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Items tagged with "esearch" (13)

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Workflows (9)
Taverna 1

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Workflow Perform a search through NCBI eUtils eSearch (v3)

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: 387 times | Downloaded: 205 times

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Taverna 1

Original Uploader

Workflow Basic eSearch/eFetch cycle (v1)

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 ...

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Viewed: 139 times | Downloaded: 46 times

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XProc

Original Uploader

Workflow Query dbsnp, transform to HTML (v1)

Created: 21/05/09 @ 22:01:55 | Last updated: 21/05/09 @ 23:12:33

Credits: User Pierre Lindenbaum

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a XProc worklow. Its input is a list of Entrez queries packed in a html list: See http://plindenbaum.blogspot.com/2009/05/xml-pipelines-xproc-for-bioinformatics.html "snp_gene_clin"[Filter] AND "snp_pubmed_cited"[Filter] AND 2[CHR] (1000[CHRPOS] : 5000[CHRPOS]) AND 2[CHR] AND "homo sapiens"[Organism] it queries entrez, download the SNPs as XML and transform the result as an HTML table:   r...

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Taverna 2

Original Uploader

Workflow Get Gene Ids for Human (v1)

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

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Taverna 2

Original Uploader

Workflow microRNA to KEGG Pathways and Abstracts (v1)

Created: 17/03/10 @ 10:53:02

Credits: User Paul Fisher

Attributions: Workflow Pathways and Gene annotations for QTL region

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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

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Taverna 2

Original Uploader

Workflow Gene to Pubmed (v3)

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

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Taverna 2

Original Uploader

Workflow Phenotype to pubmed (v3)

Created: 05/07/10 @ 14:07:33 | Last updated: 11/01/11 @ 12:07:22

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes in a phenotype search term, and searches for abstracts in the PubMed database. These are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user

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

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Taverna 2

Original Uploader

Workflow Pathway and Gene to Pubmed (v2)

Created: 10/02/11 @ 16:10:52 | Last updated: 18/02/11 @ 13:47:08

Credits: User Paul Fisher

Attributions: Workflow Cosine vector space Workflow Extract Scientific Terms Workflow Rank Phenotype Terms Workflow Cosine vector space Workflow Rank Phenotype Terms Workflow Pathway to Pubmed Workflow Extract Scientific Terms Workflow Gene to Pubmed

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes in a list of gene names and KEGG pathway descriptions, and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then used to calculate a cosine vector space between two sets of corpora (gene and phenotype, or pathway and phenotype). The workflow counts the number of articles in the pubmed database in which each term occurs, and identifies the total number of articles in the entire PubMe...

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

Viewed: 64 times | Downloaded: 19 times

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Taverna 2

Original Uploader

Workflow Download Structures from PubChem given chemical names (v1)

Created: 24/05/11 @ 13:13:52 | Last updated: 24/05/11 @ 14:19:24

Credits: User Kalai User Michael Gerlich

Attributions: Workflow Download Entries from PubChem

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes the input file containing chemical names and returns a single SDF file of structures. The names are searched against pubchem compounds via e-search. If the compound name is found an XML file containing PubChem ID is returned.The max return compound_ID is set to 1 which could be increased. If the compound name is not found then no ID is returned.  The pubchem compound_ID is then used to download structures from PubChem.  

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

Viewed: 39 times | Downloaded: 19 times

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Packs (2)

Creator:

Pack Text Mining Workflows

Created: 08/12/10 @ 11:55:03 | Last updated: 01/02/11 @ 11:33:11

This pack contains workflows to navigate from candidate Quantitative Trait genes and pathways to a given phenotype.

5 items in this pack

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Pack Trichuriasis induced Colitis

Created: 16/02/11 @ 12:49:21 | Last updated: 16/02/11 @ 15:26:36

This pack contains the workflows and data relating to Trichuriasis induced colitis.

5 items in this pack

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Files (2)

Uploader:

Blob Pathway Abstracts for Day7 Microarray Tir1 QTL

Created: 11/08/09 @ 14:08:41 | Last updated: 11/08/09 @ 14:15:58

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains all the abstracts for pathways found to be differentially expressed at day 7 post infection and intersect the Tir1 QTL region, from the African Trypanosomiasis project. Each pathway is listed as ">> [Pathway Name]", together with a PubMed identifier, date, and abstract for each article. Each pathway has been restricted to 500 abstracts, and is given in the date range 31/12/2007 to 01/01/2009. Note, some pathways do not have any abstracts available due to th...

File type: Plain text

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Blob Ondex and Taverna Tutorial

Created: 22/10/09 @ 13:50:53 | Last updated: 22/10/09 @ 13:51:51

Credits: User George

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Biological Data Integration Using Ondex and Taverna: A Tutorial 25/26th November 2009 The University of Manchester The Ondex SABR project (http://ondex.org/sabr.html) invite you to a two-day tutorial that aims to show participants how to use Ondex and Taverna to perform common biological data collection, integration and visualisation tasks.

File type: Word document

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 30 times | Downloaded: 24 times

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