myExperiment - Tags

Workflows (18)

Taverna 1 Original Uploader Marco Roos	Discover_entities (v2) Created: 10/12/07 @ 21:48:33 \| Last updated: 10/12/07 @ 22:54:42 Credits: Marco Roos Sophia katrenko AID License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow contains the 'Named Entity Recognize' web service from the AIDA toolbox, created by Sophia Katrenko. It can be used to discover entities of a certain type (determined by 'learned_model') in documents provided in a lucene output format. Known issues: The output of NErecognize contains concepts with / characters, breaking the xml. For post-processing its results it is better to use string manipulation than xml manipulations. The output is per document, which means entities will ... Rating: 5.0 / 5 (1 rating) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 103 times \| Downloaded: 50 times Tags (4): AIDA \| BioAID \| bioassist_nl \| demo	View Download (v2)
Taverna 1 Original Uploader Marco Roos	Extract_proteins (v2) Created: 10/12/07 @ 22:10:51 \| Last updated: 10/12/07 @ 22:30:53 Credits: Marco Roos License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow filters protein_molecule-labeled terms from an input string(list). The result is a tagged list of proteins (disregarding false positives in the input). Internal information: This workflow is a copy of 'filter_protein_molecule_MR3' used for the NBIC poster (now in Archive). Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 109 times \| Downloaded: 54 times Tags (4): AIDA \| BioAID \| bioassist_nl \| demo	View Download (v2)
Taverna 1 Original Uploader Marco Roos	Flatten_and_make_unique (v1) Created: 10/12/07 @ 22:12:00 Credits: Marco Roos AID License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 52 times \| Downloaded: 31 times Tags (4): bioassist_nl \| demo \| design pattern \| utility	View Download (v1)
Taverna 1 Original Uploader Marco Roos	Link_protein_to_OMIM_disease (v1) Created: 10/12/07 @ 22:13:35 Credits: Marco Roos AID License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 136 times \| Downloaded: 54 times Tags (4): AIDA \| BioAID \| bioassist_nl \| demo	View Download (v1)
Taverna 1 Original Uploader Marco Roos	Lucene_bioquery_optimizer_MR1 (v1) Created: 10/12/07 @ 22:14:26 Credits: Marco Roos AID License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow does four things: it retrieves documents relevant for the query string it discovers entities in those documents, these are considered relevant entities it filters proteins from those entities (on the tag protein_molecule) it removes all terms from the list produced by 3 (query terms temporarily considered proteins) ToDo Replace step 4 by the following procedure: 1. remove the query terms from the output of NER (probably by a regexp matching on what is inside the tag, ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 47 times \| Downloaded: 31 times Tags (4): AIDA \| BioAID \| bioassist_nl \| demo	View Download (v1)
Taverna 1 Original Uploader Marco Roos	Retrieve_bio_documents (v2) Created: 10/12/07 @ 22:15:54 \| Last updated: 10/12/07 @ 22:45:49 Credits: Marco Roos Edgar AID License: Creative Commons Attribution-Share Alike 3.0 Unported License 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. Rating: 4.5 / 5 (2 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 2 \| Citations: 0 Viewed: 117 times \| Downloaded: 43 times Tags (5): AIDA \| BioAID \| bioassist_nl \| demo \| retrieve documents	View Download (v2)
Taverna 1 Original Uploader Marco Roos	Retrieve_documents_MR1 (v1) Created: 10/12/07 @ 22:17:00 Credits: Marco Roos Edgar AID License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow applies the search web service from the AIDA toolbox. Comments: This search service is based on lucene defaults; it may be necessary to optimize the querystring to adopt the behaviour to what is most relevant in a particular domain (e.g. for medline prioritizing based on publication date is useful). Lucene favours shorter sentences, which may be bad for subsequent information extraction. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 57 times \| Downloaded: 35 times Tags (4): AIDA \| BioAID \| bioassist_nl \| demo	View Download (v1)
Taverna 1 Original Uploader Marco Roos	Demo_DiseaseDiscovery_byHumanUniprot_scaffold (v1) Created: 10/12/07 @ 23:10:00 Credits: Marco Roos AID License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow finds disease relevant to the query string via the following steps: 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. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache's Lucene)... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 89 times \| Downloaded: 64 times Tags (4): AIDA \| BioAID \| bioassist_nl \| demo	View Download (v1)
Taverna 1 Original Uploader Marco Roos	BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html (v11) Created: 28/05/09 @ 12:21:05 Credits: Marco Roos Martijn Schuemie AID AID_myGrid_collaboration Attributions: BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter 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): AIDA \| BioAID \| bioassist_nl \| demo \| nbiconworkflows \| protein \| text_mining \| text_mining_network \| VL-e	View Download (v11)
