BioAID_ProteinToDiseases

Created: 2007-11-14 12:47:57 Last updated: 2007-11-15 09:00:44

Download Workflow

This workflow was based on BioAID_DiseaseDiscovery, changes: expects only one protein name, adds protein synonyms).

This workflow finds diseases relevant to the query string via the following steps:

A user query: a single protein name
Add synonyms (service courtesy of Martijn Scheumie, Erasmus University Rotterdam)
Retrieve documents: finds relevant documents (abstract+title) based on query
Discover proteins: extract proteins discovered in the set of relevant abstracts

Link proteins to disease contained in the OMIM disease database.

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/75/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (1)

Name	Description
input_protein	One protein or enzyme name or acronym. A protein synonym service will provide synonyms (courtesy of Martijn Scheumie, Erasmus University Rotterdam). Example: EZH2 Advanced information: Internally the input query is used by an AIDA search service based on the open source information retrieval software Lucene. Please look at the Apache Lucene documentation for details on lucene queries. For this workflow one protein or enzyme name is expected; the behaviour for more elaborate queries is undefined.

Processors (10)

Name	Type	Description
search_field	stringconstant
Document_index	stringconstant
maxHits	stringconstant
Flatten_and_make_unique	workflow
Remove_xml_tag	beanshell
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.
Discover_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.
Link_proteins_to_diseases	workflow
Add_protein_synonyms	workflow
Flatten_list	local

Beanshells (3)

Name	Inputs	Outputs
Prioritise_lucene_query	query_string priority_string	lucene_query
label_OMIM_disease	OMIM_disease_string	OMIM_disease_label
Remove_xml_tag	tagged_term	term

Outputs (1)

Name	Description
discovered_diseases

Links (11)

Source	Sink
Discover_proteins:discovered_proteins	Remove_xml_tag:tagged_term
Document_index:value	Retrieve_documents:document_index
Link_proteins_to_diseases:OMIM_disease_label	Flatten_and_make_unique:input
Remove_xml_tag:term	Link_proteins_to_diseases:keyword
Retrieve_documents:relevant_documents	Discover_proteins:documents_from_lucene
input_protein	Add_protein_synonyms:query_term
Add_protein_synonyms:new_query	Retrieve_documents:query_string
Flatten_and_make_unique:flattened_unique_output	Flatten_list:inputlist
Flatten_list:outputlist	discovered_diseases
maxHits:value	Retrieve_documents:maxHits
search_field:value	Retrieve_documents:search_field

Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Marco Roos

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (3)

(People/Groups)

Information Attributions (1)

(Workflows/Files)

BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter

Information Tags (8)

Uploader tags

Log in to add Tags

Information Shared with Groups (1)

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 (1)

Nolanfyh

Information Statistics

3754 viewings

3216 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

BioAID_ProteinToDiseases

Created by Marco Roos on Wednesday 14 November 2007 12:47:57 (UTC)

Last edited by Marco Roos on Thursday 15 November 2007 09:00:44 (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 (14)

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

Taverna 1

Uploader

Marco Roos

BioAID_DiseaseDiscovery_RatHumanMouseUnipr... (4)

Download

This workflow finds disease relevant to the query string via the following steps: 1. A user query: a list of terms or boolean query - look at the Apache Lucene project for all details. E.g.: (EZH2 OR "Enhancer of Zeste" +(mutation chromatin) -clinical); consider adding 'ProteinSynonymsToQuery' in front of the input if your query is a protein. 2. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apa...

Created: 2008-12-15 | Last updated: 2011-08-11

Credits: Marco Roos AID

Taverna 1

Uploader

Marco Roos

BioAID_ProteinDiscovery_filterOnHumanUnipr... (11)

Download

This workflow finds proteins relevant to the query string via the following steps: A user query: a single gene/protein name. E.g.: (EZH2 OR "Enhancer of Zeste"). Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache's Lucene) 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 serv...

Created: 2009-05-28

Credits: Marco Roos Martijn Schuemie AID AID_myGrid_collaboration

Attributions: BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter