SPARQLthon38/GenomeRDF
提供：TogoWiki
（版間での差分）
(→サンプルデータ) |
(→Turtle形式（insdc2ttl.rb由来）) |
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| 880行： | 880行： | ||
</pre> | </pre> | ||
| - | === | + | === Turtle形式（using insdc2ttl.rb） === |
<pre> | <pre> | ||
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . | @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . | ||
2015年11月12日 (木) 03:06時点における最新版
RefSeq以外のゲノムアノテーションをRDF形式変換を目的としたbiointerchangeのRDFデータモデルとGFVOの利用について調査
目次 |
GFVOマッピング情報
- GFVO mapping http://www.biointerchange.org/ontologies.html#mappings
- 第一回RDFサミットの時の資料 → https://docs.google.com/spreadsheets/d/1y5Xzl9ak7eePX9NUwbULk55BU9vzTAawbRmiwEbaeCo/edit#gid=146873136
Biointerchange 1.0でRDFに変換
%gem install biointerchange Fetching: biointerchange-1.0.8.gem (100%) Successfully installed biointerchange-1.0.8 Parsing documentation for biointerchange-1.0.8 Installing ri documentation for biointerchange-1.0.8 Done installing documentation for biointerchange after 15 seconds 1 gem installed %/Users/tf/.rbenv/shims/biointerchange --input biointerchange.gff3 --rdf rdf.biointerchange.gfvo --file NC_000911.gb.gff > NC_000911.gb.gff.biointerchange1.ttl
Biointerchange 2.0でRDFに変換
biointerchange2.0を試用してGFF3をRDFに変換する (GeneBank→）GFF3→ JSON-LD → RDF
- GenBank → GFF3
bp_genbank2gff3.pl NC_000911.gb
- GFF3→ JSON-LD (Line Delimited JSON-LD)
%biointerchange -v 2.0.4+105 %biointerchange -o NC_000911.gb.gff.ldj NC_000911.gb.gff
- JSON-LD → Turtle
to_turtle.rb NC_000911.gb.gff.ldj > NC_000911.gb.gff.ttl
#!/usr/bin/env ruby
require 'rubygems'
require 'json'
require 'json/ld'
jsonld = "./NC_000911.gb.gff.ldj"
graph = RDF::Graph.new
i = 0
File.open(jsonld).each do |line|
input = JSON.parse line
#JSON::LD::API.toRDF(input){|st| p st}
graph << JSON::LD::API.toRdf(input)
end
require 'rdf/turtle'
puts graph.dump(:ttl, :prefixes => {:gfvosquared => "https://www.codamono.com/gfvo-squared#"})
サンプルデータ
GenBank形式
LOCUS NC_000911 3573470 bp DNA circular CON 17-AUG-2015
DEFINITION Synechocystis sp. PCC 6803 DNA, complete genome.
ACCESSION NC_000911 NZ_AB001339 NZ_D63999-NZ_D64006 NZ_D90899-NZ_D90917
VERSION NC_000911.1 GI:16329170
DBLINK BioProject: PRJNA224116
Assembly: GCF_000009725.1
KEYWORDS RefSeq.
SOURCE Synechocystis sp. PCC 6803
ORGANISM Synechocystis sp. PCC 6803
Bacteria; Cyanobacteria; Oscillatoriophycideae; Chroococcales;
Synechocystis.
REFERENCE 1
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 2
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 3 (bases 1 to 3573470)
AUTHORS Tabata,S.
TITLE Direct Submission
JOURNAL Submitted (03-JUL-2001) Contact:Satoshi Tabata Kazusa DNA Research
Institute, The First Laboratory for Plant Gene Research; Yana
1532-3, Kisarazu, Chiba 292-0812, Japan URL
:http://www.kazusa.or.jp/cyano/
COMMENT REFSEQ INFORMATION: The reference sequence was derived from
BA000022.
Potential protein coding regions were assigned on the basis of
similarity search of the ORFs and GeneMark analysis.
Annotation was added by the NCBI Prokaryotic Genome Annotation
Pipeline (released 2013). Information about the Pipeline can be
found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/
##Genome-Annotation-Data-START##
Annotation Provider :: NCBI
Annotation Date :: 08/17/2015 19:20:20
Annotation Pipeline :: NCBI Prokaryotic Genome
Annotation Pipeline
Annotation Method :: Best-placed reference
protein set; GeneMarkS+
Annotation Software revision :: 3.0
Features Annotated :: Gene; CDS; rRNA; tRNA;
ncRNA; repeat_region
Genes :: 3,673
CDS :: 3,602
Pseudo Genes :: 23
CRISPR Arrays :: 3
rRNAs :: 2, 2, 2 (5S, 16S, 23S)
complete rRNAs :: 2, 2, 2 (5S, 16S, 23S)
tRNAs :: 41
ncRNA :: 1
Frameshifted Genes :: 13
Frameshifted Genes On Monomer Runs :: 3
Frameshifted Genes Not On Monomer Runs :: 2
##Genome-Annotation-Data-END##
COMPLETENESS: full length.
FEATURES Location/Qualifiers
source 1..3573470
/organism="Synechocystis sp. PCC 6803"
/mol_type="genomic DNA"
/db_xref="taxon:1148"
gene join(3573271..3573470,1..772)
/locus_tag="SGL_RS01875"
/old_locus_tag="slr0611"
CDS join(3573271..3573470,1..772)
/locus_tag="SGL_RS01875"
/old_locus_tag="slr0611"
/inference="EXISTENCE: similar to AA
sequence:SwissProt:P72580.2"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="Prenyl transferase"
/protein_id="WP_010871207.1"
/db_xref="GI:499173620"
gene 937..1494
/locus_tag="SGL_RS01880"
/old_locus_tag="slr0612"
CDS 937..1494
/locus_tag="SGL_RS01880"
/old_locus_tag="slr0612"
/inference="EXISTENCE: similar to AA
sequence:RefSeq:WP_010871208.1"
/note="Uncharacterized RNA pseudouridine synthase slr0612;
Derived by automated computational analysis using gene
prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="WP_010871208.1"
/db_xref="GI:499173621"
GFF3形式
##gff-version 3 # sequence-region NC_000911 1 3573470 # conversion-by bp_genbank2gff3.pl # organism Synechocystis sp. PCC 6803 # date 17-AUG-2015 # Note Synechocystis sp. PCC 6803 DNA, complete genome. NC_000911 GenBank region 1 3573470 . + 1 ID=NC_000911;Dbxref=GenBank:GCF_000009725.1,taxon:1148;Name=NC_000911;Note=Synechocystis sp. PCC 6803 DNA%2C complete genome.,REFSEQ INFORMATION: The reference sequence was derived from BA000022. Potential protein coding regions were assigned on the basis of similarity search of the ORFs and GeneMark analysis. Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/ ##Genome-Annotation-Data-START## Annotation Provider :: NCBI Annotation Date :: 08/17/2015 19:20:20 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline Annotation Method :: Best-placed reference protein set,GeneMarkS+ Annotation Software revision :: 3.0 Features Annotated :: Gene,CDS,rRNA,tRNA,ncRNA,repeat_region Genes :: 3,673 CDS :: 3,602 Pseudo Genes :: 23 CRISPR Arrays :: 3 rRNAs :: 2,2,2 (5S,16S,23S) complete rRNAs :: 2,2,2 (5S,16S,23S) tRNAs :: 41 ncRNA :: 1 Frameshifted Genes :: 13 Frameshifted Genes On Monomer Runs :: 3 Frameshifted Genes Not On Monomer Runs :: 2 ##Genome-Annotation-Data-END## COMPLETENESS: full length. ;comment1=REFSEQ INFORMATION: The reference sequence was derived from BA000022. Potential protein coding regions were assigned on the basis of similarity search of the ORFs and GeneMark analysis. Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/ ##Genome-Annotation-Data-START## Annotation Provider :: NCBI Annotation Date :: 08/17/2015 19:20:20 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline Annotation Method :: Best-placed reference protein set%3B GeneMarkS+ Annotation Software revision :: 3.0 Features Annotated :: Gene%3B CDS%3B rRNA%3B tRNA%3B ncRNA%3B repeat_region Genes :: 3%2C673 CDS :: 3%2C602 Pseudo Genes :: 23 CRISPR Arrays :: 3 rRNAs :: 2%2C 2%2C 2 (5S%2C 16S%2C 23S) complete rRNAs :: 2%2C 2%2C 2 (5S%2C 16S%2C 23S) tRNAs :: 41 ncRNA :: 1 Frameshifted Genes :: 13 Frameshifted Genes On Monomer Runs :: 3 Frameshifted Genes Not On Monomer Runs :: 2 ##Genome-Annotation-Data-END## COMPLETENESS: full length. ;date=17-AUG-2015;mol_type=genomic DNA;organism=Synechocystis sp. PCC 6803 NC_000911 GenBank gene 3573271 3573470 . + 1 ID=SGL_RS01875;Name=SGL_RS01875;old_locus_tag=slr0611 NC_000911 GenBank gene 1 772 . + 1 ID=SGL_RS01875;Name=SGL_RS01875;old_locus_tag=slr0611 NC_000911 GenBank mRNA 1 3573470 . + 1 ID=SGL_RS01875.t01;Parent=SGL_RS01875 NC_000911 GenBank CDS 3573271 3573470 . + 1 ID=SGL_RS01875.p01;Parent=SGL_RS01875.t01;Dbxref=GI:499173620;Name=SGL_RS01875;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=EXISTENCE: similar to AA sequence:SwissProt:P72580.2;old_locus_tag=slr0611;product=Prenyl transferase;protein_id=WP_010871207.1;transl_table=11 NC_000911 GenBank CDS 1 772 . + 1 ID=SGL_RS01875.p01;Parent=SGL_RS01875.t01;Dbxref=GI:499173620;Name=SGL_RS01875;Note=Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=EXISTENCE: similar to AA sequence:SwissProt:P72580.2;old_locus_tag=slr0611;product=Prenyl transferase;protein_id=WP_010871207.1;transl_table=11 NC_000911 GenBank exon 3573271 3573470 . + 1 Parent=SGL_RS01875.t01 NC_000911 GenBank exon 1 772 . + 1 Parent=SGL_RS01875.t01 NC_000911 GenBank gene 937 1494 . + 1 ID=SGL_RS01880;Name=SGL_RS01880;old_locus_tag=slr0612 NC_000911 GenBank mRNA 937 1494 . + 1 ID=SGL_RS01880.t01;Parent=SGL_RS01880 NC_000911 GenBank CDS 937 1494 . + 1 ID=SGL_RS01880.p01;Parent=SGL_RS01880.t01;Dbxref=GI:499173621;Name=SGL_RS01880;Note=Uncharacterized RNA pseudouridine synthase slr0612%3B Derived by automated computational analysis using gene prediction method: Protein Homology.;codon_start=1;inference=EXISTENCE: similar to AA sequence:RefSeq:WP_010871208.1;old_locus_tag=slr0612;product=hypothetical protein;protein_id=WP_010871208.1;transl_table=11
