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DataBiNS with Kegg ID

Workflow Entry: DataBiNS with Kegg ID

Created at: 09/07/09 @ 21:39:54 Last updated: 22/11/10 @ 23:16:42

Version 3 (latest) (of 3)

Version created on: 22/11/10 @ 23:16:38 by: Mark Wilkinson | Revision comments Expand

Title: DataBiNS with Kegg ID

Type: Taverna 2

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Description

Consumes a KEGG gene id and mines for pathway, GO, PubMed and SNP information about that gene

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Workflow Components

Authors (2)

Titles (1)

Descriptions (2)

Inputs (1)

Name	Description
id	This is a gene identifer in KEGG gene-id format

Processors (56)

Name	Type	Description
Remove_duplicate_strings2	localworker
nsSNP_amino_acid_variant_list_flatter	localworker
nsSNP_allele_list_flatter	localworker
pdb_file_flatter	localworker
base64_PNG	localworker
go_term_list_flatter	beanshell
publication_pubmed_id_list_flatter	beanshell
frequency_list_flatter	localworker
gene_name_list_flatter	beanshell
KEGG_NS	stringconstant
Entrez_NS	stringconstant
article_name	stringconstant
publication_journal_name_list_flatter	beanshell
go_term_definition_list_flatter	beanshell
Remove_duplicate_strings	localworker
frequency_id_list_flatter	localworker
entrez_gene_id_list_flatter	localworker
gene_description_list_flatter	localworker
nsSNP_codon_position_list_flatter	localworker
gene_id_list_flatter	localworker
gene_summary_list_flatter	beanshell
publication_abstract_list_flatter	beanshell
nsSNP_id_list_flatter	localworker
entrez_gene_list_flatter2	localworker
nsSNP_strand_list_flatter	localworker
go_term_accession_list_flatter	beanshell
publication_title_list_flatter	beanshell
nsSNP_amino_acid_position_list_flatter	localworker
pdb_rasmol_flatter	localworker
gene_synonyms_list_flatter	beanshell
publication_author_list_flatter	beanshell
pdb_id_flatter	localworker
Parse_Moby_Data_Swiss_Prot	biomoby
Parse_Moby_Data_GO_Term	biomoby
Parse_Moby_Data_entrez_gene	biomoby
getBase64SnpFrequencyImage	biomoby
Parse_Moby_Data_nsSNP	biomoby
convertSnp2EntrezGeneID	biomoby
Parse_Moby_Data_Publication	biomoby
snp2Frequencies	biomoby
getGeneInformationByEntrezGeneID	biomoby
getEntryFromPDB	biomoby
Gene2PubMed	biomoby
convertKeggGeneId2ProtId	biomoby
Parse_Moby_Data_Frequencies	biomoby
Parse_Moby_Data_gene_ref	biomoby
getSnpsBySwissProtId	biomoby
Parse_Moby_Data_rasmol	biomoby
PDB_id2RasMolScript	biomoby
Gene2Ontology	biomoby
CreateKeggId	biomoby
CreateEntrezGeneDataType	biomoby
ExtractPdbEntry	biomoby
Parse_Moby_Data_b64_Encoded_PNG	biomoby
convertUniProtId2PDBId	biomoby
Parse Moby Data(Object)	biomoby

Beanshells (11)

Name	Inputs	Outputs
go_term_list_flatter	inputlist	outputlist
publication_pubmed_id_list_flatter	inputlist	outputlist
gene_name_list_flatter	inputlist	outputlist
publication_journal_name_list_flatter	inputlist	outputlist
go_term_definition_list_flatter	inputlist	outputlist
gene_summary_list_flatter	inputlist	outputlist
publication_abstract_list_flatter	inputlist	outputlist
go_term_accession_list_flatter	inputlist	outputlist
publication_title_list_flatter	inputlist	outputlist
gene_synonyms_list_flatter	inputlist	outputlist
publication_author_list_flatter	inputlist	outputlist

Outputs (28)

Name	Description
nsSNP_id
nsSNP_codon_position
nsSNP_allele
nsSNP_strand
nsSNP_amino_acid_variant
nsSNP_amino_acid_position
swiss_prot_id
go_term_accession
go_term
go_term_definition
frequency
frequency_id
gene_id
gene_description
gene_name
gene_summary
gene_synonyms
entrez_gene_id
publication_author
publication_pubmed_id
publication_abstract
publication_title
publication_journal_name
kegg_gene_id
pdb_id
pdb_rasmol
base64_PNG
pdb_file

