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Items tagged with "disease" (11)

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Workflows (11)

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Workflow BioAID_DiseaseDiscovery (v1)

Created: 12/11/07 @ 22:39:04 | Updated: 15/11/07 @ 09:01:44

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 License

Bioaid_diseasediscovery_28978
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) 2. Retrieve documents: finds relevant documents (abstract+title) based on query (edit maxHits to change the default maximum number of documents returned; the AIDA service inside is based on Apache Lucene) 3. Discover proteins: extract proteins ...

Rating: 4.0 / 5 (2 ratings) | Versions: 1 | Reviews: 0 | Comments: 1 | Citations: 0

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Workflow Perfrom a text based search through PubMed (v3)

Created: 03/10/07 @ 18:36:08 | Updated: 02/08/08 @ 14:35:11

License: Creative Commons Attribution-NoDerivs 3.0 License

Perfrom_a_text_based_search_through_pubmed_2447_3
This workflow takes in a number of search terms in which to perform a search over the PubMed literature database. These search terms may be input as if entered in the web based version of PubMed. The output from this workflow is a list of PubMed identifiers in xml based format

Rating: 3.0 / 5 (2 ratings) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 0

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Workflow KEGG pathways common to both QTL and microarray based investigations (v2)

Created: 03/10/07 @ 18:35:58 | Updated: 13/11/07 @ 16:22:14

License: Creative Commons Attribution-NoDerivs 3.0 License

Kegg_pathways_common_to_both_qtl_and_microarray_based_investigations_27627
This workflow takes in two lists of KEGG pathway ids. These are designed to come from pathways found from genes in a QTL (Quantitative Trait Loci) region, and from pathways found from genes differentially expressed in a microarray study. By identifying the intersecting pathways from both studies, a more informative picture is obtained of the candidate processes involved in the expression of a phenotype

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 1

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Workflow Mouse Pathways and Gene annotations for QTL Phenotype (v3)

Created: 03/10/07 @ 18:36:02 | Updated: 20/02/08 @ 16:05:44

License: Creative Commons Attribution-Share Alike 3.0 License

Pathways_and_gene_annotations_for_qtl_phenotype_28303_3
This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. 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 path...

Rating: 4.5 / 5 (2 ratings) | Versions: 3 | Reviews: 0 | Comments: 2 | Citations: 1

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Workflow Pathways from Diff Expressed Genes (v3)

Created: 03/10/07 @ 18:36:05 | Updated: 11/07/08 @ 10:52:01

License: Creative Commons Attribution-Share Alike 3.0 License

Pathways_from_diff_expressed_genes_22895_3
This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes in the QTL; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2.

Rating: 5.0 / 5 (1 rating) | Versions: 3 | Reviews: 0 | Comments: 1 | Citations: 1

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Workflow BioAID_ProteinToDiseases (v1)

Created: 14/11/07 @ 12:47:57 | Updated: 15/11/07 @ 09:00:44

Credits: User Marco Roos User Martijn Schuemie Network-member AID

Attributions: Workflow BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 License

Bioaid_proteintodiseases_16160
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: 1. A user query: a single protein name 2. Add synonyms (service courtesy of Martijn Scheumie, Erasmus University Rotterdam) 3. Retrieve documents: finds relevant documents (abstract+title) based on query 4. Discover proteins: extract proteins discovered in the set of relevant abstracts 5. Link pr...

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

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Workflow Gene annotation pipeline for the Graves disease scenario (v2)

Created: 03/10/07 @ 18:36:09 | Updated: 22/11/07 @ 16:03:15

Credits: User Katy Wolstencroft User Peter Li

License: Creative Commons Attribution-NoDerivs 3.0 License

Gene_annotation_pipeline_for_the_graves_disease_scenario_19721
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.

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 1 | Citations: 0

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Workflow BioAID_DiseaseDiscovery_count (v3)

Created: 22/11/07 @ 12:09:20 | Updated: 05/12/07 @ 23:09:13

Credits: User Marco Roos Network-member AID

Attributions: Workflow BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 License

Bioaid_diseasediscovery_count_22894_3
This adds counting to BioAID_DiseaseDiscovery, which allows you to check the results more properly. A major issue is that some false positives among the discovered proteins may have a disproportionate effect on the number of diseases found. We therefore advice to use 'BioAID_DiseaseDiscovery_byHumanUniprot' if you main interest is human proteins and diseases. This workflow finds disease relevant to the query string via the following steps: 1. A user query: a list of terms or boolean query - ...

Rating: 5.0 / 5 (1 rating) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

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Workflow BioAID_DiseaseDiscovery_byHumanUniprot (v3)

Created: 05/12/07 @ 23:11:42 | Updated: 15/05/08 @ 21:10:32

Credits: User Marco Roos User Martijn Schuemie Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 License

Bioaid_diseasediscovery_byhumanuniprot_22938_3
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 Apache's Luce...

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

Viewed: 771 times | Downloaded: 718 times

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Workflow Microarray CEL file to candidate pathways (v2)

Created: 08/02/08 @ 14:17:23 | Updated: 14/05/08 @ 15:43:16

Credits: User Paul Fisher User Saeedeh

License: Creative Commons Attribution-Share Alike 3.0 License

Microarray_cel_file_to_candidate_pathways_1844_2
This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) [http://www.bioinf.manchester.ac.uk/MADAT/index.html]. 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 ...

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

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Workflow Human Pathways from Diff Expressed Genes (v1)

Created: 08/02/08 @ 14:30:17 | Updated: 08/02/08 @ 14:30:17

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 License

Human_pathways_from_diff_expressed_genes_4391_1
This workflow takes in probesets from and AffyMetrix micorarray experiment and returns: the genes in the QTL; gene start and end positions; chromosome where genes reside; ensembl trasncripts; SwissProt ids; affy probeset identifiers for chips Mouse430_2 and Mouse430a_2. The final output of the workflow is a list of candidate pathways which are linked to the genes expressed in the microarray data

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

Viewed: 433 times | Downloaded: 5 times

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