Semantic Web Analysis Service

Transcription

1 CBRC, AIST Semantic Web Analysis Service User Manual CBRC 2013/01/15

2 1. Sync Type Analysis Services How to use Sync Type Analysis Services Blast Prepare input RDF Command for execution Results CentroidFold Prepare input RDF Command for execution Results ClustalW Prepare input RDF Command for execution Results IPknot Prepare input RDF Command for execution Results Mafft Prepare input RDF Command for execution Results Psipred Prepare input RDF Command for execution Results Raccess Prepare input RDF Command for execution Results RactIP Prepare input RDF Command for execution Results Wolfpsort Prepare input RDF... 36

3 Command for execution Results AsyncType Analysis Services How to use Async Type Analysis Services Last Prepare input RDF Command for execution Results Modelling Prepare input RDF Command for execution Results PoodleL Prepare input RDF Command for execution Results PoodleS Prepare input RDF Command for execution Results Rassie Prepare input RDF Command for execution Results Contact... 66

4 Analysis OWLClass that defines input RDF Service Name CentroidFold S IPknot S Mafft S Psipred S Raccess S RactIP S Wolfpsort S Last Modelling PoodleL A A A PoodleS A Rassie A Table 1-A OWLClass that defines input RDF: S (Synchronous), A (Asynchronous)

5 1. Sync Type Analysis Services 1.0. How to use Sync Type Analysis Services Usable SADI services will be shown by accessing (Figure 1-1). Figure 1-1 SADI service Among those, Sync type analysis services (Blast, ClustalW, CentroidFold, IPknot, Mafft, Psipred, Raccess, RactIP, Wolfpsort) can be executed by using the following curl command. 1

6 % curl RDF (refer to Table 1-A) -o outputrdf For example, output.rdf as an output RDF can be obtained by executing the following command: % curl -o output.rdf Input RDF format is as follows: <cbrc:wolfpsortinput rdf:about=" <cbrc:requireskingdominformationof>animal</cbrc:requireskingdominformationof> <cbrc:requiresqueryproteinsequence> MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWG QPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMD EYSN </cbrc:requiresqueryproteinsequence> </cbrc:wolfpsortinput> </rdf:rdf> 1-1 Input RDF for Wolfpsort - Letters in black >> start and end tags for RDF (common to each service) - Letters in green >> specify name space (common to each service) - Letters in red >> OWL class that defines input RDF (refer to table 1-A), specify corresponding URI 2

7 <for Wolfpsort> OWL class that defines input RDF: cbrc:wolfpsortinput Corresponding URI: - Letters in blue >> specify a triple required by service execution <for Wolfpsort (two triples need to be specified)> Predicate: Object: requireskingdominformationof Kingdom(animal, plant or fungi) requiresqueryproteinsequence amino acid sequence A sample input RDF file can be obtained through Figure 1-2 SADI service page 3

8 Output RDF format is as follows: <cbrc:wolfpsortoutput rdf:about=" <cbrc:requiresresultintextformat># k used for knn is: 32 queryprotein extr 19, E.R. 4, pero 4, lyso 3, E.R._mito 3, mito_pero 3 </cbrc:requiresresultintextformat> </cbrc:wolfpsortoutput> </rdf:rdf> 1-2 Output RDF for Wolfpsort - Letters in blue >> Execution results of each service are stored in triple format <for Wolfpsort > Predicate: Object: requiresresultintextformat results in text * curl (e.g. for windows) can be downloaded through the site below 4

9 1.1. Blast Prepare input RDF Create input RDF for Blast as follows: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is BlastInput class, rdf:about attribute is blast.rdf#1 - Define a triple for a query sequence. Subject: BlastInput Predicate: requiresquerysequence Object: query sequence <cbrc:requiresquerysequence>query sequence</cbrc:requiresquerysequence> - Define a triple for Blast program Subject: BlastInput Predicate: requiresblastprogramname Object: blastp, blastn, blastx, tblastn or tblastx <cbrc:requiresblastprogramname>blastp</cbrc:requiresblastprogramname> - Define a triple for target database Subject: BlastInput Predicate: requiresblastdatabase Object: SWISS, TREMBL, UNIPROT, PROTEIN, PDB etc. <cbrc:requiresblastdatabase>swiss</cbrc:requiresblastdatabase> Input RDF for Blast based on those definitions would look like 1-3. Letters in red for a query sequence, letters in blue for target database, letters in green for blast program name. 5

10 <cbrc:blastinput rdf:about=" <cbrc:requiresquerysequence>>test MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGW GQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDE YSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPVILLISFLIFLIVGMA NLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGW GQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFV HDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPVILLISFLIFLIVGMANLGCWMLV LFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHS QWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITI KQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPVILLISFLIFLIVGMANLGCWMLVLFVATWSD LGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKP KTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTT TKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPVILLISFLIFLIVG</cbrc:requiresQuerySequen ce> <cbrc:requiresblastdatabase>swiss</cbrc:requiresblastdatabase> <cbrc:requiresblastprogramname>blastp</cbrc:requiresblastprogramname> </cbrc:blastinput> </rdf:rdf> 1-3 Input RDF for Blast Command for execution Enter the command below. % curl -o outputrdf 6

11 Results Blast results will be written in RDF format defined by the following: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is BlastInput class, rdf:about attribute is blast.rdf#1 - Define a triple for a query sequence. Subject: BlastInput Predicate: requiresresultintextformat Object: Blast results <cbrc:requiresresultintextformat>blast results </cbrc:requiresresultintextformat> An example of Blast results are shown in

12 <cbrc:blastoutput rdf:about=" <cbrc:requiresresultintextformat>blastp [Aug ] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Query= test (1012 letters) Database: SWISS: SWISS sequence taken from the header [Last update Dec/02/2011] 533,049 sequences; 189,064,225 total letters Searching...done >sp P04156 PRIO_HUMAN RecName: Full=Major prion protein Short=PrP; AltName: Full=ASCR; AltName: Full=PrP27-30; AltName: Full=PrP33-35C; AltName: CD_antigen=CD230; Flags: Precursor; Length = 253 Score = 301 bits (770), Expect = 2e-80, Method: Compositional matrix adjust. Identities = 154/236 (65%), Positives = 154/236 (65%) Query: 1 MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYXXXXXXXXXXX 60 MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRY Sbjct: 1 MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQP 60 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 75 (33.5 bits)</cbrc:requiresresultintextformat> </cbrc:blastoutput> </rdf:rdf> 1-4 Blastresults 8

