Workflows

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Wsdl: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl
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Workflow Perform a search through NCBI eUtils eSearch (3)

Created: 27/11/09 @ 14:44:11 | Last updated: 03/12/09 @ 16:32:26

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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This workflow takes in a search term and a database (e.g. snp, gene, protein) in which to perfom the search over. The result is an xml file containing summary information about the search term. Example input for this workflow are given below: database: pubmed terms: cancer AND diabetes

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 8 | Citations: 0

Viewed: 426 times | Downloaded: 212 times

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Original Uploader

Workflow Escherichia coli : From cDNA Microarray Ra... (1)

Created: 08/05/08 @ 15:25:29 | Last updated: 12/05/08 @ 09:01:37

Credits: User Saeedeh User Paul Fisher

Attributions: Workflow HUMAN Microarray CEL file to candidate pathways

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes in a CDNA raw file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the R and bioconductor. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed changes in the microarray data. By identifying the candidate pathways, more detailed...

Rating: 5.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 336 times | Downloaded: 109 times

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Original Uploader

Workflow Sequence_or_ID_or_GI (1)

Created: 07/06/08 @ 16:58:14

Credits: User Hamish McWilliam

Attributions: Workflow Structure_or_ID

License: Creative Commons Attribution 3.0 Unported License

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Get a sequence in fasta format given one of: An NCBI GI number (e.g. 75251068). An entry identifier in database:identifier format (e.g. uniprot:Q96247). 3. A sequence entry in a format supported by EMBOSS seqret.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 122 times | Downloaded: 61 times

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Original Uploader

Workflow tRNAscan (1)

Created: 28/06/08 @ 09:57:33

Credits: User Hamish McWilliam

Attributions: Workflow Sequence_or_ID_or_GI

License: Creative Commons Attribution 3.0 Unported License

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Search a nucleotide sequence for tRNA genes using the tRNAscan-SE tool (see http://wiki.bioinformatics.org/TRNAscan-SE). This workflow uses the tRNAscan service at VBI PathPort (see http://pathport.vbi.vt.edu/services/#predict_7).

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 162 times | Downloaded: 57 times

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Original Uploader

Workflow NCBI_QBLAST (2)

Created: 07/06/08 @ 15:05:00 | Last updated: 07/06/08 @ 17:11:36

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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Perform an NCBI BLAST sequence similarity search using NCBI's QBLAST service (see http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 159 times | Downloaded: 80 times

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Original Uploader

Workflow Basic eSearch/eFetch cycle (1)

Created: 04/12/08 @ 22:47:43 | Last updated: 04/12/08 @ 22:51:42

Credits: User Giovanni Dall'Olio

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This is a basic eSearch/eFetch workflow created with taverna and using eUtils from NCBI. It accepts a query term as input (at the moment, for testing purposes, this is a fixed string), interrogate eSearch to retrieve the list of related sequences on the Nucleotide database, and use eFetch to retrieve the corresponding sequences. I wrote this workflow one year ago, when I was trying to understand how taverna and eUtils work; I suspect it broken, and of course it could be enhanced, so I am ...

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 160 times | Downloaded: 50 times

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Original Uploader

Workflow Search InChI in NCBI eSearch (pccompound) (1)

Created: 30/03/09 @ 09:26:25 | Last updated: 30/03/09 @ 09:47:00

Credits: User Michael Gerlich

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes in a search term (e.g. InChI) for search in PubChem pccompound database. The result is an xml file containing summary information about the search term and also a compound image and the compound webpage fetched from Pubchem.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 103 times | Downloaded: 50 times

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Original Uploader

Workflow Get Gene Ids for Human (1)

Created: 04/02/10 @ 12:47:16 | Last updated: 04/02/10 @ 12:48:11

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow gets a list of gene ids (number depending on Ret_Max_value variable) for Homo sapiens. The species may be changed according to that desired, by altering the term_value string constant

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 78 times | Downloaded: 24 times

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Original Uploader

Workflow Pathway to Pubmed (1)

Created: 02/09/08 @ 20:53:53 | Last updated: 08/09/08 @ 15:35:53

Credits: User Stian Soiland-Reyes User Paul Fisher

Attributions: Workflow ProteinSynonymsToQuery

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes in a list of KEGG pathway descriptions and searches the PubMed database for corresponding articles. Any matches to the pathways are then retrieved (abstracts only). These abstracts are then returned to the user.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 29 times | Downloaded: 13 times

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Original Uploader

Workflow Gene to Pubmed (3)

Created: 05/07/10 @ 13:14:36 | Last updated: 26/01/11 @ 16:57:39

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes in a list of gene names and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then returned to the user.

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 55 times | Downloaded: 32 times

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