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Workflow Entry: BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html

Created at: 29/02/08 @ 01:34:47 Last updated: 14/12/08 @ 21:44:19

Version 9 (latest) (of 9)

Version created on: 14/12/08 @ 21:42:40 by: Marco Roos | Revision comments Expand

Last edited on: 14/12/08 @ 21:44:19 by: Marco Roos

Title: BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html

Type: Taverna 1

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Description

This workflow finds proteins relevant to the query string via the following steps: 1. A user query: a single gene/protein name. E.g.: (EZH2 OR "Enhancer of Zeste"). 2. Retrieve documents: finds ‘maximumNumberOfHits’ relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache’s Lucene) 3. Discover proteins: extract proteins discovered in the set of relevant abstracts with a ‘named entity recognizer’ trained on genomic terms using a Bayesian approach; the AIDA service inside is based on LingPipe. This subworkflow also ‘filters’ false positives from the discovered protein by requiring a discovery has a valid UniProt ID. Martijn Schuemie’s service to do that contains only human UniProt IDs, which is why this workflow only works for human proteins. Workflow by Marco Roos (AID = Adaptive Information Disclosure, University of Amsterdam; http://adaptivedisclosure.org) Text mining services by Sophia Katrenko and Edgar Meij (AID), and Martijn Schuemie (BioSemantics, Erasmus University Rotterdam). Changes to our original BioAID_DiseaseDiscovery workflow: * Stops at protein discovery * Use of Martijn Schuemie’s synsets service to * add synonyms to the query. * provide uniprot ids to discovered proteins * filter false positive discoveries, only proteins with a uniprot id go through; this introduces some false negatives (e.g. discovered proteins with a name shorter than 3 characters) * Counting of results in various ways, but no outputs defined in this simplified workflow. * Output into simple html table.

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Option 1:

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Note: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.

Option 2:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/154/download?version=9
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Workflow Components

Inputs (1)

Name	Description
query_protein	A protein name to query. A sinlge gene/protein name is expected, because the 'ProteinSynonymsToQuery' workflow is used on the query.

Processors (22)

Name	Type	Description
PubMedURLstub	stringconstant
search_field	stringconstant
Concatenate_URLstub_ID	local
DummyRankScore	stringconstant
Results_pending_html_doc	stringconstant
default_max_hits	stringconstant	Default maximum number of documents to retrieve from medline by the query from which to extract proteins.
NotAppendHtmlDoc	stringconstant
AppendToHtmlDoc	stringconstant
Document_index	stringconstant
Clone	beanshell
AIDAHtmlScaffold	beanshell
CountDocuments	beanshell
CountProteins	beanshell
Proteins_to_html_table	beanshell
save_html_top	arbitrarywsdl
save_html_bottom	arbitrarywsdl
save_html	arbitrarywsdl
SynonymsToQuery	workflow	This workflow creates a query string from the query term using Martijn Schuemie's synonym service. The service is limited to proteins, enzymes and genes. An input query that is a boolean string will be split and processed, but the boolean logic of the input query will be lost.
Discover_HumanUniProt_proteins	workflow	This workflow applies the discovery workflow built around the AIDA 'Named Entity Recognize' web service by Sophia Katrenko. It uses the pre-learned genomics model, named 'MedLine', to find genomics concepts in a set of documents in lucene output format.
Retrieve_documents	workflow	This workflow retrieves relevant documents, based on a query optimized by adding a string to the original query that will rank the search output according to the most recent years. The added string adds years with priorities (most recent is highest); it starts at 2007.
save_html_init	arbitrarywsdl
html_ref	beanshell

Outputs (3)

Name	Description
discovery_html_table
discovery_table_url
discovery_html_ref

Links (29)