13 1.2. CentroidFold Prepare input RDF Create input RDF for CentroidFold as follows: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is CentroidFoldInput class, rdf:about attribute is <cbrc:centroidfoldinput rdf:about= > - Define a triple for a RNA sequence. Subject: CentroidFoldInput Predicate: requiresqueryrnasequence Object: RNA sequence <cbrc:requiresqueryrnasequence>rnasequence</cbrc:requiresqueryrnaseq uence> - Define a triple for multiple alignment in ClutsalW format Subject: CentroidFoldInput Predicate: requiresclustalwmultiplealignment Object: multiple alignment in ClutsalW format <cbrc:requiresclustalwmultiplealignment> multiple alignment in ClutsalW format </cbrc:requiresclutalwmultiplealignment> - Define a triple for command line options Subject: CentroidFoldInput Predicate: hasoptions Object: options <cbrc:hasoptions>-g 4</cbrc:hasOptions> 9

14 Input RDF for CentroidFold based on those definitions would look like 1-5. Letters in red for a RNA sequence, letters in blue for command line options. <cbrc:centroidfoldinput rdf:about=" <cbrc:requiresqueryrnasequence>>af / RF00381;Antizyme_FSE; UGAUGCCCCUCACCCAUCAGUGAAGAUCCCGGGUGGGCGAGGGAACGGAA GGGAUC >AAVX / RF00381;Antizyme_FSE; UGAUGUCCCUCACCCACCCUUGAAGAUCCCAGGUGGGCGAGGGAAUGGUC AAAGGGAUC >BAAE / RF00381;Antizyme_FSE; UGAUGCCCCUCACCCACAGCUGAAGAUCCCGGGUGGGCGAGGGACUGUCA GGGAUC </cbrc:requiresqueryrnasequence> <cbrc:hasoptions>-g 4</cbrc:hasOptions> </cbrc:centroidfoldinput> </rdf:rdf> 1-5 Input RDF for CentroidFold Command for execution Enter the command below. % curl -o outputrdf 10

15 Results CentroidFold results will be written in RDF format defined by the following: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is CentroidFoldOutput class, rdf:about attribute is centroid.rdf#1 <cbrc:centroidfoldoutput rdf:about= > - Define a triple for CentroidFold. Subject: CentroidFoldOutput Predicate: requiresresultintextformat Object: results <cbrc:requiresresultintextformat>centroidfold results </cbrc:requiresresultintextformat> - Define a triple for CentroidFold graphic base64 conversion. Subject: CentroidFoldOutput Predicate: requiresresultinbase64binaryformat Object: results <cbrc:requiresresultinbase64binaryformat>centroidfold results </cbrc:requiresresultinbase64binaryformat> * This triple will not be written if noimage is defined for hasoptions in input RDF. An example of CentroidFold results are shown in 1-6. Letters in red for a CentroidFold graphic conversion, letters in blue for CentroidFold results. 11

16 <cbrc:centroidfoldoutput rdf:about=" <cbrc:requiresresultinbase64binaryformat>png:1 ivborw0kggoaaaansuheugaadrcaaa63caiaaaddrqitaacaaeleqvr42uzcw3ltxpfauu7h32dq Cv/0iHoMHhzazSNRFJ8A6pWZtVbgU9dE0b6OSmhHvhwAAAAAAAAAAAAAQC0vfgUAAAAAAAAAAAAA UIxKGAAAAAAAAAAAAACqUQkDAAAAAAAAAAAAQDUqYQAAAAAAAAAAAACoRiUMAAAAAAAAAAAAANWo haeaaaaaaaaaaacggpuwaaaaaaaaaaaaafsjegyaaaaaaaaaaacaaltcaaaaaaaaaaaaafcnshga AAAAAAAAAAAAqlEJAwAAAAAAAAAAAEA1KmEAAAAAAAAAAAAAqEYlDAAAAAAAAAAAAADVqIQBAAAA AACAiVTCcyrhzLS/EmEAAAAAAACYwtQNAABgrlQLd1uGwvkpgCXCAAAAAAAAMJ7BGwAAwFwWCauE 30iBJcIAAAAAAAAwktkbAADAdCrhcZVwLYJgfTAAAAAAAAAMYwIHAACwwsJVu41D4YqUwRJhAAAA AAAAGMMQDgAAYJG9FwnHV8J16YMlwgAAAAAAADCAORwAAMA6KuGoSrg6iTAAAAAAAAAQzSgOAABg qr9urmevnvtbaaaaaaaaqbwdoed/t2vhnaaaaaia+rf2nycbd+qaaiarx9csboowaaaaaaaambjs jjufyd3svaaaaabjru5erkjggg== </cbrc:requiresresultinbase64binaryformat> <cbrc:requiresresultintextformat>>af / RF00381;Antizyme_FSE; UGAUGCCCCUCACCCAUCAGUGAAGAUCCCGGGUGGGCGAGGGAACGGAAGGGAUC...(.(((((.((((((.(...)...)))))).)))))..)... (g=4,th=0.2,e=-10.39) >AAVX / RF00381;Antizyme_FSE; UGAUGUCCCUCACCCACCCUUGAAGAUCCCAGGUGGGCGAGGGAAUGGUCAAAGGGAUC ((((.((((((.((((((..((...)))))))).))))))...))))... (g=4,th=0.2,e=-13.76) >BAAE / RF00381;Antizyme_FSE; UGAUGCCCCUCACCCACAGCUGAAGAUCCCGGGUGGGCGAGGGACUGUCAGGGAUC (((((.(((((.(((((..(((...)))))))).)))))..)))))... (g=4,th=0.2,e=-12.51) </cbrc:requiresresultintextformat> </cbrc:centroidfoldoutput> </rdf:rdf> 1-6 CentroidFold results 12

