Parsed UniProt to PubMed

Created: 2011-04-01 12:51:20 Last updated: 2011-04-01 12:52:02

Download Workflow

Uses the parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve information from PubMed.

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/2030/download?version=1
[ More Info Expand ]

Workflow Components

Authors (0)

Titles (4)

Descriptions (3)

Uses the parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve information from PubMed.

Comparison of the genome of Bacillus anthracis to closely related strains will allow the discovery of proteins which may be involved in pathogenicity. Based on the biochemical pathways where the protein interacts, vaccines can be designed for these unique proteins. By gaining insight into the biochemical pathways that the unique proteins are involved in, the proteins can also be assessed for potential quality as vaccines. The key components of the vaccine finding system are the following: The vaccine finding system reads in at least two annotated whole genome sequences in EMBL or GenBank format; the source (non-pathogen) and the target (Bacillus anthracis). At this point, the workflow runs a BlastP search to compare the two strains of bacteria. Assessment of the evolutionary relationship between the two genomes ascertains whether they are closely related enough to derive meaningful comparisons. The vaccine finding system then parses the proteins from the data set that are only coded for in the target genome Bacillus anthracis, giving a new data set of unique proteins which can then be assessed in the KEGG PATHWAY database. The position of the unique proteins in the pathways will give a good indication of the enzymatic role of the proteins in Bacillus anthracis. The vaccine finding system then records its findings in an HTML file, as well as additional information such as annotations from Gene Ontology, functional annotations and literature references.

The drug repurposing workflow system screens at least 20 bacterial proteomes against this set of proteins that are already being treated against using established drugs. By screening the bacterial proteomes it will be possible to find proteins of highly similar structure to those that are existing drug protein targets and so this will infer that it is highly likely that the drugs can be used as antimicrobials against these proteins of highly similar structure. Proteomes that will be screened belong to Gram positive bacteria, with special focus on Staphylococcus aureus. We look at a variety of species and strains as the company advised. A mixture of screening targets could potentially identify targets for broad-spectrum antimicrobial development. The drug repurposing workflow shows where in the KEGG pathways the proteins are active and therefore where the action of the drug will be in the biochemical pathways of the bacteria. The workflow will update the Ondex database where new information on Gene Ontology annotations, functional annotation and literature references are available. All information about each unique protein is made available in an HTML document.

Dependencies (0)

Inputs (1)

Name	Description
parsed_uniprot	The parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html). (File location) The parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html).

Processors (10)

Name	Type	Description
get_identifiers_from_uniprot_2_2	beanshell	Script String [] lines = parsed_uniprot.split("\n"); List list = new ArrayList(); for (String line: lines) { if (line.startsWith(identifier_name)) { list.add(line.substring(identifier_name.length()+1,line.length()).trim()); } } out1 = list;
PubMed	stringconstant	Value PubMed
searchCitations	wsdl	Wsdl http://www.ebi.ac.uk/webservices/citexplore/v1.0/service?wsdl Wsdl Operation searchCitations
searchCitations_input	xmlsplitter
searchCitations_output	xmlsplitter
email	stringconstant	Value m.l.taschuk@ncl.ac.uk
core	stringconstant	Value core
zero	stringconstant	Value 0
deXMLer	beanshell	Script String input = in1; String pat = "<[^>]+>[^<]+"; java.util.regex.Pattern p = java.util.regex.Pattern.compile(pat); java.util.regex.Matcher matcher = p.matcher(input); String output = ""; List list = new ArrayList(); while(matcher.find()) { String match = input.substring(matcher.start()+1, matcher.end()); if (match.contains("abstractText") \|\| match.contains("fullName") \|\| match.contains("title") \|\| match.contains("dx.doi.org") \|\| match.contains("yearOfPublication") \|\| match.contains("volume") \|\| match.contains("pageInfo")) { list.add(match); } } String authors = ""; String abstractText =""; String year = ""; String volume =""; String pageInfo =""; String link =""; String journal = ""; String title = ""; for (Object o: list) { String word = o.toString(); int length = word.length(); if (word.contains("abstractText")) { abstractText = word.substring(13, length); } else if (word.contains("fullName")) { authors += word.substring(9) +", "; } else if (word.contains("dx.doi.org")) { link = word.substring(4); } else if (word.contains("yearOfPublication")) { year = word.substring(18); } else if (word.contains("volume")) { volume = word.substring(7); } else if (word.contains("pageInfo")) { pageInfo = word.substring(9); } else if (word.contains("title") && journal.equals("")) { journal = word.substring(6); } else if (word.contains("title")) { title = word.substring(6); } } output = authors.substring(0,authors.length()-2) + " ("+year+"). "+title+". "+journal+", "+volume+ " :" + pageInfo+ ". "+link; out1 = output;
Merge_String_List_to_a_String	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = data.iterator(); i.hasNext();) { String id = (String) i.next(); sb.append(id); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();

Beanshells (2)

Name	Description	Inputs	Outputs
get_identifiers_from_uniprot_2_2		parsed_uniprot identifier_name	out1
deXMLer		in1	out1

Outputs (1)

Name	Description
PubMed_Results_2

Datalinks (11)

Source	Sink
PubMed:value	get_identifiers_from_uniprot_2_2:identifier_name
parsed_uniprot	get_identifiers_from_uniprot_2_2:parsed_uniprot
searchCitations_input:output	searchCitations:parameters
get_identifiers_from_uniprot_2_2:out1	searchCitations_input:luceneQueryString
email:value	searchCitations_input:email
core:value	searchCitations_input:outputFormat
zero:value	searchCitations_input:offSet
searchCitations:parameters	searchCitations_output:input
searchCitations_output:return	deXMLer:in1
deXMLer:out1	Merge_String_List_to_a_String:data
Merge_String_List_to_a_String:concatenated	PubMed_Results_2

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Morgan Taschuk

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Morgan Taschuk

Information Attributions (0)

(Workflows/Files)

None

Information Tags (0)

None

Log in to add Tags

Information Shared with Groups (1)

A Team

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

1489 viewings

1401 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Parsed UniProt to PubMed

Created by Morgan Taschuk on Friday 01 April 2011 12:51:20 (UTC)

Last edited by Morgan Taschuk on Friday 01 April 2011 12:52:02 (UTC)

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (4)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.

Taverna 1

Uploader

Hamish McWilliam

EBI_CiteXplore (1)

Download

Perform a literature search using the EBI's CiteXplore service (http://www.ebi.ac.uk/citexplore/), and get the results in a minimal XML format containing the citation information (i.e. title, author, journal, etc.), the identifier of the citation in the source database (PubMed/Medline, Agricola, Patent Abstracts, CBA, CiteSeer, etc.) and information about abstract and full article availablity including URLs.