Datalinks (84)

Source	Sink
entrez_gene_id_list_flatter:outputlist	Remove_duplicate_strings2:stringlist
Parse_Moby_Data_nsSNP:snps_'aa_var'	nsSNP_amino_acid_variant_list_flatter:inputlist
Parse_Moby_Data_nsSNP:snps_'allele'	nsSNP_allele_list_flatter:inputlist
ExtractPdbEntry:entry_'content'	pdb_file_flatter:inputlist
Parse_Moby_Data_b64_Encoded_PNG:image_'content'	base64_PNG:inputlist
Parse_Moby_Data_GO_Term:terms_'Term'	go_term_list_flatter:inputlist
Parse_Moby_Data_Publication:id	publication_pubmed_id_list_flatter:inputlist
Parse_Moby_Data_Frequencies:Frequencies_'Frequency'	frequency_list_flatter:inputlist
Parse_Moby_Data_gene_ref:gene_info_'name'	gene_name_list_flatter:inputlist
Parse_Moby_Data_Publication:publications_'Journal'	publication_journal_name_list_flatter:inputlist
Parse_Moby_Data_GO_Term:terms_'Definition'	go_term_definition_list_flatter:inputlist
entrez_gene_list_flatter2:outputlist	Remove_duplicate_strings:stringlist
Parse_Moby_Data_Frequencies:id	frequency_id_list_flatter:inputlist
Parse_Moby_Data_entrez_gene:id	entrez_gene_id_list_flatter:inputlist
Parse_Moby_Data_gene_ref:gene_info_'description'	gene_description_list_flatter:inputlist
Parse_Moby_Data_nsSNP:snps_'codon_pos'	nsSNP_codon_position_list_flatter:inputlist
Parse_Moby_Data_gene_ref:id	gene_id_list_flatter:inputlist
Parse_Moby_Data_gene_ref:gene_info_'summary'	gene_summary_list_flatter:inputlist
Parse_Moby_Data_Publication:publications_'Abstract'	publication_abstract_list_flatter:inputlist
Parse_Moby_Data_nsSNP:id	nsSNP_id_list_flatter:inputlist
Parse_Moby_Data_entrez_gene:id	entrez_gene_list_flatter2:inputlist
Parse_Moby_Data_nsSNP:snps_'strand'	nsSNP_strand_list_flatter:inputlist
Parse_Moby_Data_GO_Term:id	go_term_accession_list_flatter:inputlist
Parse_Moby_Data_Publication:publications_'Title'	publication_title_list_flatter:inputlist
Parse_Moby_Data_nsSNP:snps_'aa_pos'	nsSNP_amino_acid_position_list_flatter:inputlist
Parse_Moby_Data_rasmol:rasmol_text_'content'	pdb_rasmol_flatter:inputlist
Parse_Moby_Data_gene_ref:gene_info_'synonyms'	gene_synonyms_list_flatter:inputlist
Parse_Moby_Data_Publication:publications_'Author'	publication_author_list_flatter:inputlist
Parse Moby Data(Object):id	pdb_id_flatter:inputlist
convertKeggGeneId2ProtId:Object(prot_id)	Parse_Moby_Data_Swiss_Prot:mobyData('Object')
Gene2Ontology:GO_Term(Collection - 'terms' As Simples)	Parse_Moby_Data_GO_Term:mobyData('GO_Term')
convertSnp2EntrezGeneID:Object(geneid)	Parse_Moby_Data_entrez_gene:mobyData('Object')
snp2Frequencies:Frequencies(Frequencies)	getBase64SnpFrequencyImage:Object(snpId)
getSnpsBySwissProtId:nsSNP(Collection - 'snps' As Simples)	Parse_Moby_Data_nsSNP:mobyData('nsSNP')
getSnpsBySwissProtId:nsSNP(Collection - 'snps' As Simples)	convertSnp2EntrezGeneID:Object(snp)
Gene2PubMed:Publication(Collection - 'publications' As Simples)	Parse_Moby_Data_Publication:mobyData('Publication')
getSnpsBySwissProtId:nsSNP(Collection - 'snps' As Simples)	snp2Frequencies:Object(snpid)
CreateEntrezGeneDataType:mobyData	getGeneInformationByEntrezGeneID:Object(geneid)
PDB_id2RasMolScript:text-formatted(rasmol_text)	getEntryFromPDB:Object(id)
CreateEntrezGeneDataType:mobyData	Gene2PubMed:Object(geneid)
CreateKeggId:mobyData	convertKeggGeneId2ProtId:Object(kegg_gene)
snp2Frequencies:Frequencies(Frequencies)	Parse_Moby_Data_Frequencies:mobyData('Frequencies')
getGeneInformationByEntrezGeneID:gene_ref(gene_info)	Parse_Moby_Data_gene_ref:mobyData('gene_ref')
convertKeggGeneId2ProtId:Object(prot_id)	getSnpsBySwissProtId:Object(id)
