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Items tagged with "demo" (11)

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Blob From biologist to web service to Taverna to myExperiment to biologist

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

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

Attributions: Workflow BioAID_DiseaseDiscovery_byHumanUniprot

License: Creative Commons Attribution-Share Alike 3.0 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: video/x-msvideo

Rating: 1.0 / 5 (1 rating) | Comments: 0 | Viewed: 361 times | Downloaded: 289 times

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Workflows (10)

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Workflow Discover_entities (v2)

Created: 10/12/07 @ 21:48:33 | Updated: 10/12/07 @ 22:54:42

Credits: User Marco Roos User Sophia katrenko Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 License

Discover_entities_29989_2
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: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 486 times | Downloaded: 436 times

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Workflow Extract_proteins (v2)

Created: 10/12/07 @ 22:10:51 | Updated: 10/12/07 @ 22:30:53

Credits: User Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 License

Extract_proteins_31269_2
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).

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Workflow Flatten_and_make_unique (v1)

Created: 10/12/07 @ 22:12:00 | Updated: 10/12/07 @ 22:12:00

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 License

Flatten_and_make_unique_9537_1
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Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow Link_protein_to_OMIM_disease (v1)

Created: 10/12/07 @ 22:13:35 | Updated: 10/12/07 @ 22:13:35

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 License

Link_protein_to_omim_disease_31835_1
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Workflow Lucene_bioquery_optimizer_MR1 (v1)

Created: 10/12/07 @ 22:14:26 | Updated: 10/12/07 @ 22:14:26

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 License

Lucene_bioquery_optimizer_mr1_7699_1
This workflow does four things: 1. it retrieves documents relevant for the query string 2. it discovers entities in those documents, these are considered relevant entities 3. it filters proteins from those entities (on the tag protein_molecule) 4. 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...

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Workflow Retrieve_bio_documents (v2)

Created: 10/12/07 @ 22:15:54 | Updated: 10/12/07 @ 22:45:49

Credits: User Marco Roos User Edgar Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 License

Retrieve_bio_documents_524_2
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

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Workflow Retrieve_documents_MR1 (v1)

Created: 10/12/07 @ 22:17:00 | Updated: 10/12/07 @ 22:17:00

Credits: User Marco Roos User Edgar Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 License

Retrieve_documents_mr1_16960_1
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

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Workflow Demo_DiseaseDiscovery_byHumanUniprot_scaffold (v1)

Created: 10/12/07 @ 23:10:00 | Updated: 10/12/07 @ 23:10:00

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 License

Demo_diseasediscovery_byhumanuniprot_scaffold_28715_1
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: 1 | 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

Viewed: 771 times | Downloaded: 718 times

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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

Viewed: 728 times | Downloaded: 580 times

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