Workflows

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Tag: ebi User: Rafael C. Jimenez
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Workflow Find PRIDE experiments by GO (1)

Created: 29/05/11 @ 19:07:59 | Last updated: 29/05/11 @ 19:08:01

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Find PRIDE experiments in Human with related information like Cell Type and Tissue location filtering results by Gene Ontology terms. This is an example of how to use the PRIDE Biomart service in Taverna. Many other options are possible by modifying the filters and attributes of this service.

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

Viewed: 52 times | Downloaded: 8 times

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Original Uploader

Workflow EBI NCBI BLAST Multi FASTA (2)

Created: 16/07/11 @ 19:08:38 | Last updated: 16/07/11 @ 19:35:11

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow performs multiple sequence similarity searches using the 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. If you want to make a blast search for more than 10 sequences I would recommend you to run the workflow using the comm...

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

Viewed: 44 times | Downloaded: 31 times

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Original Uploader

Workflow EBI PICR, find cross-references for protei... (2)

Created: 18/05/11 @ 09:36:26 | Last updated: 29/05/11 @ 17:35:20

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Find cross-references (based on 100% sequence identity) for protein accessions from more than 95 distinct databases. For instance input a list of IPI accessions and find cross-references for Swissprot and Ensembl. Mappings can be limited by source database, taxonomic ID and activity status.

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

Viewed: 14 times | Downloaded: 14 times

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Original Uploader

Workflow Find Reactome pathways and reactions by GO (1)

Created: 29/05/11 @ 19:09:23 | Last updated: 29/05/11 @ 19:09:25

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Find Reactome pathways and reactions (names and accessions) in Human querying by a Gene Ontology term. This is an example of how to use the Reactome Biomart service in Taverna. Many other possibilities are possible by modifying the filters and attributes options of the service.

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

Viewed: 34 times | Downloaded: 8 times

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Original Uploader

Workflow Molecular Interactions from IntAct PSICQUI... (2)

Created: 29/05/11 @ 01:32:18 | Last updated: 05/10/11 @ 00:20:00

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Get molecular interaction data in psi-mitab25 from IntAct through its REST PSICQUIC service. As input you can use an Uniprot Acc like "P99999" or a MIQL query like "alias:KHDRBS1".

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

Viewed: 16 times | Downloaded: 9 times

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Original Uploader

Workflow Find Biological Models by GO. (1)

Created: 29/05/11 @ 21:44:22 | Last updated: 29/05/11 @ 21:44:23

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Find Biological Models (Ids and Names) from Biomodels querying by Gene Ontology terms.

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

Viewed: 19 times | Downloaded: 8 times

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Original Uploader

Workflow Molecular Interactions from IntAct PSICQUI... (2)

Created: 17/05/11 @ 07:09:30 | Last updated: 20/07/11 @ 15:14:56

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Get molecular interaction data in psi-mitab25 from IntAct through its PSICQUIC service. As input you can use an Uniprot Acc like "P99999" or a MIQL query like "alias:(KHDRBS1 OR HCK)". This workflow finds by itself how many queries needs to make (SOAP service limited to 200 binary interactions per call) to be able to return all the results in one file.

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

Viewed: 28 times | Downloaded: 8 times

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