Workflows in this Topic

Gene annotation pipeline for the Graves di... (2)

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This is a revised workflow for the Graves disease scenario gene annotation pipeline used in the myGrid project. The workflow had to be re-written due to the loss of the services invoked in the original workflow.

Created: 2007-10-03 | Last updated: 2007-11-22

Credits: Katy Wolstencroft Peter Li

ProteinSynonymsToQuery (2)

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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

Created: 2007-10-03 | Last updated: 2007-11-13

Credits: Marco Roos Martijn Schuemie AID

DiscoverProteinLink (2)

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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 ...

Created: 2007-10-03 | Last updated: 2007-11-15

Credits: Marco Roos AID

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: Niall Haslam

CountListElements (5)

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Very simple workflow to count the number of items in a list (top level only in case of nested lists). Does no more than count = list.size();

Created: 2007-10-17 | Last updated: 2007-10-17

BioAID_DiseaseDiscovery_RatHumanMouseUnipr... (4)

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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...

Created: 2008-12-15 | Last updated: 2011-08-11

Credits: Marco Roos AID

BioAID_ProteinDiscovery (8)

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The 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.

Created: 2010-05-10 | Last updated: 2013-08-16

Credits: Marco Roos AID

BioAID_ProteinToDiseases (1)

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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 ...

Created: 2007-11-14 | Last updated: 2007-11-15

Credits: Marco Roos Martijn Schuemie AID

Attributions: BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter

Discover_proteins_from_text (2)

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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.

Created: 2007-11-15 | Last updated: 2007-11-15

Credits: Marco Roos AID

BioAID_Discover_proteins_from_text_plus_sy... (1)

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: Marco Roos Martijn Schuemie AID

TestIterator (1)

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Workflow to experiment with list iteration strategies. Look at metadata of nested workflow 'Concatenate' to see the current iteration strategy.

Created: 2007-11-28

Credits: Marco Roos

TestIteratorStrategy_withNesting (1)

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Implementation of the iteration workaround by Tom Oin conform the Q&A below. The nested workflow 'NestedProcessor' is called that to conform to Tom's explanation. For an alternative solution using a java beanshell to clone list items see 'TestIteratorStrategy_withCloning. This workflow implements the following Q&A: Marco Roos wrote: > Dear Taverna user, > > Issue 1: Complex iteration > > I would like to perform an iteration including a dot product between > a list and a list of li...

Created: 2007-11-29

Credits: Marco Roos Tomoinn

CloneItemsInList (1)

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Utility workflow that clones an item copy_number times. You can use this to work around standard iteration strategies, e.g. in combination with the CountListItems workflow. Workflow examples: TestIterationStrategy_withClones. For an alternative approach see TestIterationStrategy_withNesting. Example I/O: input: A copy_number: 3 result: [A,A,A] input: [A,B,C] copy_number: 3 result: [[A,A,A][B,B,B][C,C,C]] input: [A,B,C] copy_number: [3,2] result: [[[A,A,A],[A,A]][[B,B,B],[B,B]],[[C,C,C],...

Created: 2007-11-29

Credits: Marco Roos

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: Marco Roos

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: Marco Roos Sophia katrenko AID

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: Marco Roos

Flatten_and_make_unique (1)

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No description

Created: 2007-12-10

Credits: Marco Roos AID

Link_protein_to_OMIM_disease (1)

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No description

Created: 2007-12-10

Credits: Marco Roos AID

Lucene_bioquery_optimizer_MR1 (1)

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This workflow does four things: it retrieves documents relevant for the query string it discovers entities in those documents, these are considered relevant entities it filters proteins from those entities (on the tag protein_molecule) it removes all terms from the list produced by 3 (query terms temporarily considered proteins) ToDo Replace step 4 by the following procedure: 1. remove the query terms from the output of NER (probably by a regexp matching on what is inside the tag, ...

Created: 2007-12-10

Credits: Marco Roos AID

Retrieve_bio_documents (2)

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This workflow retrieves relevant documents, based on a query optimized by adding a string to the original query that will rank the search output according to the most recent years. The added string adds years with priorities (most recent is highest); it starts at 2007.

