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Items tagged with "VL-e" (15)
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Created: 14/11/07 @ 12:47:57 | Last updated: 15/11/07 @ 09:00:44
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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
5. Link proteins ...
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 188 times | Downloaded: 90 times Tags (8): |
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Created: 15/12/08 @ 20:46:09 | Last updated: 11/08/11 @ 09:22:23
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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...
Rating: 4.0 / 5 (2 ratings) | Versions: 4 | Reviews: 0 | Comments: 3 | Citations: 0 Viewed: 4030 times | Downloaded: 616 times Tags (9): |
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Created: 03/10/07 @ 18:36:12 | Last updated: 15/11/07 @ 09:02:44
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
COMPETITION:
For friends only:
If you find any two topics that return true positives with this workflow I will buy you a bottle of wine (or equivalent).
Terms: if we confirm that the protein was indeed never mentioned together with both input topics in one article, we will publish this together.
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This workflow implements Swanson's prinicple with services from the AIDA toolbox. It tries to find proteins that link two topics, while they never mentioned together with both topics in ...
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 291 times | Downloaded: 62 times Tags (8): |
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Created: 15/11/07 @ 08:58:00 | Last updated: 15/11/07 @ 09:12:34
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow discovers proteins from plain text. It is built around the AIDA 'Named Entity Recognize' web service by Sophia Katrenko (service based on LingPipe), from which output it filters out proteins. The Named Recognizer services uses the pre-learned genomics model, named 'MedLine', to find genomics concepts in plain text.
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 182 times | Downloaded: 68 times Tags (7): |
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Created: 29/11/07 @ 15:31:32
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Implementation of the iteration workaround by Tom Oin conform the Q&A below. The nested workflow 'NestedProcessor' is called that to conform to Tom's explanation. For an alternative solution using a java beanshell to clone list items see 'TestIteratorStrategy_withCloning.
This workflow implements the following Q&A:
Marco Roos wrote:
> Dear Taverna user,
>
> Issue 1: Complex iteration
>
> I would like to perform an iteration including a dot product between
> a list and a list of li...
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Created: 29/11/07 @ 15:34:52
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Utility workflow that clones an item copy_number times. You can use this to work around standard iteration strategies, e.g. in combination with the CountListItems workflow.
Workflow examples: TestIterationStrategy_withClones. For an alternative approach see TestIterationStrategy_withNesting.
Example I/O:
input: A
copy_number: 3
result: [A,A,A]
input: [A,B,C]
copy_number: 3
result: [[A,A,A][B,B,B][C,C,C]]
input: [A,B,C]
copy_number: [3,2]
result: [[[A,A,A],[A,A]][[B,B,B],[B,B]],[[C,C,C],...
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Original Uploader |
Created: 29/11/07 @ 15:35:48 | Last updated: 29/11/07 @ 15:40:30
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow implements a strategy for this problem:
> I would like to perform an iteration including a dot product between
> a list and a list of lists; example:
> Input:
>
> [1] (1)
> [A,B,C] (2)
> [[a,b],[c,d],[e,f]] (3)
>
> Desired output:
>
> [1Aa, 1Ab, 1Bc, 1Bd, 1Ce, 1Cf]
In this implementation a java beanshell is used to clone the items in list 2 as many times per item as there are items in the sublists of list 3. The iteration stra...
Rating: 5.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 66 times | Downloaded: 49 times Tags (6): |
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Created: 28/05/09 @ 12:21:05
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
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...
Rating: 0.0 / 5 (0 ratings) | Versions: 11 | Reviews: 0 | Comments: 1 | Citations: 0 Viewed: 454 times | Downloaded: 167 times Tags (9): |
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Created: 03/10/07 @ 18:36:27 | Last updated: 02/05/08 @ 13:09:07
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License: Creative Commons Attribution-No Derivative Works 3.0 Unported License
Simple workflow to retrieve the sequence of a phospho.ELM entry given the Instance identifier. Input requires xml as the namespace is not correctly handled by the xml splitter. Example input:
I000299
Further outputs can easily be added, most are text with some xml. See list in InstanceXML.
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Created: 16/05/09 @ 01:06:26 | Last updated: 16/05/09 @ 01:13:18
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License: Creative Commons Attribution-No Derivative Works 3.0 Unported License
This workflow is for demonstration purposes only. Please contact the authors if you wish to try it. We will gladly collaborate with you.
Summary
This workflow extracts proteins and protein relations from Medline. Extracted protein names (symbols of at least 3 characters) are validated against mouse, rat, and human UniProt symbols, so the results are limited to these species. This workflow follows the following basic steps:
it retrieves documents relevant for the query string
i...
Rating: 0.0 / 5 (0 ratings) | Versions: 7 | Reviews: 0 | Comments: 1 | Citations: 0 Viewed: 150 times | Downloaded: 31 times Tags (10): |
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Created: 10/05/10 @ 16:21:09 | Last updated: 20/03/12 @ 17:16:11
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
This protein discovery workflow extracts protein names from documents retrieved from MedLine based on a user Query (cf Apache Lucene syntax). The protein names are filtered by checking if there exists a valid UniProt ID for the given protein name.
Rating: 0.0 / 5 (0 ratings) | Versions: 7 | Reviews: 0 | Comments: 1 | Citations: 0 Viewed: 292 times | Downloaded: 131 times Tags (12): |
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Created: 14/12/08 @ 21:35:43 | Last updated: 01/05/09 @ 17:35:26
Pack with AIDA demo material
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Created: 15/05/09 @ 15:45:32 | Last updated: 11/08/11 @ 10:01:23
Supporting material for BMC Bioinformatics, supplement for Semantic Web Applications and Tools for Life Science (2009)
Structuring and extracting knowledge for the support of hypothesis generation in molecular biology
Marco Roos, M. Scott Marshall, Andrew P. Gibson, Martijn Schuemie, Edgar Meij, Sophia Katrenko, Willem Robert van Hage, Konstantinos Krommydas, Pieter W. Adriaans
Acknowledgements
We thank the myGrid team and OMII-UK for their support in applying their e-Science tools, and M...
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Created: 15/05/09 @ 16:08:03 | Last updated: 15/05/09 @ 16:11:20
Runners for AIDA demonstrations and testing
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Created: Wednesday 23 January 2008 @ 15:17:17 (GMT)
Group of researchers of the Virtual Laboratory e-Science (VL-e) project in the Netherlands. This is a large nation wide e-science research project funded by BSIK grants from the Dutch ministry of Economic Affairs. Its activities range from Grid infrastructure, to middleware, to (six) applications. The projects BioRange and BioAssist (also groups here) are tightly associated with VL-e.
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