17 1.3. ClustalW Prepare input RDF Create input RDF for ClustalW as follows: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is ClustalWInput class, rdf:about attribute is clustalw.rdf#1 <cbrc:clustalwinput rdf:about= > - Define a triple for a sequence. Subject: ClustalWInput Predicate: requiressequence Object: sequence <cbrc:requiressequence>more than 3 sequences </cbrc:requiressequence> - Define a triple for command line options Subject: ClustalWInput Predicate: hasoptions Object: options <cbrc:hasoptions>-gapopen=10 -GAPEXT=0.5</cbrc:hasOptions> 13

18 An example of ClustalW results are shown in 1-7. Letters in red for a sequence, letters in blue for options. <cbrc:clustalwinput rdf:about=" <cbrc:requiressequence>>1lyla FNDELRNRREKLAALRQQGVAFPNDFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRMMTRRIMGKASFVTLQDVGGRI QLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRLLTKALRPLPDQEVRYRQRYLDLIANDKSRQTFVVRSK ILAAIRQFMVARGFMEVETPMMQVIPGGASARPFITHHNALDLDMYLRIAPELYLKRLVVGGFERVFEINRNFRNEGISVRHNPEFT MMELYMAYADYHDLIELTESLFRTLAQEVLGTTKVTYGEHVFDFGKPFEKLTMREAIKKYRPETDMADLDNFDAAKALAESIGITVE KSWGLGRIVTEIFDEVAEAHLIQPTFITEYPAEVSPLARRNDVNPEITDRFEFFIGGREIGNGFSELNDAEDQAERFQEQVNAKAAG DDEAMFYDEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVILFPAMRP >1B8AA MYRTHYSSEITEELNGQKVKVAGWVWEVKDLGGIKFLWIRDRDGIVQITAPKKKVDPELFKLIPKLRSEDVVAVEGVVNFT PKAKLGFEILPEKIVVLNRAETPLPLDPTGKVKAELDTRLNNRFMDLRRPEVMAIFKIRSSVFKAVRDFFHENGFIEIHTPKIIATA TEGGTELFPMKYFEEDAFLAESPQLYKEIMMASGLDRVYEIAPIFRAEEHNTTRHLNEAWSIDSEMAFIEDEEEVMSFLERLVAHAI NYVREHNAKELDILNFELEEPKLPFPRVSYDKALEILGDLGKEIPWGEDIDTEGERLLGKYMMENENAPLYFLYQYPSEAKPFYIMK YDNKPEICRAFDLEYRGVEISSGGQREHRHDILVEQIKEKGLNPESFEFYLKAFRYGMPPHGGFGLGAERLIKQMLDLPNIREVILF PRDRRRLTP </cbrc:requiressequence> <cbrc:hasoptions>-gapopen=10 GAPEXT=2</cbrc:hasOptions> </cbrc:clustalwinput> </rdf:rdf> 1-7 Input RDF for ClustalW Command for execution Enter the command below. % curl -o outputrdf 14

19 Results ClustalW results will be written in RDF format defined by the following: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is ClustalWOutput class, rdf:about attribute is clustalw.rdf#1 <cbrc:clustalwoutput rdf:about= > - Define a triple for ClustalW. Subject: ClustalWOutput Predicate: requiresresultintextformat Object: results <cbrc:requiresresultintextformat>clustalw results </cbrc:requiresresultintextformat> An example of ClustalW results are shown in 1-8. Letters in red for ClustalW results. 15

20 <cbrc:clustalwoutput rdf:about=" <cbrc:requiresresultintextformat>clustal W (1.83) Multiple Sequence Alignments 1ATIA E64328 B64744 E64454 G ADJA G64930 D SESA A PYSA y Pyrococcus JT0942 1B8AA 1ASZB 1LYLA S WTPPRYFNMMFQDLRGPRGGRGLLAYLRPETAQGIFVNFKNVLDATSRKLGFGIAQIGK ELGEVKKFNLMFVTSIGPGGKR--TGYMRPETAQGIFIQFRRLAQFFRNKLPFGVVQIGK KFRDEVRPRFGVMRSREFLMKDAYSFHTSQESLQETYDAMYAAYSKIFSRMGLDFRAVQA HGGKTQLDVKLALRPTSETPIYYMMK-LWVKVHTDLPIKIYQIVN DHGGREMALRPEMTSPVVRFYLNELKNLQKPL--RLYYFAN DRGGRSLTLRPEGTAAMVRAYLEHGMKVWPQP-VRLWMAGP VDMCRGPHVPNMRFCHHFKLMKTAGAYWRGDSNNKMLQRIYGTAWADKKALNAYLQRLEE KGHPLSELSRKIVAKEEKKEEGEESKFYLLNPETEEIIELNENNINIIKDEELLALAKHE KALGEEAKRLEEALREKEARLEALLLQVPLPPWPGAPVGGE KLGEELDAAKAELDALQAEIRDIALTIPNLPADEVPVGKD EGFRLEGPLGEEVEGRLLLRTHTSPMQVRYMVAHTP LKAIVGVLRKEGWAEVSKTKEGLTLKLSEKGKKAEKRAIDIALEVL RPEMAQRLKTRAKITSLVRRFMDDHGFLDIETPMLTKATPE FTPKAKLGFEILPEKIVVLNRAETPLPLDPTGKVKAELD IVKKVDEPIKSATVQNLEIHITKIYTISETPEALPILLEDASRSEAE DSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCTELRL FETRFVGPGHSQGMNLWLMTSPEYHMKRLLVAGCGPVFQ ( D64449: , G64930: ) : ) : );</cbrc:requiresResultInTextFormat> </cbrc:clustalwoutput> </rdf:rdf> 1-8 ClustalW results 16

21 1.4. IPknot Prepare input RDF Create input RDF for IPknot as follows: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is IPknotInput class, rdf:about attribute is ipknot.rdf#1 <cbrc:ipknotinput rdf:about= > - Define a triple for a RNA sequence. Subject: IPknotInput Predicate: requiresqueryrnasequence Object: RNA sequence <cbrc:requiresqueryrnasequence>rnasequence</cbrc:requiresqueryrnaseq uence> - Define a triple for multiple alignment in ClutsalW format Subject: IPknotInput Predicate: requiresclustalwmultiplealignment Object: multiple alignment in ClutsalW format <cbrc:requiresclustalwmultiplealignment> multiple alignment in ClutsalW format </cbrc:requiresclutalwmultiplealignment> - Define a triple for command line options Subject: IPknotInput Predicate: hasoptions Object: options <cbrc:hasoptions>-i</cbrc:hasoptions> 17