PDB_id2RasMolScript:text-formatted(rasmol_text)	Parse_Moby_Data_rasmol:mobyData('text-formatted')
convertUniProtId2PDBId:Object(Collection - 'pdb_ids')	PDB_id2RasMolScript:Object(pdb_id)
CreateEntrezGeneDataType:mobyData	Gene2Ontology:Object(gene)
KEGG_NS:value	CreateKeggId:namespace
article_name:value	CreateKeggId:article name
id	CreateKeggId:id
Entrez_NS:value	CreateEntrezGeneDataType:namespace
Remove_duplicate_strings:strippedlist	CreateEntrezGeneDataType:id
getEntryFromPDB:PDB-Text(entry)	ExtractPdbEntry:mobyData('PDB-Text')
getBase64SnpFrequencyImage:b64_Encoded_PNG(image)	Parse_Moby_Data_b64_Encoded_PNG:mobyData('b64_Encoded_PNG')
convertKeggGeneId2ProtId:Object(prot_id)	convertUniProtId2PDBId:Object(kegg_gene)
convertUniProtId2PDBId:Object(Collection - 'pdb_ids' As Simples)	Parse Moby Data(Object):mobyData('Object')
nsSNP_id_list_flatter:outputlist	nsSNP_id
nsSNP_codon_position_list_flatter:outputlist	nsSNP_codon_position
nsSNP_allele_list_flatter:outputlist	nsSNP_allele
nsSNP_strand_list_flatter:outputlist	nsSNP_strand
nsSNP_amino_acid_variant_list_flatter:outputlist	nsSNP_amino_acid_variant
nsSNP_amino_acid_position_list_flatter:outputlist	nsSNP_amino_acid_position
Parse_Moby_Data_Swiss_Prot:id	swiss_prot_id
go_term_accession_list_flatter:outputlist	go_term_accession
go_term_list_flatter:outputlist	go_term
go_term_definition_list_flatter:outputlist	go_term_definition
frequency_list_flatter:outputlist	frequency
frequency_id_list_flatter:outputlist	frequency_id
gene_id_list_flatter:outputlist	gene_id
gene_description_list_flatter:outputlist	gene_description
gene_name_list_flatter:outputlist	gene_name
gene_summary_list_flatter:outputlist	gene_summary
gene_synonyms_list_flatter:outputlist	gene_synonyms
Remove_duplicate_strings2:strippedlist	entrez_gene_id
publication_author_list_flatter:outputlist	publication_author
publication_pubmed_id_list_flatter:outputlist	publication_pubmed_id
publication_abstract_list_flatter:outputlist	publication_abstract
publication_title_list_flatter:outputlist	publication_title
publication_journal_name_list_flatter:outputlist	publication_journal_name
id	kegg_gene_id
pdb_id_flatter:outputlist	pdb_id
pdb_rasmol_flatter:outputlist	pdb_rasmol
base64_PNG:outputlist	base64_PNG
pdb_file_flatter:outputlist	pdb_file

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Information Workflow Type

Taverna 2

Information Original Uploader

Mark Wilkinson

Information License

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Information Ratings (2)

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Information Statistics

726 viewings

853 downloads

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Citations (0)

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Version History

Earliest Version:
[1] - DataBiNS

Created on: Tuesday 19 May 2009 @ 18:25:40 (GMT)

Created by: Mark Wilkinson

Revision comments:

None

Previous Versions:
[2] - DataBiNS

Created on: Thursday 09 July 2009 @ 21:39:54 (GMT)

Created by: Mark Wilkinson

Last edited on: Monday 22 November 2010 @ 23:15:14 (GMT)

Last edited by: Mark Wilkinson

Revision comments:

Previous workflow was not properly flattening some of the PubMed information, so it never made it into the output bin. This version is also properly annotated with an example input.

Latest Version:
[3] - DataBiNS with Kegg ID

Created on: Monday 22 November 2010 @ 23:16:38 (GMT)

Created by: Mark Wilkinson

Revision comments:

switched default input suggestion to a new valid KEGG gene Identifier (previous one didn't return hits in all cases)