Workflows

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Workflow Extract_proteins (2)

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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).

Created: 2007-12-10 | Last updated: 2007-12-10

Credits: User Marco Roos

Workflow Discover_entities (2)

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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 ...

Created: 2007-12-10 | Last updated: 2007-12-10

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

Workflow TestIteratorStrategy_withCloning (2)

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This workflow implements a strategy for this problem: > I would like to perform an iteration including a dot product between > a list and a list of lists; example: > Input: > > [1] (1) > [A,B,C] (2) > [[a,b],[c,d],[e,f]] (3) > > Desired output: > > [1Aa, 1Ab, 1Bc, 1Bd, 1Ce, 1Cf] In this implementation a java beanshell is used to clone the items in list 2 as many times per item as there are items in the sublists of list 3. The iteration stra...

Created: 2007-11-29 | Last updated: 2007-11-29

Credits: User Marco Roos

Workflow kegg_gene_to_swissprot_identifier (1)

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Takes a KEGG gene identifier, e.g. sce:YAL038W (yeast pyruvate kinase) and converts to the corresponding Swissprot identifier.

Created: 2007-11-27 | Last updated: 2007-11-28

Credits: User Sirisha Gollapudi

Workflow BioAID_Discover_proteins_from_text_plus_sy... (1)

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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.

Created: 2007-11-15

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

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Workflow Query Maxd microarray database (1)

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Retrieves data from the maxd database given name of data set

Created: 2007-11-14 | Last updated: 2007-11-22

Credits: User Peter Li

Workflow pELM_getInstance_Return_Seq (2)

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Simple workflow to retrieve the sequence of a phospho.ELM entry given the Instance identifier. Input requires xml as the namespace is not correctly handled by the xml splitter. Example input: I000299 Further outputs can easily be added, most are text with some xml. See list in InstanceXML.

Created: 2007-10-03 | Last updated: 2008-05-02

Credits: User Niall Haslam

Workflow getFragWithClosure (2)

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Bit of a hack, but it works now, adds trailing "%90" to the output.

Created: 2007-10-03

Workflow getFragWithClosure (2)

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getFragment with closure "workflow", actually just one service, but need example inputs for smiles string, group and closure parameters.

Created: 2007-10-03

Workflow MrBayesPPtest (13)

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robust connection

Created: 2013-12-11 | Last updated: 2014-11-27

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