Define one query and retrieve Molecular Interactions from PSICQUIC Services registered in the PSICQUIC registry.

Value

Wsdl

Wsdl Operation

Value

Value

Script

List fastaOut = new ArrayList();
for (Iterator i = fastaIn.iterator(); i.hasNext();) {
    List temp = (ArrayList) i.next();
    String content = "";
    for(Object line:temp){
        if(content.length() == 0){
            content += line;
            content += "\n";
        } else {
            content += line;
        }              
    }
    fastaOut.add(content);
}

Script

List accsOut = new ArrayList();
List accsOutPrefix = new ArrayList();
Iterator j = uniprotAccs.iterator();
String nucleusTerms = "GO:0005634,nucleus,GO:0048555,generative cell nucleus,GO:0031039,macronucleus,GO:0048556,microsporocyte nucleus,GO:0044428,nuclear part,GO:0034978,PDX1-PBX1b-MRG1 complex,GO:0031595,nuclear proteasome complex,GO:0031601,nuclear proteasome core complex,GO:0031604,nuclear proteasome core complex, alpha-subunit complex,GO:0031607,nuclear proteasome core complex, beta-subunit complex,GO:0031598,nuclear proteasome regulatory particle,GO:0031610,nuclear proteasome regulatory particle, base subcomplex,GO:0031613,nuclear proteasome regulatory particle, lid subcomplex,GO:0030870,Mre11 complex,GO:0070532,BRCA1-B complex,GO:0070531,BRCA1-A complex,GO:0031499,TRAMP complex,GO:0070533,BRCA1-C complex,GO:0034980,FHL2-CREB complex,GO:0034981,FHL3-CREB complex,GO:0000347,THO complex,GO:0000445,THO complex part of transcription export complex,GO:0000446,nucleoplasmic THO complex,GO:0005697,telomerase holoenzyme complex,GO:0000333,telomerase catalytic core complex,GO:0031533,mRNA cap methyltransferase complex,GO:0000346,transcription export complex,GO:0032116,SMC loading complex,GO:0030689,Noc complex,GO:0030691,Noc2p-Noc3p complex,GO:0030690,Noc1p-Noc2p complex,GO:0030692,Noc4p-Nop14p complex,GO:0033597,mitotic checkpoint complex,GO:0034064,Tor2-Mei2-Ste11 complex,GO:0031080,Nup107-160 complex,GO:0000176,nuclear exosome (RNase complex),GO:0034992,microtubule organizing center attachment site,GO:0034993,SUN-KASH complex,GO:0030895,apolipoprotein B mRNA editing enzyme complex,GO:0070467,RC-1 DNA recombination complex,GO:0055125,Nic96 complex,GO:0055126,Nup82 complex,GO:0031380,nuclear RNA-directed RNA polymerase complex,GO:0005635,nuclear envelope,GO:0031965,nuclear membrane,GO:0005640,nuclear outer membrane,GO:0031308,intrinsic to nuclear outer membrane,GO:0031309,integral to nuclear outer membrane,GO:0031316,extrinsic to nuclear outer membrane,GO:0044453,nuclear membrane part,GO:0031229,intrinsic to nuclear inner membrane,GO:0005639,integral to nuclear inner membrane,GO:0005637,nuclear inner membrane,GO:0005643,nuclear pore,GO:0031015,karyopherin docking complex,GO:0070762,NDC1 complex,GO:0044195,nucleoplasmic reticulum,GO:0005641,nuclear envelope lumen,GO:0000214,tRNA-intron endonuclease complex,GO:0005638,lamin filament,GO:0016363,nuclear matrix,GO:0000109,nucleotide-excision repair complex,GO:0008622,epsilon DNA polymerase complex,GO:0000113,nucleotide-excision repair factor 4 complex,GO:0000111,nucleotide-excision repair factor 2 complex,GO:0070522,ERCC4-ERCC1 complex,GO:0000112,nucleotide-excision repair factor 3 complex,GO:0000442,SSL2-core TFIIH complex portion of NEF3 complex,GO:0000440,core TFIIH complex portion