22 Input RDF for IPknotbased on those definitions would look like 1-9. Letters in red for a RNA sequence, letters in blue for command line options. <cbrc:ipknotinput rdf:about=" <cbrc:requiresqueryrnasequence>>tomato_mosaic_virus.1 GUGUCUUGGAGCGCGCGGAGUAAACAUAUAUGGUUCAUAUAUGUCCGUAGGCACGUAAAAAAAGCGA >Tobacco_mosaic_virus.1 GUGUCUUGGAUCGCGCGGGUCAAAUGUAUAUGGUUCAUAUACAUCCGCAGGCACGUAAUAAA-GCGA >Rehmannia_mosaic_vir.1 GUGUCUUGGUUCGCGCGGGUCAAGUGUAUAUGGUGCAUAUACAUCCGUAGGCACGUAAUAAA-GCGA >B.pepper.1 GUGUCUUGGAACGCGCGGGUCAAAUAUAAGUGGUUCACUUAUAUCCGUAGGCACGAAAAAUU-GCGU</cbrc:requi resqueryrnasequence> <cbrc:hasoptions>-i</cbrc:hasoptions> </cbrc:ipknotinput> </rdf:rdf> 1-9 Input RDF for IPknot Command for execution Enter the following command: % curl -o outputrdf 18

23 Results IPknot results will be written in RDF format defined by the following: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is IPknotOutput class, rdf:about attribute is ipknot.rdf#1 <cbrc:ipknotoutput rdf:about= > - Define a triple for IPknot. Subject: IPknotOutput Predicate: requiresresultintextformat Object: results <cbrc:requiresresultintextformat>ipknot results </cbrc:requiresresultintextformat> An example of IPknot results are shown in Letters in red for a IPknot results. <cbrc:ipknotoutput rdf:about=" <cbrc:requiresresultintextformat>>tomato_mosaic_virus.1 GUGUCUUGGAGCGCGCGGAGUAAACAUAUAUGGUUCAUAUAUGUCCGUAGGCACGUAAAAAAAGCGA ((((((...((((...(((((((((...)))))))))))))))))))... >Rehmannia_mosaic_vir.1 GUGUCUUGGUUCGCGCGGGUCAAGUGUAUAUGGUGCAUAUACAUCCGUAGGCACGUAAUAAA-GCGA (((((..(((...[[[[)))...((((((((...)))))))).]]]].)))))... </cbrc:requiresresultintextformat> </cbrc:ipknotoutput> </rdf:rdf> 1-10 IPknot results 19

24 1.5. Mafft Prepare input RDF Create input RDF for Mafft as follows: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is MafftInput class, rdf:about attribute is mafft.rdf#1 <cbrc:mafftinput rdf:about= > - Define a triple for a sequence. Subject: MafftInput Predicate: requiressequence Object: sequence <cbrc:requiressequence>more than 3 sequences </cbrc:requiressequence> - Define a triple for command line options Subject: MafftInput Predicate: hasoptions Object: options <cbrc:hasoptions>--retree 2 --maxiterate 0 --bl 62 --op ep clustalout</cbrc:hasoptions> An example of Mafft results are shown in Letters in red for a sequence, letters in blue for options. 20

25 <cbrc:mafftinput rdf:about=" <cbrc:requiressequence>>1lyla FNDELRNRREKLAALRQQGVAFPNDFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRM MTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTG ELSIHCTELRLLTKALRPLPDQEVRYRQRYLDLIANDKSRQTFVVRSKILAAIRQFMVAR EQVNAKAAGDDEAMFYDEDYVTALEYGLPPTAGLGIGIDRMIMLFTNSHTIRDVILFPAM RP >1B8AA MYRTHYSSEITEELNGQKVKVAGWVWEVKDLGGIKFLWIRDRDGIVQITAPKKKVDPELF KLIPKLRSEDVVAVEGVVNFTPKAKLGFEILPEKIVVLNRAETPLPLDPTGKVKAELDTR LNNRFMDLRRPEVMAIFKIRSSVFKAVRDFFHENGFIEIHTPKIIATATEGGTELFPMKY PNIREVILFPRDRRRLTP >1ASZB EDTAKDNYGKLPLIQSRDSDRTGQKRVKFVDLDEAKDSDKEVLFRARVHNTRQQGATLAF LTLRQQASLIQGLVKANKEGTISKNMVKWAGSLNLESIVLVRGIVKKVDEPIKSATVQNL EIHITKIYTISETPEALPILLEDASRSEAEAEAAGLPVVNLDTRLDYRVIDLRTVTNQAI FRIQAGVCELFREYLATKKFTEVHTPKLLGAPSEGGSSVFEVTYFKGKAYLAQSPQFNKQ QLIVADFERVYEIGPVFRAENSNTHRHMTEFTGLDMEMAFEEHYHEVLDTLSELFVFIFS KFLGKLVRDKYDTDFYILDKFPLEIRPFYTMPDPANPKYSNSYDFFMRGEEILSGAQRIH EIYEKLKGKFRVHIDDRDIRPGRKFNDWEIKGVPLRIEVGPKDIENKKITLFRRDTMEKF QVDETQLMEVVEKTLNNIMENIKNRAWEKFENFITILEDINPDEIKNILSEKRGVILVPF KEEIYNEELEEKVEATILGETEYKGNKYIAIAKTY </cbrc:requiressequence> <cbrc:hasoptions></cbrc:hasoptions> </cbrc:mafftinput> </rdf:rdf> 1-11 Input RDF for Mafft 21

26 Command for execution Enter the command below. % curl -o outputrdf Results Mafft results will be written in RDF format defined by the following: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is MafftOutput class, rdf:about attribute is mafft.rdf#1 - Define a triple for Mafft results Subject: MafftOutput Predicate: requiresresultintextformat Object: Mafft results <cbrc:requiresresultintextformat>mafft results </cbrc:requiresresultintextformat> An example of Mafft results are shown in Letters in red for Mafft results 22

