Dear Sir, Thank you for the information. That was very helpful.
Regards, Jitesh Dundas On Mon, Dec 21, 2009 at 5:24 PM, Thasso Griebel < [email protected]> wrote: > Hi, > > probably the wrong place to discuss such things, but your file looks > like you forgot to reappend the newline characters after you read your > line. When you write out the line, append a "\n". This results in a > file similar to this: > > stringId ncbiTaxonId taxonName preferredName annotation > 9606.ENSP00000333813 9606 Homo sapiens ALG12 > Dolichyl-P-Man:Man(7)... > ... > > So String-DB seems to report in some tab delimited format. I don't > know String-DB and can only guess what sort of information is > provided, but for me, this simply maps the String-ID to an NCBI Taxons > (and its preferred name) and reports the prefered name (ALG12 in this > example) of the mapped protien and its String-DB annotation. > > cheers, > -thasso > > On Dec 18, 2009, at 22:00 , jitesh dundas wrote: > > > Dear Dr. Thasso Griebel , > > > > Finally I have got the output! It was a simple mistake from my side. > > > > The program needed was for just to read from the URL and not POST to > > the URL. > > > > I have attached the working code now. > > > > Now the problem is that I dont understand what that means. How to I > > understand what part is the list of protein interactors for the > > given term. > > > > Can some one help me in this ? All this is new to me. > > > > Regards, > > Jitesh > > > > On Fri, Dec 18, 2009 at 11:47 PM, Thasso Griebel < > [email protected] > > > wrote: > > Hi, > > > > uh yeah...bioinformatics...sort of :) > > > > In general I think you have to be a bit more precise about the error > > you get and you might want to append a stacktrace or something. > > "Version number" error sounds like a "class version number" ? But I > > have no idea, could be anything. > > > > I can confirm though that the data URL is fine > http://string-db.org/api/tsv/resolve?identifier=ADD&species=9606 > > . Here is the method I used to fetch the data: > > > > public static void write2File(URL url, File file) throws IOException { > > FileOutputStream out = null; > > InputStream in = null; > > try { > > in = url.openStream(); > > out = new FileOutputStream(file); > > byte[] buff = new byte[4096]; > > int len = 0; > > while (-1 != (len = in.read(buff))) { > > out.write(buff, 0, len); > > } > > } finally{ > > if(out != null)out.close(); > > if(in != null) in.close(); > > } > > } > > > > > > with this and your URL a simple > > > > write2File(new URL(" > http://string-db.org/api/tsv/resolve?identifier=ADD&species=9606 > > "), new File("/tmp/test.embl")); > > > > works as expected. > > > > On the other hand, please note that the String-DB guys explicitly > > state: > > > > "Please note that we currently discourage robot access, due to the > > heavy load on our server. If you require a large portion of the > > interaction data which is contained in STRING, please contact one of > > the authors" > > (http://string.embl.de/newstring_cgi/show_robot_regulations.pl) > > > > So if you want to integrate this in some sort of service/agent/robot > > thingy, a local copy of the database might be a good idea ! > > > > cheers, > > -thasso > > > > On Dec 18, 2009, at 18:02 , jitesh dundas wrote: > > > > > Dear Sir/Madam, > > > > > > I am trying to fetch data from EMBL STRING Database ( > http://string.embl.de/ > > > ) for a list of protein interactors. The file is attached with this > > > email. > > > > > > On executing the code, it gives me a "version number" error. The > > > same code is working fine when I fetch data from NCBI databases. > > > Thus, I am trying to know what is going wrong here. > > > > > > I request your reply. Please let me know if you need anything else > > > from my side. > > > > > > Regards, > > > Jitesh Dundas > > > > > > > > > > > > > > -- > > > > > > You received this message because you are subscribed to the Google > > > Groups "The Java Posse" group. > > > To post to this group, send email to [email protected]. > > > To unsubscribe from this group, send email to > [email protected]<javaposse%[email protected]> > > > . > > > For more options, visit this group at > http://groups.google.com/group/javaposse?hl=en > > > . > > > <ImportGet.jsp> > > > > -- > > Dipl. Inf. Thasso Griebel-------------------Lehrstuhl fuer > > Bioinformatik > > Office 3426--http://bio.informatik.uni-jena.de--Institut fuer > > Informatik > > Phone +49 (0)3641 9-46454-----------Friedrich-Schiller-Universitaet > > Jena > > Fax +49 (0)3641 9-46452----------Ernst-Abbe-Platz 2, 07743 Jena, > > Germany > > > > > > > > > > > > -- > > > > You received this message because you are subscribed to the Google > > Groups "The Java Posse" group. > > To post to this group, send email to [email protected]. > > To unsubscribe from this group, send email to > [email protected]<javaposse%[email protected]> > > . > > For more options, visit this group at > http://groups.google.com/group/javaposse?hl=en > > . > > > > > > > > > > -- > > > > You received this message because you are subscribed to the Google > > Groups "The Java Posse" group. > > To post to this group, send email to [email protected]. > > To unsubscribe from this group, send email to > [email protected]<javaposse%[email protected]> > > . > > For more options, visit this group at > http://groups.google.com/group/javaposse?hl=en > > . > > <output_File.txt><import.jsp> > > -- > > You received this message because you are subscribed to the Google Groups > "The Java Posse" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]<javaposse%[email protected]> > . > For more options, visit this group at > http://groups.google.com/group/javaposse?hl=en. > > > -- You received this message because you are subscribed to the Google Groups "The Java Posse" group. 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