JSON-LD形式
{"@context":"https://www.codamono.com/jsonld/gff3-c1.json","@type":"https://www.codamono.com/gfvo-squared#Context","biointerchange-version":"2.0.4+105","input-file":"NC_000911.gb.gff","output-file":"NC_000911.gb.gff.ldj","input-filetype":"GFF3","user-parameter":null,"python-callback":null}
{"@context":"https://www.codamono.com/jsonld/gff3-x1.json","@type":"https://www.codamono.com/gfvo-squared#Meta","gff-version":"3"}
{"@context":"https://www.codamono.com/jsonld/gff3-f1.json","@type":"https://www.codamono.com/gfvo-squared#Feature","comment":"sequence-region NC_000911 1 3573470\nconversion-by bp_genbank2gff3.pl\norganism Synechocystis sp. PCC 6803\ndate 17-AUG-2015\nNote Synechocystis sp. PCC 6803 DNA, complete genome.","id":"NC_000911","name":"NC_000911","note":"Synechocystis sp. PCC 6803 DNA%2C complete genome.,REFSEQ INFORMATION: The reference sequence was derived from BA000022. Potential protein coding regions were assigned on the basis of similarity search of the ORFs and GeneMark analysis. Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/ ##Genome-Annotation-Data-START## Annotation Provider :: NCBI Annotation Date :: 08/17/2015 19:20:20 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline Annotation Method :: Best-placed reference protein set,GeneMarkS+ Annotation Software revision :: 3.0 Features Annotated :: Gene,CDS,rRNA,tRNA,ncRNA,repeat_region Genes :: 3,673 CDS :: 3,602 Pseudo Genes :: 23 CRISPR Arrays :: 3 rRNAs :: 2,2,2 (5S,16S,23S) complete rRNAs :: 2,2,2 (5S,16S,23S) tRNAs :: 41 ncRNA :: 1 Frameshifted Genes :: 13 Frameshifted Genes On Monomer Runs :: 3 Frameshifted Genes Not On Monomer Runs :: 2 ##Genome-Annotation-Data-END## COMPLETENESS: full length. ","source":"GenBank","type":"region","score":null,"codon-phase":1,"dbxref":["GenBank:GCF_000009725.1","taxon:1148"],"locus":{"landmark":"NC_000911","start":1,"end":3573470,"strand":"+"},"user-defined":{"comment1":"REFSEQ INFORMATION: The reference sequence was derived from BA000022. Potential protein coding regions were assigned on the basis of similarity search of the ORFs and GeneMark analysis. Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/ ##Genome-Annotation-Data-START## Annotation Provider :: NCBI Annotation Date :: 08/17/2015 19:20:20 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline Annotation Method :: Best-placed reference protein set%3B GeneMarkS+ Annotation Software revision :: 3.0 Features Annotated :: Gene%3B CDS%3B rRNA%3B tRNA%3B ncRNA%3B repeat_region Genes :: 3%2C673 CDS :: 3%2C602 Pseudo Genes :: 23 CRISPR Arrays :: 3 rRNAs :: 2%2C 2%2C 2 (5S%2C 16S%2C 23S) complete rRNAs :: 2%2C 2%2C 2 (5S%2C 16S%2C 23S) tRNAs :: 41 ncRNA :: 1 Frameshifted Genes :: 13 Frameshifted Genes On Monomer Runs :: 3 Frameshifted Genes Not On Monomer Runs :: 2 ##Genome-Annotation-Data-END## COMPLETENESS: full length. ","date":"17-AUG-2015","mol_type":"genomic DNA","organism":"Synechocystis sp. PCC 6803"}}
{"@context":"https://www.codamono.com/jsonld/gff3-f1.json","@type":"https://www.codamono.com/gfvo-squared#Feature","id":"SGL_RS01875","name":"SGL_RS01875","source":"GenBank","type":"gene","score":null,"codon-phase":1,"locus":{"landmark":"NC_000911","start":3573271,"end":3573470,"strand":"+"},"user-defined":{"old_locus_tag":"slr0611"}}
{"@context":"https://www.codamono.com/jsonld/gff3-f1.json","@type":"https://www.codamono.com/gfvo-squared#Feature","id":"SGL_RS01875","name":"SGL_RS01875","source":"GenBank","type":"gene","score":null,"codon-phase":1,"locus":{"landmark":"NC_000911","start":1,"end":772,"strand":"+"},"user-defined":{"old_locus_tag":"slr0611"}}
{"@context":"https://www.codamono.com/jsonld/gff3-f1.json","@type":"https://www.codamono.com/gfvo-squared#Feature","id":"SGL_RS01875.t01","source":"GenBank","type":"mRNA","score":null,"codon-phase":1,"parent":["SGL_RS01875"],"locus":{"landmark":"NC_000911","start":1,"end":3573470,"strand":"+"}}
{"@context":"https://www.codamono.com/jsonld/gff3-f1.json","@type":"https://www.codamono.com/gfvo-squared#Feature","id":"SGL_RS01875.p01","name":"SGL_RS01875","note":"Derived by automated computational analysis using gene prediction method: Protein Homology.","source":"GenBank","type":"CDS","score":null,"codon-phase":1,"parent":["SGL_RS01875.t01"],"dbxref":["GI:499173620"],"locus":{"landmark":"NC_000911","start":3573271,"end":3573470,"strand":"+"},"user-defined":{"codon_start":1,"inference":"EXISTENCE: similar to AA sequence:SwissProt:P72580.2","old_locus_tag":"slr0611","product":"Prenyl transferase","protein_id":"WP_010871207.1","transl_table":11}}
{"@context":"https://www.codamono.com/jsonld/gff3-f1.json","@type":"https://www.codamono.com/gfvo-squared#Feature","id":"SGL_RS01875.p01","name":"SGL_RS01875","note":"Derived by automated computational analysis using gene prediction method: Protein Homology.","source":"GenBank","type":"CDS","score":null,"codon-phase":1,"parent":["SGL_RS01875.t01"],"dbxref":["GI:499173620"],"locus":{"landmark":"NC_000911","start":1,"end":772,"strand":"+"},"user-defined":{"codon_start":1,"inference":"EXISTENCE: similar to AA sequence:SwissProt:P72580.2","old_locus_tag":"slr0611","product":"Prenyl transferase","protein_id":"WP_010871207.1","transl_table":11}}
{"@context":"https://www.codamono.com/jsonld/gff3-f1.json","@type":"https://www.codamono.com/gfvo-squared#Feature","source":"GenBank","type":"exon","score":null,"codon-phase":1,"parent":["SGL_RS01875.t01"],"locus":{"landmark":"NC_000911","start":3573271,"end":3573470,"strand":"+"}}
{"@context":"https://www.codamono.com/jsonld/gff3-f1.json","@type":"https://www.codamono.com/gfvo-squared#Feature","source":"GenBank","type":"exon","score":null,"codon-phase":1,"parent":["SGL_RS01875.t01"],"locus":{"landmark":"NC_000911","start":1,"end":772,"strand":"+"}}
{"@context":"https://www.codamono.com/jsonld/gff3-f1.json","@type":"https://www.codamono.com/gfvo-squared#Feature","id":"SGL_RS01880","name":"SGL_RS01880","source":"GenBank","type":"gene","score":null,"codon-phase":1,"locus":{"landmark":"NC_000911","start":937,"end":1494,"strand":"+"},"user-defined":{"old_locus_tag":"slr0612"}}
{"@context":"https://www.codamono.com/jsonld/gff3-f1.json","@type":"https://www.codamono.com/gfvo-squared#Feature","id":"SGL_RS01880.t01","source":"GenBank","type":"mRNA","score":null,"codon-phase":1,"parent":["SGL_RS01880"],"locus":{"landmark":"NC_000911","start":937,"end":1494,"strand":"+"}}
{"@context":"https://www.codamono.com/jsonld/gff3-f1.json","@type":"https://www.codamono.com/gfvo-squared#Feature","id":"SGL_RS01880.p01","name":"SGL_RS01880","note":"Uncharacterized RNA pseudouridine synthase slr0612%3B Derived by automated computational analysis using gene prediction method: Protein Homology.","source":"GenBank","type":"CDS","score":null,"codon-phase":1,"parent":["SGL_RS01880.t01"],"dbxref":["GI:499173621"],"locus":{"landmark":"NC_000911","start":937,"end":1494,"strand":"+"},"user-defined":{"codon_start":1,"inference":"EXISTENCE: similar to AA sequence:RefSeq:WP_010871208.1","old_locus_tag":"slr0612","product":"hypothetical protein","protein_id":"WP_010871208.1","transl_table":11}}
{"@context":"https://www.codamono.com/jsonld/gff3-f1.json","@type":"https://www.codamono.com/gfvo-squared#Feature","source":"GenBank","type":"exon","score":null,"codon-phase":1,"parent":["SGL_RS01880.t01"],"locus":{"landmark":"NC_000911","start":937,"end":1494,"strand":"+"}}
Turtle形式 (biointerchange1.0由来)
@prefix dc: <http://purl.org/dc/terms/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix faldo: <http://biohackathon.org/resource/faldo#> .
@prefix gfvo: <http://www.biointerchange.org/gfvo#> .
@prefix sio: <http://semanticscience.org/resource/> .
@base <biointerchange://gff3/featureset/self/ba2f6e614a28f25e528d249702161dc812ceb941/> .
