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

Created: 2007-12-04 23:43:01 Last updated: 2007-12-04 23:45:25

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DataBiNS (Data Mining Workflow for Biological Pathways and Non-Synonymous SNPs) is a workflow that takes an identifier (list of gene ids, or list of KEGG pathway ids) and proceeds to mine for Single Nucleotide Polymorphism (SNP) data that is associated with the identifiers.

This particular variation of DataBiNS can take in several gene identifiers. The version of DataBiNS that takes in a KEGG pathway id can be found as a separate workflow on myExperiment. The identifers can be from the following sources:

1) KEGG (Kyoto Encyclopedia of Genes and Genomes) 2) OMIM (Online Mendelian Inheritance in Man) 3) PMID (Pubmed Identifier) 4) UniGene 5) UniProt 6) GenBank 7) NCBI_gi

When entering the inputs for the workflow, enter the id in the id input, and the source of the identifer into the namespace. The source name must be EXACTLY the same name as the mentioned above. So for example, searching by kegg id hsa:10, the namespace input must be KEGG. Searching by OMIM id 603028, the namespace must be OMIM, etc. etc. See also the related workflow on KEGG pathway id.

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Workflow Components

Inputs (2)

Name	Description
id
namespace

Processors (31)

Name	Type	Description
Entrez_NS	stringconstant
Remove_duplicate_strings	local
Remove_duplicate_strings2	local
entrez_gene_id_list_flatter	local
entrez_gene_list_flatter2	local
Parse_Moby_Data_Swiss_Prot	biomobyparser	Processor to parse the datatype Object
Parse_Moby_Data_Frequencies	biomobyparser	Processor to parse the datatype Frequencies
Parse_Moby_Data_nsSNP	biomobyparser	Processor to parse the datatype nsSNP
Parse_Moby_Data_GO_Term	biomobyparser	Processor to parse the datatype GO_Term
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
convertKeggGeneId2ProtId	biomobywsdl	This service consumes an identifier under the KEGG namespace. This identifier is then 'transformed' into a corresponding swissprot/uniprot identifier.
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.
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.
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.
getSnpsBySwissProtId	biomobywsdl	This service consumes an identifier under the Swiss-Prot / UniProt namespace. Using the input identifier, relevant snp data is returned.
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.
Parse_Moby_Data_Kegg	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.
convertIdentifier2KeggID	biomobywsdl	This service consumes an identifier from the following namespaces: NCBI_gi, GenBank, UniProt, UniGene, PMID or OMIM and returns a KEGG identifier that represents the KEGG id mapped to the input identifier. An example input would be (in <Object, ns, id> triple format, <Object, omim, 153240>
getEntryFromPDB	biomobywsdl	Retrieves an entry from PDB database.
Parse_Moby_Data_Publication	biomobyparser	Processor to parse the datatype Publication
getBase64SnpFrequencyImage	biomobywsdl	This service returns the hapmap SNP frequency image in a base64 format.
Parse_Moby_Data_rasmol	biomobyparser	Processor to parse the datatype text-formatted
CreateMobyObject	biomobyobject	an object
Parse_Moby_Data_gene_ref	biomobyparser	Processor to parse the datatype gene_ref
CreateEntrezGeneDataType	biomobyobject	an object
Parse_Moby_Data_b64_Encoded_PNG	biomobyparser	Processor to parse the datatype b64_Encoded_PNG
Parse_Moby_Data_PDB_Text	biomobyparser	Processor to parse the datatype PDB-Text
Parse_Moby_Data_entrez_gene	biomobyparser	Processor to parse the datatype Object

Beanshells (0)

Outputs (29)

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
original_id

Links (61)

