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Items tagged with "ncbi" (27)

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Workflows (25)

Taverna 1 Original Uploader Paul Fisher	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 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: 368 times \| Downloaded: 192 times Tags (4): esearch \| eutils \| ncbi \| pubmed	View Download (v3)
Taverna 1 Original Uploader Alan Williams	GBSeq test (v2) Created: 05/03/08 @ 14:15:35 \| Last updated: 31/03/08 @ 15:55:09 Credits: Franck Tanoh License: Creative Commons Attribution 3.0 Unported License This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 222 times \| Downloaded: 87 times Tags (9): bioinformatics \| example \| mygrid \| ncbi \| nucleotide \| protein \| retrieval \| shim \| taverna	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	NCBI_QBLAST (v2) Created: 07/06/08 @ 15:05:00 \| Last updated: 07/06/08 @ 17:11:36 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License 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: 130 times \| Downloaded: 67 times Tags (5): bioinformatics \| BLAST \| ncbi \| ncbi blast \| sequence similarity search	View Download (v2)
Taverna 1 Original Uploader Hamish McWilliam	Sequence_or_ID_or_GI (v1) Created: 07/06/08 @ 16:58:14 Credits: Hamish McWilliam Attributions: Structure_or_ID License: Creative Commons Attribution 3.0 Unported License 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: 110 times \| Downloaded: 56 times Tags (9): bioinformatics \| dbfetch \| ebi \| efetch \| fasta format \| gi \| ncbi \| sequence identifier \| sequence retrieval	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	Pathways and Gene annotations for Arabidopsis affy data (v2) Created: 06/03/09 @ 17:18:13 \| Last updated: 03/12/09 @ 16:59:11 Credits: Paul Fisher Peter Li Attributions: Pathways and Gene annotations for QTL region License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow searches for genes obtained from affy_ath1 affymetrix probeset identifiers. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway database. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 216 times \| Downloaded: 1 time Tags (12): affymetrix \| arabidopsis \| binfo \| entrez \| gene \| kegg \| Kegg Pathways \| ncbi \| pathway \| pathways \| swissprot \| uniprot	View
Taverna 1 Original Uploader Michael Gerlich	Search InChI in NCBI eSearch (pccompound) (v1) Created: 30/03/09 @ 09:26:25 \| Last updated: 30/03/09 @ 09:47:00 Credits: Michael Gerlich License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 89 times \| Downloaded: 44 times Tags (12): bioinformatics \| compound \| compound info + image \| database \| image \| inchi \| information \| ncbi \| pccompound \| pubchem \| search \| xml	View Download (v1)
Taverna 1 Original Uploader Michael Gerlich	MassBank to KEGG (v1) Created: 30/03/09 @ 09:30:32 \| Last updated: 30/03/09 @ 09:49:13 Credits: Michael Gerlich License: Creative Commons Attribution-Share Alike 3.0 Unported License Workflow that queries MassBank DB to retrieve database identifiers (KEGG, PubChem, InChI) and continue search with them to retrieve pathways from KEGG for given compound identifier,searches PubChem via eutils and PUG, queries ChemSpider for compound information and image. Note: Usage of ChemSpider web services requires a valid security token - receive one by registering at ChemSpider (look at your profile to see your token) Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 194 times \| Downloaded: 0 times Tags (21): bget \| bioinformatics \| chemspider \| compound \| compound info + image \| database \| eutils \| image \| inchi \| information \| mass spectrometry \| massbank \| metabolomics \| ncbi \| pathway \| pccompound \| pubchem \| pug \| search \| summary \| xml	View
Taverna 1 Original Uploader Paul Fisher	NCBI Gi to Kegg Pathways (v1) Created: 08/06/09 @ 18:39:38 \| Last updated: 14/12/09 @ 11:51:20 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow converts a list of NCBI gi numbers and converts them to a list of KEGG genes. Those KEGG gene ids are subsequently turned into KEGG pathway identifiers and descriptions. It also removes any null values from a list of strings. Example input for this workflow is as follows (new line separated): gi:215422388 gi:120407068 Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 220 times \| Downloaded: 144 times Tags (6): bconv \| gene \| genes \| ncbi \| pathway \| pathways	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	Rank Phenotype Terms (v1) Created: 