BH12.12/TogoStanza

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[[Category:TogoStanza]]

2013年8月21日 (水) 10:45時点における最新版

目次

TogoStanza

UniProt 

% 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

RefSeq 

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"

TogoGenome 

% less wget_prokaryotes/PRJNA57659/NC_000911.1

% less wget_prokaryotes.v5/PRJNA57659/NC_000911.1.ttl

in Virtuoso (w/o predicate paths) 

% 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'

in OWLIM (w/ predicate paths) 

% 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

% 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

in UniProt (P16033.ttl) 

<http://purl.uniprot.org/refseq/NP_439906.1>
    :database <http://purl.uniprot.org/database/RefSeq> ;
    a :Resource ;
    rdfs:comment "NC_000911.1" .

<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> .

add some links between Identifiers.org and UniProt 

% 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

Notes 

% 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

% 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

% 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

% 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

% 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
  :
「/mw/BH12.12/TogoStanza」より作成