of NEF3 complex,GO:0000110,nucleotide-excision repair factor 1 complex,GO:0070912,Ddb1-Ckn1 complex,GO:0071942,XPC complex,GO:0070913,Ddb1-Wdr21 complex,GO:0070312,RAD52-ERCC4-ERCC1 complex,GO:0070516,CAK-ERCC2 complex,GO:0032389,MutLalpha complex,GO:0070310,ATR-ATRIP complex,GO:0002111,BRCA2-BRAF35 complex,GO:0000228,nuclear chromosome,GO:0001740,Barr body,GO:0000794,condensed nuclear chromosome,GO:0000780,condensed nuclear chromosome, centromeric region,GO:0000778,condensed nuclear chromosome kinetochore,GO:0000942,condensed nuclear chromosome outer kinetochore,GO:0000941,condensed nuclear chromosome inner kinetochore,GO:0000818,nuclear MIS12/MIND type complex,GO:0000817,COMA complex,GO:0042729,DASH complex,GO:0030998,linear element,GO:0030896,checkpoint clamp complex,GO:0000795,synaptonemal complex,GO:0000802,transverse filament,GO:0000801,central element,GO:0000800,lateral element,GO:0000798,nuclear cohesin complex,GO:0034990,nuclear mitotic cohesin complex,GO:0034991,nuclear meiotic cohesin complex,GO:0000799,nuclear condensin complex,GO:0005712,chiasma,GO:0005713,recombination nodule,GO:0005715,late recombination nodule,GO:0005714,early recombination nodule,GO:0044454,nuclear chromosome part,GO:0043625,delta DNA polymerase complex,GO:0000790,nuclear chromatin,GO:0034974,Swi5-Swi2 complex,GO:0005719,nuclear euchromatin,GO:0034967,Set3 complex,GO:0030874,nucleolar chromatin,GO:0030875,rDNA protrusion,GO:0005731,nucleolus organizer region,GO:0000812,Swr1 complex,GO:0070209,ASTRA complex,GO:0005726,perichromatin fibrils,GO:0031011,Ino80 complex,GO:0005720,nuclear heterochromatin,GO:0005724,nuclear telomeric heterochromatin,GO:0005725,intercalary heterochromatin,GO:0031618,nuclear centromeric heterochromatin,GO:0002137,nuclear cluster,GO:0030958,RITS complex,GO:0001739,sex chromatin,GO:0001741,XY body,GO:0032798,Swi5-Sfr1 complex,GO:0000788,nuclear nucleosome,GO:0070822,Sin3-type complex,GO:0032221,Rpd3S complex,GO:0016580,Sin3 complex,GO:0033698,Rpd3L complex,GO:0070211,Snt2C complex,GO:0070823,HDA1 complex,GO:0070210,Rpd3L-Expanded complex,GO:0043601,nuclear replisome,GO:0005658,alpha DNA polymerase:primase complex,GO:0043599,nuclear DNA replication factor C complex,GO:0070517,DNA replication factor C core complex,GO:0005662,DNA replication factor A complex,GO:0000811,GINS complex,GO:0005664,nuclear origin of replication recognition complex,GO:0043596,nuclear replication fork,GO:0031298,replication fork protection complex,GO:0000784,nuclear chromosome, telomeric region,GO:0000783,nuclear telomere cap complex,GO:0070187,telosome,GO:0070188,Stn1-Ten1 complex,GO:0042555,MCM complex,GO:0033557,Slx1-Slx4 complex,GO:0071162,CMG complex,GO:0070313,RGS6-DNMT1-DMAP1 complex,GO:0032807,DNA ligase IV complex,GO:0032301,MutSalpha complex,GO:0032806,carboxy-terminal domain protein kinase complex,GO:0008024,positive transcription elongation factor complex b,GO:0070691,dimeric positive transcription elongation factor complex b,GO:0070692,trimeric positive transcription elongation factor complex b,GO:0000439,core TFIIH complex,GO:0000438,core TFIIH complex portion of holo TFIIH complex,GO:0032302,MutSbeta complex,GO:0000943,retrotransposon nucleocapsid,GO:0034753,nuclear aryl hydrocarbon receptor complex,GO:0032390,MutLbeta complex,GO:0033061,DNA recombinase mediator