27 <cbrc:mafftoutput rdf:about=" <cbrc:requiresresultintextformat>clustal format alignment by MAFFT FFT-NS-2 (v6.717b) 1LYLA 1B8AA 1ASZB FNDELRNRREKLAALRQQGVAFPNDFRRDHTSDQLHEEFDAKDNQELESLNIEVSVAGRM MYRTHY------SSEITEELNGQKVKVAGWV EDTAKDNYGKLPLIQSRDSDRTGQKRVKFVD-L 1ADJA PYSA LYLA 1B8AA 1ASZB 1ADJA 1PYSA LVVGGFER------VFEINR-NFRNE MMASGLDR------VYEIAP-IFRAE LIVADFER------VYEIGP-VFRAE YLEHGMKVWPQ-----PVRLWMAGP-MFRAE MVAHTP-----PFRIVVPGR-VFRFE----- * 1LYLA 1B8AA 1ASZB 1ADJA 1PYSA -----AMRP RDRRRLTP RDPKRLRP FLGEDELRAGEVTLKRLATGEQVRLSREEVPGYLLQALG ----KFLEQFKGVL </cbrc:requiresresultintextformat> </cbrc:mafftoutput> </rdf:rdf> 1-12 Mafft results 23

28 1.6. Psipred Prepare input RDF Create input RDF for Psipred as follows: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is PsiPredInput class, rdf:about attribute is psipred.rdf#1 <cbrc:psipredinput rdf:about= > - Define a triple for an amino acid sequence. Subject: PsiPredInput Predicate: requiresqueryproteinsequence Object: amino acid sequence <cbrc:requiresqueryproteinsequence> amino acid sequence </cbrc:requiresqueryproteinsequence> 24

29 Input RDF for Psipred based on those definitions would look like Letters in red for a sequence. <cbrc:psipredinput rdf:about=" <cbrc:requiresqueryproteinsequence>>test MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGW GQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDE YSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPVILLISFLIFLIVGMA NLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGW GQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFV HDCVNIMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTT TKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPVILLISFLIFLIVG</cbrc:requiresQueryProtei nsequence> </cbrc:psipredinput> </rdf:rdf> 1-13 Input RDF for Psipred Command for execution Enter the command below. % curl -o outputrdf 25

30 Results Psipred results will be written in RDF format defined by the following: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is PsiPredOutput class, rdf:about attribute is psipred.rdf#1 - <cbrc:psipredoutput rdf:about= > - Define a triple for Psipred. Subject: PsiPredOutput Predicate: requiresresultintextformat Object: results <cbrc:requiresresultintextformat>psipred results </cbrc:requiresresultintextformat> An example of Psipred results are shown in Letters in red for Psipred results. 26

31 <cbrc:psipredoutput rdf:about=" <cbrc:requiresresultintextformat># PSIPRED HFORMAT (PSIPRED V2.5 by David Jones) Conf: Pred: CCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC AA: MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQP Conf: Pred: CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCHHHHH AA: HGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGA Conf: Pred: HHHCCHHHHHHHHHCCCEECCCCCCCHHHHHHHHHHCCCCCEECCCHHHCCCCCCEEEEE AA: VVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCV Conf: Pred: HHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHCCC AA: DVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPVILLISFLIFLIVG </cbrc:requiresresultintextformat> </cbrc:psipredoutput> </rdf:rdf> 1-14 Psipred results 27

32 1.7. Raccess Prepare input RDF Create input RDF for Raccess as follows: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is RaccessInput class, rdf:about attribute is raccess.rdf#1 - <cbrc:raccessinput rdf:about= > - Define a triple for a RNA sequence. Subject: RaccessInput Predicate: requiresqueryrnasequence Object: sequence <cbrc:requiresqueryrnasequence>rna sequence </cbrc:requiresqueryrnasequence> - Define a triple for command line options Subject: RaccessInput Predicate: hasoptions Object: options <cbrc:hasoptions>-access_len=50 </cbrc:hasoptions> Input RDF for Raccess based on those definitions would look like Letters in red for a RNA sequence, letters in blue for command line options. 28

33 <cbrc:raccessinput rdf:about=" <cbrc:requiresqueryrnasequence>>gi ref NM_ Homo sapiens vasohibin 1 (VASH1), mrna GCCCCTGCGCGCCGCCCGAGCCGGTCCCGCTGAGCCGCGGGCCCCGTGCCCTGCGATGGCTCGGCTGGTG CAGCGCGGCGCCAGGTGCCAGCCGTCCTCCCGCTGAGACGCGCCCGAGTGGGGACCCGCTGGGCCTCGGG GCTCGCAGCCTTCGCCTCCCCGCCGCGCCCGCTCCCTTTCTGGGGACTCCGCCGCTGTTTCTGGGGACGA GGGGACAGGGGACCCAGACAAAGCCCACTTTGTGCAGGGAGTTGGCCGCAGGCGGGGAATGTGCGCGTCG GCGCGCGCCCCCTCCCCGCTCCCGGCCAGCTGCGAGTCTTGGCTCCCGGACTTGTCTCGTCGCGTCGGAG AAATCGCCCCCCAGCGCCGCTCTCCCGCCCGGGGGTCTTGGTTCCGAGCTCGCGCGGCCGGGAGTCGCCT CGGTCTTCCTTGGGGCGCGCGCAGATGTGAGCGTGCGAGAGTTGTGTAGGGGATTTTGTTCCCTCCGAAA CTGAGACCCAGGGCGCCCAGTGGGCACCCGTGCCTTGACTCTGTCCTTTCTGCAGCCGCTGGTCCGAGCT GTCTGGCCTCAGTTTCCCTCCGACTTTTCTCCGCTCTGCCAGCCCTCACTGCTGCCCGTCATTGTTCTCG CAGTTAGATGGGGGTGCTTTGTGACGGCTGCCAAGTTGGGGTGTGTTCTCTTTATTCCGTTTTTCAAACA GAACAAGGCCTCCAAGGCTGACCCCAGACAACCCACCCCCTCGGACCCTAATTCACCTTATTGCACTGAT TTTTTTTATCAAGTCGTATTTTATTGTACAGGAGCCACGCCCTGATTTCTTAAAGGCGCCTTGCACTCTG GCCATGTGTTATCTCTGCAGCCGGTGTGTGGGAGGCCTCTTGTGAGCCAGTTGTTTTCCCGCCTCCACCA CCCCCCTCGAAGATTTAGGGATGCCAGGGGGGAAGAAGGTGGCTGGGGGTGGCAGCAGCGGTGCCACTCC AACGTCCGCTGCGGCCACCGCCCCCTCTGGGGTCAGGCGTTTGGAGACCAGCGAAGGAACCTCAGCCCAG CCAAGCTGCTCTCGCTCCCACTGAGCCAAGCCCCCTAACTTTGGGCCTAGAGGCCGTTAGTAT. </cbrc:requiresqueryrnasequence> <cbrc:hasoptions></cbrc:hasoptions> </cbrc:raccessinput> </rdf:rdf> 1-15 Input RDF for Raccess Command for execution Enter the command below. % curl -o outputrdf 29

