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Items tagged with "text_mining_network" (8)

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Workflows (7)
Original Uploader

Workflow Discover_proteins_from_text (2)

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

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 194 times | Downloaded: 71 times

Tags (7):

Original Uploader

Workflow BioAID_ProteinToDiseases (1)

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

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

Attributions: Workflow BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 197 times | Downloaded: 94 times

Tags (8):

Original Uploader

Workflow BioAID_ProteinDiscovery (7)

Created: 10/05/10 @ 16:21:09 | Last updated: 20/03/12 @ 17:16:11

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 389 times | Downloaded: 144 times

Tags (12):

Original Uploader

Workflow BioAID_DiseaseDiscovery_RatHumanMouseUnipr... (4)

Created: 15/12/08 @ 20:46:09 | Last updated: 11/08/11 @ 09:22:23

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 4266 times | Downloaded: 664 times

Tags (9):

Original Uploader

Workflow DiscoverProteinLink (2)

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

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 303 times | Downloaded: 65 times

Tags (8):

Original Uploader

Workflow BioAID_Discover_proteins_from_text_plus_sy... (1)

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

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 97 times | Downloaded: 2 times

Tags (7):

Original Uploader

Workflow BioAID_ProteinDiscovery_filterOnHumanUnipr... (11)

Created: 28/05/09 @ 12:21:05

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

Attributions: Workflow BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 471 times | Downloaded: 173 times

Tags (9):

Packs (1)
Creator

Pack AIDA toolbox


Created: 01/08/08 @ 11:33:03 | Last updated: 14/02/10 @ 16:04:25

Adaptive Information Disclosure Application toolbox: AIDA web services for automated knowledge extraction and knowledge management Documentation    

9 items in this pack

Comments: 0 | Viewed: 182 times | Downloaded: 23 times

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