complex,GO:0033065,Rad51C-XRCC3 complex,GO:0033064,XRCC2-RAD51D complex,GO:0033066,Rad51B-Rad51C complex,GO:0033063,Rad51B-Rad51C-Rad51D-XRCC2 complex,GO:0033062,Rhp55-Rhp57 complex,GO:0046536,dosage compensation complex,GO:0016456,X chromosome located dosage compensation complex, transcription activating,GO:0070877,microprocessor complex,GO:0070876,SOSS complex,GO:0070274,RES complex,GO:0034692,E.F.G complex,GO:0030532,small nuclear ribonucleoprotein complex,GO:0071009,U4atac/U6atac x U5 tri-snRNP complex,GO:0005693,U12 snRNP,GO:0071019,U12-type post-mRNA release spliceosomal complex,GO:0005692,U11 snRNP,GO:0005691,U6atac snRNP,GO:0005690,U4atac snRNP,GO:0071024,SL snRNP,GO:0071001,U4/U6 snRNP,GO:0071002,U4atac/U6atac snRNP,GO:0071003,penta-snRNP complex,GO:0034693,U11/U12 snRNP,GO:0005683,U7 snRNP,GO:0005682,U5 snRNP,GO:0005687,U4 snRNP,GO:0046540,U4/U6 x U5 tri-snRNP complex,GO:0005688,U6 snRNP,GO:0005685,U1 snRNP,GO:0005686,U2 snRNP,GO:0016585,chromatin remodeling complex,GO:0070603,SWI/SNF-type complex,GO:0071565,nBAF complex,GO:0070604,PBAF complex,GO:0016514,SWI/SNF complex,GO:0035060,brahma complex,GO:0071778,WINAC complex,GO:0071564,npBAF complex,GO:0008623,chromatin accessibility complex,GO:0031213,RSF complex,GO:0031010,ISWI complex,GO:0016589,NURF complex,GO:0016587,ISW1 complex,GO:0070311,nucleosomal methylation activator complex,GO:0035059,RCAF complex,GO:0048189,Lid2 complex,GO:0000118,histone deacetylase complex,GO:0016581,NuRD complex,GO:0070824,SHREC complex,GO:0048188,Set1C/COMPASS complex,GO:0005677,chromatin silencing complex,GO:0030869,RENT complex,GO:0016586,RSC complex,GO:0030530,heterogeneous nuclear ribonucleoprotein complex,GO:0035145,exon-exon junction complex,GO:0019907,cyclin-dependent protein kinase activating kinase holoenzyme complex,GO:0070390,transcription export complex 2,GO:0019908,nuclear cyclin-dependent protein kinase holoenzyme complex,GO:0016533,cyclin-dependent protein kinase 5 holoenzyme complex,GO:0033203,DNA helicase A complex,GO:0034399,nuclear periphery,GO:0005652,nuclear lamina,GO:0005654,nucleoplasm,GO:0044451,nucleoplasm part,GO:0071821,FANCM-MHF complex,GO:0071180,MAML3-RBP-Jkappa-ICN2 complex,GO:0071181,MAML3-RBP-Jkappa-ICN3 complex,GO:0071182,MAML3-RBP-Jkappa-ICN4 complex,GO:0005656,pre-replicative complex,GO:0000418,DNA-directed RNA polymerase IV complex,GO:0000420,DNA-directed RNA polymerase IVa complex,GO:0000419,DNA-directed RNA polymerase IVb complex,GO:0030015,CCR4-NOT core complex,GO:0017053,transcriptional repressor complex,GO:0070439,Mad-Max-mSin3A complex,GO:0070176,DRM complex,GO:0070443,Mad-Max complex,GO:0017054,negative cofactor 2 complex,GO:0070722,Tle3-Aes complex,GO:0070440,Mad-Max-mSin3B complex,GO:0000123,histone acetyltransferase complex,GO:0070775,H3 histone acetyltransferase complex,GO:0070776,MOZ/MORF histone acetyltransferase complex,GO:0033100,NuA3 histone acetyltransferase complex,GO:0072487,MSL complex,GO:0005671,Ada2/Gcn5/Ada3 transcription activator complex,GO:0043189,H4/H2A histone acetyltransferase complex,GO:0032777,Piccolo NuA4 histone acetyltransferase complex,GO:0033255,SAS acetyltransferase complex,GO:0035267,NuA4 histone acetyltransferase complex,GO:0070461,SAGA-type complex,GO:0046695,SLIK (SAGA-like) complex,GO:0030914,STAGA complex,GO:0000125,PCAF complex,GO:0000124,SAGA