10/08/09 @ 15:43:48 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This 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 PubMed database. It also identified the total number of articles within pubmed so that a term enrichment score may be calculated. The workflow also takes in a document containing abstracts that are related to a particular phenotype. Scientiifc terms are then extracted from this text and given a weighting according to the number of terms that ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 119 times \| Downloaded: 0 times Tags (24): abstracts \| append term \| authors \| concept \| cosine vector space \| data-driven \| enrichment \| gene identifier \| geneid \| genes \| genotype \| information \| mining \| ncbi \| pathways \| phenotype \| pubmed \| ranking \| term \| term extraction \| terms \| text \| text mining \| text mining; term extraction; entity recognition	View
Taverna 2 Original Uploader Francois Belleau	What is [query] from NCBI, EBI, UniProt and KEGG ? (v2) Created: 03/11/09 @ 04:29:15 \| Last updated: 03/11/09 @ 04:29:19 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License test values: query = paget disease query = pdb4 query = hk1 query = h1n1 This rdfiser query those four federated search services EB-Eye, KEGG LinkDB, NCBI Entrez and UniProt knowledgebase. RDF triples are returned for search statistics with Bio2RDF normalised URIs. This workflow should be used responsibly because it can generate high load at the provider resources. test values: query = paget disease query = pdb4 query = hk1 query = h1n1 query = paget disease query = pdb4 query = hk1 que... Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 120 times \| Downloaded: 25 times Tags (8): bio2rdf \| cognoscope \| eb-eye \| kegg \| ncbi \| rdfiser \| search \| uniprot	View Download (v2)
Taverna 2 Original Uploader Francois Belleau	Triplify namespace list from global search services from EBI, KEGG, NCBI and UniProt [myexperiment:search_services_namespace2rdf] (v1) Created: 30/11/09 @ 21:38:23 \| Last updated: 30/11/09 @ 21:44:57 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 19 times \| Downloaded: 11 times Tags (7): banff_manifesto \| bio2rdf \| cognoscope \| ebi \| kegg \| ncbi \| uniprot	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Triplify NCBI databases list [myexperiment:ncbi_namespace2rdf] (v1) Created: 30/11/09 @ 21:47:05 \| Last updated: 01/12/09 @ 02:49:34 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License List NCBI's database name. Using this URL service: http://www.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi? This is NCBI's namespace list supported by Bio2RDF : pubmed protein nucleotide gene=geneid homologene mesh omim pccompound=cid pcsubstance=sid taxonomy unigene unists Rating: 1.0 / 5 (1 rating) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 24 times \| Downloaded: 10 times Tags (4): banff_manifesto \| bio2rdf \| cognoscope \| ncbi	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Triplify NCBI databases external reference list [myexperiment:ncbi_xref_namespace2rdf] (v1) Created: 01/12/09 @ 03:01:28 \| Last updated: 01/12/09 @ 03:03:24 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License Get NCBI external database list from http://www.ncbi.nlm.nih.gov/projects/collab/db_xref.html Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 27 times \| Downloaded: 13 times Tags (5): banff_manifesto \| bio2rdf \| ncbi \| rdf \| xref	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Get Gene Ids for Human (v1) Created: 04/02/10 @ 12:47:16 \| Last updated: 04/02/10 @ 12:48:11 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 67 times \| Downloaded: 18 times Tags (8): database \| esearch \| gene \| gene identifier \| homo sapiens \| human \| ncbi \| species	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	microRNA to KEGG Pathways and Abstracts (v1) Created: 17/03/10 @ 10:53:02 Credits: Paul Fisher Attributions: Pathways and Gene annotations for QTL region License: Creative Commons Attribution-Share Alike 3.0 Unported License 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 Viewed: 129 times \| Downloaded: 2 times Tags (21): bconv \| beanshell \| elico \| ensembl \| esearch \| eutils \| gene identifier \| geneid \| genes \| homo sapiens \| kegg \| KeggID \| microrna \| ncbi \| pathway \| pathway-driven \| pathways \| pubmed \| swissprot \| text mining \| uniprot	View
