Workflow Entry: DataBiNS - Data Mining Workflow for Biological Pathways and Non-Synonymous SNPs

Created at: 04/12/07 @ 23:43:03 Last updated: 04/12/07 @ 23:45:25

Version 2 (latest) (of 2)

Version created on: 04/12/07 @ 23:43:01 by: Fong Chun Chan | Revision comments Expand

Last edited on: 04/12/07 @ 23:45:25 by: Fong Chun Chan

Title: DataBiNS - Data Mining Workflow for Biological Pathways and Non-Synonymous SNPs

Type: Taverna 1

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Workflow Components

Inputs (1)

Name	Description
id

Processors (32)

Name	Type	Description
KEGG_NS	stringconstant
Entrez_NS	stringconstant
entrez_gene_id_list_flatter	local
Remove_duplicate_strings	local
entrez_gene_list_flatter2	local
Remove_duplicate_strings2	local
Parse_Moby_Data_nsSNP	biomobyparser	Processor to parse the datatype nsSNP
Parse_Moby_Data_GO_Term	biomobyparser	Processor to parse the datatype GO_Term
getGeneInformationByEntrezGeneID	biomobywsdl	This service consumes an identifier under the EntrezGene_ID / EntrezGene_EntrezGeneID namespaces. Using the input identifier, any relevant gene information is returned regarding that particular gene id.
Gene2Ontology	biomobywsdl	This service consumes an identifier under the EntrezGene_EntrezGeneID / EntrezGene_ID namespaces. This identifier is then used to query for any associated GO_Terms.
Parse_Moby_Data_Frequencies	biomobyparser	Processor to parse the datatype Frequencies
Parse_Moby_Data_entrez_gene	biomobyparser	Processor to parse the datatype Object
getSnpsBySwissProtId	biomobywsdl	This service consumes an identifier under the Swiss-Prot / UniProt namespace. Using the input identifier, relevant snp data is returned.
convertKeggGeneId2PDBId	biomobywsdl	This service consumes an identifier under the KEGG namespace. This identifier is then queried against the KEGG DB and all PDB records are returned.
getBase64SnpFrequencyImage	biomobywsdl	This service returns the hapmap SNP frequency image in a base64 format.
Parse_Moby_Data_Publication	biomobyparser	Processor to parse the datatype Publication
Parse_Moby_Data_Swiss_Prot	biomobyparser	Processor to parse the datatype Object
getEntryFromPDB	biomobywsdl	Retrieves an entry from PDB database.
convertSnp2EntrezGeneID	biomobywsdl	This service consumes an identifier under the NCBI_dbSNP namespace. The identifier is then converted into an EntrezGene_ID
Parse_Moby_Data_pdb_id	biomobyparser	Processor to parse the datatype Object
snp2Frequencies	biomobywsdl	Retrieves a list of genotype and allele frequencies for non-synonymous SNPs genotyped by HapMap (www.hapmap.org) from the snp input identifier.
getKeggIdsByKeggPathway	biomobywsdl	This service, given a KEGG pathway, searches for all known genes on that pathway.
Gene2PubMed	biomobywsdl	Enter the EntrezGene ID (ie. 5211 for gene pfkl - phosphofructokinase, liver) to lretrieve list of references and abstracts of publications related to the gene of your interest.
convertKeggGeneId2ProtId	biomobywsdl	This service consumes an identifier under the KEGG namespace. This identifier is then 'transformed' into a corresponding swissprot/uniprot identifier.
Parse_Moby_Data_kegg_gene	biomobyparser	Processor to parse the datatype Object
Parse_Moby_Data_rasmol	biomobyparser	Processor to parse the datatype text-formatted
CreateEntrezGeneDataType	biomobyobject	an object
Parse_Moby_Data_gene_ref	biomobyparser	Processor to parse the datatype gene_ref
Parse_Moby_Data_b64_Encoded_PNG	biomobyparser	Processor to parse the datatype b64_Encoded_PNG
CreateKeggPathwayDataType	biomobyobject	an object
Parse_Moby_Data_PDB_Text	biomobyparser	Processor to parse the datatype PDB-Text
PDB_id2RasMolScript	biomobywsdl	Given a pdb_id, it returns a RasMol script that can be used in conjunction to the PDB file of the protein to produce SNP sites labelled on the 3D representation.

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

Links (60)