Taverna 2 Original Uploader Francois Belleau	Bio2rdf: Bind search, rdfise and load demo (v1) Created: 19/02/09 @ 05:07:30 \| Last updated: 19/02/09 @ 05:39:51 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License INSERT IN GRAPH <http://localhost/sesame/mem_rdf_db> { CONSTRUCT { ?s, ?p, ?o . } FROM <http://soap.bind.ca/wsdl/bind.wsdl> WHERE { SELECT ?s FROM <http://soap.bind.ca/wsdl/bind.wsdl> WHERE { ?s, ?p, ?o . ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 54 times \| Downloaded: 29 times Tags (4): bind \| bio2rdf \| demo \| search	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Bio2RDF: CPath search, rdfise and load demo (step 1) (v1) Created: 19/02/09 @ 07:06:58 \| Last updated: 19/02/09 @ 07:08:28 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License Search for a list of genes into the Pathway Commons interaction database and load the fetched triples into a triplestore. INSERT IN GRAPH < http://localhost/sesame/mem_rdf_db> { CONSTRUCT{ ?s, ?p, ?o . } FROM < http://www.pathwaycommons.org/pc/webservice.do> WHERE { SELECT ?s FROM <http://www.pathwaycommons.org/pc/webservice.do> ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 49 times \| Downloaded: 28 times Tags (5): bio2rdf \| cpath \| demo \| pathway commons \| protein interaction	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Bio2RDF: CPath search, rdfise and load demo (step 2) (v1) Created: 19/02/09 @ 07:14:23 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 35 times \| Downloaded: 24 times Tags (4): bio2rdf \| cpath \| demo \| pathway commons	View Download (v1)
Excel 2007 Macro-Enabled Workbook Original Uploader David De Roure	Demo of ChemSpider InChi to SMILES webservice invoked from Excel (v1) Created: 28/03/09 @ 18:38:07 \| Last updated: 28/03/09 @ 19:13:05 Credits: David De Roure License: Creative Commons Attribution-Share Alike 3.0 Unported License This demo was created in Excel 2007, with the Office XP Webservices toolkit. Using the spreadsheet, the formula InChiToSMILES invokes the corresponding ChemSpider web service. How I made this: 1. Installed Office XP Webservices toolkit from the Microsoft Download Center. 2. In Excel 2007 I turned on the Developer tab (hit Office button, then Excel options). 3. In the Developer ribbon I selected Visual Basic 4. In Tools->Web Services References I selected Web Service URL and ente... Rating: 5.0 / 5 (2 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 1 \| Citations: 0 Viewed: 160 times \| Downloaded: 135 times Tags (5): chemspider \| demo \| excel \| spreadflow \| spreadsheet	View Download (v1)
Excel 2007 Macro-Enabled Workbook Original Uploader David De Roure	Demo of statistics webservice invoked from Excel (v1) Created: 29/03/09 @ 17:56:04 Credits: David De Roure License: Creative Commons Attribution-Share Alike 3.0 Unported License This "spreadflow" was created by searching Seekda for a statistics webservice, adding it using "Web Services References" in Excel, and creating a simple VBA module to implement the corresponding Excel functions (sum, average, standard deviation etc) . The module simply gathers data from the cells to build an array of doubles that can be passed to the webservice. For more details about adding webservices to Excel see the inchidemo workflow http://www.myexperiment.org/workf... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 91 times \| Downloaded: 34 times Tags (4): demo \| excel \| spreadflow \| statistics	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Get the list of GeneID for all pathways of a specified taxon (v1) Created: 28/04/09 @ 07:48:40 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 55 times \| Downloaded: 33 times Tags (6): bio2rdf \| broken \| demo \| hcls2009 \| kegg \| pathways	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Insert in local triplestore GeneID and KEGG pathway (v1) Created: 28/04/09 @ 07:55:10 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 54 times \| Downloaded: 30 times Tags (7): bio2rdf \| demo \| hcls2009 \| kegg \| pathway \| pathways \| triplestore	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	ChEBI mashup from searched string (v1) Created: 29/04/10 @ 14:09:37 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License A demo showing hoe to use SOAP services from Bio2RDF ChEBI SPARQL endpoint.A demo showing hoe to use SOAP services from Bio2RDF ChEBI SPARQL endpoint. First a full text search query is done, then we do a reverse link query to get all the related topic. Finally with a describe queries we obtain the complete graph of each topic. The ntriples result is a mashup of what is known about this searched topic form ChEBI. This graph can then be loaded in a triplestore for further exploration. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 20 times \| Downloaded: 12 times Tags (5): bio2rdf \| chebi \| demo \| mashup \| soap	View Download (v1)
Taverna 2 Original Uploader Reinout van Schouwen	ExplainScores demo (v2) Created: 07/02/12 @ 11:05:50 \| Last updated: 21/03/12 @ 15:10:04 Credits: Reinout van Schouwen License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow demonstrates the explainScores method from the Anni web services. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 31 times \| Downloaded: 11 times Tags (3): anni \| concept \| demo	View Download (v2)

