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Network-member VL-e

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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Workflow BioAID_ProteinToDiseases (v1)

Created: 14/11/07 @ 12:47:57 | Updated: 15/11/07 @ 09:00:44

Credits: User Marco Roos User Martijn Schuemie Network-member AID

Attributions: Workflow BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 License

Bioaid_proteintodiseases_16160
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: 1. A user query: a single protein name 2. Add synonyms (service courtesy of Martijn Scheumie, Erasmus University Rotterdam) 3. Retrieve documents: finds relevant documents (abstract+title) based on query 4. Discover proteins: extract proteins discovered in the set of relevant abstracts 5. Link pr...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow BioAID_protein_discovery (v1)

Created: 14/11/07 @ 12:46:33 | Updated: 15/11/07 @ 09:01:12

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 License

Bioaid_protein_discovery_1051
This workflow finds proteins 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 2. Retrieve documents: finds relevant documents (abstract+title) based on query (edit maxHits to change the default maximum number of documents returned) 3. Discover proteins: extract proteins discovered in the set of relevant abstracts. Servic...

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Workflow BioAID_DiseaseDiscovery (v1)

Created: 12/11/07 @ 22:39:04 | Updated: 15/11/07 @ 09:01:44

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 License

Bioaid_diseasediscovery_28978
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) 2. Retrieve documents: finds relevant documents (abstract+title) based on query (edit maxHits to change the default maximum number of documents returned; the AIDA service inside is based on Apache Lucene) 3. Discover proteins: extract proteins ...

Rating: 4.0 / 5 (2 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

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Workflow DiscoverProteinLink (v2)

Created: 03/10/07 @ 18:36:12 | Updated: 15/11/07 @ 09:02:44

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 License

Discoverproteinlink_6189
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. ---- 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

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Workflow Discover_proteins_from_text (v2)

Created: 15/11/07 @ 08:58:00 | Updated: 15/11/07 @ 09:12:34

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 License

Discover_proteins_from_text_18980_2
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.

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Workflow BioAID_DiseaseDiscovery_count (v3)

Created: 22/11/07 @ 12:09:20 | Updated: 05/12/07 @ 23:09:13

Credits: User Marco Roos Network-member AID

Attributions: Workflow BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 License

Bioaid_diseasediscovery_count_22894_3
This adds counting to BioAID_DiseaseDiscovery, which allows you to check the results more properly. A major issue is that some false positives among the discovered proteins may have a disproportionate effect on the number of diseases found. We therefore advice to use 'BioAID_DiseaseDiscovery_byHumanUniprot' if you main interest is human proteins and diseases. This workflow finds disease relevant to the query string via the following steps: 1. A user query: a list of terms or boolean query - ...

Rating: 5.0 / 5 (1 rating) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow TestIteratorStrategy_withNesting (v1)

Created: 29/11/07 @ 15:31:32 | Updated: 29/11/07 @ 15:31:32

Credits: User Marco Roos User Tomoinn

License: Creative Commons Attribution-Share Alike 3.0 License

Testiteratorstrategy_withnesting_29185_1
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 list...

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Workflow CloneItemsInList (v1)

Created: 29/11/07 @ 15:34:52 | Updated: 29/11/07 @ 15:34:52

Credits: User Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 License

Cloneitemsinlist_10203_1
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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Workflow TestIteratorStrategy_withCloning (v2)

Created: 29/11/07 @ 15:35:48 | Updated: 29/11/07 @ 15:40:30

Credits: User Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 License

Testiteratorstrategy_withcloning_21054_2
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 strategy...

Rating: 5.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow BioAID_DiseaseDiscovery_byHumanUniprot (v3)

Created: 05/12/07 @ 23:11:42 | Updated: 15/05/08 @ 21:10:32

Credits: User Marco Roos User Martijn Schuemie Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 License

Bioaid_diseasediscovery_byhumanuniprot_22938_3
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 Apache's Luce...

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html (v8)

Created: 29/02/08 @ 01:34:46 | Updated: 28/07/08 @ 21:43:42

Credits: User Marco Roos User Martijn Schuemie Network-member AID Network-member AID_myGrid_collaboration

Attributions: Workflow BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 License

Bioaid_proteindiscovery_filteronhumanuniprot_perdoc_html_14081_8
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...

Rating: 0.0 / 5 (0 ratings) | Versions: 8 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow pELM_getInstance_Return_Seq (v2)

Created: 03/10/07 @ 18:36:27 | Updated: 02/05/08 @ 13:09:07

Credits: User Niall Haslam

License: Creative Commons Attribution-NoDerivs 3.0 License

Pelm_getinstance_return_seq_4755
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.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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