Source	Sink
CreateEntrezGeneDataType:mobyData	Gene2Ontology:Object(gene)
CreateEntrezGeneDataType:mobyData	Gene2PubMed:Object(geneid)
CreateEntrezGeneDataType:mobyData	getGeneInformationByEntrezGeneID:Object(geneid)
Entrez_NS:value	CreateEntrezGeneDataType:namespace
Gene2Ontology:GO_Term(Collection - 'terms' As Simples)	Parse_Moby_Data_GO_Term:mobyData('GO_Term')
Gene2PubMed:Publication(Collection - 'publications' As Simples)	Parse_Moby_Data_Publication:mobyData('Publication')
PDB_id2RasMolScript:text-formatted(rasmol_text)	Parse_Moby_Data_rasmol:mobyData('text-formatted')
PDB_id2RasMolScript:text-formatted(rasmol_text)	getEntryFromPDB:Object(id)
Parse_Moby_Data_entrez_gene:id	entrez_gene_id_list_flatter:inputlist
Parse_Moby_Data_entrez_gene:id	entrez_gene_list_flatter2:inputlist
Remove_duplicate_strings:strippedlist	CreateEntrezGeneDataType:id
convertKeggGeneId2PDBId:Object(Collection - 'pdb_ids' As Simples)	PDB_id2RasMolScript:Object(pdb_id)
convertKeggGeneId2PDBId:Object(Collection - 'pdb_ids' As Simples)	Parse_Moby_Data_pdb_id:mobyData('Object')
convertKeggGeneId2ProtId:Object(prot_id)	Parse_Moby_Data_Swiss_Prot:mobyData('Object')
convertKeggGeneId2ProtId:Object(prot_id)	getSnpsBySwissProtId:Object(id)
convertSnp2EntrezGeneID:Object(geneid)	Parse_Moby_Data_entrez_gene:mobyData('Object')
getBase64SnpFrequencyImage:b64_Encoded_PNG(image)	Parse_Moby_Data_b64_Encoded_PNG:mobyData('b64_Encoded_PNG')
getEntryFromPDB:PDB-Text(entry)	Parse_Moby_Data_PDB_Text:mobyData('PDB-Text')
getGeneInformationByEntrezGeneID:gene_ref(gene_info)	Parse_Moby_Data_gene_ref:mobyData('gene_ref')
getSnpsBySwissProtId:nsSNP(Collection - 'snps' 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)
id	CreateMobyObject:id
entrez_gene_id_list_flatter:outputlist	Remove_duplicate_strings2:stringlist
entrez_gene_list_flatter2:outputlist	Remove_duplicate_strings:stringlist
namespace	CreateMobyObject:namespace
convertIdentifier2KeggID:Object(keggID)	convertKeggGeneId2PDBId:Object(kegg_gene)
Parse_Moby_Data_Frequencies:Frequencies_'Frequency'	frequency
Parse_Moby_Data_Frequencies:Frequencies_'Frequency'_id	frequency_id
Parse_Moby_Data_GO_Term:id	go_term_accession
Parse_Moby_Data_GO_Term:terms_'Definition'	go_term_definition
Parse_Moby_Data_GO_Term:terms_'Term'	go_term
Parse_Moby_Data_PDB_Text:entry_'content'	pdb_file
Parse_Moby_Data_Publication:id	publication_pubmed_id
Parse_Moby_Data_Publication:publications_'Abstract'	publication_abstract
Parse_Moby_Data_Publication:publications_'Author'	publication_author
Parse_Moby_Data_Publication:publications_'Journal'	publication_journal_name
Parse_Moby_Data_Publication:publications_'Title'	publication_title
Parse_Moby_Data_Swiss_Prot:id	swiss_prot_id
Parse_Moby_Data_b64_Encoded_PNG:image_'content'	base64_PNG
Parse_Moby_Data_gene_ref:gene_info_'description'	gene_description
Parse_Moby_Data_gene_ref:gene_info_'name'	gene_name
Parse_Moby_Data_gene_ref:gene_info_'summary'	gene_summary
Parse_Moby_Data_gene_ref:gene_info_'synonyms'	gene_synonyms
Parse_Moby_Data_gene_ref:id	gene_id
Parse_Moby_Data_nsSNP:id	nsSNP_id
Parse_Moby_Data_nsSNP:snps_'aa_pos'	nsSNP_amino_acid_position
Parse_Moby_Data_nsSNP:snps_'aa_var'	nsSNP_amino_acid_variant
Parse_Moby_Data_nsSNP:snps_'allele'	nsSNP_allele
Parse_Moby_Data_nsSNP:snps_'codon_pos'	nsSNP_codon_position
Parse_Moby_Data_nsSNP:snps_'strand'	nsSNP_strand
Parse_Moby_Data_pdb_id:id	pdb_id
Parse_Moby_Data_rasmol:rasmol_text_'content'	pdb_rasmol
Remove_duplicate_strings2:strippedlist	entrez_gene_id
convertIdentifier2KeggID:Object(keggID)	convertKeggGeneId2ProtId:Object(kegg_gene)
id	original_id
CreateMobyObject:mobyData	convertIdentifier2KeggID:Object(identifier)
convertIdentifier2KeggID:Object(keggID)	Parse_Moby_Data_Kegg:mobyData('Object')
Parse_Moby_Data_Kegg:id	kegg_gene_id
snp2Frequencies:Frequencies(Frequencies)	Parse_Moby_Data_Frequencies:mobyData('Frequencies')
snp2Frequencies:Frequencies(Frequencies)	getBase64SnpFrequencyImage:Object(snpId)

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Fong Chun Chan

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Fong Chun Chan

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Version History

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DataBiNS with Single Unique Idenitifers

Created by Fong Chun Chan on Tuesday 04 December 2007 23:43:01 (UTC)

Last edited by Fong Chun Chan on Tuesday 04 December 2007 23:43:03 (UTC)
DataBiNS - Data Mining Workflow for Biological Pathways and Non-Synonymous SNPs

Created by Fong Chun Chan on Tuesday 04 December 2007 23:43:01 (UTC)

Last edited by Fong Chun Chan on Tuesday 04 December 2007 23:45:25 (UTC)

Revision comment:

This version of the workflow is just another variation of the workflow that works with KEGG pathways as an input.

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