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

Credits: Marco Roos Edgar AID

Retrieve_documents_MR1 (1)

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This workflow applies the search web service from the AIDA toolbox. Comments: This search service is based on lucene defaults; it may be necessary to optimize the querystring to adopt the behaviour to what is most relevant in a particular domain (e.g. for medline prioritizing based on publication date is useful). Lucene favours shorter sentences, which may be bad for subsequent information extraction.

Created: 2007-12-10

Credits: Marco Roos Edgar AID

Demo_DiseaseDiscovery_byHumanUniprot_scaffold (1)

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This workflow finds disease relevant to the query string via the following steps: 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. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache's Lucene)...

Created: 2007-12-10

Credits: Marco Roos AID

BioAID_ProteinDiscovery_filterOnHumanUnipr... (11)

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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...

Created: 2009-05-28

Credits: Marco Roos Martijn Schuemie AID AID_myGrid_collaboration

Attributions: BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter

lister.xml (1)

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No description

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

Ensembl_id_2_Swissport_id.xml (1)

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No description

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

bind-idsearch.xml (1)

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No description

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

blast_GO.xml (1)

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No description

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

metabolic.xml (1)

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An example of how a more complex workflow can federate multiple resources to perform data mining. In this case a single input data item in the form of a probe set identifier is cross referenced to data sets in multiple locations to answer a kind of 'show me everything about this data' question.

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

BioAID_EnirchBioModelWithProteinsFromText (7)

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This workflow is for demonstration purposes only. Please contact the authors if you wish to try it. We will gladly collaborate with you. Summary This workflow extracts proteins and protein relations from Medline. Extracted protein names (symbols of at least 3 characters) are validated against mouse, rat, and human UniProt symbols, so the results are limited to these species. This workflow follows the following basic steps: it retrieves documents relevant for the query string i...

Created: 2009-05-16 | Last updated: 2009-05-16

Credits: Marco Roos Sophia katrenko Andrew Gibson M. Scott Marshall Willem van Hage Edgar Martijn Schuemie AID

Structural alignment of arbitrary number o... (1)

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This grid-executed Mustang application performs a structural alignment of protein sequences. The number of arguments is variable, in principle, but is shown here for three. The application is executed via the Taverna-ARC plugin on a machine of the NorduGrid. Although your machine can be a part of it, you may prefer to wait for a later version of that interface that does not require grid certificates.

Created: 2008-09-02

Credits: Steffen Möller Fxtentacle

Attributions: Fetch PDB flatfile from RCSB server

Cove_NetCDF_visualization (1)

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The Cove workflow reads oceanographic NetCDF data, does a simple processing step, writes the data out, then sends a web service message to the COVE visualization tool. It is a four step, sequential workflow.

Created: 2008-10-08 | Last updated: 2008-10-08

Credits: Trident

Blast against ENSEMBLE Danio_rerio_Genome (1)

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This workflow invokes the blast service provided at www.bioinformatics.nl, written by Pieter Neerincx. The workflow takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and a set of sequences in fasta format. The blast service is invoked (using polling) and the result is a tab separated blast report.   To run this workflow, a certificate to access www.bioinformatics.nl needs to installed (Some services use an SSL connection). Look at the link below how to ins...

Created: 2008-10-15 | Last updated: 2008-10-15

Credits: Wassinki

NETCDFMean (1)

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This WF reads a netCDF file to a hyper cube data structure. Then this WF applies the mean transform to a variable in the netCDF file. The calculated mean is produced as part of the output.

Created: 2008-10-21

Credits: Trident

Demo of ChemSpider InChi to SMILES webserv... (1)

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Created: 2009-03-28 | Last updated: 2009-03-28

Credits: David De Roure

Demo of statistics webservice invoked from... (1)

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Created: 2009-03-29

Credits: David De Roure

snpNeighbours (1)

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My first Taverna workflow:  the input is the SNP "rs25". The Web Services invoked finds its position on the human genome and find its neighbours at 100bp. The XML result is then saved to a local file. The web services used here are under developpement and might be turned off in a near future.

