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<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]. For more options, visit this group at http://groups.google.com/group/javaposse?hl=en.
stringId ncbiTaxonId taxonName preferredName annotation 9606.ENSP00000333813 9606 Homo sapiens ALG12 Dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl-alpha-1,6- mannosyltransferase (EC 2.4.1.-) (Mannosyltransferase ALG12 homolog) (hALG12) (Membrane protein SB87); Adds the eighth mannose residue in an alpha-1,6 linkage onto the dolichol-PP-oligosaccharide precursor (dolichol-PP- Man(7)GlcNAc(2)) required for protein glycosylation 9606.ENSP00000366165 9606 Homo sapiens NMT1 Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) (Peptide N- myristoyltransferase 1) (Myristoyl-CoA:protein N-myristoyltransferase 1) (NMT 1) (Type I N-myristoyltransferase); Adds a myristoyl group to the N-terminal glycine residue of certain cellular proteins (By similarity) 9606.ENSP00000369637 9606 Homo sapiens PAPD4 PAP associated domain containing 4; Cytoplasmic poly(A) RNA polymerase that adds successive AMP monomers to the 3'-end of specific RNAs, forming a poly(A) tail. In contrast to the canonical nuclear poly(A) RNA polymerase, it only adds poly(A) to selected cytoplasmic mRNAs 9606.ENSP00000299626 9606 Homo sapiens ALG8 Probable dolichyl pyrophosphate Glc1Man9GlcNAc2 alpha-1,3- glucosyltransferase (EC 2.4.1.-) (Dolichyl-P-Glc:Glc1Man9GlcNAc2-PP- dolichyl glucosyltransferase) (Asparagine-linked glycosylation protein 8 homolog); Adds the second glucose residue to the lipid-linked oligosaccharide precursor for N-linked glycosylation. Transfers glucose from dolichyl phosphate glucose (Dol-P-Glc) onto the lipid-linked oligosaccharide Glc(1)Man(9)GlcNAc(2)-PP-Dol (By similarity) 9606.ENSP00000263440 9606 Homo sapiens ALG6 Dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase (EC 2.4.1.-) (Dolichyl-P-Glc:Man9GlcNAc2-PP-dolichyl glucosyltransferase); Adds the first glucose residue to the lipid-linked oligosaccharide precursor for N-linked glycosylation. Transfers glucose from dolichyl phosphate glucose (Dol-P-Glc) onto the lipid-linked oligosaccharide Man(9)GlcNAc(2)-PP-Dol 9606.ENSP00000310120 9606 Homo sapiens ALG10B Putative alpha-1,2-glucosyltransferase ALG10-B (EC 2.4.1.-) (Alpha-2- glucosyltransferase ALG10-B) (Asparagine-linked glycosylation protein 10 homolog B) (Potassium channel regulator 1); Putative alpha-1,2-glucosyltransferase, which adds the third glucose residue to the lipid-linked oligosaccharide precursor for N-linked glycosylation. Transfers glucose from dolichyl phosphate glucose (Dol-P-Glc) onto the lipid-linked oligosaccharide Glc(2)Man(9)GlcNAc(2)-PP-Dol. When coupled to KCNH2 may reduce KCNH2 sensitivity to classic proarrhythmic drug blockade, possibly by mediating glycosylati [...] 9606.ENSP00000308546 9606 Homo sapiens BCDIN3 bin3, bicoid-interacting 3; S-adenosyl-L-methionine-dependent methyltransferase that adds a methylphosphate cap at the 5'-end of 7SK snRNA, leading to stabilize it 9606.ENSP00000309572 9606 Homo sapiens TERT Telomerase reverse transcriptase (EC 2.7.7.49) (Telomerase catalytic subunit) (HEST2) (Telomerase-associated protein 2) (TP2); Telomerase is a ribonucleoprotein enzyme essential for the replication of chromosome termini in most eukaryotes. It elongates telomeres. It is a reverse transcriptase that adds simple sequence repeats to chromosome ends by copying a template sequence within the RNA component of the enzyme 9606.ENSP00000367385 9606 Homo sapiens NMT2 Glycylpeptide N-tetradecanoyltransferase 2 (EC 2.3.1.97) (Peptide N- myristoyltransferase 2) (Myristoyl-CoA:protein N-myristoyltransferase 2) (NMT 2) (Type II N-myristoyltransferase); Adds a myristoyl group to the N-terminal glycine residue of certain cellular proteins (By similarity) 9606.ENSP00000266483 9606 Homo sapiens ALG10 Alpha-1,2-glucosyltransferase ALG10-A (EC 2.4.1.-) (Alpha-2- glucosyltransferase ALG10-A) (Asparagine-linked glycosylation protein 10 homolog A); Adds the third glucose residue to the lipid-linked oligosaccharide precursor for N-linked glycosylation. Transfers glucose from dolichyl phosphate glucose (Dol-P-Glc) onto the lipid-linked oligosaccharide Glc(2)Man(9)GlcNAc(2)-PP-Dol 9606.ENSP00000280591 9606 Homo sapiens TRNT1 tRNA-nucleotidyltransferase 1, mitochondrial precursor (EC 2.7.7.25) (Mitochondrial tRNA nucleotidyl transferase, CCA-adding) (mt tRNA adenylyltransferase) (mt tRNA CCA-pyrophosphorylase) (mt tRNA CCA- diphosphorylase) (mt CCA-adding enzyme); Adds and repairs the conserved 3'-CCA sequence necessary for the attachment of amino acids to the 3' terminus of tRNA molecules, using CTP and ATP as substrates 9606.ENSP00000231198 9606 Homo sapiens THG1L interphase cytoplasmic foci protein 45; Adds a GMP to the 5'-end of tRNA(His) after transcription and RNase P cleavage (By similarity)
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