BH12.12/TogoStanza

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== TogoStanza == * http://togo-stanza.herokuapp.com/ === UniProt === <pre> % wget http://www.uniprot.org/uniprot/P16033.rdf % rapper -i rdfxml -o turtle P16033.rdf > P16033.ttl rapper: Parsing URI file:///Users/ktym/P16033.rdf with parser rdfxml rapper: Serializing with serializer turtle rapper: Parsing returned 702 triples % export SPARQL_ENDPOINT="http://beta.sparql.uniprot.org/sparql" % sparql.rb query ' prefix up: <http://purl.uniprot.org/core/> prefix tax: <http://purl.uniprot.org/taxonomy/> select * where { ?s up:locusName "slr1311" . ?s ?p ?o . }' s p o _5031363033330011 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.uniprot.org/core/Gene> _5031363033330011 <http://purl.uniprot.org/core/locusName> slr1311 _5031363033330011 <http://www.w3.org/2004/02/skos/core#prefLabel> psbA2 _5031363033330011 <http://www.w3.org/2004/02/skos/core#altLabel> psbA-2 </pre> === RefSeq === <pre> LOCUS NC_000911 3573470 bp DNA circular BCT 19-JAN-2012 DEFINITION Synechocystis sp. PCC 6803 chromosome, complete genome. ACCESSION NC_000911 VERSION NC_000911.1 GI:16329170 DBLINK Project: 57659 KEYWORDS . SOURCE Synechocystis sp. PCC 6803 ORGANISM Synechocystis sp. PCC 6803 Bacteria; Cyanobacteria; Chroococcales; Synechocystis. REFERENCE 1 (bases 1 to 3573470) AUTHORS Thelwell,C., Robinson,N.J. and Turner-Cavet,J.S. TITLE An SmtB-like repressor from Synechocystis PCC 6803 regulates a zinc exporter JOURNAL Proc. Natl. Acad. Sci. U.S.A. 95 (18), 10728-10733 (1998) PUBMED 9724772 REFERENCE 2 (bases 1 to 3573470) AUTHORS Kaneko,T., Sato,S., Kotani,H., Tanaka,A., Asamizu,E., Nakamura,Y., Miyajima,N., Hirosawa,M., Sugiura,M., Sasamoto,S., Kimura,T., Hosouchi,T., Matsuno,A., Muraki,A., Nakazaki,N., Naruo,K., Okumura,S., Shimpo,S., Takeuchi,C., Wada,T., Watanabe,A., Yamada,M., Yasuda,M. and Tabata,S. TITLE Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions JOURNAL DNA Res. 3 (3), 109-136 (1996) PUBMED 8905231 REFERENCE 3 (bases 1 to 3573470) AUTHORS Kaneko,T., Tanaka,A., Sato,S., Kotani,H., Sazuka,T., Miyajima,N., Sugiura,M. and Tabata,S. TITLE Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. I. Sequence features in the 1 Mb region from map positions 64% to 92% of the genome JOURNAL DNA Res. 2 (4), 153-166 (1995) PUBMED 8590279 REFERENCE 4 (bases 1 to 3573470) CONSRTM NCBI Genome Project TITLE Direct Submission JOURNAL Submitted (10-SEP-2004) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA REFERENCE 5 (bases 1 to 3573470) AUTHORS Tabata,S. TITLE Direct Submission JOURNAL Submitted (28-JUN-1996) Kazusa DNA Research Institute, The First Laboratory for Plant Gene Research, Yana 1532-3, Kisarazu, Chiba 292-0812, Japan COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence was derived from BA000022. COMPLETENESS: full length. FEATURES Location/Qualifiers source 1..3573470 /organism="Synechocystis sp. PCC 6803" /mol_type="genomic DNA" /strain="PCC 