Created: 2009-05-14 | Last updated: 2009-05-14

Credits: PL

Index MyExperiment Workflow (2)

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This workflow uses AIDA components to index all of the workflows on MyExperiment. First, it lists and downloads each workflow's xml file. Then, the titles and descriptions are parsed and submitted to an Indexer webservice. After it's finished, your index will be searchable by visiting http://aida.science.uva.nl:9999/search.

Created: 2009-05-26 | Last updated: 2009-05-27

Credits: Edgar

Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2009-07-03

Credits: Stian Soiland-Reyes Ian Dunlop

t ... (2)

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Created: 2009-08-21 | Last updated: 2009-10-09

Credits: Ctindal

Spreadsheet Importer (1)

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This workflow is designed to import a spreadhseet from a local computer. The imported spreadsheet is parsed to extract the first two columns, A and B, for all rows in the spreadsheet. These are returned as two separate outputs.

Created: 2009-08-24

Credits: Paul Fisher

OJAX++ feed retrieval (1)

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No description

Created: 2009-09-01 | Last updated: 2009-09-01

Credits: Davej

Get locations from postcode (1)

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 This workflow will return all the areas that correspond to a postcode. Enter the first part of the postcode only, e.g. SW19

Created: 2010-03-08 | Last updated: 2010-03-08

Credits: Rory

EBI_InterProScan for Taverna 2 (1)

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Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the s...

Created: 2010-07-08 | Last updated: 2010-07-08

Credits: Benb

Performing a double sided T-test on Brunn ... (1)

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Created: 2010-09-13 | Last updated: 2010-09-13

Credits: jonalv

Using a Create_List script with a dot-prod... (1)

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Create_lots_of_strings gives implicit iteration over the service add_a_and_b - assume this is a service that returns two values which you now want to keep in a list [a,b]. The shim Create_list takes two single inputs, and returns a list of [in1, in2]. Configured with the Dot product list strategy it means that it will pipeline out [a1,b1], [a2,b2], [a3,b3] etc.Create_lots_of_strings gives implicit iteration over the service add_a_and_b - assume this is a service that returns two values which...

Created: 2011-02-02 | Last updated: 2011-02-02

Credits: Stian Soiland-Reyes

Create a molecules table from a list of IU... (1)

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 Scripts that uses OPSIN to convert IUPAC names into chemical structures, which are saved as SD file and openend in the Bioclipse molecules table.

Created: 2011-05-25 | Last updated: 2011-05-25

Credits: Egon Willighagen

Comparison of Birth and Death Rates for a ... (1)

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This workflow extracts the relevant data from two spreadsheets, formats the data strings, and puts that data through a REST to Google Charts. Data collected for this project comes from data.un.org. Currently, the workflow supports data from only one country at a time (data from data.un.org can be filtered and exported directly from the website). Data from the Live births by month and Deaths by month works best with this workflow.

Created: 2011-11-27 | Last updated: 2011-11-27

Credits: tpacurtis

FFmpeg convert audio2aac (REST) (1)

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Converts supported audio files to AAC using FFmpeg through a REST webservice.

Created: 2012-01-16 | Last updated: 2012-01-16

Credits: Rui Castro

Explain concept scores (7)

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Purpose of workflow: This workflow takes two concept 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 pe...

Created: 2012-02-07 | Last updated: 2014-07-14

Credits: Reinout van Schouwen

Temporal Expression Extraction (1)

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This experiment evaluates a method of extracting temporal expressions from documents. It uses the WikiWars-corpus, a time-annotated corpus of descriptions of the course of wars and conflicts. An evaluation component compares the experimently identified expressions with the pre-annotated expressions of the corpus and calculates precision, recall and  f-score.

Created: 2012-05-22 | Last updated: 2012-05-22

Credits: AGeduldig

Sample workflow for usability testing (1)

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Created: 2012-06-18

Credits: Wotan