Workflows

List Concept Sets (1)

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Pupose: The workflow returns a list of all Concept Set IDs currently available in the database. The Concept Sets have an hierarchical structure that can be inferred by referring to the parent Concept Set ID.

Created: 2015-04-03

Credits: Eleni BioSemantics

Explain score between two concepts (1)

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Purpose of workflow: This workflow takes two ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the percentage...

Created: 2015-04-03

Credits: Eleni BioSemantics

Galaxy workflow for the identification of ... (1)

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This approach screens three proteins against a given genome sequence, leading to a genome position were all three genes are located nearby. As usual in Galaxy workflows every parameter, including the proximity distance, can be changed and additional steps can be easily added. For example additional filtering to refine the initial BLAST hits, or inclusion of a third query sequence.https://github.com/bgruening/galaxytools/tree/master/workflows/ncbi_blast_plus/find_three_genes_located_nearby

Created: 2015-03-17

Credits: Björn Grüning

Get concept suggestions from term (1)

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This workflow suggests concept ids that match the query term. The user can run this workflow with any term of interest as for example "human", "htt", "Transcription" etc, and will get suggestions for concept ids together with descriptions. Then can choose the concept id that matches the best to her/his needs and use it to the rest of the CPA workflows.

Created: 2015-02-18

Credits: Eelke van der Horst Kristina Hettne Marco Roos Eleni

Attributions: Get concept suggestions from term

North - Chapter 11 process (1)

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Testing myExperiment.org

Created: 2015-02-11

Store Receipts to structured information (1)

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As the title suggests, this process is a tool to transform receipts into a table sheet. The process is made for receipts that are already scanned and processed with an OCR Tool.Input: txt. FilesOutput: table with the following columns: Date, price, category, receipt index, buyer, product description  Roughly speaking this process is divided in the following steps:1.    .txt2exset: In this sub process a receipt.txt file is segmented. Every line represents one example. ...

Created: 2015-02-08 | Last updated: 2015-02-08

Galaxy workflow for the identification of ... (1)

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This approach screens two proteins against all nucleotide sequence from the NCBI nt database within hours on our cluster, leading to all organisms with an inter- esting gene structure for further investigation. As usual in Galaxy workflows every parameter, including the proximity distance, can be changed and additional steps can be easily added. For example additional filtering to refine the initial BLAST hits, or inclusion of a third query sequence.https://github.com/bgruening/galaxytools/tr...

Created: 2015-01-25

Credits: Björn Grüning

Example SPARQL on Wikidata using the Linke... (1)

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This Bioclipse script (in Groovy) uses the Linked Data Fragments (ldf) manager that uses the LDF Java client library to run a SPARQL query on the LDF server wrapping Wikidata.

Created: 2015-01-23 | Last updated: 2015-01-23

Credits: Egon Willighagen

Groovy script to convert (part of) CGN dat... (1)

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Created: 2015-01-22

Credits: Egon Willighagen

connect to WoS Web services lite concept (1)

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This workflow is a concept for how Taverna could connect to the Thomson Reuters Web of Science (WoS) Web services lite. However, at this moment (2015-01-20), the authentication generate a session ID, but the other services (here search and closeSession) do not have an input port for this session ID. According to the documentation, this is required. The error message from the Web service also show this is missing. This workflow is "work in progress", but may nevertheless be of interest to an...

Created: 2015-01-20 | Last updated: 2015-08-19

Credits: Magnus Palmblad Arzu Tugce Guler Cathelijn Waaijer

pipeline5 (1)

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Created: 2015-01-09 | Last updated: 2015-01-09

Credits: Chetan Joshi

OCR_NE (1)

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Takes as input an image, and extracts the NE

Created: 2015-01-06

Metabolite pathway search (1)

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The workflow searches for metabolomic pathways that match the entered keywords and returns information about the chosen pathway

Created: 2014-12-18

Credits: Alan Williams

Choose_id (1)

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Make a choice based upon displayed names and return the id corresponding to the choice

Created: 2014-12-18 | Last updated: 2014-12-18

Extract columns (3)

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Extracts column data from a newline and tab separated string

Created: 2014-12-18 | Last updated: 2014-12-18

Example Process using the RapidMiner Linke... (1)

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This example process uses the operator SPARQL Data Importer provided by the RapidMiner LOD Extension to receive additional data about books including the author, isbn, country, abstract, number of pages and language from dbpedia (www.dbpedia.org).

Created: 2014-12-04

RapidMiner process created by the MLWizard... (1)

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This process was created by the MLWizard Extension. Start RapidMiner Studio, download the extension from the RapidMiner Marketplace, open the menu Tools and click on "Automatic System Construction". A wizard opens, which suggests some models which fit best to build a model from your data. You can choose the one which has the most accuracy and the wizard creates the RapidMiner process for you.

Created: 2014-12-04

Example Process using the WHIBO Extension (1)

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This example shows simply the operator Generic decision tree of the WHIBO extension for RapidMiner Studio, which allows the creation and usage of an individual Decision Tree algorithm.

Created: 2014-12-04

Example process of the Text and Web Mining... (1)

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This example process crawls the web (RapidMiner forum) for entries, extracts the information with the Process Documents operator and applies Clustering on the results. The process shows the interaction between the Web Mining Extension and the Text Mining Extension from RapidMiner.

Created: 2014-12-04

Example Process RapidMiner Multimedia Mini... (1)

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This example process can be used with the Multimedia Extension (http://www.burgsys.com/) in RapidMiner Studio. It shows how to create a QR code with the extension, and how to make image transformations.

Created: 2014-12-04 | Last updated: 2014-12-04

BioMaS Illumina Workflow (1)

BioMaS (Bioinformatic analysis of Metagenomic AmpliconS) is a bioinformatic pipeline designed to support biomolecular researchers involved in taxonomic studies of environmental microbial communities by a completely automated workflow, comprehensive of all the fundamental steps, from raw sequence data arrangement to final taxonomic identification, that are absolutely required in a typical Meta-barcoding HTS-based experiment. This BioMaS version allows the analysis of both bacterial a...

Created: 2014-11-27 | Last updated: 2014-11-27

Credits: Pasquale Notarangelo