6803" /db_xref="taxon:1148" : gene 7229..8311 /gene="psbA2" /locus_tag="slr1311" /db_xref="GeneID:951890" CDS 7229..8311 /gene="psbA2" /locus_tag="slr1311" /codon_start=1 /transl_table=11 /product="photosystem II D1 protein" /protein_id="NP_439906.1" /db_xref="GI:16329178" /db_xref="GeneID:951890" /translation="MTTTLQQRESASLWEQFCQWVTSTNNRIYVGWFGTLMIPTLLTA TTCFIIAFIAAPPVDIDGIREPVAGSLLYGNNIISGAVVPSSNAIGLHFYPIWEAASL DEWLYNGGPYQLVVFHFLIGIFCYMGRQWELSYRLGMRPWICVAYSAPVSAATAVFLI YPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSL VTSSLVRETTEVESQNYGYKFGQEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLG AWPVIGIWFTAMGVSTMAFNLNGFNFNQSILDSQGRVIGTWADVLNRANIGFEVMHER NAHNFPLDLASGEQAPVALTAPAVNG" </pre> === TogoGenome === <pre> % less wget_prokaryotes/PRJNA57659/NC_000911.1 % less wget_prokaryotes.v5/PRJNA57659/NC_000911.1.ttl </pre> in Virtuoso (w/o predicate paths) <pre> % sparql.rb query ' prefix obo: <http://purl.obolibrary.org/obo/> prefix faldo: <http://biohackathon.org/resource/faldo#> prefix insdc: <http://rdf.insdc.org/> prefix up: <http://purl.uniprot.org/core/> prefix tax: <http://purl.uniprot.org/taxonomy/> select * from <http://v5.genome.db/> where { ?seq rdfs:seeAlso <http://identifiers.org/taxonomy/1148> . ?gene obo:so_part_of ?seq . ?cds obo:so_part_of ?gene . ?cds a obo:SO_0000316 . # CDS ?cds rdfs:label "slr1311" . # ?cds ?p ?o . ?gene ?p2 ?o2 . } limit 100' </pre> in OWLIM (w/ predicate paths) <pre> % export SPARQL_ENDPOINT="http://lod.dbcls.jp/openrdf-sesame/repositories/togogenome" % sparql.rb query ' prefix obo: <http://purl.obolibrary.org/obo/> prefix faldo: <http://biohackathon.org/resource/faldo#> prefix insdc: <http://rdf.insdc.org/> select * where { ?seq rdfs:seeAlso <http://identifiers.org/taxonomy/1148> . ?s obo:so_part_of+ ?seq . ?s a obo:SO_0000316 . ?s rdfs:label "slr1311" . ?s ?p ?o . } ' seq s p o <urn:uuid:182f171a-7928-4324-8d41-f3e820a872fd> <urn:uuid:aaf399d2-f84a-4feb-a689-966311a3b116> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://purl.obolibrary.org/obo/SO_0000316> <urn:uuid:182f171a-7928-4324-8d41-f3e820a872fd> <urn:uuid:aaf399d2-f84a-4feb-a689-966311a3b116> <http://biohackathon.org/resource/faldo#location> <urn:uuid:3114165b-ffee-4816-b9bf-811dbbcb9b06> <urn:uuid:182f171a-7928-4324-8d41-f3e820a872fd> <urn:uuid:aaf399d2-f84a-4feb-a689-966311a3b116> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://identifiers.org/ncbigene/951890> <urn:uuid:182f171a-7928-4324-8d41-f3e820a872fd> <urn:uuid:aaf399d2-f84a-4feb-a689-966311a3b116> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://identifiers.org/ncbigi/16329178> <urn:uuid:182f171a-7928-4324-8d41-f3e820a872fd> <urn:uuid:aaf399d2-f84a-4feb-a689-966311a3b116> <http://www.w3.org/2000/01/rdf-schema#seeAlso> <http://identifiers.org/ncbiprotein/NP_439906.1> <urn:uuid:182f171a-7928-4324-8d41-f3e820a872fd> <urn:uuid:aaf399d2-f84a-4feb-a689-966311a3b116> <http://www.w3.org/2000/01/rdf-schema#label> slr1311 <urn:uuid:182f171a-7928-4324-8d41-f3e820a872fd> <urn:uuid:aaf399d2-f84a-4feb-a689-966311a3b116> <http://rdf.insdc.org/feature_gene> psbA2 <urn:uuid:182f171a-7928-4324-8d41-f3e820a872fd> <urn:uuid:aaf399d2-f84a-4feb-a689-966311a3b116> <http://rdf.insdc.org/feature_locus_tag> slr1311 <urn:uuid:182f171a-7928-4324-8d41-f3e820a872fd> <urn:uuid:aaf399d2-f84a-4feb-a689-966311a3b116> <http://purl.obolibrary.org/obo/so_part_of> <urn:uuid:8683a33d-e496-43da-a4ce-a454faeb228c> <urn:uuid:182f171a-7928-4324-8d41-f3e820a872fd> <urn:uuid:aaf399d2-f84a-4feb-a689-966311a3b116> <http://rdf.insdc.org/feature_translation> MTTTLQQRESASLWEQFCQWVTSTNNRIYVGWFGTLMIPTLLTATTCFIIAFIAAPPVDIDGIREPVAGSLLYGNNIISGAVVPSSNAIGLHFYPIWEAASLDEWLYNGGPYQLVVFHFLIGIFCYMGRQWELSYRLGMRPWICVAYSAPVSAATAVFLIYPIGQGSFSDGMPLGISGTFNFMIVFQAEHNILMHPFHMLGVAGVFGGSLFSAMHGSLVTSSLVRETTEVESQNYGYKFGQEEETYNIVAAHGYFGRLIFQYASFNNSRSLHFFLGAWPVIGIWFTAMGVSTMAFNLNGFNFNQSILDSQGRVIGTWADVLNRANIGFEVMHERNAHNFPLDLASGEQAPVALTAPAVNG <urn:uuid:182f171a-7928-4324-8d41-f3e820a872fd> <urn:uuid:aaf399d2-f84a-4feb-a689-966311a3b116> <http://purl.obolibrary.org/obo/so_has_part> node9 <urn:uuid:182f171a-7928-4324-8d41-f3e820a872fd> <urn:uuid:aaf399d2-f84a-4feb-a689-966311a3b116> <http://rdf.insdc.org/feature_codon_start> 1 <urn:uuid:182f171a-7928-4324-8d41-f3e820a872fd> <urn:uuid:aaf399d2-f84a-4feb-a689-966311a3b116> <http://rdf.insdc.org/feature_transl_table> 11 <urn:uuid:182f171a-7928-4324-8d41-f3e820a872fd> <urn:uuid:aaf399d2-f84a-4feb-a689-966311a3b116> <http://rdf.insdc.org/feature_product> photosystem II D1 protein </pre> <pre> % sparql.rb query ' select * where { <http://identifiers.org/ncbiprotein/NP_439906.1> ?p ?o . }' p o <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://rdf.insdc.org/Protein> <http://www.w3.org/2000/01/rdf-schema#label> Protein:NP_439906.1 </pre> in UniProt (P16033.ttl) <pre> <http://purl.uniprot.org/refseq/NP_439906.1> :database <http://purl.uniprot.org/database/RefSeq> ; a :Resource ; rdfs:comment "NC_000911.1" . </pre> <pre> <http://purl.uniprot.org/uniprot/P16033> :alternativeName <http://purl.uniprot.org/SHA-384/63DA65DE404AF09310FCB840EDB66B43F33A99437BE6B168EAA56CB750697BD770D0AF1352224737D950375500334306>, <http://purl.uniprot.org/SHA-384/EAD38724FC2B221349C148590947FAC022608F9163892 A8655BADDABAED4C601851DBB74C938735F74B87EF124B1360F> ; :annotation <http://purl.uniprot.org/SHA-384/0A12089C8DC290CBBD8D8103B12CEB67A4E6D0C2A7EDB14E2526E07E6C19A0D8E7136E5980D425920C5592597C839D1C>, <http://purl.uniprot.org/SHA-384/38793A73EC12E67AE573E8D2AFA1C5103C22D40D6A6BF9932A 6B44C0E58BA2D1BAB3AFA7B90690213AD739E0333AEA99>, <http://purl.uniprot.org/SHA-384/3D4275B11E23026B6EF0BE4CA7C603B256C2C8561EA924F27B61086765DD71154A8A25933F28502973394A8BFEAD15FA>, <http://purl.uniprot.org/SHA-384/3E9A71260346FD57F 7B9329143014B76A05C3B0ECE448D7BA2C7C58144C48C4C1C0B95B4B110272E5D0473DD9F0C506B>, <http://purl.uniprot.org/SHA-384/45985780EEA20147BA2739E59E023F00FF07A031FF00B7A0714D4C6F5028C96225F04CB0AC407CDA585F36D5FBE08A49>, <http://purl.unip