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Items tagged with "pubchem" (9)
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Created: 30/03/09 @ 09:20:42 | Last updated: 30/03/09 @ 09:34:37
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Given a list of identifiers (e.g. CID) and their appropriate type (eID_CID - note that these differ slightly from the original identifier name -> CID <-> eID_CID), this workflow queries PubChem via PUG to retrieve a download URL for the resulting XML file containing the results.
Adding support for downloading this XML file and writing it to filesystem is planned.
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 74 times | Downloaded: 52 times Tags (4): |
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Original Uploader |
Created: 30/03/09 @ 09:26:25 | Last updated: 30/03/09 @ 09:47:00
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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: 93 times | Downloaded: 47 times Tags (12): |
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Original Uploader |
Created: 30/03/09 @ 09:30:32 | Last updated: 30/03/09 @ 09:49:13
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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: 198 times | Downloaded: 0 times Tags (21): |
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Original Uploader |
Created: 16/07/10 @ 09:34:45 | Last updated: 16/07/10 @ 09:43:39
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Performs a 2D structure similarity search on PubChem. The input structure has to be in the form of a SDF file. The original SDF-based similarity search workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 18 times | Downloaded: 16 times Tags (2): |
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Original Uploader |
Created: 16/07/10 @ 09:50:50 | Last updated: 16/07/10 @ 09:53:16
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Searches for similar structures in PubChem to an input SMILES string. This workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).
Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 11 times | Downloaded: 14 times Tags (3): |
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Original Uploader |
Created: 16/07/10 @ 10:20:48 | Last updated: 16/07/10 @ 10:25:06 License: Creative Commons Attribution-Share Alike 3.0 Unported License
Performs a search in Pubchem for compounds similar to an input compound represented in SMILES notation. This workflow is based on the original smiles-identity-idlist workflow written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 15 times | Downloaded: 14 times Tags (3): |
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Original Uploader |
Created: 16/07/10 @ 10:31:51 | Last updated: 16/07/10 @ 10:52:28 License: Creative Commons Attribution-Share Alike 3.0 Unported License
Search PubChem Compound for structures containing the one given by the structure key input, based on a user-selected level of chemical identity: connectivity only, match isotopes and/or stereo, etc. The original workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 32 times | Downloaded: 25 times Tags (3): |
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Original Uploader |
Created: 16/07/10 @ 10:41:38 | Last updated: 16/07/10 @ 10:53:32
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License: Creative Commons Attribution-Share Alike 3.0 Unported License
Given a list key, prepare for download a file containing those records in the selected format. The original workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).
Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 29 times | Downloaded: 24 times Tags (2): |
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Creator: |
Created: 23/07/10 @ 11:13:09 | Last updated: 23/07/10 @ 11:21:05
This pack contains example pipelines showing how the PubChem, ChEBI and ChemSpider web services can be called from Taverna workflows.
Descriptions of the operations found in the PubChem, ChEBI and ChemSpider web services are available at http://www.taverna.org.uk/introduction/related-projects/chemtaverna/chemistry-web-services.
40 items in this pack Comments: 0 | Viewed: 41 times | Downloaded: 14 times Tags: |
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