<biointerchange://gff3/featureset/self/ba2f6e614a28f25e528d249702161dc812ceb941> a gfvo:File ;
gfvo:hasIdentifier <version> .
<version> a gfvo:Version ;
gfvo:hasValue "gff-version 3.0" .
<biointerchange://gff3/featureset/self/ba2f6e614a28f25e528d249702161dc812ceb941> gfvo:hasMember <feature/NC_000911> .
<feature/NC_000911> a gfvo:Feature ,
<http://purl.obolibrary.org/obo/SO_0000001> .
<landmark/NC_000911> a gfvo:Landmark ;
gfvo:hasIdentifier <landmark/NC_000911/id> .
<landmark/NC_000911/id> gfvo:hasValue "NC_000911" .
<landmark/NC_000911> gfvo:hasAttribute <landmark/NC_000911/region> .
<feature/NC_000911> gfvo:isLocatedOn <landmark/NC_000911> ;
gfvo:isCreatedBy <feature/NC_000911/source> .
<feature/NC_000911/source> a gfvo:ExperimentalMethod ;
gfvo:hasValue "GenBank" .
<feature/NC_000911> gfvo:hasQuality <feature/NC_000911/phase> .
<feature/NC_000911/phase> a gfvo:CodingFrameOffset ;
gfvo:hasValue 1 .
<feature/NC_000911> gfvo:hasPart <feature/NC_000911/locus> .
<feature/NC_000911/locus> a gfvo:Locus ;
gfvo:hasAttribute <feature/NC_000911/locus/region> ;
gfvo:isLocatedOn <feature/NC_000911/locus/region> .
<feature/NC_000911/locus/region> a faldo:Region ;
faldo:begin <feature/NC_000911/locus/region/start> .
<feature/NC_000911/locus/region/start> a faldo:ForwardStrandPosition ;
faldo:position 1 .
<feature/NC_000911/locus/region> faldo:end <feature/NC_000911/locus/region/end> .
<feature/NC_000911/locus/region/end> a faldo:ForwardStrandPosition .
<feature/NC_000911/locus/region/start> faldo:position 3573470 .
<feature/NC_000911> gfvo:hasIdentifier <feature/NC_000911/id> .
<feature/NC_000911/id> a gfvo:Identifier ;
gfvo:hasValue "NC_000911" .
<feature/NC_000911> gfvo:references <feature/NC_000911/dbxref/GenBank> .
<feature/NC_000911/dbxref/GenBank> a gfvo:ExternalReference .
<feature/NC_000911> gfvo:references <feature/NC_000911/attribute/dbxref/0> .
<feature/NC_000911/attribute/dbxref/0> a gfvo:ExternalReference ;
gfvo:hasValue "GenBank:GCF_000009725.1" .
<feature/NC_000911> gfvo:references <feature/NC_000911/dbxref/taxon> .
<feature/NC_000911/dbxref/taxon> a gfvo:ExternalReference .
<feature/NC_000911> gfvo:references <feature/NC_000911/attribute/dbxref/1> .
<feature/NC_000911/attribute/dbxref/1> a gfvo:ExternalReference ;
gfvo:hasValue "taxon:1148" .
<feature/NC_000911> gfvo:hasAttribute <feature/NC_000911/name> .
<feature/NC_000911/name> a gfvo:Name ;
gfvo:hasValue "NC_000911" .
<feature/NC_000911> gfvo:hasAnnotation <feature/NC_000911/note/0> .
<feature/NC_000911/note/0> a gfvo:Note ;
gfvo:hasValue "Synechocystis sp. PCC 6803 DNA, complete genome." .
<feature/NC_000911> gfvo:hasAnnotation <feature/NC_000911/note/1> .
<feature/NC_000911/note/1> a gfvo:Note ;
gfvo:hasValue "REFSEQ INFORMATION: The reference sequence was derived from BA000022. Potential protein coding regions were assigned on the basis of similarity search of the ORFs and GeneMark analysis. Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/ ##Genome-Annotation-Data-START## Annotation Provider :: NCBI Annotation Date :: 08/17/2015 19:20:20 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline Annotation Method :: Best-placed reference protein set" .
<feature/NC_000911> gfvo:hasAnnotation <feature/NC_000911/note/2> .
<feature/NC_000911/note/2> a gfvo:Note ;
gfvo:hasValue "GeneMarkS+ Annotation Software revision :: 3.0 Features Annotated :: Gene" .
<feature/NC_000911> gfvo:hasAnnotation <feature/NC_000911/note/3> .
<feature/NC_000911/note/3> a gfvo:Note ;
gfvo:hasValue "CDS" .
<feature/NC_000911> gfvo:hasAnnotation <feature/NC_000911/note/4> .
<feature/NC_000911/note/4> a gfvo:Note ;
gfvo:hasValue "rRNA" .
<feature/NC_000911> gfvo:hasAnnotation <feature/NC_000911/note/5> .
<feature/NC_000911/note/5> a gfvo:Note ;
gfvo:hasValue "tRNA" .
<feature/NC_000911> gfvo:hasAnnotation <feature/NC_000911/note/6> .
<feature/NC_000911/note/6> a gfvo:Note ;
gfvo:hasValue "ncRNA" .
<feature/NC_000911> gfvo:hasAnnotation <feature/NC_000911/note/7> .
<feature/NC_000911/note/7> a gfvo:Note ;
gfvo:hasValue "repeat_region Genes :: 3" .
<feature/NC_000911> gfvo:hasAnnotation <feature/NC_000911/note/8> .
<feature/NC_000911/note/8> a gfvo:Note ;
gfvo:hasValue "673 CDS :: 3" .
<feature/NC_000911> gfvo:hasAnnotation <feature/NC_000911/note/9> .
<feature/NC_000911/note/9> a gfvo:Note ;
gfvo:hasValue "602 Pseudo Genes :: 23 CRISPR Arrays :: 3 rRNAs :: 2" .
<feature/NC_000911> gfvo:hasAnnotation <feature/NC_000911/note/10> .
<feature/NC_000911/note/10> a gfvo:Note ;
gfvo:hasValue "2" .
<feature/NC_000911> gfvo:hasAnnotation <feature/NC_000911/note/11> .
<feature/NC_000911/note/11> a gfvo:Note ;
gfvo:hasValue "2 (5S" .
<feature/NC_000911> gfvo:hasAnnotation <feature/NC_000911/note/12> .
<feature/NC_000911/note/12> a gfvo:Note ;
gfvo:hasValue "16S" .
<feature/NC_000911> gfvo:hasAnnotation <feature/NC_000911/note/13> .
<feature/NC_000911/note/13> a gfvo:Note ;
gfvo:hasValue "23S) complete rRNAs :: 2" .
<feature/NC_000911> gfvo:hasAnnotation <feature/NC_000911/note/14> .
<feature/NC_000911/note/14> a gfvo:Note ;
gfvo:hasValue "2" .
<feature/NC_000911> gfvo:hasAnnotation <feature/NC_000911/note/15> .
<feature/NC_000911/note/15> a gfvo:Note ;
gfvo:hasValue "2 (5S" .
<feature/NC_000911> gfvo:hasAnnotation <feature/NC_000911/note/16> .
<feature/NC_000911/note/16> a gfvo:Note ;
gfvo:hasValue "16S" .
<feature/NC_000911> gfvo:hasAnnotation <feature/NC_000911/note/17> .
<feature/NC_000911/note/17> a gfvo:Note ;
gfvo:hasValue "23S) tRNAs :: 41 ncRNA :: 1 Frameshifted Genes :: 13 Frameshifted Genes On Monomer Runs :: 3 Frameshifted Genes Not On Monomer Runs :: 2 ##Genome-Annotation-Data-END## COMPLETENESS: full length." .
<feature/NC_000911> gfvo:hasAttribute <feature/NC_000911/attribute/comment1> .
<feature/NC_000911/attribute/comment1> a gfvo:InformationContentEntity ;
gfvo:hasValue "REFSEQ INFORMATION: The reference sequence was derived from BA000022. Potential protein coding regions were assigned on the basis of similarity search of the ORFs and GeneMark analysis. Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/ ##Genome-Annotation-Data-START## Annotation Provider :: NCBI Annotation Date :: 08/17/2015 19:20:20 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline Annotation Method :: Best-placed reference protein set; GeneMarkS+ Annotation Software revision :: 3.0 Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes :: 3,673 CDS :: 3,602 Pseudo Genes :: 23 CRISPR Arrays :: 3 rRNAs :: 2, 2, 2 (5S, 16S, 23S) complete rRNAs :: 2, 2, 2 (5S, 16S, 23S) tRNAs :: 41 ncRNA :: 1 Frameshifted Genes :: 13 Frameshifted Genes On Monomer Runs :: 3 Frameshifted Genes Not On Monomer Runs :: 2 ##Genome-Annotation-Data-END## COMPLETENESS: full length." .
<feature/NC_000911/attribute/comment1/tag/comment1> a gfvo:Label ;
gfvo:hasValue "comment1" .
<feature/NC_000911> gfvo:hasAttribute <feature/NC_000911/attribute/date> .
<feature/NC_000911/attribute/date> a gfvo:InformationContentEntity ;
gfvo:hasValue "17-AUG-2015" .
<feature/NC_000911/attribute/date/tag/date> a gfvo:Label ;
gfvo:hasValue "date" .
<feature/NC_000911> gfvo:hasAttribute <feature/NC_000911/attribute/mol_type> .
<feature/NC_000911/attribute/mol_type> a gfvo:InformationContentEntity ;
gfvo:hasValue "genomic DNA" .
<feature/NC_000911/attribute/mol_type/tag/mol_type> a gfvo:Label ;
gfvo:hasValue "mol_type" .
<feature/NC_000911> gfvo:hasAttribute <feature/NC_000911/attribute/organism> .
<feature/NC_000911/attribute/organism> a gfvo:InformationContentEntity ;
gfvo:hasValue "Synechocystis sp. PCC 6803" .
<feature/NC_000911/attribute/organism/tag/organism> a gfvo:Label ;
gfvo:hasValue "organism" .
