Hi Matthias I don't have a workflow for you, but it might use the EMBOSS application "entret" (http://emboss.sourceforge.net/apps/release/6.0/emboss/apps/entret.html) for steps 1-3. As for output, entret (or something else) could easily be customised. If you think that might help you, mail your requirements to [email protected].
Cheers Jon > Hello, > First of all I'm pretty new to Taverna. I already downloaded and > installed version 2 and played a bit with it. I even managed to get it > working through our dreaded proxy server ;-) > Now I've been thinking of using Taverna to semi-automate some data > extractions from Genbank. > This is what I would like to do: > 1) input list = a list of GI or accession numbers > 2) do a search in the NCBI nucleotide database for this list of GI > numbers > 3) retrieve the results in Genbank format > 4) extract some data fields out of the Genbank records (for example: > "product" or "info" fields > 5) finally create a csv file with the following columns: GI number, > "product" field, "info" field > Is it difficult to do this with Taverna? I guess I will have to register > the NCBI Entrez web services as activities, probably the ESearch and > EFetch utilities? > Has anyone created a workflow like this before? > Thanks, > Matthias > _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ > > This e-mail and any attachments thereto may contain information > which is confidential and/or protected by intellectual property > rights and are intended for the sole use of the recipient(s) named above. > Any use of the information contained herein (including, but not limited to, > total or partial reproduction, communication or distribution in any form) > by persons other than the designated recipient(s) is prohibited. > If you have received this e-mail in error, please notify the sender either > by telephone or by e-mail and delete the material from any computer. > > Any views expressed in this message are those of the individual > sender, except where the sender specifies and with authority, > states them to be the views of Devgen NV. > > Thank you for your cooperation. > ------------------------------------------------------------------------------ > Enter the BlackBerry Developer Challenge > This is your chance to win up to $100,000 in prizes! For a limited time, > vendors submitting new applications to BlackBerry App World(TM) will have > the opportunity to enter the BlackBerry Developer Challenge. See full prize > details at: > http://p.sf.net/sfu/Challenge_______________________________________________ > taverna-users mailing list > [email protected] > [email protected] > Web site: http://www.taverna.org.uk > Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/ > ------------------------------------------------------------------------------ Enter the BlackBerry Developer Challenge This is your chance to win up to $100,000 in prizes! For a limited time, vendors submitting new applications to BlackBerry App World(TM) will have the opportunity to enter the BlackBerry Developer Challenge. See full prize details at: http://p.sf.net/sfu/Challenge _______________________________________________ taverna-users mailing list [email protected] [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/