34 Results Raccess results will be written in RDF format defined by the following: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is RaccessOutput class, rdf:about attribute is raccess.rdf#1 <cbrc:raccessoutput rdf:about= > - Define a triple for Raccess. Subject: RaccessOutput Predicate: requiresresultintextformat Object: results <cbrc:requiresresultintextformat> Raccess results </cbrc:requiresresultintextformat> An example of Raccess results are shown in Letters in red for Raccess results. 30

35 <cbrc:raccessoutput rdf:about=" <cbrc:requiresresultintextformat>>gi ref NM_ Homo sapiens vasohibin 1 (VASH1), mrna /cbrc:requiresResultInTextFormat> </cbrc:raccessoutput> </rdf:rdf> 1-16 Raccess results 31

36 1.8. RactIP Prepare input RDF Create input RDF for RactIPInput as follows: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is RactIPInput class, rdf:about attribute is ractip.rdf#1 <cbrc:ractipinput rdf:about= > - Define a triple for a RNA sequence. Subject: RactIPInput Predicate: requiresqueryrnasequence Object: RNA sequence <cbrc:requiresqueryrnasequence>rnasequence</cbrc:requiresqueryrnaseq uence> - Define a triple for target RNA sequence Subject: RactIPInput Predicate: requiressubjectrnasequence Object: sequence - <cbrc:requiressubjectrnasequence>rna sequence - </cbrc:requiressubjectrnasequence> - Define a triple for command line options Subject: RactIPInput Predicate: hasoptions Object: options <cbrc:hasoptions>-i</cbrc:hasoptions> 32

37 Input RDF for RactIP based on those definitions would look like Letters in red for a RNA sequence, letters in blue for command line options. <cbrc:ractipinput rdf:about=" <cbrc:requiresqueryrnasequence>>r1inv GGCAACGGAUGGUUCGUUGCC</cbrc:requiresQueryRNASequence> <cbrc:requiressubjectrnasequence>>r2inv GCACCGAACCAUCCGGUGC</cbrc:requiresSubjectRNASequence> <cbrc:hasoptions>-i</cbrc:hasoptions> </cbrc:ractipinput> </rdf:rdf> 1-17 Input RDF for RactIP Command for execution Enter the command below. % curl -o outputrdf 33

38 Results RactIP results will be written in RDF format defined by the following: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is RactIPOutput class, rdf:about attribute is ractip.rdf#1 <cbrc:ractipoutput rdf:about= > - Define a triple for RactIP. Subject: RactIPOutput Predicate: requiresresultintextformat Object: results <cbrc:requiresresultintextformat> RactIP results </cbrc:requiresresultintextformat> An example of RactIP results are shown in Letters in red for RactIP results. 34

39 <cbrc:ractipoutput rdf:about=" <cbrc:requiresresultintextformat>* 0: objval = e+00 infeas = e+00 (0) * 36: objval = e+01 infeas = e+00 (0) OPTIMAL SOLUTION FOUND Integer optimization begins : mip = not found yet <= +inf (1; 0) + 36: >>>>> e+01 <= e % (1; 0) + 36: mip = e+01 <= tree is empty 0.0% (0; 1) INTEGER OPTIMAL SOLUTION FOUND >R1inv GGCAACGGAUGGUUCGUUGCC ((((((([[[[[[[))))))) >R2inv GCACCGAACCAUCCGGUGC ((((((]]]]]]]))))))</cbrc:requiresresultintextformat> </cbrc:ractipoutput> </rdf:rdf> 1-18 RactIP results 35

40 1.9. Wolfpsort Prepare input RDF Create input RDF for Wolfpsort as follows: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is WolfPsortInput class, rdf:about attribute is wolfpsort.rdf#1 <cbrc:wolfpsortinput rdf:about= > - Define a triple for kingdom. Subject: WolfPsortInput Predicate: requireskingdominformation Object: animal plant or fungi <cbrc:requirekingomdinfomationof> string </cbrc:requirekingdominformationof> - Define a triple for an amino acid sequence Subject: WolfPsortInput Predicate: requiresqueryproteinsequence Object: sequence <cbrc:requiresqueryproteinsequence> sequence </cbrc:requiresqueryproteinsequence> 36

41 Input RDF for Wolfpsort based on those definitions would look like Letters in red for a sequence, letters in blue for a kingdom. <cbrc:wolfpsortinput rdf:about=" <cbrc:requireskingdominformationof>animal</cbrc:requireskingdominformationof> <cbrc:requiresqueryproteinsequence>manlgcwmlvlfvatwsdlglckkrpkpggwntggsrypgqgspgg NRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSA MSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYER ESQAYYQRGSSMVLFSSPPVILLISFLIFLIVG</cbrc:requiresQueryProteinSequence> </cbrc:wolfpsortinput> </rdf:rdf> 1-19 Input RDF for Wolfpsort Command for execution Enter the command below. % curl -o outputrdf 37

42 Results Wolfpsort results will be written in RDF format defined by the following: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is WolfPsortOutput class, rdf:about attribute is wolfpsort.rdf#1 <cbrc:wolfpsortoutput rdf:about= > - Define a triple for Wolfpsort results. Subject: WolfPsortOutput Predicate: requiresresultintextformat Object: results <cbrc:requiresresultintextformat>wolfpsort results </cbrc:requiresresultintextformat> An example of Wolfpsort results are shown in Letters in red for a Wolfpsort results. <cbrc:wolfpsortoutput rdf:about=" <cbrc:requiresresultintextformat># k used for knn is: 32 queryprotein extr 19, E.R. 4, pero 4, lyso 3, E.R._mito 3, mito_pero 3 </cbrc:requiresresultintextformat> </cbrc:wolfpsortoutput> </rdf:rdf> 1-20 Wolfpsort results 38

43 2. AsyncType Analysis Services 2.0. How to use Async Type Analysis Services Async type services (Last, Modelling, PoodleL, PoodleS, Rassie) can be executed by using the following curl command. 1) Obtain polling URI % curl to Table 1-A) For example, input.rdf as an input RDF can be used to execute PoodleL as follows: % curl RDF storing polling URI (in red) will be written to standard out. <cbrc:poodleloutput rdf:about=" <rdfs:isdefinedby rdf:resource= /> </cbrc:poodleloutput> </rdf:rdf> 2-1 RDF storing polling URL 2) Polling to SADI server % curl For example, PoodleL can be executed as follows: 39

44 %curl Results URL will then be written to standard out upon completion of the service. % curl COMPLETE: poodlelresult.rdf ** This standard output is shown only once so that the results cannot be obtained if it ( poodlelresult.rdf ) is lost. Xxx/yyy indicates the location of the data on the CBRC server. 3) Obtain results % curl poodlelresult.rdf -o outputrdf Refer to section 1-1 and 1-2 for input/output RDF format. 40

45 2.1. Last Prepare input RDF Create input RDF for Last as follows: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is LastInput class, rdf:about attribute is last.rdf#1 <cbrc:lastinput rdf:about= > - Define a triple for a query sequence. Subject: LastInput Predicate: requiresquerysequence Object: sequence <cbrc:requiresquerysequence>sequence</cbrc:requiresquerysequence> - Define a triple for a subject sequence. Subject: LastInput Predicate: requiressubjectsequence Object: sequence <cbrc:requiressubjectsequence>subject sequence </cbrc:requiressubjectsequence> - Define a triple forlastdb command line options Subject: LastInput Predicate: hasoptionsforlastdb Object: options - <cbrc:hasoptionsforlastdb>-m110 -w1</cbrc:hasoptionsforlastdb> - Define a triple for Lastal command line options Subject: LastInput Predicate: hasoptionsforlastal Object: options 41

46 <cbrc:hasoptionsforlastal>-j4 -u0 -m10 -l1 -k1 -w0 -g1.0 -s2 -e30 </cbrc:hasoptionsforlastal> Input RDF for Last based on those definitions would look like 2-2. Letters in red for a sequence, letters in blue for command line options. <cbrc:lastinput rdf:about=" <cbrc:requiresquerysequence>>gi ref NC_ Pyrococcus abyssi GE5, complete genome GGGCTTTAGCCTCCTTCACCGCTTCCACGATTTTCTGCCTGTCAAAGGGCATTCTAGACATCCCTCCTTA GGTTTTTAATTAAAAATTCAAGGTGGAGTAAAAAGGGATGTTTTTAAATTTTTCTCACTCTTTCTCGGCC TTCTCAAATAGCTCGTCGTAAACCCCTTCATCTATTTCTCTCTGAACTTCCCTTGGATCCTTGCCTTCGA CGGTAACTCCCATGCTTAAAGCCGTTCCAATGACTTCCTTGGCGGCAGCCTTAAGAGTCAATGCTAGCAT CTGGTTTCTCTTCATCTTAGCTATCTTGATAACTTGCTCCATCGTTAAGTTCCCAACGATATTGTGCTTC CTATCTCGAACTGCTTGGTTACTGGATCTACGATGATCTTCACTGGGACCTGCATCCCAGCGAACTCTTT AACATCAAGAAGCTGACCTACCACGGCCCTGAACTTCCTAGGATCTCCATGTCCCTCATCCTCTTCTTCA</cbrc:requ iresquerysequence> <cbrc:requiressubjectsequence> AGATCCTTAGCCTTGTTGTTCCTTTTCTCAAGGAGCTTTACGCTACCGTCTTCACAGATCTCATAGATCG CGAAAAACTCTGAATCTCCGTAGTGAGCGTCTATGAGATGTTCATCATCCTCCATTCCAAAGGCTACCTT GTTCCTGGGACCTAGGTATCTACCGAGGTACCTACCTATCTTGGGCATTAATGGGGCCTCAGCTATGAAG TAATAACGTCAAGCCCGAGCCTCCTCGCCGCTTCGGCAACTGCACCATCAGCGATGACCGCGATCTTTAC TCTTTAAGGTTCACTGCCACCTCGACACTCTGTGTGAAGTTACGCGGCTTGGCCC</cbrc:requiresSubjectSequ ence> <cbrc:hasoptionsforlastdb>-m110 -w1</cbrc:hasoptionsforlastdb> <cbrc:hasoptionsforlastal>-j4 -u0 -m10 -l1 -k1 -w0 -g1.0 -s2 -e30</cbrc:hasoptionsforlastal> </cbrc:lastinput> </rdf:rdf> 2-2 Input RDF for Last 42

47 Command for execution Enter the command below. % curl In case of Last, because of asynchronous communication, RDF corresponding HTTP response code 202 is returned to standard out (2-3) Polling to SADI server is performed using defined by.isdefinedby. % curl COMPLETE: <cbrc:lastoutput rdf:about=" <rdfs:isdefinedby rdf:resource= /> </cbrc:lastoutput> </rdf:rdf> 2-3 RDF corresponding HTTP response code 202 % curl seq1_seq2result.rdf -ooutputrdf 43

