatabase:output	current_database
getgenesbyspecies:output	genes_in_region

Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Antoon Goderis

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Paul Fisher

Information Attributions (0)

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None

Information Tags (1)

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benchmarks

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Information Shared with Groups (0)

None

Information Featured In Packs (1)

Paul Fisher workflows for benchmarks PR and CA2

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Information Attributed By (0)

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Information Favourited By (0)

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Information Statistics

2029 viewings

1984 downloads

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Citations (0)

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Version History

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complete_2_text_mining.xml

Created by Antoon Goderis on Saturday 12 July 2008 09:33:56 (UTC)

Last edited by Antoon Goderis on Saturday 12 July 2008 09:35:15 (UTC)