Taverna 2 Original Uploader Ian Laycock	NCBI Gi to Kegg Pathways (v1) Created: 19/03/10 @ 13:47:39 \| Last updated: 19/03/10 @ 13:52:45 Credits: Ian Laycock nclteamc Attributions: color_pathway_by_objects NCBI Gi to Kegg Pathways License: Creative Commons Attribution-Share Alike 3.0 Unported License User inputs background and foreground colour to be used to highlight proteins in KEGG pathway image. User provides NCBI GI numbers. Worflow calculates KEGG ID and pathway ID and sends value to colour service, which adds colour to that KEGG id on pathway image. Also outputs kegg description, pathway description and url of image. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 72 times \| Downloaded: 30 times Tags (5): bconv \| color \| kegg \| ncbi \| pathway	View Download (v1)
Taverna 2 Original Uploader Paul Fisher	Phenotype to pubmed (v3) Created: 05/07/10 @ 14:07:33 \| Last updated: 11/01/11 @ 12:07:22 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License 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 Viewed: 107 times \| Downloaded: 24 times Tags (18): abstracts \| african trypanosomiasis \| disease \| efetch \| entrez \| esearch \| loci \| ncbi \| phenotype \| pubmed \| qtl \| quanitative \| sleeping sickness \| term \| text \| text mining \| text mining; term extraction; entity recognition \| trait	View Download (v3)
Taverna 1 Original Uploader Paul Fisher	Entrez Gene to KEGG Pathway (v5) Created: 04/12/09 @ 16:04:38 \| Last updated: 30/11/10 @ 12:18:53 Credits: Paul Fisher License: Creative Commons Attribution 3.0 Unported License This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned. Rating: 4.8 / 5 (4 ratings) \| Versions: 5 \| Reviews: 0 \| Comments: 2 \| Citations: 0 Viewed: 1034 times \| Downloaded: 442 times Tags (9): entrez \| genotype \| kegg \| ncbi \| pathway \| pathway-driven \| pathways \| phenotype \| shim	View Download (v5)
Taverna 2 Original Uploader Katy Wolstencroft	EBI_NCBI_BLAST (v1) Created: 17/01/11 @ 12:51:58 \| Last updated: 17/01/11 @ 12:52:03 Credits: Katy Wolstencroft Hamish McWilliam Attributions: EBI_NCBI_BLAST License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow performs an NCBI blast at the EBI. It uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 61 times \| Downloaded: 28 times Tags (13): async \| asynchronous services \| BLAST \| blastp \| database \| ebi \| example \| looping \| ncbi \| ncbi blast \| protein sequence \| sequence \| uniprot	View Download (v1)
Taverna 2 Original Uploader Kalai	Download Structures from PubChem given chemical names (v1) Created: 24/05/11 @ 13:13:52 \| Last updated: 24/05/11 @ 14:19:24 Credits: Kalai Michael Gerlich Attributions: Download Entries from PubChem License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 30 times \| Downloaded: 12 times Tags (26): bioinformatics \| cheminformatics \| compound \| data \| download file \| esearch \| eutils \| file \| list \| ncbi \| open science \| open source \| pccompound \| split \| string \| structure \| structure retrieval \| synthetic \| taverna 2 \| taverna2 \| url2list \| workflow \| workflows \| wsdl \| xml \| xpath	View Download (v1)
Taverna 2 Original Uploader Rafael C. Jimenez	Get homologous from NCBI homoloGene (v1) Created: 13/10/11 @ 18:35:58 \| Last updated: 13/10/11 @ 18:36:01 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Get homologous from NCBI homoloGene for a list of Refseq protein accessions. Be patient, the workflows has to bring a file around 11Mb. ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/README Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 3 times \| Downloaded: 1 time Tags (3): homologene \| ncbi \| orthologous	View Download (v1)
Taverna 2 Original Uploader Rafael C. Jimenez	Get homologous from an NCBI homoloGene.data file using a list of UniProt accessions (v1) Created: 20/10/11 @ 17:53:28 \| Last updated: 27/10/11 @ 10:38:33 Credits: Rafael C. Jimenez License: Creative Commons Attribution-Share Alike 3.0 Unported License Get homologous from NCBI homoloGene for a lsit of UniProt protein accession. This workflow is useful if you have a long list of protein accessions. Use PICR to convert UniProt to RefSeq, get homologous from homoloGene and convert RefSeq results to UniProt. Be patient, the workflows has to bring a file around 11Mb. ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/README Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 9 times \| Downloaded: 4 times Tags (3): homologene \| ncbi \| orthologous	View Download (v1)