48 Results Last results will be written in RDF format defined by the following: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is LastOutput class, rdf:about attribute is last.rdf#1 <cbrc:lastoutput rdf:about= > - Define a triple for Last. Subject: LastOutput Predicate: requiresresultintextformat Object: results <cbrc:requiresresultintextformat>last results </cbrc:requiresresultintextformat> - Define a triple for Last graphic base64 conversion. Subject: LastOutput Predicate: requiresresultinbase64binaryformat Object: results <cbrc:requiresresultinbase64binaryformat>last results </cbrc:requiresresultinbase64binaryformat> * This triple will not be written if noimage is defined for lastaloptions in input RDF. An example of Last results are shown in 2-4. Letters in red for a Last graphic conversion, letters in blue for Last results. 44

49 <cbrc:lastoutput rdf:about=" <cbrc:requiresresultinbase64binaryformat>ivborw0kggoaaaansuheugaaa8caaapocaaaaadw ntnlaaanoeleqvr42u3daxijrrzf0dz/zmsj ohblqllzburnnc73occmgmiw0gp7kvm/rhlsqlrhuwa65k9+dcah37/91/jh/spjw8fhgl/6q42v /lbjh3/7ya8khfp61+ie7ltqj98b93xph79/5bf/ubjvf/j4/euf/6uv//mifvjo0tgvhcrjpbdz AAAASUVORK5CYII=</cbrc:requiresResultInBase64BinaryFormat> <cbrc:requiresresultintextformat># LAST version 58 # # a=7 b=1 c= e=30 d=18 x=27 y=10 # u=0 s=2 m=10 l=1 k=1 i= w=0 t= g=1 j=4 # seq1 a score=30 s gi ref NC_ GTTGAGAGTTCCAATAAGACTAAAATAGGATTGAAA s GATCCTTAGCCTTGTTGTTCCTTTTCTCAAGGAGCTTTACGCTACCGTCTTCACAGATCTCATAGATCG GTGGCGAGTTCCAATAAGACTAAAATAGAATTGAAA p # CPU time: 0.36 seconds </cbrc:requiresresultintextformat> </cbrc:lastoutput> </rdf:rdf> 2-4 Last results 45

50 2.2. Modelling Prepare input RDF Create input RDF for Modelling as follows: - Define vocabulary RDF and CBRC OWL in RDF header xmlns:rdf xmlns:cbrc > - Subject is ModellingInput class, rdf:about attribute is modelling.rdf#1 <cbrc:modellinginput rdf:about= > - Define a triple for an amino acid sequence. Subject: ModellingInput Predicate: requiresqueryproteinsequence Object: sequence <cbrc:requiresqueryproteinsequence>sequence </cbrc:requiresqueryproteinsequence> - Define a triple for BLAST. Subject: ModellingInput Predicate: requiresblastprogramname Object: BLAST or PSI-BLAST <cbrc:requiresblastprogramname>blast or PSI-BLAST</cbrc:requiresBlastProgramName> - Define a triple for Iteration (PSI-BLAST) Subject: ModellingInput Predicate: setupiterationnumber Object: Iteration <cbrc:setupiterationnumber>3</cbrc:setupiterationnumber> - Define a triple for E-value Subject: ModellingInput Predicate: setupevaluethreshold 46

51 Object: E-Value <cbrc:setupevaluethreshold> </cbrc:setupevaluethreshold> - Define a triple for hit region coverage threshold. Subject: ModellingInput Predicate: setuphitregioncoveragethreshold Object: threshold <cbrc:setuphitregioncoveragethreshold>60.0 </cbrc:setuphitregioncoveragethreshold> - Define a triple for hit region identity. Subject: ModellingInput Predicate: setuphitregionidentitythreshold Object: identity <cbrc:setuphitregionidentitythreshold>30.0 </cbrc:setuphitregionidentitythreshold> - Define a triple for minimum sequence length Subject: ModellingInput Predicate: setupminimumsequencelength Object: identity <cbrc:setupminimumsequencelength>30 </cbrc:setupminimumsequencelength> - Define a triple for template coverage threshold. Subject: ModellingInput Predicate: setuptemplatecoveragethreshold Object: threshold <cbrc:setuptemplatecoveragethreshold>90.0 </cbrc:setuptemplatecoveragethreshold> - Define a triple for template coverage identity. Subject: ModellingInput Predicate: setuptemplateidentitythreshold Object: identity <cbrc:setuptemplateidentitythreshold>90.0 </cbrc:setuptemplateidentitythreshold> - Define a triple for MODELLER license key. Subject: ModellingInput Predicate: requireslicensekey Object: key 47

52 <cbrc:requireslicensekey>***</cbrc:requireslicensekey> ** Modelling cannot be used without MODELLER license key. A key must be obtained through - Define a triple for number of models. Subject: ModellingInput Predicate: setupmodelnumber Object: number <cbrc:setupmodelnumber>10</cbrc:setupmodelnumber> Input RDF for Modelling based on those definitions would look like 2-5. Letters in red for a sequence, letters in blue for command line options. 48

53 <cbrc:modellinginput rdf:about=" <cbrc:requiresqueryproteinsequence>>sample MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAV ADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACA APPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVI IMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNKREIRLMKNREAAREC RRKKKEYVKCLENRVAVLENQNKTLIEELKTLKDLYSNKMSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDS VEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQ DKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYK AQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPYSNASQMGNT GSGGYDNAW</cbrc:requiresQueryProteinSequence> <cbrc:requiresblastprogramname>blast</cbrc:requiresblastprogramname> <cbrc:setupevaluethreshold> </cbrc:setupevaluethreshold> <cbrc:setuphitregioncoveragethreshold>60.0</cbrc:setuphitregioncoveragethreshold> <cbrc:setuphitregionidentitythreshold>30.0</cbrc:setuphitregionidentitythreshold> <cbrc:setupminimumsequencelength>30</cbrc:setupminimumsequencelength> <cbrc:setuptemplatecoveragethreshold>95.0</cbrc:setuptemplatecoveragethreshold> <cbrc:setuptemplateidentitythreshold>95.0</cbrc:setuptemplateidentitythreshold> <cbrc:requireslicensekey>***</cbrc:requireslicensekey> <cbrc:setupmodelnumber>10</cbrc:setupmodelnumber> </cbrc:modellinginput> </rdf:rdf> 2-5 Input RDF for Modelling 49