Sink	Source
Clone:copy_number	CountProteins:count
CountProteins:list	Discover_HumanUniProt_proteins:discovered_proteins
Concatenate_URLstub_ID:string2	Discover_HumanUniProt_proteins:doc_ids
CountDocuments:list	Discover_HumanUniProt_proteins:doc_ids
Retrieve_documents:document_index	Document_index:value
Concatenate_URLstub_ID:string1	PubMedURLstub:value
Discover_HumanUniProt_proteins:documents_from_lucene	Retrieve_documents:relevant_documents
Retrieve_documents:maxHits	default_max_hits:value
Proteins_to_html_table:query_protein	query_protein
SynonymsToQuery:query_term	query_protein
save_html_bottom:content	AIDAHtmlScaffold:html_bottom
save_html_top:content	AIDAHtmlScaffold:html_top
save_html:append	AppendToHtmlDoc:value
save_html_bottom:append	AppendToHtmlDoc:value
Proteins_to_html_table:ranking_score_list	Clone:clones
Proteins_to_html_table:discovered_protein_list	Discover_HumanUniProt_proteins:discovered_proteins
Proteins_to_html_table:discovered_uniprot_id_list	Discover_HumanUniProt_proteins:discovered_uniprot_ids
Proteins_to_html_table:pubmed_id_list	Discover_HumanUniProt_proteins:doc_ids
Clone:input	DummyRankScore:value
save_html_init:append	NotAppendHtmlDoc:value
save_html_top:append	NotAppendHtmlDoc:value
save_html:content	Proteins_to_html_table:html_table
save_html_init:content	Results_pending_html_doc:value
Retrieve_documents:query_string	SynonymsToQuery:new_query
discovery_html_table	Proteins_to_html_table:html_table
discovery_html_ref	html_ref:html_ref
html_ref:url	save_html_bottom:save_htmlReturn
Retrieve_documents:search_field	search_field:value
discovery_table_url	save_html_bottom:save_htmlReturn

Coordinations (4)

Controller	Target
save_html_init	SynonymsToQuery
Proteins_to_html_table	save_html_top
save_html_top	save_html
save_html	save_html_bottom

Citations (0)

None

Version History

Earliest Version:
[1] - BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html

Created on: Friday 29 February 2008 @ 01:34:46 (GMT)

Created by: Marco Roos

Last edited on: Friday 29 February 2008 @ 01:34:47 (GMT)

Last edited by: Marco Roos

Revision comments:

None

Previous Versions:
[2] - BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html

Created on: Friday 29 February 2008 @ 01:34:46 (GMT)

Created by: Marco Roos

Last edited on: Wednesday 05 March 2008 @ 08:12:04 (GMT)

Last edited by: Marco Roos

Revision comments:

Demo

[3] - BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html

Created on: Friday 29 February 2008 @ 01:34:46 (GMT)

Created by: Marco Roos

Last edited on: Thursday 15 May 2008 @ 11:41:50 (BST)

Last edited by: Marco Roos

Revision comments:

Balanced list levels for I/O of all beanshells.
Temporarily switched to development service for document search service due to problems with index files.

[4] - BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html

Created on: Friday 29 February 2008 @ 01:34:46 (GMT)

Created by: Marco Roos

Last edited on: Thursday 15 May 2008 @ 17:37:31 (BST)

Last edited by: Marco Roos

Revision comments:

Added new simple web service that provides the html document on a publicly accessible URL.

[5] - BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html

Created on: Friday 29 February 2008 @ 01:34:46 (GMT)

Created by: Marco Roos

Last edited on: Thursday 15 May 2008 @ 22:26:46 (BST)

Last edited by: Marco Roos

Revision comments:

Added initial 'results pending' html doc.

[6] - BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html

Created on: Friday 29 February 2008 @ 01:34:46 (GMT)

Created by: Marco Roos

Last edited on: Thursday 15 May 2008 @ 23:22:52 (BST)

Last edited by: Marco Roos

Revision comments:

updated mime type of url output

[7] - BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html

Created on: Friday 29 February 2008 @ 01:34:46 (GMT)

Created by: Marco Roos

Last edited on: Monday 28 July 2008 @ 20:48:45 (BST)

Last edited by: Marco Roos

Revision comments:

Repaired this workflow. Creating the html is done by a beanshell again.

[8] - BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html

Created on: Friday 29 February 2008 @ 01:34:46 (GMT)

Created by: Marco Roos

Last edited on: Wednesday 29 October 2008 @ 09:29:36 (GMT)

Last edited by: Marco Roos

Revision comments:

Repaired this workflow. Creating the html is done by a beanshell again.

Latest Version:
[9] - BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html

Created on: Sunday 14 December 2008 @ 21:42:40 (GMT)

Created by: Marco Roos

Last edited on: Sunday 14 December 2008 @ 21:44:19 (GMT)

Last edited by: Marco Roos

Revision comments:

Workflow running from production servers

Comments (1)

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Giovanni Dall'Olio

I am not sure I understand what this workflow does.

Can you please add some use case/example of how to use it?
What do you mean exactly with 'proteins relevant to the query string'? Proteins that interact with the query gene? Or that are involved in the same metabolism?

With which data have you tested this workflow? Which queries have you tried?

Workflow Entry: BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html

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