<biointerchange://gff3/featureset/self/ba2f6e614a28f25e528d249702161dc812ceb941> gfvo:hasMember <feature/SGL_RS01875> .
<feature/SGL_RS01875> a gfvo:Feature ,
<http://purl.obolibrary.org/obo/SO_0000704> ;
gfvo:isLocatedOn <landmark/NC_000911> ;
gfvo:isCreatedBy <feature/SGL_RS01875/source> .
<feature/SGL_RS01875/source> a gfvo:ExperimentalMethod ;
gfvo:hasValue "GenBank" .
<feature/SGL_RS01875> gfvo:hasQuality <feature/SGL_RS01875/phase> .
<feature/SGL_RS01875/phase> a gfvo:CodingFrameOffset ;
gfvo:hasValue 1 .
<feature/SGL_RS01875> gfvo:hasPart <feature/SGL_RS01875/locus> .
<feature/SGL_RS01875/locus> a gfvo:Locus ;
gfvo:hasAttribute <feature/SGL_RS01875/locus/region> ;
gfvo:isLocatedOn <feature/SGL_RS01875/locus/region> .
<feature/SGL_RS01875/locus/region> a faldo:Region ;
faldo:begin <feature/SGL_RS01875/locus/region/start> .
<feature/SGL_RS01875/locus/region/start> a faldo:ForwardStrandPosition ;
faldo:position 3573271 .
<feature/SGL_RS01875/locus/region> faldo:end <feature/SGL_RS01875/locus/region/end> .
<feature/SGL_RS01875/locus/region/end> a faldo:ForwardStrandPosition .
<feature/SGL_RS01875/locus/region/start> faldo:position 3573470 .
<feature/SGL_RS01875> gfvo:hasIdentifier <feature/SGL_RS01875/id> .
<feature/SGL_RS01875/id> a gfvo:Identifier ;
gfvo:hasValue "SGL_RS01875" .
<feature/SGL_RS01875> gfvo:hasAttribute <feature/SGL_RS01875/name> .
<feature/SGL_RS01875/name> a gfvo:Name ;
gfvo:hasValue "SGL_RS01875" .
<feature/SGL_RS01875> gfvo:hasAttribute <feature/SGL_RS01875/attribute/old_locus_tag> .
<feature/SGL_RS01875/attribute/old_locus_tag> a gfvo:InformationContentEntity ;
gfvo:hasValue "slr0611" .
<feature/SGL_RS01875/attribute/old_locus_tag/tag/old_locus_tag> a gfvo:Label ;
gfvo:hasValue "old_locus_tag" .
<biointerchange://gff3/featureset/self/ba2f6e614a28f25e528d249702161dc812ceb941> gfvo:hasMember <feature/SGL_RS01875> .
<feature/SGL_RS01875> a gfvo:Feature ,
<http://purl.obolibrary.org/obo/SO_0000704> ;
gfvo:isLocatedOn <landmark/NC_000911> ;
gfvo:isCreatedBy <feature/SGL_RS01875/source> .
<feature/SGL_RS01875/source> a gfvo:ExperimentalMethod ;
gfvo:hasValue "GenBank" .
<feature/SGL_RS01875> gfvo:hasQuality <feature/SGL_RS01875/phase> .
<feature/SGL_RS01875/phase> a gfvo:CodingFrameOffset ;
gfvo:hasValue 1 .
<feature/SGL_RS01875> gfvo:hasPart <feature/SGL_RS01875/locus> .
<feature/SGL_RS01875/locus> a gfvo:Locus ;
gfvo:hasAttribute <feature/SGL_RS01875/locus/region> ;
gfvo:isLocatedOn <feature/SGL_RS01875/locus/region> .
<feature/SGL_RS01875/locus/region> a faldo:Region ;
faldo:begin <feature/SGL_RS01875/locus/region/start> .
<feature/SGL_RS01875/locus/region/start> a faldo:ForwardStrandPosition ;
faldo:position 1 .
<feature/SGL_RS01875/locus/region> faldo:end <feature/SGL_RS01875/locus/region/end> .
<feature/SGL_RS01875/locus/region/end> a faldo:ForwardStrandPosition .
<feature/SGL_RS01875/locus/region/start> faldo:position 772 .
<feature/SGL_RS01875> gfvo:hasIdentifier <feature/SGL_RS01875/id> .
<feature/SGL_RS01875/id> a gfvo:Identifier ;
gfvo:hasValue "SGL_RS01875" .
<feature/SGL_RS01875> gfvo:hasAttribute <feature/SGL_RS01875/name> .
<feature/SGL_RS01875/name> a gfvo:Name ;
gfvo:hasValue "SGL_RS01875" .
<feature/SGL_RS01875> gfvo:hasAttribute <feature/SGL_RS01875/attribute/old_locus_tag> .
<feature/SGL_RS01875/attribute/old_locus_tag> a gfvo:InformationContentEntity ;
gfvo:hasValue "slr0611" .
<feature/SGL_RS01875/attribute/old_locus_tag/tag/old_locus_tag> a gfvo:Label ;
gfvo:hasValue "old_locus_tag" .
<biointerchange://gff3/featureset/self/ba2f6e614a28f25e528d249702161dc812ceb941> gfvo:hasMember <feature/SGL_RS01875.t01> .
<feature/SGL_RS01875.t01> a gfvo:Feature ,
<http://purl.obolibrary.org/obo/SO_0000234> ;
gfvo:isLocatedOn <landmark/NC_000911> ;
gfvo:isCreatedBy <feature/SGL_RS01875.t01/source> .
<feature/SGL_RS01875.t01/source> a gfvo:ExperimentalMethod ;
gfvo:hasValue "GenBank" .
<feature/SGL_RS01875.t01> gfvo:hasQuality <feature/SGL_RS01875.t01/phase> .
<feature/SGL_RS01875.t01/phase> a gfvo:CodingFrameOffset ;
gfvo:hasValue 1 .
<feature/SGL_RS01875.t01> gfvo:hasPart <feature/SGL_RS01875.t01/locus> .
<feature/SGL_RS01875.t01/locus> a gfvo:Locus ;
gfvo:hasAttribute <feature/SGL_RS01875.t01/locus/region> ;
gfvo:isLocatedOn <feature/SGL_RS01875.t01/locus/region> .
<feature/SGL_RS01875.t01/locus/region> a faldo:Region ;
faldo:begin <feature/SGL_RS01875.t01/locus/region/start> .
<feature/SGL_RS01875.t01/locus/region/start> a faldo:ForwardStrandPosition ;
faldo:position 1 .
<feature/SGL_RS01875.t01/locus/region> faldo:end <feature/SGL_RS01875.t01/locus/region/end> .
<feature/SGL_RS01875.t01/locus/region/end> a faldo:ForwardStrandPosition .
<feature/SGL_RS01875.t01/locus/region/start> faldo:position 3573470 .
<feature/SGL_RS01875.t01> gfvo:hasIdentifier <feature/SGL_RS01875.t01/id> .
<feature/SGL_RS01875.t01/id> a gfvo:Identifier ;
gfvo:hasValue "SGL_RS01875.t01" .
<feature/SGL_RS01875.t01> gfvo:hasSource <feature/SGL_RS01875> .
<biointerchange://gff3/featureset/self/ba2f6e614a28f25e528d249702161dc812ceb941> gfvo:hasMember <feature/SGL_RS01875.p01> .
<feature/SGL_RS01875.p01> a gfvo:Feature ,
<http://purl.obolibrary.org/obo/SO_0000316> ;
gfvo:isLocatedOn <landmark/NC_000911> ;
gfvo:isCreatedBy <feature/SGL_RS01875.p01/source> .
<feature/SGL_RS01875.p01/source> a gfvo:ExperimentalMethod ;
gfvo:hasValue "GenBank" .
<feature/SGL_RS01875.p01> gfvo:hasQuality <feature/SGL_RS01875.p01/phase> .
<feature/SGL_RS01875.p01/phase> a gfvo:CodingFrameOffset ;
gfvo:hasValue 1 .
<feature/SGL_RS01875.p01> gfvo:hasPart <feature/SGL_RS01875.p01/locus> .
<feature/SGL_RS01875.p01/locus> a gfvo:Locus ;
gfvo:hasAttribute <feature/SGL_RS01875.p01/locus/region> ;
gfvo:isLocatedOn <feature/SGL_RS01875.p01/locus/region> .
<feature/SGL_RS01875.p01/locus/region> a faldo:Region ;
faldo:begin <feature/SGL_RS01875.p01/locus/region/start> .
<feature/SGL_RS01875.p01/locus/region/start> a faldo:ForwardStrandPosition ;
faldo:position 3573271 .
<feature/SGL_RS01875.p01/locus/region> faldo:end <feature/SGL_RS01875.p01/locus/region/end> .
<feature/SGL_RS01875.p01/locus/region/end> a faldo:ForwardStrandPosition .
<feature/SGL_RS01875.p01/locus/region/start> faldo:position 3573470 .
<feature/SGL_RS01875.p01> gfvo:hasIdentifier <feature/SGL_RS01875.p01/id> .
<feature/SGL_RS01875.p01/id> a gfvo:Identifier ;
gfvo:hasValue "SGL_RS01875.p01" .
<feature/SGL_RS01875.p01> gfvo:hasSource <feature/SGL_RS01875.t01> ;
gfvo:references <feature/SGL_RS01875.p01/dbxref/GI> .
<feature/SGL_RS01875.p01/dbxref/GI> a gfvo:ExternalReference .
<feature/SGL_RS01875.p01> gfvo:references <feature/SGL_RS01875.p01/attribute/dbxref/2> .
<feature/SGL_RS01875.p01/attribute/dbxref/2> a gfvo:ExternalReference ;
gfvo:hasValue "GI:499173620" .
<feature/SGL_RS01875.p01> gfvo:hasAttribute <feature/SGL_RS01875.p01/name> .
<feature/SGL_RS01875.p01/name> a gfvo:Name ;
gfvo:hasValue "SGL_RS01875" .
<feature/SGL_RS01875.p01> gfvo:hasAnnotation <feature/SGL_RS01875.p01/note/0> .
<feature/SGL_RS01875.p01/note/0> a gfvo:Note ;
gfvo:hasValue "Derived by automated computational analysis using gene prediction method: Protein Homology." .