complex,GO:0033276,transcription factor TFTC complex,GO:0005665,DNA-directed RNA polymerase II, core complex,GO:0005666,DNA-directed RNA polymerase III complex,GO:0042272,nuclear RNA export factor complex,GO:0071175,MAML2-RBP-Jkappa-ICN1 complex,GO:0071177,MAML2-RBP-Jkappa-ICN3 complex,GO:0071176,MAML2-RBP-Jkappa-ICN2 complex,GO:0071179,MAML3-RBP-Jkappa-ICN1 complex,GO:0071178,MAML2-RBP-Jkappa-ICN4 complex,GO:0005667,transcription factor complex,GO:0071150,TEAD-3-YAP complex,GO:0071151,TEAD-4-YAP complex,GO:0070985,TFIIK complex,GO:0071943,Myc-Max complex,GO:0030014,CCR4-NOT complex,GO:0070514,SRF-myogenin-E12 complex,GO:0000127,transcription factor TFIIIC complex,GO:0034735,transcription factor TFIIIC2 complex,GO:0034734,transcription factor TFIIIC1 complex,GO:0016513,core-binding factor complex,GO:0000126,transcription factor TFIIIB complex,GO:0034733,transcription factor TFIIIB-beta complex,GO:0034732,transcription factor TFIIIB-alpha complex,GO:0034740,TFIIIC-TOP1-SUB1 complex,GO:0035189,Rb-E2F complex,GO:0030232,insulin control element activator complex,GO:0030907,MBF transcription complex,GO:0070264,transcription factor TFIIIE complex,GO:0005669,transcription factor TFIID complex,GO:0070556,TAF4B-containing transcription factor TFIID complex,GO:0000120,RNA polymerase I transcription factor complex,GO:0005668,RNA polymerase transcription factor SL1 complex,GO:0000500,RNA polymerase I upstream activating factor complex,GO:0070860,RNA polymerase I core factor complex,GO:0071148,TEAD-1-YAP complex,GO:0071149,TEAD-2-YAP complex,GO:0019185,snRNA-activating protein complex,GO:0032444,activin responsive factor complex,GO:0033309,SBF transcription complex,GO:0016602,CCAAT-binding factor complex,GO:0008230,ecdysone receptor holocomplex,GO:0005672,transcription factor TFIIA complex,GO:0005673,transcription factor TFIIE complex,GO:0005674,transcription factor TFIIF complex,GO:0005675,holo TFIIH complex,GO:0070721,ISGF3 complex,GO:0008023,transcription elongation factor complex,GO:0070449,elongin complex,GO:0035101,FACT complex,GO:0032044,DSIF complex,GO:0032783,ELL-EAF complex,GO:0032021,NELF complex,GO:0016593,Cdc73/Paf1 complex,GO:0070847,core mediator complex,GO:0043240,Fanconi anaemia nuclear complex,GO:0016604,nuclear body,GO:0042382,paraspeckles,GO:0015030,Cajal body,GO:0016607,nuclear speck,GO:0035062,omega speckle,GO:0010445,nuclear dicing body,GO:0035363,histone locus body,GO:0035061,interchromatin granule,GO:0016605,PML body,GO:0016606,LYSP100-associated nuclear domain,GO:0033620,Mei2 nuclear dot,GO:0071920,cleavage body,GO:0071601,sphere organelle,GO:0035097,histone methyltransferase complex,GO:0035098,ESC/E(Z) complex,GO:0070688,MLL5-L complex,GO:0071339,MLL1 complex,GO:0016592,mediator complex,GO:0016591,DNA-directed RNA polymerase II, holoenzyme,GO:0032039,integrator complex,GO:0000443,SSL2-core TFIIH complex portion of holo TFIIH complex,GO:0071819,DUBm complex,GO:0005849,mRNA cleavage factor complex,GO:0005847,mRNA cleavage and polyadenylation specificity factor complex,GO:0005848,mRNA cleavage stimulating factor complex,GO:0031261,DNA replication preinitiation complex,GO:0071204,histone pre-mRNA 3'end processing complex,GO:0042405,nuclear inclusion body,GO:0005880,nuclear microtubule,GO:0005678,chromatin assembly complex,GO:0033186,CAF-1 complex,GO:0016590,ACF complex,GO:0000417,HIR