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Showing 35 results. Use the filters on the left and the search box below to refine the results.
Tag: text mining Licence: by-sa

Workflow Termine with c-value threshold (1)

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This workflow accepts a list of sentences from a single document and returns the terms found by the TerMine web service. It also allows you to set a threshold c-value score so that only terms with a user-controlled probability (of being a real term) are returned as an output.   To get sentences to supply to this workflow you can use the sentence splitting workflow.  The TerMine service (used in this workflow) only accepts text in ASCII encoding, so you should also use the Clean p...

Created: 2010-02-19 | Last updated: 2011-12-13

Credits: User James Eales

Workflow PDF to plain text (1)

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This workflow will extract the plain text content of PDF files supplied to the input port.  You can connect the Load PDF from directory workflow to this workflows input. We recommend you send the output from this workflow to the Clean plain text workflow, because the PDF to text process can add characters into the text that are XML-invalid and therefore can not be sent to most services as plain text.  Another way round this problem is to encode the text as Base64 using the handy loc...

Created: 2010-02-19 | Last updated: 2011-12-13

Credits: User James Eales

Workflow GeneIlluminator_GetPubMedQuery (2)

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Example workflow demonstrating how to use GeneIlluminator_GetPubMedQuery, a synchronous BioMOBY service for gene symbol disambiguation. If a gene symbol is ambiguous this service uses GeneIlluminator to create clusters describing which different genes, sharing the same symbol, exist in different parts of the tree of life. GeneIlluminator provides also aliases associated to the input gene symbol. Finally, using the cluster characteristics it creates a boolean PubMed query that could be used to...

Created: 2008-02-27 | Last updated: 2008-03-03

Credits: User Pieter Neerincx User Alako

Workflow GeneIlluminator_Disambiguate (2)

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Example workflow demonstrating how to use GeneIlluminator_Disambiguate, a synchronous BioMOBY service for gene symbol disambiguation. If a gene symbol is ambiguous this service provides GI_Clusters describing which different genes, sharing the same symbol, exist in different parts of the tree of life. Provides also gene symbol aliases associated to the input gene symbol. (This is the same output as the one from the GeneIlluminator_GetClusters service.) In addition this service takes an Organi...

Created: 2008-02-27 | Last updated: 2008-03-03

Credits: User Pieter Neerincx User Alako

Workflow microRNA to KEGG Pathways and Abstracts (1)

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Workflow takes in a text file of microRNAs from microCOSM (at the EBI) and outputs a list of KEGG pathway information, including genes in pathways and pathway abstracts from PubMed. The results can then be used in various text mining applications/workflows to rank the results against a given disease.Workflow takes in a file of microRNAs

Created: 2010-03-17

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

Workflow Sentence splitting (1)

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This workflow will attempt to split up text into sentences, returning a list of sentences to the output port.  The sentence splitting service makes use of the OpenNLP sentence detector and has been trained to work on english text. This workflow can be used to provide input to the Termine with c-value threshold workflow. This is a workflow component, designed to be used as a nested workflow inside a larger text mining or text processing workflow.

Created: 2010-02-19 | Last updated: 2011-12-13

Credits: User James Eales

Workflow GeneIlluminator_GetGraph (2)

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Example workflow demonstrating how to use GeneIlluminator_GetGraph, a synchronous BioMOBY service for gene symbol disambiguation. If a gene symbol is ambiguous this service uses GeneIlluminator to create clusters describing which different genes, sharing the same symbol, exist in different parts of the tree of life. GeneIlluminator provides also aliases associated to the input gene symbol. Finally, a graphical overview of the clusters and gene symbols is created in SVG format and returned to ...

Created: 2008-02-27 | Last updated: 2008-03-03

Credits: User Pieter Neerincx User Alako

Workflow GeneIlluminator_GetClusters (2)

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Example workflow demonstrating how to use GeneIlluminator_GetClusters, a synchronous BioMOBY service for gene symbol disambiguation. If a gene symbol is ambiguous this service provides GI_Clusters describing which different genes, sharing the same symbol, exist in different parts of the tree of life. Provides also gene symbol aliases associated to the input gene symbol. (Use GeneIlluminator_GetGraph for a graphical representation of the clusters or GeneIlluminator_Disambiguate to get the mos...

Created: 2008-02-27 | Last updated: 2008-03-03

Credits: User Pieter Neerincx User Alako

Workflow Terms from collection of PDF files (2)

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This workflow will give you a set of candidate terms for each PDF document in a user-specified directory. You can also specify a c-value threshold that will restrict the terms to those with higher scores. This workflow was created using only nested workflows.  These workflow components work on their own and can be linked together to form more complex workflows such as this. You can view the text mining workflow components in this pack. If you receive errors when running this workflow t...

Created: 2010-02-19 | Last updated: 2011-12-13

Credits: User James Eales

Workflow Extract Scientific Terms (1)

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This workflow takes in a document containg text and removes any non-ascii characters. The cleaned text is then sent to a service in Dresden, to extract all scientific terms. These terms represent a concept profile for the input concpet. Any null values are also removed.

Created: 2009-08-10 | Last updated: 2009-08-10

Credits: User Paul Fisher

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