<feature/SGL_RS01875.p01> gfvo:hasAttribute <feature/SGL_RS01875.p01/attribute/codon_start> .
<feature/SGL_RS01875.p01/attribute/codon_start> a gfvo:InformationContentEntity ;
gfvo:hasValue "1" .
<feature/SGL_RS01875.p01/attribute/codon_start/tag/codon_start> a gfvo:Label ;
gfvo:hasValue "codon_start" .
<feature/SGL_RS01875.p01> gfvo:hasAttribute <feature/SGL_RS01875.p01/attribute/inference> .
<feature/SGL_RS01875.p01/attribute/inference> a gfvo:InformationContentEntity ;
gfvo:hasValue "EXISTENCE: similar to AA sequence:SwissProt:P72580.2" .
<feature/SGL_RS01875.p01/attribute/inference/tag/inference> a gfvo:Label ;
gfvo:hasValue "inference" .
<feature/SGL_RS01875.p01> gfvo:hasAttribute <feature/SGL_RS01875.p01/attribute/old_locus_tag> .
<feature/SGL_RS01875.p01/attribute/old_locus_tag> a gfvo:InformationContentEntity ;
gfvo:hasValue "slr0611" .
<feature/SGL_RS01875.p01/attribute/old_locus_tag/tag/old_locus_tag> a gfvo:Label ;
gfvo:hasValue "old_locus_tag" .
<feature/SGL_RS01875.p01> gfvo:hasAttribute <feature/SGL_RS01875.p01/attribute/product> .
<feature/SGL_RS01875.p01/attribute/product> a gfvo:InformationContentEntity ;
gfvo:hasValue "Prenyl transferase" .
<feature/SGL_RS01875.p01/attribute/product/tag/product> a gfvo:Label ;
gfvo:hasValue "product" .
<feature/SGL_RS01875.p01> gfvo:hasAttribute <feature/SGL_RS01875.p01/attribute/protein_id> .
<feature/SGL_RS01875.p01/attribute/protein_id> a gfvo:InformationContentEntity ;
gfvo:hasValue "WP_010871207.1" .
<feature/SGL_RS01875.p01/attribute/protein_id/tag/protein_id> a gfvo:Label ;
gfvo:hasValue "protein_id" .
<feature/SGL_RS01875.p01> gfvo:hasAttribute <feature/SGL_RS01875.p01/attribute/transl_table> .
<feature/SGL_RS01875.p01/attribute/transl_table> a gfvo:InformationContentEntity ;
gfvo:hasValue "11" .
<feature/SGL_RS01875.p01/attribute/transl_table/tag/transl_table> a gfvo:Label ;
gfvo:hasValue "transl_table" .
<biointerchange://gff3/featureset/self/ba2f6e614a28f25e528d249702161dc812ceb941> gfvo:hasMember <feature/SGL_RS01875.p01> .
<feature/SGL_RS01875.p01> a gfvo:Feature ,
<http://purl.obolibrary.org/obo/SO_0000316> ;
gfvo:isLocatedOn <landmark/NC_000911> ;
gfvo:isCreatedBy <feature/SGL_RS01875.p01/source> .
<feature/SGL_RS01875.p01/source> a gfvo:ExperimentalMethod ;
gfvo:hasValue "GenBank" .
<feature/SGL_RS01875.p01> gfvo:hasQuality <feature/SGL_RS01875.p01/phase> .
<feature/SGL_RS01875.p01/phase> a gfvo:CodingFrameOffset ;
gfvo:hasValue 1 .
<feature/SGL_RS01875.p01> gfvo:hasPart <feature/SGL_RS01875.p01/locus> .
<feature/SGL_RS01875.p01/locus> a gfvo:Locus ;
gfvo:hasAttribute <feature/SGL_RS01875.p01/locus/region> ;
gfvo:isLocatedOn <feature/SGL_RS01875.p01/locus/region> .
<feature/SGL_RS01875.p01/locus/region> a faldo:Region ;
faldo:begin <feature/SGL_RS01875.p01/locus/region/start> .
<feature/SGL_RS01875.p01/locus/region/start> a faldo:ForwardStrandPosition ;
faldo:position 1 .
<feature/SGL_RS01875.p01/locus/region> faldo:end <feature/SGL_RS01875.p01/locus/region/end> .
<feature/SGL_RS01875.p01/locus/region/end> a faldo:ForwardStrandPosition .
<feature/SGL_RS01875.p01/locus/region/start> faldo:position 772 .
<feature/SGL_RS01875.p01> gfvo:hasIdentifier <feature/SGL_RS01875.p01/id> .
<feature/SGL_RS01875.p01/id> a gfvo:Identifier ;
gfvo:hasValue "SGL_RS01875.p01" .
<feature/SGL_RS01875.p01> gfvo:hasSource <feature/SGL_RS01875.t01> ;
gfvo:references <feature/SGL_RS01875.p01/dbxref/GI> .
<feature/SGL_RS01875.p01/dbxref/GI> a gfvo:ExternalReference .
<feature/SGL_RS01875.p01> gfvo:references <feature/SGL_RS01875.p01/attribute/dbxref/3> .
<feature/SGL_RS01875.p01/attribute/dbxref/3> a gfvo:ExternalReference ;
gfvo:hasValue "GI:499173620" .
<feature/SGL_RS01875.p01> gfvo:hasAttribute <feature/SGL_RS01875.p01/name> .
<feature/SGL_RS01875.p01/name> a gfvo:Name ;
gfvo:hasValue "SGL_RS01875" .
<feature/SGL_RS01875.p01> gfvo:hasAnnotation <feature/SGL_RS01875.p01/note/0> .
<feature/SGL_RS01875.p01/note/0> a gfvo:Note ;
gfvo:hasValue "Derived by automated computational analysis using gene prediction method: Protein Homology." .
<feature/SGL_RS01875.p01> gfvo:hasAttribute <feature/SGL_RS01875.p01/attribute/codon_start> .
<feature/SGL_RS01875.p01/attribute/codon_start> a gfvo:InformationContentEntity ;
gfvo:hasValue "1" .
<feature/SGL_RS01875.p01/attribute/codon_start/tag/codon_start> a gfvo:Label ;
gfvo:hasValue "codon_start" .
<feature/SGL_RS01875.p01> gfvo:hasAttribute <feature/SGL_RS01875.p01/attribute/inference> .
<feature/SGL_RS01875.p01/attribute/inference> a gfvo:InformationContentEntity ;
gfvo:hasValue "EXISTENCE: similar to AA sequence:SwissProt:P72580.2" .
<feature/SGL_RS01875.p01/attribute/inference/tag/inference> a gfvo:Label ;
gfvo:hasValue "inference" .
<feature/SGL_RS01875.p01> gfvo:hasAttribute <feature/SGL_RS01875.p01/attribute/old_locus_tag> .
<feature/SGL_RS01875.p01/attribute/old_locus_tag> a gfvo:InformationContentEntity ;
gfvo:hasValue "slr0611" .
<feature/SGL_RS01875.p01/attribute/old_locus_tag/tag/old_locus_tag> a gfvo:Label ;
gfvo:hasValue "old_locus_tag" .
<feature/SGL_RS01875.p01> gfvo:hasAttribute <feature/SGL_RS01875.p01/attribute/product> .
<feature/SGL_RS01875.p01/attribute/product> a gfvo:InformationContentEntity ;
gfvo:hasValue "Prenyl transferase" .
<feature/SGL_RS01875.p01/attribute/product/tag/product> a gfvo:Label ;
gfvo:hasValue "product" .
<feature/SGL_RS01875.p01> gfvo:hasAttribute <feature/SGL_RS01875.p01/attribute/protein_id> .
<feature/SGL_RS01875.p01/attribute/protein_id> a gfvo:InformationContentEntity ;
gfvo:hasValue "WP_010871207.1" .
<feature/SGL_RS01875.p01/attribute/protein_id/tag/protein_id> a gfvo:Label ;
gfvo:hasValue "protein_id" .
<feature/SGL_RS01875.p01> gfvo:hasAttribute <feature/SGL_RS01875.p01/attribute/transl_table> .
<feature/SGL_RS01875.p01/attribute/transl_table> a gfvo:InformationContentEntity ;
gfvo:hasValue "11" .
<feature/SGL_RS01875.p01/attribute/transl_table/tag/transl_table> a gfvo:Label ;
gfvo:hasValue "transl_table" .
<biointerchange://gff3/featureset/self/ba2f6e614a28f25e528d249702161dc812ceb941> gfvo:hasMember <feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1> .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1> a gfvo:Feature ,
<http://purl.obolibrary.org/obo/SO_0000147> ;
gfvo:isLocatedOn <landmark/NC_000911> ;
gfvo:isCreatedBy <feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1/source> .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1/source> a gfvo:ExperimentalMethod ;
gfvo:hasValue "GenBank" .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1> gfvo:hasQuality <feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1/phase> .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1/phase> a gfvo:CodingFrameOffset ;
gfvo:hasValue 1 .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1> gfvo:hasPart <feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1/locus> .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1/locus> a gfvo:Locus ;
gfvo:hasAttribute <feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1/locus/region> ;
gfvo:isLocatedOn <feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1/locus/region> .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1/locus/region> a faldo:Region ;
faldo:begin <feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1/locus/region/start> .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1/locus/region/start> a faldo:ForwardStrandPosition ;
faldo:position 3573271 .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1/locus/region> faldo:end <feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1/locus/region/end> .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1/locus/region/end> a faldo:ForwardStrandPosition .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1/locus/region/start> faldo:position 3573470 .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,3573271,3573470,2,1> gfvo:hasSource <feature/SGL_RS01875.t01> .