complex,GO:0070421,DNA ligase III-XRCC1 complex,GO:0000152,nuclear ubiquitin ligase complex,GO:0033768,SUMO-targeted ubiquitin ligase complex,GO:0043224,nuclear SCF ubiquitin ligase complex,GO:0005680,anaphase-promoting complex,GO:0031436,BRCA1-BARD1 complex,GO:0070552,BRISC complex,GO:0008180,signalosome,GO:0019035,viral integration complex,GO:0046809,replication compartment,GO:0019036,viral transcriptional complex,GO:0046808,assemblon,GO:0070557,PCNA-p21 complex,GO:0019034,viral replication complex,GO:0055029,nuclear DNA-directed RNA polymerase complex,GO:0080137,DNA-directed RNA polymerase V complex,GO:0005736,DNA-directed RNA polymerase I complex,GO:0005681,spliceosomal complex,GO:0071023,trans spliceosomal complex,GO:0071010,prespliceosome,GO:0071004,U2-type prespliceosome,GO:0071015,U12-type prespliceosome,GO:0005684,U2-type spliceosomal complex,GO:0071005,U2-type precatalytic spliceosome,GO:0071006,U2-type catalytic step 1 spliceosome,GO:0071007,U2-type catalytic step 2 spliceosome,GO:0071008,U2-type post-mRNA release spliceosomal complex,GO:0000243,commitment complex,GO:0071021,U2-type post-spliceosomal complex,GO:0071013,catalytic step 2 spliceosome,GO:0071018,U12-type catalytic step 2 spliceosome,GO:0071014,post-mRNA release spliceosomal complex,GO:0071020,post-spliceosomal complex,GO:0071022,U12-type post-spliceosomal complex,GO:0071011,precatalytic spliceosome,GO:0071016,U12-type precatalytic spliceosome,GO:0005689,U12-type spliceosomal complex,GO:0071017,U12-type catalytic step 1 spliceosome,GO:0071012,catalytic step 1 spliceosome,GO:0071687,horsetail nucleus leading edge,GO:0005958,DNA-dependent protein kinase-DNA ligase 4 complex,GO:0070353,GATA1-TAL1-TCF3-Lmo2 complex,GO:0070693,P-TEFb-cap methyltransferase complex,GO:0070354,GATA2-TAL1-TCF3-Lmo2 complex,GO:0031519,PcG protein complex,GO:0035102,PRC1 complex,GO:0035517,PR-DUB complex,GO:0070767,BRCA1-Rad51 complex,GO:0032545,CURI complex,GO:0005730,nucleolus,GO:0044452,nucleolar part,GO:0031428,box C/D snoRNP complex,GO:0001652,granular component,GO:0031429,box H/ACA snoRNP complex,GO:0034388,Pwp2p-containing subcomplex of 90S preribosome,GO:0070545,PeBoW complex,GO:0001651,dense fibrillar component,GO:0001650,fibrillar center,GO:0005655,nucleolar ribonuclease P complex,GO:0034455,t-UTP complex,GO:0034456,UTP-C complex,GO:0030685,nucleolar preribosome,GO:0034457,Mpp10 complex,GO:0031510,SUMO activating enzyme complex,GO:0031981,nuclear lumen,GO:0046818,dense nuclear body,GO:0043564,Ku70:Ku80 complex,GO:0070418,DNA-dependent protein kinase complex,GO:0033167,ARC complex,GO:0031040,micronucleus,GO:0048353,primary endosperm nucleus,GO:0043073,germ cell nucleus,GO:0001674,female germ cell nucleus,GO:0042585,germinal vesicle,GO:0001673,male germ cell nucleus,GO:0071686,horsetail nucleus,GO:0045120,pronucleus,GO:0001939,female pronucleus,GO:0001940,male pronucleus,GO:0043076,megasporocyte nucleus,GO:0043079,antipodal cell nucleus,GO:0043078,polar nucleus,GO:0043082,megagametophyte egg cell nucleus";
for (Iterator i = goAccs.iterator(); i.hasNext();) {
  String goAcc = (String)i.next();
  if(nucleusTerms.indexOf(goAcc) != -1){
    String uniprotAcc = (String)j.next();
    if(!accsOut.contains(uniprotAcc)){
      accsOut.add(uniprotAcc);
      accsOutPrefix.add("uniprot:"+uniprotAcc);
    }
  }  
}