rot.org/SHA-384/4BA37B67329EB5CA13971C6B80B63177B08707C016E85FECAD16D920A3A78551B339401DD16EB987C6F2ADA53F96790D>, <http://purl.uniprot.org/SHA-384/4BA6E00208715C9F97005D140C55724519E59F4D003F6AA12EEBFF476B441453F38B8A189CC04FB9475 B99B212016071>, <http://purl.uniprot.org/SHA-384/4EF0E156B484A48AB5218FAD0B1A9C13A6025EA158E5C040FB8D2784A92CBE85B98BEB81E81CD0791B0F52C91DCC582F>, <http://purl.uniprot.org/SHA-384/544178BF8F549741F1E6D37A8D6C136EC7A8904549747CD8C0 7AC4685BCE363F295FE2A7465ACBD490842C4E796DD070>, <http://purl.uniprot.org/SHA-384/6053A5ADB44A67383A68345CCE74A13BE6B7D36CF58FAC445E84E9848833A873AA81CC36361300FBC24F05827DFAC423>, <http://purl.uniprot.org/SHA-384/6A5872379CA70C029 A451EAD2C53B87C9F6EACCC8FAB4B4A394CD0BA8E7415680D5EBA00C9187BAB64E35B9632DEE4F7>, <http://purl.uniprot.org/SHA-384/75BF329FEE3F451FF77AF5A3803F6D29B261FD591ABF4E07B293FEE7CDD018DB9C85536E068C228AB350DE6D139885D8>, <http://purl.unip rot.org/SHA-384/85C78400E36858ADC0071231FD8A6709C38BF701671845B6CE0F5C45072CF26768E232486B9B03447192F854FDC7A1DB>, <http://purl.uniprot.org/SHA-384/87F9AA3AA9878DF4C4FA702DCA7D6F1EB446807D4671341993D8D5AD314D5B9070951C4A35FCDEB2E17 274BC5DB8F146>, <http://purl.uniprot.org/SHA-384/9B01722321188DB4D6BBAEF28AF09A62F521F68D6D582732A40BAFBF2655E270E79B05021F8505FC834C3ADBEB651E84>, <http://purl.uniprot.org/SHA-384/A3D9739FD7880EA11D08891C9C7C7F7DB81A75F5A841C2411F 1604269DC66845DAE6896B16890981E0D063B6B0790018>, <http://purl.uniprot.org/SHA-384/AFD4449E781236F710E3EE1DE22FA44E7CC6048DB880064D069D4357AE91AE8165ECD5437DAF4CB13C51ED3FD014D647>, <http://purl.uniprot.org/SHA-384/B5DF4D8C0FCF36A77 E232288948A178235B0A6BC4CB7321156210ABA4DDB093524BC71D117B96A46A49FD7B2533BA13C>, <http://purl.uniprot.org/SHA-384/CA8CEE0DF4CC11BF7B206AB2744628FD475856E4AF7F456DEEC61A941A8040A6ED92DAA23FB417268E7C583C34BEE3B1>, <http://purl.unip rot.org/SHA-384/E88D7DCCE1290A2CF157170747A81E75132EA0584A0A84FD066D480F8BFCE8439A118C05C8C81DBBC4134D7FE47DB70C>, <http://purl.uniprot.org/SHA-384/EA46197EDC149F2C44230CCA8CD64D18C45903399D17A5413D3CAAB1F669BAF1C5256D54CB7832E6734 07065325213B7>, <http://purl.uniprot.org/SHA-384/EC6B9B2DD6E9B53D60CFF23C106C370CC16BC354AA5F1EBB9EE08D1A0C22B0338B794E7E14D65E9CDED5B4342E86D2CB>, <http://purl.uniprot.org/SHA-384/F941CD576798E06F86C2E10F0F65517031010C14B9F0021A5C B96E45ABD9DC6D80FAD0498772BAE34F6D2ED257C12D93>, <http://purl.uniprot.org/SHA-384/FCE2EE65D2F3B1104A46D8054D58B795F1FC5944B8189D0C041F8B3D2A2EB2F535216DCFA4AD9E67591F8F23A79318CB>, <http://purl.uniprot.org/annotation/PRO_0000090493 >, <http://purl.uniprot.org/annotation/PRO_0000316429> ; :attribution <file:///Users/ktym/P16033.rdf#_5031363033330015>, <file:///Users/ktym/P16033.rdf#_503136303333004F>, <file:///Users/ktym/P16033.rdf#_5031363033330051>, <file:///Users/ktym/P16033.rdf#_5031363033330053>, <file:///U