<biointerchange://gff3/featureset/self/ba2f6e614a28f25e528d249702161dc812ceb941> gfvo:hasMember <feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1> .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1> a gfvo:Feature ,
<http://purl.obolibrary.org/obo/SO_0000147> ;
gfvo:isLocatedOn <landmark/NC_000911> ;
gfvo:isCreatedBy <feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1/source> .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1/source> a gfvo:ExperimentalMethod ;
gfvo:hasValue "GenBank" .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1> gfvo:hasQuality <feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1/phase> .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1/phase> a gfvo:CodingFrameOffset ;
gfvo:hasValue 1 .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1> gfvo:hasPart <feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1/locus> .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1/locus> a gfvo:Locus ;
gfvo:hasAttribute <feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1/locus/region> ;
gfvo:isLocatedOn <feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1/locus/region> .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1/locus/region> a faldo:Region ;
faldo:begin <feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1/locus/region/start> .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1/locus/region/start> a faldo:ForwardStrandPosition ;
faldo:position 1 .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1/locus/region> faldo:end <feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1/locus/region/end> .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1/locus/region/end> a faldo:ForwardStrandPosition .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1/locus/region/start> faldo:position 772 .
<feature/NC_000911,GenBank,purl.obolibrary.org/obo/SO_0000147,1,772,2,1> gfvo:hasSource <feature/SGL_RS01875.t01> .
<biointerchange://gff3/featureset/self/ba2f6e614a28f25e528d249702161dc812ceb941> gfvo:hasMember <feature/SGL_RS01880> .
<feature/SGL_RS01880> a gfvo:Feature ,
<http://purl.obolibrary.org/obo/SO_0000704> ;
gfvo:isLocatedOn <landmark/NC_000911> ;
gfvo:isCreatedBy <feature/SGL_RS01880/source> .
<feature/SGL_RS01880/source> a gfvo:ExperimentalMethod ;
gfvo:hasValue "GenBank" .
<feature/SGL_RS01880> gfvo:hasQuality <feature/SGL_RS01880/phase> .
<feature/SGL_RS01880/phase> a gfvo:CodingFrameOffset ;
gfvo:hasValue 1 .
<feature/SGL_RS01880> gfvo:hasPart <feature/SGL_RS01880/locus> .
<feature/SGL_RS01880/locus> a gfvo:Locus ;
gfvo:hasAttribute <feature/SGL_RS01880/locus/region> ;
gfvo:isLocatedOn <feature/SGL_RS01880/locus/region> .
<feature/SGL_RS01880/locus/region> a faldo:Region ;
faldo:begin <feature/SGL_RS01880/locus/region/start> .
<feature/SGL_RS01880/locus/region/start> a faldo:ForwardStrandPosition ;
faldo:position 937 .
<feature/SGL_RS01880/locus/region> faldo:end <feature/SGL_RS01880/locus/region/end> .
<feature/SGL_RS01880/locus/region/end> a faldo:ForwardStrandPosition .
<feature/SGL_RS01880/locus/region/start> faldo:position 1494 .
<feature/SGL_RS01880> gfvo:hasIdentifier <feature/SGL_RS01880/id> .
<feature/SGL_RS01880/id> a gfvo:Identifier ;
gfvo:hasValue "SGL_RS01880" .
<feature/SGL_RS01880> gfvo:hasAttribute <feature/SGL_RS01880/name> .
<feature/SGL_RS01880/name> a gfvo:Name ;
gfvo:hasValue "SGL_RS01880" .
<feature/SGL_RS01880> gfvo:hasAttribute <feature/SGL_RS01880/attribute/old_locus_tag> .
<feature/SGL_RS01880/attribute/old_locus_tag> a gfvo:InformationContentEntity ;
gfvo:hasValue "slr0612" .
<feature/SGL_RS01880/attribute/old_locus_tag/tag/old_locus_tag> a gfvo:Label ;
gfvo:hasValue "old_locus_tag" .
<biointerchange://gff3/featureset/self/ba2f6e614a28f25e528d249702161dc812ceb941> gfvo:hasMember <feature/SGL_RS01880.t01> .
<feature/SGL_RS01880.t01> a gfvo:Feature ,
<http://purl.obolibrary.org/obo/SO_0000234> ;
gfvo:isLocatedOn <landmark/NC_000911> ;
gfvo:isCreatedBy <feature/SGL_RS01880.t01/source> .
<feature/SGL_RS01880.t01/source> a gfvo:ExperimentalMethod ;
gfvo:hasValue "GenBank" .
<feature/SGL_RS01880.t01> gfvo:hasQuality <feature/SGL_RS01880.t01/phase> .
<feature/SGL_RS01880.t01/phase> a gfvo:CodingFrameOffset ;
gfvo:hasValue 1 .
<feature/SGL_RS01880.t01> gfvo:hasPart <feature/SGL_RS01880.t01/locus> .
<feature/SGL_RS01880.t01/locus> a gfvo:Locus ;
gfvo:hasAttribute <feature/SGL_RS01880.t01/locus/region> ;
gfvo:isLocatedOn <feature/SGL_RS01880.t01/locus/region> .
<feature/SGL_RS01880.t01/locus/region> a faldo:Region ;
faldo:begin <feature/SGL_RS01880.t01/locus/region/start> .
<feature/SGL_RS01880.t01/locus/region/start> a faldo:ForwardStrandPosition ;
faldo:position 937 .
<feature/SGL_RS01880.t01/locus/region> faldo:end <feature/SGL_RS01880.t01/locus/region/end> .
<feature/SGL_RS01880.t01/locus/region/end> a faldo:ForwardStrandPosition .
<feature/SGL_RS01880.t01/locus/region/start> faldo:position 1494 .
<feature/SGL_RS01880.t01> gfvo:hasIdentifier <feature/SGL_RS01880.t01/id> .
<feature/SGL_RS01880.t01/id> a gfvo:Identifier ;
gfvo:hasValue "SGL_RS01880.t01" .
<feature/SGL_RS01880.t01> gfvo:hasSource <feature/SGL_RS01880> .
<biointerchange://gff3/featureset/self/ba2f6e614a28f25e528d249702161dc812ceb941> gfvo:hasMember <feature/SGL_RS01880.p01> .
<feature/SGL_RS01880.p01> a gfvo:Feature ,
<http://purl.obolibrary.org/obo/SO_0000316> ;
gfvo:isLocatedOn <landmark/NC_000911> ;
gfvo:isCreatedBy <feature/SGL_RS01880.p01/source> .
<feature/SGL_RS01880.p01/source> a gfvo:ExperimentalMethod ;
gfvo:hasValue "GenBank" .
<feature/SGL_RS01880.p01> gfvo:hasQuality <feature/SGL_RS01880.p01/phase> .
<feature/SGL_RS01880.p01/phase> a gfvo:CodingFrameOffset ;
gfvo:hasValue 1 .
<feature/SGL_RS01880.p01> gfvo:hasPart <feature/SGL_RS01880.p01/locus> .
<feature/SGL_RS01880.p01/locus> a gfvo:Locus ;
gfvo:hasAttribute <feature/SGL_RS01880.p01/locus/region> ;
gfvo:isLocatedOn <feature/SGL_RS01880.p01/locus/region> .
<feature/SGL_RS01880.p01/locus/region> a faldo:Region ;
faldo:begin <feature/SGL_RS01880.p01/locus/region/start> .
<feature/SGL_RS01880.p01/locus/region/start> a faldo:ForwardStrandPosition ;
faldo:position 937 .
<feature/SGL_RS01880.p01/locus/region> faldo:end <feature/SGL_RS01880.p01/locus/region/end> .
<feature/SGL_RS01880.p01/locus/region/end> a faldo:ForwardStrandPosition .
<feature/SGL_RS01880.p01/locus/region/start> faldo:position 1494 .
<feature/SGL_RS01880.p01> gfvo:hasIdentifier <feature/SGL_RS01880.p01/id> .
<feature/SGL_RS01880.p01/id> a gfvo:Identifier ;
gfvo:hasValue "SGL_RS01880.p01" .
<feature/SGL_RS01880.p01> gfvo:hasSource <feature/SGL_RS01880.t01> ;
gfvo:references <feature/SGL_RS01880.p01/dbxref/GI> .
<feature/SGL_RS01880.p01/dbxref/GI> a gfvo:ExternalReference .
<feature/SGL_RS01880.p01> gfvo:references <feature/SGL_RS01880.p01/attribute/dbxref/4> .
<feature/SGL_RS01880.p01/attribute/dbxref/4> a gfvo:ExternalReference ;
gfvo:hasValue "GI:499173621" .
<feature/SGL_RS01880.p01> gfvo:hasAttribute <feature/SGL_RS01880.p01/name> .
<feature/SGL_RS01880.p01/name> a gfvo:Name ;
gfvo:hasValue "SGL_RS01880" .
<feature/SGL_RS01880.p01> gfvo:hasAnnotation <feature/SGL_RS01880.p01/note/0> .
<feature/SGL_RS01880.p01/note/0> a gfvo:Note ;
gfvo:hasValue "Uncharacterized RNA pseudouridine synthase slr0612; Derived by automated computational analysis using gene prediction method: Protein Homology." .
<feature/SGL_RS01880.p01> gfvo:hasAttribute <feature/SGL_RS01880.p01/attribute/codon_start> .
<feature/SGL_RS01880.p01/attribute/codon_start> a gfvo:InformationContentEntity ;
gfvo:hasValue "1" .
<feature/SGL_RS01880.p01/attribute/codon_start/tag/codon_start> a gfvo:Label ;
gfvo:hasValue "codon_start" .
<feature/SGL_RS01880.p01> gfvo:hasAttribute <feature/SGL_RS01880.p01/attribute/inference> .
<feature/SGL_RS01880.p01/attribute/inference> a gfvo:InformationContentEntity ;
gfvo:hasValue "EXISTENCE: similar to AA sequence:RefSeq:WP_010871208.1" .
<feature/SGL_RS01880.p01/attribute/inference/tag/inference> a gfvo:Label ;
gfvo:hasValue "inference" .
<feature/SGL_RS01880.p01> gfvo:hasAttribute <feature/SGL_RS01880.p01/attribute/old_locus_tag> .
<feature/SGL_RS01880.p01/attribute/old_locus_tag> a gfvo:InformationContentEntity ;
gfvo:hasValue "slr0612" .
<feature/SGL_RS01880.p01/attribute/old_locus_tag/tag/old_locus_tag> a gfvo:Label ;
Turtle形式 (biointerchange2.0由来)
@prefix gfvosquared: <https://www.codamono.com/gfvo-squared#> .