Wsdl

Wsdl Operation

Wsdl

Wsdl Operation

Script

String uniprotAccs = "";
String[] enxmlSplit= entries.split("primaryRef db=\"SWISSPROT\" id=\"");
for(int i=1; i<(enxmlSplit.length); i++){
    String[] enxmlSplitSplit = enxmlSplit[i].split("\" refType=\"primary-reference\"");
    uniprotAccs += enxmlSplitSplit[0];
    if(i != enxmlSplit.length-1){
        uniprotAccs += ",";
    }
}
enxmlSplit= entries.split("primaryRef db=\"TREMBL\" id=\"");
for(int i=1; i<(enxmlSplit.length); i++){
    String[] enxmlSplitSplit = enxmlSplit[i].split("\" refType=\"primary-reference\"");
    uniprotAccs += enxmlSplitSplit[0];
    if(i != enxmlSplit.length-1){
        uniprotAccs += ",";
    }
}

Script

String selectedAccs = "";
String uniprotAcc = "";

String[] uniprotSplit = iepInput.split("IEP of ");
for(int i=1; i<(uniprotSplit.length); i++){
    String[] uniprotSplitSplit = uniprotSplit[i].split(" from ");
    uniprotAcc = uniprotSplitSplit[0];
}

String[] ipSplit = iepInput.split("Isoelectric Point = ");
for(int i=1; i<(ipSplit.length); i++){
    String[] ipSplitSplit = ipSplit[i].split("\n");
    String ip = ipSplitSplit[0];
    Float ipValue = Float.parseFloat(ip);
    if(ipValue > Integer.parseInt(minIpValue) && ipValue < Integer.parseInt(maxIpValue)){
        selectedAccs = uniprotAcc;       
    }
}

Endpoint

Script

List utilityInput = new ArrayList();
String[] protAccsSplit = protAccs.split(",");
int runLimit = Integer.parseInt(accsPerRun);
int count = 0;
List temp = new ArrayList();
for(Object acc:protAccsSplit){
    count++;
    temp.add((String)acc);
    if(count == runLimit){
        utilityInput.add(temp);
        count = 0;
        temp = new ArrayList();
    }
}
if(temp.size() > 0){
    utilityInput.add(temp);
}

Script

String output = "";
for(Object list:input){
    for(Object list2:list){
       for (Iterator j = list2.iterator(); j.hasNext();) {         
    	  String acc = (String)j.next();
          if(output.indexOf(acc) == -1 && acc.length() > 0){
              if(output.length() != 0){
                  output += ",";
              }
      	      output += acc;
          }
       }
    }
}

Value

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