sers/ktym/P16033.rdf#_5031363033330054>, <file:///Users/ktym/P16033.rdf#_5031363033330056>, <file:///Users/ktym/P16033.rdf#_5031363033330058>, <file:///Users/ktym/P16033.rdf#_503136303333005A>, <file:///Users/ktym/P16033.rdf#_50313 6303333005C>, <file:///Users/ktym/P16033.rdf#_503136303333005E>, <file:///Users/ktym/P16033.rdf#_5031363033330060> ; :citation <http://purl.uniprot.org/citations/1498597>, <http://purl.uniprot.org/citations/2123543>, <http://purl.uniprot.org/citations/2499875>, <http://purl.uniprot.org/citations/8068689>, <http://purl.uniprot.org/citations/89 05231>, <http://purl.uniprot.org/citations/9512353> ; :classifiedWith <http://purl.uniprot.org/go/0009635>, <http://purl.uniprot.org/go/0009772>, <http://purl.uniprot.org/go/0016021>, <http://purl.uniprot.org/go/0016491>, <http://purl.uniprot.org/go/0030076>, <http://purl.uniprot. org/go/0030096>, <http://purl.uniprot.org/go/0042651>, <http://purl.uniprot.org/go/0045156>, <http://purl.uniprot.org/go/0046872>, <http://purl.uniprot.org/keywords/1133>, <http://purl.uniprot.org/keywords/1185>, <http://purl.unipr ot.org/keywords/249>, <http://purl.uniprot.org/keywords/359>, <http://purl.uniprot.org/keywords/408>, <http://purl.uniprot.org/keywords/479>, <http://purl.uniprot.org/keywords/560>, <http://purl.uniprot.org/keywords/604>, <http://p url.uniprot.org/keywords/793> ; :created "1990-04-01"^^<http://www.w3.org/2001/XMLSchema#date> ; :encodedBy <file:///Users/ktym/P16033.rdf#_5031363033330011>, <file:///Users/ktym/P16033.rdf#_5031363033330012> ; :enzyme <http://purl.uniprot.org/enzyme/1.10.3.9> ; :existence :Evidence_at_Protein_Level_Existence ; :mnemonic "PSBA2_SYNY3" ; :modified "2012-11-28"^^<http://www.w3.org/2001/XMLSchema#date> ; :oldMnemonic "PSB2_SYNY3" ; :organism <http://purl.uniprot.org/taxonomy/1111708> ; :recommendedName <http://purl.uniprot.org/SHA-384/6EE72299671F7B6AC21B0F83D7FD7531E50CE30DB2B45C3A58AB32A23D9CEB01EEF80F689B5BBADF6A9579BB420C5123> ; :reviewed true ; :sequence <http://purl.uniprot.org/isoforms/P16033-1> ; :version "111"^^<http://www.w3.org/2001/XMLSchema#int> ; a :Protein ; rdfs:seeAlso <http://purl.uniprot.org/eggnog/NOG04871>, <http://purl.uniprot.org/embl-cds/BAA16586.1>, <http://purl.uniprot.org/embl-cds/BAA18230.1>, <http://purl.uniprot.org/embl-cds/CAA31899.1>, <http://purl.uniprot.org/embl- cds/CAA39472.1>, <http://purl.uniprot.org/gene3d/1.20.85.10>, <http://purl.uniprot.org/geneid/12254260>, <http://purl.uniprot.org/geneid/12255303>, <http://purl.uniprot.org/geneid/951890>, <http://purl.uniprot.org/geneid/953105>, < http://purl.uniprot.org/genomereviews/BA000022_GR>, <http://purl.uniprot.org/hamap/MF_01379>, <http://purl.uniprot.org/hogenom/HOG000246913>, <http://purl.uniprot.org/intact/P16033>, <http://purl.uniprot.org/interpro/IPR000484>, <h ttp://purl.uniprot.org/interpro/IPR005867>, <http://purl.uniprot.org/kegg/syn:sll1867>, <http://purl.uniprot.org/kegg/syn:slr1311>, <http://purl.uniprot.org/kegg/syy:SYNGTS_0008>, <http://purl.uniprot.org/kegg/syy:SYNGTS_1655>, <ht tp://purl.uniprot.org/ko/K02703>, <http://purl.uniprot.org/oma/CFTIAFI>, <http://purl.uniprot.org/patric/23836870>, <http://purl.uniprot.org/pfam/PF00124>, <http://purl.uniprot.org/pir/F2YB16>, <http://purl.uniprot.org/prints/PR002 56>, <http://purl.uniprot.org/prosite/PS00244>, <http://purl.uniprot.org/protclustdb/CLSK892431>, <http://purl.uniprot.org/proteinmodelportal/P16033>, <http://purl.uniprot.org/refseq/NP_439906.1>, <http://purl.uniprot.org/refseq/NP _441550.1>, <http://purl.uniprot.org/refseq/YP_005649961.1>, <http://purl.uniprot.org/refseq/YP_005651608.1>, <http://purl.uniprot.org/smr/P16033>, <http://purl.uniprot.org/string/P16033>, <http://purl.uniprot.org/supfam/SSF81483>, <http://purl.uniprot.org/tcdb/3.E.2.2.2>, <http://purl.uniprot.org/tigrfams/TIGR01151> . </pre> add some links between Identifiers.org and UniProt <pre> % cut -f 3 wget_prokaryotes.v5.ttl | grep ncbiprotein | perl -pe 's/ .*//' | perl -pe 's|(.._.*)>|$1> rdfs:seeAlso <http://purl.uniprot.org/refseq/$1> .|' > wget_prokaryotes.v5.rs-up.ttl : <http://identifiers.org/ncbiprotein/NP_439906.1> rdfs:seeAlso <http://purl.uniprot.org/refseq/NP_439906.1> . : % wc wget_prokaryotes.v5.rs-up.ttl 6485705 25942820 738098573 wget_prokaryotes.v5.rs-up.ttl </pre> == Notes == <pre> % sparql.rb query ' prefix obo: <http://purl.obolibrary.org/obo/> prefix faldo: <http://biohackathon.org/resource/faldo#> prefix insdc: <http://rdf.insdc.org/> prefix up: <http://purl.uniprot.org/core/> prefix tax: <http://purl.uniprot.org/taxonomy/> select count(?cds) as ?num_cds count(?gene) as ?num_genes from <http://v5.genome.db/> where { ?seq rdfs:seeAlso <http://identifiers.org/taxonomy/1148> . ?gene obo:so_part_of ?seq . ?cds obo:so_part_of ?gene . ?cds a obo:SO_0000316 . # CDS }' num_cds num_genes 6745 6745 </pre> <pre> % sparql.rb query ' prefix obo: <http://purl.obolibrary.org/obo/> prefix faldo: <http://biohackathon.org/resource/faldo#> prefix insdc: <http://rdf.insdc.org/> prefix up: <http://purl.uniprot.org/core/> prefix tax: <http://purl.uniprot.org/taxonomy/> select ?cds ?label from <http://v5.genome.db/> where { ?seq rdfs:seeAlso <http://identifiers.org/taxonomy/1148> . ?gene obo:so_part_of ?seq . ?cds obo:so_part_of ?gene . ?cds a obo:SO_0000316 . # CDS ?cds rdfs:label ?label . } limit 10' cds label <urn:uuid:c73b48d2-e65a-43c5-86e1-26945386b6b4> sll5004 <urn:uuid:24ecccd5-bf11-48d0-948f-9bd89f370a91> slr5005 <urn:uuid:52ca1690-60ce-477f-bfe2-022de04c167a> sll5006 <urn:uuid:e551fa78-b90c-435f-b528-9a8b5bac8296> ssl5007 <urn:uuid:fa2a53e8-a500-4b8b-b7ab-5e0623cd72e5> ssl5008 <urn:uuid:125a0827-d81d-47c7-b13b-506cd49e2989> ssr5009 <urn:uuid:ce6e08ac-adbf-429b-a057-2a4284d3e1cd> ssr5011 <urn:uuid:c24d24cd-5a0d-499f-b899-a31415dc9d6b> sll5014 <urn:uuid:e03852ac-57d9-4d6b-b995-0b0ffa33e163> ssl5015 <urn:uuid:6cc65822-e4b1-40a4-82ac-df2d9cc24775> ssr5019 </pre> <pre> % sparql.rb query ' prefix obo: <http://purl.obolibrary.org/obo/> prefix faldo: <http://biohackathon.org/resource/faldo#> prefix insdc: <http://rdf.insdc.org/> prefix up: <http://purl.uniprot.org/core/> prefix tax: <http://purl.uniprot.org/taxonomy/> select ?cds ?l ?b ?e from <http://v5.genome.db/> where { ?seq rdfs:seeAlso <http://identifiers.org/taxonomy/1148> . ?gene obo:so_part_of ?seq . ?cds obo:so_part_of ?gene . ?cds a obo:SO_0000316 . # CDS ?cds rdfs:label "slr1311" . ?cds faldo:location ?location . ?location insdc:location_string ?l . ?location faldo:begin ?begin . ?location faldo:end ?end . ?begin faldo:position ?b . ?end faldo:position ?e . } limit 100' cds l b e <urn:uuid:aaf399d2-f84a-4feb-a689-966311a3b116> 7229..8311 7229 8311 </pre> <pre> % sparql.rb query ' prefix obo: <http://purl.obolibrary.org/obo/> prefix faldo: <http://biohackathon.org/resource/faldo#> prefix insdc: <http://rdf.insdc.org/> prefix up: <http://purl.uniprot.org/core/> prefix tax: <http://purl.uniprot.org/taxonomy/> select ?label ?l ?b ?e from <http://v5.genome.db/> where { ?seq rdfs:seeAlso <http://identifiers.org/taxonomy/1148> . ?gene obo:so_part_of ?seq . ?cds obo:so_part_of ?gene . ?cds a obo:SO_0000316 . # CDS ?cds rdfs:label ?label . ?cds faldo:location ?location . ?location insdc:location_string ?l . ?location faldo:begin ?begin . ?location faldo:end ?end . ?begin faldo:position ?b . ?end faldo:position ?e . } limit 10' label l b e ssl5001 complement(195..374) 195 374 sll5002 complement(574..921) 574 921 sll5003 complement(1136..1540) 1136 1540 slr5005 2528..13921 2528 13921 sll5006 complement(14579..15133) 14579 15133 ssl5008 complement(15639..15812) 15639 15812 slr5012 17880..18800 17880 18800 slr5013 18822..20513 18822 20513 sll5014 complement(20523..21479) 20523 21479 ssr5020 24181..24462 24181 24462 </pre> <pre> % sparql.rb query ' prefix obo: <http://purl.obolibrary.org/obo/> prefix faldo: <http://biohackathon.org/resource/faldo#> prefix insdc: <http://rdf.insdc.org/> prefix up: <http://purl.uniprot.org/core/> prefix tax: <http://purl.uniprot.org/taxonomy/> select ?label ?l ?b ?e from <http://v5.genome.db/> where { ?seq rdfs:seeAlso <http://identifiers.org/taxonomy/1148> . ?gene obo:so_part_of ?seq . ?cds obo:so_part_of ?gene . ?cds a obo:SO_0000316 . # CDS ?cds rdfs:label ?label . ?cds faldo:location ?location . ?location insdc:location_string ?l . ?location faldo:begin ?begin . ?location faldo:end ?end . ?begin faldo:position ?b . ?end faldo:position ?e . filter (?b > 10000 && ?e < 20000) } limit 100' label l b e sll5006 complement(14579..15133) 14579 15133 ssl5008 complement(15639..15812) 15639 15812 slr5012 17880..18800 17880 18800 slr7012 11524..12513 11524 12513 slr7013 12674..13438 12674 13438 ssl7021 complement(19594..19779) 19594 19779 slr8016 10998..11867 10998 11867 sll8017 complement(12618..13151) 12618 13151 sll8019 complement(15590..17317) 15590 17317 slr8021 18529..19311 18529 19311 slr8022 19356..19691 19356 19691 : </pre> [[Category:TogoStanza]]

BH12.12/TogoStanzaに戻る。