Sink	Source
Gene2Ontology:Object(gene)	CreateEntrezGeneDataType:mobyData
Gene2PubMed:Object(geneid)	CreateEntrezGeneDataType:mobyData
getGeneInformationByEntrezGeneID:Object(geneid)	CreateEntrezGeneDataType:mobyData
getKeggIdsByKeggPathway:Object(pathway)	CreateKeggPathwayDataType:mobyData
CreateEntrezGeneDataType:namespace	Entrez_NS:value
Parse_Moby_Data_GO_Term:mobyData('GO_Term')	Gene2Ontology:GO_Term(Collection - 'terms' As Simples)
Parse_Moby_Data_Publication:mobyData('Publication')	Gene2PubMed:Publication(Collection - 'publications' As Simples)
CreateKeggPathwayDataType:namespace	KEGG_NS:value
Parse_Moby_Data_rasmol:mobyData('text-formatted')	PDB_id2RasMolScript:text-formatted(rasmol_text)
getEntryFromPDB:Object(id)	PDB_id2RasMolScript:text-formatted(rasmol_text)
entrez_gene_id_list_flatter:inputlist	Parse_Moby_Data_entrez_gene:id
entrez_gene_list_flatter2:inputlist	Parse_Moby_Data_entrez_gene:id
CreateEntrezGeneDataType:id	Remove_duplicate_strings:strippedlist
PDB_id2RasMolScript:Object(pdb_id)	convertKeggGeneId2PDBId:Object(Collection - 'pdb_ids' As Simples)
Parse_Moby_Data_pdb_id:mobyData('Object')	convertKeggGeneId2PDBId:Object(Collection - 'pdb_ids' As Simples)
Parse_Moby_Data_Swiss_Prot:mobyData('Object')	convertKeggGeneId2ProtId:Object(prot_id)
getSnpsBySwissProtId:Object(id)	convertKeggGeneId2ProtId:Object(prot_id)
Parse_Moby_Data_entrez_gene:mobyData('Object')	convertSnp2EntrezGeneID:Object(geneid)
Remove_duplicate_strings2:stringlist	entrez_gene_id_list_flatter:outputlist
Remove_duplicate_strings:stringlist	entrez_gene_list_flatter2:outputlist
Parse_Moby_Data_b64_Encoded_PNG:mobyData('b64_Encoded_PNG')	getBase64SnpFrequencyImage:b64_Encoded_PNG(image)
Parse_Moby_Data_PDB_Text:mobyData('PDB-Text')	getEntryFromPDB:PDB-Text(entry)
Parse_Moby_Data_gene_ref:mobyData('gene_ref')	getGeneInformationByEntrezGeneID:gene_ref(gene_info)
Parse_Moby_Data_kegg_gene:mobyData('Object')	getKeggIdsByKeggPathway:Object(Collection - 'keggIds' As Simples)
convertKeggGeneId2PDBId:Object(kegg_gene)	getKeggIdsByKeggPathway:Object(Collection - 'keggIds' As Simples)
convertKeggGeneId2ProtId:Object(kegg_gene)	getKeggIdsByKeggPathway:Object(Collection - 'keggIds' As Simples)
Parse_Moby_Data_nsSNP:mobyData('nsSNP')	getSnpsBySwissProtId:nsSNP(Collection - 'snps' As Simples)
convertSnp2EntrezGeneID:Object(snp)	getSnpsBySwissProtId:nsSNP(Collection - 'snps' As Simples)
snp2Frequencies:Object(snpid)	getSnpsBySwissProtId:nsSNP(Collection - 'snps' As Simples)
CreateKeggPathwayDataType:id	id
frequency	Parse_Moby_Data_Frequencies:Frequencies_'Frequency'
frequency_id	Parse_Moby_Data_Frequencies:Frequencies_'Frequency'_id
go_term_accession	Parse_Moby_Data_GO_Term:id
go_term_definition	Parse_Moby_Data_GO_Term:terms_'Definition'
go_term	Parse_Moby_Data_GO_Term:terms_'Term'
pdb_file	Parse_Moby_Data_PDB_Text:entry_'content'
publication_pubmed_id	Parse_Moby_Data_Publication:id
publication_abstract	Parse_Moby_Data_Publication:publications_'Abstract'
publication_author	Parse_Moby_Data_Publication:publications_'Author'
publication_journal_name	Parse_Moby_Data_Publication:publications_'Journal'
publication_title	Parse_Moby_Data_Publication:publications_'Title'
swiss_prot_id	Parse_Moby_Data_Swiss_Prot:id
base64_PNG	Parse_Moby_Data_b64_Encoded_PNG:image_'content'
gene_description	Parse_Moby_Data_gene_ref:gene_info_'description'
gene_name	Parse_Moby_Data_gene_ref:gene_info_'name'
gene_summary	Parse_Moby_Data_gene_ref:gene_info_'summary'
gene_synonyms	Parse_Moby_Data_gene_ref:gene_info_'synonyms'
gene_id	Parse_Moby_Data_gene_ref:id
kegg_gene_id	Parse_Moby_Data_kegg_gene:id
nsSNP_id	Parse_Moby_Data_nsSNP:id
nsSNP_amino_acid_position	Parse_Moby_Data_nsSNP:snps_'aa_pos'
nsSNP_amino_acid_variant	Parse_Moby_Data_nsSNP:snps_'aa_var'
nsSNP_allele	Parse_Moby_Data_nsSNP:snps_'allele'
nsSNP_codon_position	Parse_Moby_Data_nsSNP:snps_'codon_pos'
nsSNP_strand	Parse_Moby_Data_nsSNP:snps_'strand'
pdb_id	Parse_Moby_Data_pdb_id:id
pdb_rasmol	Parse_Moby_Data_rasmol:rasmol_text_'content'
entrez_gene_id	Remove_duplicate_strings2:strippedlist
Parse_Moby_Data_Frequencies:mobyData('Frequencies')	snp2Frequencies:Frequencies(Frequencies)
getBase64SnpFrequencyImage:Object(snpId)	snp2Frequencies:Frequencies(Frequencies)