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Uploader:

Marco Roos

DiscoverProteinLink (v2)

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

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 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. ---- 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: 746 times | Downloaded: 624 times

Uploader:

Marco Roos

ProteinSynonymsToQuery (v2)

Created: 03/10/07 @ 18:36:10 | Updated: 13/11/07 @ 23:47:41

Credits: Marco Roos Martijn Schuemie AID

License: Creative Commons Attribution-Share Alike 3.0 License

This workflow uses Martijn Schuemie's protein synonym service to produce synonyms and a new query string from the input query term. The service is limited to proteins, enzymes and genes. An input query that is a boolean string will be split and processed, but the boolean logic of the input query will be lost. Workflow URL: http://rdf.adaptivedisclosure.org/~marco/BioAID/Public/Workflows/BioAID/ProteinSynonymsToQuery.xml

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

Viewed: 705 times | Downloaded: 571 times

Uploader:

Marco Roos

BioAID_ProteinToDiseases (v1)

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

Credits: Marco Roos Martijn Schuemie AID

Attributions: BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 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: 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

Viewed: 568 times | Downloaded: 643 times

Uploader:

Marco Roos

BioAID_Discover_proteins_from_text_plus_synonyms (v1)

Created: 15/11/07 @ 09:40:24 | Updated: 15/11/07 @ 09:40:24

Credits: Marco Roos Martijn Schuemie AID

License: Creative Commons Attribution-Share Alike 3.0 License

This workflow discovers proteins from plain text and adds synonyms using Martijn Schuemie's proteins synonym service. Proteins are discovered with 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: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 439 times | Downloaded: 0 times

Uploader:

Marco Roos

BioAID_DiseaseDiscovery_byHumanUniprot (v3)

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

Credits: Marco Roos Martijn Schuemie AID

License: Creative Commons Attribution-Share Alike 3.0 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 Apache's Luce...

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

Viewed: 771 times | Downloaded: 718 times

Uploader:

Marco Roos

BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html (v8)

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

Credits: Marco Roos Martijn Schuemie AID AID_myGrid_collaboration

Attributions: BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 License

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

Uploader:

Alan Williams

GBSeq test (v2)

Created: 05/03/08 @ 14:15:35 | Updated: 31/03/08 @ 15:55:09

Credits: Franck Tanoh

License: Creative Commons Attribution 3.0 License

This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

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Viewed: 461 times | Downloaded: 314 times

Uploader:

Hamish McWilliam

EBI_Phobius (v2)

Created: 01/06/08 @ 11:08:45 | Updated: 02/06/08 @ 21:39:06

Credits: Hamish McWilliam

License: Creative Commons Attribution 3.0 License

The Phobius tool predicts transmembrane domains and signal peptide region from a protein sequence. This workflow uses the EBI's WSPhobius web service (see http://www.ebi.ac.uk/Tools/webservices/services/phobius) to access the tool. The predicted features are returned in a UniProtKB style feature listing.

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

Viewed: 180 times | Downloaded: 135 times

Uploader:

Hamish McWilliam

Protein_alignment_transmembrane (v1)

Created: 01/06/08 @ 12:20:29 | Updated: 01/06/08 @ 12:20:29

Credits: Hamish McWilliam

Attributions: EBI_FASTA EBI_ClustalW2 EBI_dbfetch_fetchBatch

License: Creative Commons Attribution 3.0 License

Transmembrane domain prediction using EMBOSS tmap with an input sequence alignment of homolouges: 1. Sequence similarity search (SSS) to find homologues 2. Fetch sequences of hits 3. Multiple sequence alignment (MSA) of hit sequences 4. EMBOSS tmap with alignment from 3. Uses the EBI web services: 1. WSFasta (see http://www.ebi.ac.uk/Tools/webservices/services/fasta) 2. WSDbfetch (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) 3. WSClustalW2 (see http://www.ebi.ac.uk/Tools/webs...

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

Viewed: 125 times | Downloaded: 124 times

Uploader:

Hamish McWilliam

Protein_transmembrane_prediction (v1)

Created: 01/06/08 @ 17:49:30 | Updated: 01/06/08 @ 17:49:30

Credits: Hamish McWilliam

Attributions: EBI_InterProScan_tmhmm_signalp EBI_Phobius tmap_single_sequence

License: Creative Commons Attribution 3.0 License

Transmembrane and signal peptide prediction using three methods: 1. EMBOSS tmap with a single sequence. Uses Soaplab tmap. 2. Phobius. Uses EBI's WSPhobius web service. 3. TMHMM and SignalP. Uses the TMHMM and SignalP methods of InterProScan via the EBI's WSInterProScan service. The results of the three methods are converted into GFF format and collated.

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

Viewed: 188 times | Downloaded: 137 times

Uploader:

Hamish McWilliam

EBI_ScanPS (v1)

Created: 03/06/08 @ 05:57:09 | Updated: 03/06/08 @ 05:57:09

Credits: Hamish McWilliam

License: Creative Commons Attribution 3.0 License

Perform a Smith-Waterman sequence similarity search using the ScanPS tool (see http://www.compbio.dundee.ac.uk/Software/Scanps/scanps.html). In the case the EBI's WSScanPS web service (see http://www.ebi.ac.uk/Tools/webservices/services/scanps) is used to run the tool.

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

Viewed: 121 times | Downloaded: 107 times

Uploader:

Hamish McWilliam

Structure_or_ID (v1)

Created: 06/06/08 @ 05:57:31 | Updated: 06/06/08 @ 05:57:31

Credits: Hamish McWilliam

License: Creative Commons Attribution 3.0 License