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 version of DataBiNS can take in a KEGG pathway. An example KEGG pathway is hsa00030. The version of DataBiNS that works with single unqiue identifiers can be found as a separate version of the DataBiNS workflow under myExperiment.
KEGG_PATHWAY
EntrezGene_EntrezGeneID
org.embl.ebi.escience.scuflworkers.java.FlattenList
org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
org.embl.ebi.escience.scuflworkers.java.FlattenList
org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates
Processor to parse the datatype nsSNP
http://moby.ucalgary.ca/moby/MOBY-Central.pl
nsSNP
snps
Processor to parse the datatype nsSNP
Processor to parse the datatype GO_Term
http://moby.ucalgary.ca/moby/MOBY-Central.pl
GO_Term
terms
Processor to parse the datatype GO_Term
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.
http://moby.ucalgary.ca/moby/MOBY-Central.pl
getGeneInformationByEntrezGeneID
bioinfo.icapture.ubc.ca
This service consumes an identifier under the EntrezGene_EntrezGeneID / EntrezGene_ID namespaces. This identifier is then used to query for any associated GO_Terms.
http://moby.ucalgary.ca/moby/MOBY-Central.pl
Gene2Ontology
icapture.ubc.ca
Processor to parse the datatype Frequencies
http://moby.ucalgary.ca/moby/MOBY-Central.pl
Frequencies
Frequencies
Processor to parse the datatype Frequencies
Processor to parse the datatype Object
http://moby.ucalgary.ca/moby/MOBY-Central.pl
Object
geneid
Processor to parse the datatype Object
This service consumes an identifier under the Swiss-Prot / UniProt namespace.
Using the input identifier, relevant snp data is returned.
http://moby.ucalgary.ca/moby/MOBY-Central.pl
getSnpsBySwissProtId
bioinfo.icapture.ubc.ca
This service consumes an identifier under the KEGG namespace.
This identifier is then queried against the KEGG DB and all PDB records are returned.
http://moby.ucalgary.ca/moby/MOBY-Central.pl
convertKeggGeneId2PDBId
bioinfo.icapture.ubc.ca
This service returns the hapmap SNP frequency image in a base64 format.
http://moby.ucalgary.ca/moby/MOBY-Central.pl
getBase64SnpFrequencyImage
bioinfo.icapture.ubc.ca
Processor to parse the datatype Publication
http://moby.ucalgary.ca/moby/MOBY-Central.pl
Publication
publications
Processor to parse the datatype Publication
Processor to parse the datatype Object
http://moby.ucalgary.ca/moby/MOBY-Central.pl
Object
prot_id
Processor to parse the datatype Object
Retrieves an entry from PDB database.
http://moby.ucalgary.ca/moby/MOBY-Central.pl
getEntryFromPDB
inb.bsc.es
This service consumes an identifier under the NCBI_dbSNP namespace.
The identifier is then converted into an EntrezGene_ID
http://moby.ucalgary.ca/moby/MOBY-Central.pl
convertSnp2EntrezGeneID
bioinfo.icapture.ubc.ca
Processor to parse the datatype Object
http://moby.ucalgary.ca/moby/MOBY-Central.pl
Object
pdb_ids
Processor to parse the datatype Object
Retrieves a list of genotype and allele frequencies for non-synonymous SNPs genotyped by HapMap (www.hapmap.org) from the snp input identifier.
http://moby.ucalgary.ca/moby/MOBY-Central.pl
snp2Frequencies
bioinfo.icapture.ubc.ca
This service, given a KEGG pathway, searches for all known genes on that pathway.
http://moby.ucalgary.ca/moby/MOBY-Central.pl
getKeggIdsByKeggPathway
bioinfo.icapture.ubc.ca
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.
http://moby.ucalgary.ca/moby/MOBY-Central.pl
Gene2PubMed
icapture.ubc.ca
20
This service consumes an identifier under the KEGG namespace.
This identifier is then 'transformed' into a corresponding swissprot/uniprot identifier.
http://moby.ucalgary.ca/moby/MOBY-Central.pl
convertKeggGeneId2ProtId
bioinfo.icapture.ubc.ca
Processor to parse the datatype Object
http://moby.ucalgary.ca/moby/MOBY-Central.pl
Object
keggIds
Processor to parse the datatype Object
Processor to parse the datatype text-formatted
http://moby.ucalgary.ca/moby/MOBY-Central.pl
text-formatted
rasmol_text
Processor to parse the datatype text-formatted
an object
http://moby.ucalgary.ca/moby/MOBY-Central.pl
Object
Processor to parse the datatype gene_ref
http://moby.ucalgary.ca/moby/MOBY-Central.pl
gene_ref
gene_info
Processor to parse the datatype gene_ref
Processor to parse the datatype b64_Encoded_PNG
http://moby.ucalgary.ca/moby/MOBY-Central.pl
b64_Encoded_PNG
image
Processor to parse the datatype b64_Encoded_PNG
an object
http://moby.ucalgary.ca/moby/MOBY-Central.pl
Object
Processor to parse the datatype PDB-Text
http://moby.ucalgary.ca/moby/MOBY-Central.pl
PDB-Text
entry
Processor to parse the datatype PDB-Text
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.
http://moby.ucalgary.ca/moby/MOBY-Central.pl
PDB_id2RasMolScript
bioinfo.icapture.ubc.ca