[
a gfvosquared:Context;
gfvosquared:biointerchangeVersion "2.0.4+105";
gfvosquared:inputFile "NC_000911.gb.gff";
gfvosquared:inputFiletype "GFF3";
gfvosquared:outputFile "NC_000911.gb.gff.ldj"
] .
[
a gfvosquared:Meta;
gfvosquared:gffVersion "3"
] .
[
a gfvosquared:Feature;
gfvosquared:codonPhase 1;
gfvosquared:comment """sequence-region NC_000911 1 3573470
conversion-by bp_genbank2gff3.pl
organism Synechocystis sp. PCC 6803
date 17-AUG-2015
Note Synechocystis sp. PCC 6803 DNA, complete genome.""";
gfvosquared:dbxref ("GenBank:GCF_000009725.1" "taxon:1148");
gfvosquared:id "NC_000911";
gfvosquared:locus [
gfvosquared:end 3573470;
gfvosquared:landmark "NC_000911";
gfvosquared:start 1;
gfvosquared:strand "+"
];
gfvosquared:source "GenBank";
gfvosquared:type "region";
gfvosquared:unknownProperty-name "NC_000911";
gfvosquared:unknownProperty-note "Synechocystis sp. PCC 6803 DNA%2C complete genome.,REFSEQ INFORMATION: The reference sequence was derived from BA000022. Potential protein coding regions were assigned on the basis of similarity search of the ORFs and GeneMark analysis. Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/ ##Genome-Annotation-Data-START## Annotation Provider :: NCBI Annotation Date :: 08/17/2015 19:20:20 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline Annotation Method :: Best-placed reference protein set,GeneMarkS+ Annotation Software revision :: 3.0 Features Annotated :: Gene,CDS,rRNA,tRNA,ncRNA,repeat_region Genes :: 3,673 CDS :: 3,602 Pseudo Genes :: 23 CRISPR Arrays :: 3 rRNAs :: 2,2,2 (5S,16S,23S) complete rRNAs :: 2,2,2 (5S,16S,23S) tRNAs :: 41 ncRNA :: 1 Frameshifted Genes :: 13 Frameshifted Genes On Monomer Runs :: 3 Frameshifted Genes Not On Monomer Runs :: 2 ##Genome-Annotation-Data-END## COMPLETENESS: full length. ";
gfvosquared:userDefined [
gfvosquared:unknownProperty-comment1 "REFSEQ INFORMATION: The reference sequence was derived from BA000022. Potential protein coding regions were assigned on the basis of similarity search of the ORFs and GeneMark analysis. Annotation was added by the NCBI Prokaryotic Genome Annotation Pipeline (released 2013). Information about the Pipeline can be found here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/ ##Genome-Annotation-Data-START## Annotation Provider :: NCBI Annotation Date :: 08/17/2015 19:20:20 Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline Annotation Method :: Best-placed reference protein set%3B GeneMarkS+ Annotation Software revision :: 3.0 Features Annotated :: Gene%3B CDS%3B rRNA%3B tRNA%3B ncRNA%3B repeat_region Genes :: 3%2C673 CDS :: 3%2C602 Pseudo Genes :: 23 CRISPR Arrays :: 3 rRNAs :: 2%2C 2%2C 2 (5S%2C 16S%2C 23S) complete rRNAs :: 2%2C 2%2C 2 (5S%2C 16S%2C 23S) tRNAs :: 41 ncRNA :: 1 Frameshifted Genes :: 13 Frameshifted Genes On Monomer Runs :: 3 Frameshifted Genes Not On Monomer Runs :: 2 ##Genome-Annotation-Data-END## COMPLETENESS: full length. ";
gfvosquared:unknownProperty-date "17-AUG-2015";
gfvosquared:unknownProperty-mol_type "genomic DNA";
gfvosquared:unknownProperty-organism "Synechocystis sp. PCC 6803"
]
] .
[
a gfvosquared:Feature;
gfvosquared:codonPhase 1;
gfvosquared:locus [
gfvosquared:end 772;
gfvosquared:landmark "NC_000911";
gfvosquared:start 1;
gfvosquared:strand "+"
];
gfvosquared:source "GenBank";
gfvosquared:type "exon";
gfvosquared:unknownProperty-parent "SGL_RS01875.t01"
] .
[
a gfvosquared:Feature;
gfvosquared:codonPhase 1;
gfvosquared:locus [
gfvosquared:end 3573470;
gfvosquared:landmark "NC_000911";
gfvosquared:start 3573271;
gfvosquared:strand "+"
];
gfvosquared:source "GenBank";
gfvosquared:type "exon";
gfvosquared:unknownProperty-parent "SGL_RS01875.t01"
] .
[
a gfvosquared:Feature;
gfvosquared:codonPhase 1;
gfvosquared:dbxref ("GI:499173620");
gfvosquared:id "SGL_RS01875.p01";
gfvosquared:locus [
gfvosquared:end 772;
gfvosquared:landmark "NC_000911";
gfvosquared:start 1;
gfvosquared:strand "+"
];
gfvosquared:source "GenBank";
gfvosquared:type "CDS";
gfvosquared:unknownProperty-name "SGL_RS01875";
gfvosquared:unknownProperty-note "Derived by automated computational analysis using gene prediction method: Protein Homology.";
gfvosquared:unknownProperty-parent "SGL_RS01875.t01";
gfvosquared:userDefined [
gfvosquared:unknownProperty-codon_start 1;
gfvosquared:unknownProperty-inference "EXISTENCE: similar to AA sequence:SwissProt:P72580.2";
gfvosquared:unknownProperty-old_locus_tag "slr0611";
gfvosquared:unknownProperty-product "Prenyl transferase";
gfvosquared:unknownProperty-protein_id "WP_010871207.1";
gfvosquared:unknownProperty-transl_table 11
]
] .
[
a gfvosquared:Feature;
gfvosquared:codonPhase 1;
gfvosquared:dbxref ("GI:499173620");
gfvosquared:id "SGL_RS01875.p01";
gfvosquared:locus [
gfvosquared:end 3573470;
gfvosquared:landmark "NC_000911";
gfvosquared:start 3573271;
gfvosquared:strand "+"
];
gfvosquared:source "GenBank";
gfvosquared:type "CDS";
gfvosquared:unknownProperty-name "SGL_RS01875";
gfvosquared:unknownProperty-note "Derived by automated computational analysis using gene prediction method: Protein Homology.";
gfvosquared:unknownProperty-parent "SGL_RS01875.t01";
gfvosquared:userDefined [
gfvosquared:unknownProperty-codon_start 1;
gfvosquared:unknownProperty-inference "EXISTENCE: similar to AA sequence:SwissProt:P72580.2";
gfvosquared:unknownProperty-old_locus_tag "slr0611";
gfvosquared:unknownProperty-product "Prenyl transferase";
gfvosquared:unknownProperty-protein_id "WP_010871207.1";
gfvosquared:unknownProperty-transl_table 11
]
] .
[
a gfvosquared:Feature;
gfvosquared:codonPhase 1;
gfvosquared:id "SGL_RS01875";
gfvosquared:locus [
gfvosquared:end 3573470;
gfvosquared:landmark "NC_000911";
gfvosquared:start 3573271;
gfvosquared:strand "+"
];
gfvosquared:source "GenBank";
gfvosquared:type "gene";
gfvosquared:unknownProperty-name "SGL_RS01875";
gfvosquared:userDefined [ gfvosquared:unknownProperty-old_locus_tag "slr0611"]
] .
[
a gfvosquared:Feature;
gfvosquared:codonPhase 1;
gfvosquared:id "SGL_RS01875";
gfvosquared:locus [
gfvosquared:end 772;
gfvosquared:landmark "NC_000911";
gfvosquared:start 1;
gfvosquared:strand "+"
];
gfvosquared:source "GenBank";
gfvosquared:type "gene";
gfvosquared:unknownProperty-name "SGL_RS01875";
gfvosquared:userDefined [ gfvosquared:unknownProperty-old_locus_tag "slr0611"]
] .
[
a gfvosquared:Feature;
gfvosquared:codonPhase 1;
gfvosquared:id "SGL_RS01875.t01";
gfvosquared:locus [
gfvosquared:end 3573470;
gfvosquared:landmark "NC_000911";
gfvosquared:start 1;
gfvosquared:strand "+"
];
gfvosquared:source "GenBank";
gfvosquared:type "mRNA";
gfvosquared:unknownProperty-parent "SGL_RS01875"
] .