Taverna 2 Original Uploader Katy Wolstencroft	NCBI Gi to Kegg Pathway Images (v2) Created: 12/01/12 @ 09:38:10 \| Last updated: 12/01/12 @ 15:04:00 Credits: Katy Wolstencroft Paul Fisher Attributions: NCBI Gi to Kegg Pathways License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow accepts a list of genbank gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in, according to the KEGG database. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 3 times \| Downloaded: 5 times Tags (6): genbank \| genes \| gi \| image \| ncbi \| pathways	View Download (v2)
Taverna 2 Original Uploader Katy Wolstencroft	NCBI Gi to Kegg Pathway Descriptions (v2) Created: 12/01/12 @ 09:46:31 \| Last updated: 12/01/12 @ 14:54:37 Credits: Katy Wolstencroft Attributions: NCBI Gi to Kegg Pathways License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow accepts a list of genbank gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in, according to the KEGG database. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 3 times \| Downloaded: 2 times Tags (8): bconv \| genbank \| gene \| genes \| gi \| ncbi \| pathway \| pathways	View Download (v2)
Taverna 2 Original Uploader Paul martin	Define Associated Regions and Genes (v1) Created: 08/02/12 @ 16:08:08 \| Last updated: 08/02/12 @ 16:08:09 Credits: Paul martin License: Creative Commons Attribution-Share Alike 3.0 Unported License Defines regions and genes from associated SNPs Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 0 times \| Downloaded: 0 times Tags (14): association \| disease \| disease-associated genes \| ensembl \| gene \| genes \| genome wide association studies \| gwas \| mapping \| ncbi \| ngs \| sequencing \| snp \| ucsc	View Download (v1)

Packs (1)

Creator:

Paul Fisher

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

Comments: 0 | Viewed: 75 times | Downloaded: 12 times

Tags:

concept profile
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cosine vector space
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data-driven
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efetch
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entity recognition
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esearch
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gene
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gene identifier
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geneid
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genes
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genotype
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kegg
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Kegg Pathways
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KeggID
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literature
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loci
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locus
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ncbi
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pathway
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pathway-driven
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pathways
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phenotype
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pubmed
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qtl
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quanitative
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ranking
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space
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term
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term extraction
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terms
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text
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text mining
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text mining; term extraction; entity recognition
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trait
|
vector

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Files (1)

Uploader:

Paul Fisher

Gene Cosine Scores

Created: 10/08/09 @ 16:00:45

Credits: Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This excel file contains a list of genes linked to the resistance to African trypanosomiasis in the mouse. Genes from the Tir1 QTL were used in a search through PubMed. The results were then correlated to the trypanosomiasis resistance phenotype. The higher the score (and ranking) the more related to the phenotype the gene is likely to be. This is based on the co-occurrence of terms within the gene and phentoype corpora.

File type: Excel workbook

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 13 times | Downloaded: 0 times

Tags: