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Items tagged with "ncbi" (28)

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Files (1)
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Blob Gene Cosine Scores

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

Credits: User 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

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Workflows (26)
Original Uploader

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 GBSeq test (2)

Created: 05/03/08 @ 14:15:35 | Last updated: 31/03/08 @ 15:55:09

Credits: User Franck Tanoh

License: Creative Commons Attribution 3.0 Unported License

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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: 249 times | Downloaded: 93 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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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 Pathways and Gene annotations for Arabidop... (2)

Created: 06/03/09 @ 17:18:13 | Last updated: 03/12/09 @ 16:59:11

Credits: User Paul Fisher User Peter Li

Attributions: Workflow Pathways and Gene annotations for QTL region

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

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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: 237 times | Downloaded: 1 time

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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 MassBank to KEGG (1)

Created: 30/03/09 @ 09:30:32 | Last updated: 30/03/09 @ 09:49:13

Credits: User Michael Gerlich

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 215 times | Downloaded: 0 times

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Original Uploader

Workflow NCBI Gi to Kegg Pathways (1)

Created: 08/06/09 @ 18:39:38 | Last updated: 14/12/09 @ 11:51:20

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 260 times | Downloaded: 159 times

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Original Uploader

Workflow Rank Phenotype Terms (1)

Created: 10/08/09 @ 15:43:48

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 139 times | Downloaded: 0 times

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Original Uploader

Workflow What is [query] from NCBI, EBI, UniProt an... (2)

Created: 03/11/09 @ 04:29:15 | Last updated: 03/11/09 @ 04:29:19

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 134 times | Downloaded: 30 times

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Original Uploader
Original Uploader

Workflow Triplify NCBI databases list [myexperiment... (1)

Created: 30/11/09 @ 21:47:05 | Last updated: 01/12/09 @ 02:49:34

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 42 times | Downloaded: 13 times

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Original Uploader

Workflow Triplify NCBI databases external reference... (1)

Created: 01/12/09 @ 03:01:28 | Last updated: 01/12/09 @ 03:03:24

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 37 times | Downloaded: 16 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 microRNA to KEGG Pathways and Abstracts (1)

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

Viewed: 163 times | Downloaded: 2 times

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Original Uploader

Workflow NCBI Gi to Kegg Pathways (1)

Created: 19/03/10 @ 13:47:39 | Last updated: 19/03/10 @ 13:52:45

Credits: User Ian Laycock Network-member nclteamc

Attributions: Workflow color_pathway_by_objects Workflow NCBI Gi to Kegg Pathways

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 94 times | Downloaded: 47 times

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Original Uploader

Workflow Phenotype to pubmed (3)

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

Viewed: 130 times | Downloaded: 45 times

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Original Uploader

Workflow Entrez Gene to KEGG Pathway (5)

Created: 04/12/09 @ 16:04:38 | Last updated: 30/11/10 @ 12:18:53

Credits: User Paul Fisher

License: Creative Commons Attribution 3.0 Unported License

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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: 1282 times | Downloaded: 504 times

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Original Uploader

Workflow EBI_NCBI_BLAST (1)

Created: 17/01/11 @ 12:51:58 | Last updated: 17/01/11 @ 12:52:03

Credits: User Katy Wolstencroft User Hamish McWilliam

Attributions: Workflow EBI_NCBI_BLAST

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 91 times | Downloaded: 41 times

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Original Uploader

Workflow Download Structures from PubChem given che... (1)

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: 57 times | Downloaded: 26 times

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Original Uploader

Workflow Get homologous from NCBI homoloGene (1)

Created: 13/10/11 @ 18:35:58 | Last updated: 13/10/11 @ 18:36:01

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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Viewed: 18 times | Downloaded: 5 times

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Original Uploader

Workflow Get homologous from an NCBI homoloGene.dat... (1)

Created: 20/10/11 @ 17:53:28 | Last updated: 27/10/11 @ 10:38:33

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 43 times | Downloaded: 11 times

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Original Uploader

Workflow NCBI Gi to Kegg Pathway Images (2)

Created: 12/01/12 @ 09:38:10 | Last updated: 12/01/12 @ 15:04:00

Credits: User Katy Wolstencroft User Paul Fisher

Attributions: Workflow NCBI Gi to Kegg Pathways

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 23 times | Downloaded: 21 times

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Original Uploader

Workflow NCBI Gi to Kegg Pathway Descriptions (2)

Created: 12/01/12 @ 09:46:31 | Last updated: 12/01/12 @ 14:54:37

Credits: User Katy Wolstencroft

Attributions: Workflow NCBI Gi to Kegg Pathways

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 21 times | Downloaded: 19 times

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Original Uploader

Workflow Define Associated Regions and Genes (2)

Created: 08/02/12 @ 16:08:08 | Last updated: 09/05/12 @ 09:52:18

Credits: User Paul martin

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Defines regions and genes from associated SNPs A JAVA MySQL connector is required to run the workflow and must be placed in the $TAVERNA_HOME/lib directory.

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

Viewed: 37 times | Downloaded: 35 times

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Original Uploader

Workflow SNPs to Concept Set through Concept Profil... (5)

Created: 26/06/12 @ 10:27:33 | Last updated: 14/09/12 @ 10:10:23

Credits: User Kristina Hettne User Eleni User Harish Dharuri User Reinout van Schouwen User Marco Roos User Martijn Schuemie Network-member BioSemantics

Attributions: Workflow Find Supporting Documents Workflow SNP_ID2EntrezGene_ID Workflow DatabaseID_to_ConceptID Workflow Match gene lists based on information in literature Workflow Match concept profiles Workflow Explain concept scores

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Purpose: Currently, this workflow takes one SNP and a concept set as input, calculates the matching score between these, finds co-occuring documents between the query concept and the match concept, finds the concept that contributes the most to the match, and the documents that support this finding. Author comments: The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www...

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

Viewed: 48 times | Downloaded: 6 times

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Packs (1)
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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.

0 items in this pack

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