Packs (2)

Creator:

Marco Roos

AIDA demo pack

Created: 14/12/08 @ 21:35:43 | Last updated: 01/05/09 @ 17:35:26

Pack with AIDA demo material

5 items in this pack

Comments: 0 | Viewed: 119 times | Downloaded: 0 times

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Creator:

Marco Roos

AIDA remote runners

Created: 15/05/09 @ 16:08:03 | Last updated: 15/05/09 @ 16:11:20

Runners for AIDA demonstrations and testing

2 items in this pack

Comments: 0 | Viewed: 16 times | Downloaded: 7 times

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AIDA
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demo
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e-science
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VL-e

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Groups (1)

Administrator:

Simon Fischer

RapidMiner Demo

Unique name: rapidminer_demo Created: Saturday 01 May 2010 @ 09:49:28 (GMT)

This group is created for demo processes used in RapidMiner documentation, manual, or training. Feel free to add workflows if you consider them instructive examples.

5 shared items | 1 announcements

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Latest announcement:: RCOMM 2011

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Files (1)

Uploader:

Marco Roos

From biologist to web service to Taverna to myExperiment to biologist

Created: 21/03/08 @ 19:00:12 | Last updated: 23/03/08 @ 10:39:27

Credits: Marco Roos Martijn Schuemie AID myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A movie to show the principle of the round trip from a biology question via pieces of code wrapped as web services and combined into a workflow (computational experiment) in Taverna, via uploading to myExperiment and back to the biologist through myExperiment's run facility. NB: at the time of uploading this movie the runner-option was in test-phase. It is important to note that the workflow combines the work of various scientists with different expertise and some at remote locations around ...

File type: AVI video

Rating: 1.0 / 5 (1 rating) | Comments: 1 | Viewed: 261 times | Downloaded: 244 times

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Items tagged with "demo" (22)