Turtle形式（using insdc2ttl.rb）
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . @prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . @prefix xsd: <http://www.w3.org/2001/XMLSchema#> . @prefix skos: <http://www.w3.org/2004/02/skos/core#> . @prefix sio: <http://semanticscience.org/resource/> . @prefix obo: <http://purl.obolibrary.org/obo/> . @prefix faldo: <http://biohackathon.org/resource/faldo#> . @prefix insdc: <http://ddbj.nig.ac.jp/ontologies/nucleotide/> . @prefix insdcdiv: <http://ddbj.nig.ac.jp/ontologies/nucleotide/Division#> . @prefix insdcref: <http://ddbj.nig.ac.jp/ontologies/nucleotide/reference#> . <http://identifiers.org/insdc/NC_000911.1> rdf:type insdc:Entry . <http://identifiers.org/insdc/NC_000911.1> insdc:definition "Synechocystis sp. PCC 6803 DNA, complete genome." . <http://identifiers.org/insdc/NC_000911.1> rdfs:label "Synechocystis sp. PCC 6803 DNA, complete genome." . <http://identifiers.org/insdc/NC_000911.1> insdc:sequence_version "NC_000911.1" . <http://identifiers.org/insdc/NC_000911.1> insdc:sequence_date "2015-08-17"^^xsd:date . <http://identifiers.org/insdc/NC_000911.1> insdc:sequence <http://identifiers.org/insdc/NC_000911.1#sequence> . <http://identifiers.org/insdc/NC_000911.1#sequence> rdfs:seeAlso <http://www.ncbi.nlm.nih.gov/nuccore/NC_000911.1?report=fasta> . <http://identifiers.org/insdc/NC_000911.1#sequence> rdfs:seeAlso <http://www.ebi.ac.uk/ena/data/view/NC_000911.1&display=fasta> . <http://identifiers.org/insdc/NC_000911.1#sequence> rdfs:seeAlso <http://getentry.ddbj.nig.ac.jp/getentry/na/NC_000911.1?format=fasta> . <http://identifiers.org/insdc/NC_000911.1#sequence> rdfs:subClassOf obo:SO_0000001 . # SO:sequence <http://identifiers.org/insdc/NC_000911.1#sequence> insdc:sequence_length 3573470 . <http://identifiers.org/insdc/NC_000911.1#sequence> insdc:topology insdc:circular . <http://identifiers.org/insdc/NC_000911.1#sequence> obo:so_has_quality obo:SO_0000988 . # SO:circular <http://identifiers.org/insdc/NC_000911.1> insdc:division insdcdiv:CON . <http://identifiers.org/insdc/NC_000911.1> rdfs:seeAlso <http://identifiers.org/ncbigi/GI:16329170> . <http://identifiers.org/ncbigi/GI:16329170> rdfs:label "GI:16329170" . <http://identifiers.org/ncbigi/GI:16329170> rdf:type insdc:GI . <http://identifiers.org/ncbigi/GI:16329170> sio:SIO_000068 <http://identifiers.org/ncbigi> . # sio:is-part-of <http://identifiers.org/insdc/NC_000911.1> insdc:dblink <http://identifiers.org/bioproject/PRJNA224116> . <http://identifiers.org/bioproject/PRJNA224116> rdfs:label "PRJNA224116" . <http://identifiers.org/bioproject/PRJNA224116> rdf:type insdc:BioProject . <http://identifiers.org/bioproject/PRJNA224116> sio:SIO_000068 <http://identifiers.org/bioproject> . # sio:is-part-of <http://identifiers.org/insdc/NC_000911.1> insdc:keyword <http://ddbj.nig.ac.jp/ontologies/nucleotide/Keyword#RefSeq> . <http://ddbj.nig.ac.jp/ontologies/nucleotide/Keyword#RefSeq> rdfs:label "RefSeq" . <http://identifiers.org/insdc/NC_000911.1> insdc:source "Synechocystis sp. PCC 6803" . <http://identifiers.org/insdc/NC_000911.1> insdc:organism "Synechocystis sp. PCC 6803" . <http://identifiers.org/insdc/NC_000911.1> insdc:taxonomy "Bacteria; Cyanobacteria; Oscillatoriophycideae; Chroococcales; Synechocystis." . <http://identifiers.org/insdc/NC_000911.1> insdc:reference <http://identifiers.org/insdc/NC_000911.1#reference.1> . <http://identifiers.org/insdc/NC_000911.1#reference.1> sio:SIO_000300 1 . # sio:has-value <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref: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" . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Kaneko, T." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Sato, S." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Kotani, H." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Tanaka, A." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Asamizu, E." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Nakamura, Y." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Miyajima, N." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Hirosawa, M." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Sugiura, M." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Sasamoto, S." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Kimura, T." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Hosouchi, T." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Matsuno, A." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Muraki, A." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Nakazaki, N." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Naruo, K." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Okumura, S." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Shimpo, S." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Takeuchi, C." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Wada, T." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Watanabe, A." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Yamada, M." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Yasuda, M." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:author "Tabata, S." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:journal "DNA Res." . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:volume "3" . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:issue "3" . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:pages "109-136" . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:year "1996" . <http://identifiers.org/insdc/NC_000911.1#reference.1> insdcref:pubmed "8905231" . <http://identifiers.org/insdc/NC_000911.1> rdfs:seeAlso <http://identifiers.org/pubmed/8905231> . <http://identifiers.org/pubmed/8905231> rdfs:label "8905231" . <http://identifiers.org/pubmed/8905231> rdf:type insdc:PubMed . <http://identifiers.org/pubmed/8905231> sio:SIO_000068 <http://identifiers.org/pubmed> . # sio:is-part-of <http://identifiers.org/insdc/NC_000911.1> insdc:reference <http://identifiers.org/insdc/NC_000911.1#reference.2> . <http://identifiers.org/insdc/NC_000911.1#reference.2> sio:SIO_000300 2 . # sio:has-value <http://identifiers.org/insdc/NC_000911.1#reference.2> insdcref: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" . <http://identifiers.org/insdc/NC_000911.1#reference.2> insdcref:author "Kaneko, T." . <http://identifiers.org/insdc/NC_000911.1#reference.2> insdcref:author "Tanaka, A." . <http://identifiers.org/insdc/NC_000911.1#reference.2> insdcref:author "Sato, S." . <http://identifiers.org/insdc/NC_000911.1#reference.2> insdcref:author "Kotani, H." . <http://identifiers.org/insdc/NC_000911.1#reference.2> insdcref:author "Sazuka, T." . <http://identifiers.org/insdc/NC_000911.1#reference.2> insdcref:author "Miyajima, N." . <http://identifiers.org/insdc/NC_000911.1#reference.2> insdcref:author "Sugiura, M." . <http://identifiers.org/insdc/NC_000911.1#reference.2> insdcref:author "Tabata, S." . <http://identifiers.org/insdc/NC_000911.1#reference.2> insdcref:journal "DNA Res." . <http://identifiers.org/insdc/NC_000911.1#reference.2> insdcref:volume "2" . <http://identifiers.org/insdc/NC_000911.1#reference.2> insdcref:issue "4" . <http://identifiers.org/insdc/NC_000911.1#reference.2> insdcref:pages "153-166" . <http://identifiers.org/insdc/NC_000911.1#reference.2> insdcref:year "1995" . <http://identifiers.org/insdc/NC_000911.1#reference.2> insdcref:pubmed "8590279" . <http://identifiers.org/insdc/NC_000911.1> rdfs:seeAlso <http://identifiers.org/pubmed/8590279> . <http://identifiers.org/pubmed/8590279> rdfs:label "8590279" . <http://identifiers.org/pubmed/8590279> rdf:type insdc:PubMed . <http://identifiers.org/pubmed/8590279> sio:SIO_000068 <http://identifiers.org/pubmed> . # sio:is-part-of <http://identifiers.org/insdc/NC_000911.1> insdc:reference <http://identifiers.org/insdc/NC_000911.1#reference.3> . <http://identifiers.org/insdc/NC_000911.1#reference.3> sio:SIO_000300 3 . # sio:has-value <http://identifiers.org/insdc/NC_000911.1#reference.3> insdcref:title "Direct Submission" . <http://identifiers.org/insdc/NC_000911.1#reference.3> insdcref:author "Tabata, S." . <http://identifiers.org/insdc/NC_000911.1#reference.3> insdcref:journal "Submitted (03-JUL-2001) Contact:Satoshi Tabata Kazusa DNA Research Institute, The First Laboratory for Plant Gene Research; Yana 1532-3, Kisarazu, Chiba 292-0812, Japan URL :http://www.kazusa.or.jp/cyano/" . <http://identifiers.org/insdc/NC_000911.1> insdc:comment "REFSEQ INFORMATION: The reference sequence was derived from\\nBA000022.\\nPotential protein coding regions were assigned on the basis of\\nsimilarity search of the ORFs and GeneMark analysis.\\nAnnotation was added by the NCBI Prokaryotic Genome Annotation\\nPipeline (released 2013). Information about the Pipeline can be\\nfound here: http://www.ncbi.nlm.nih.gov/genome/annotation_prok/\\n\\n##Genome-Annotation-Data-START##\\nAnnotation Provider :: NCBI\\nAnnotation Date :: 08/17/2015 19:20:20\\nAnnotation Pipeline :: NCBI Prokaryotic Genome\\n Annotation Pipeline\\nAnnotation Method :: Best-placed reference\\n protein set; GeneMarkS+\\nAnnotation Software revision :: 3.0\\nFeatures Annotated :: Gene; CDS; rRNA; tRNA;\\n ncRNA; repeat_region\\nGenes :: 3,673\\nCDS :: 3,602\\nPseudo Genes :: 23\\nCRISPR Arrays :: 3\\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\\ntRNAs :: 41\\nncRNA :: 1\\nFrameshifted Genes :: 13\\nFrameshifted Genes On Monomer Runs :: 3\\nFrameshifted Genes Not On Monomer Runs :: 2\\n##Genome-Annotation-Data-END##\\nCOMPLETENESS: full length." . <http://identifiers.org/insdc/NC_000911.1#sequence> insdc:location "1..3573470" . <http://identifiers.org/insdc/NC_000911.1#sequence> faldo:location <http://identifiers.org/insdc/NC_000911.1#region:1-3573470:1> . <http://identifiers.org/insdc/NC_000911.1#region:1-3573470:1> rdf:type faldo:Region . <http://identifiers.org/insdc/NC_000911.1#region:1-3573470:1> faldo:begin <http://identifiers.org/insdc/NC_000911.1#position:1:1> . <http://identifiers.org/insdc/NC_000911.1#region:1-3573470:1> faldo:end <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> . <http://identifiers.org/insdc/NC_000911.1#position:1:1> faldo:position 1 . <http://identifiers.org/insdc/NC_000911.1#position:1:1> faldo:reference <http://identifiers.org/insdc/NC_000911.1#sequence> . <http://identifiers.org/insdc/NC_000911.1#position:1:1> rdf:type faldo:ForwardStrandPosition . <http://identifiers.org/insdc/NC_000911.1#position:1:1> rdf:type faldo:ExactPosition . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> faldo:position 3573470 . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> faldo:reference <http://identifiers.org/insdc/NC_000911.1#sequence> . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> rdf:type faldo:ForwardStrandPosition . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> rdf:type faldo:ExactPosition . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:source> rdfs:seeAlso <http://identifiers.org/taxonomy/1148> . <http://identifiers.org/taxonomy/1148> rdfs:label "1148" . <http://identifiers.org/taxonomy/1148> rdf:type insdc:Taxonomy . <http://identifiers.org/taxonomy/1148> sio:SIO_000068 <http://identifiers.org/taxonomy> . # sio:is-part-of <http://identifiers.org/insdc/NC_000911.1#sequence> obo:RO_0002162 <http://identifiers.org/taxonomy/1148> . # RO:in taxon <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:source> insdc:organism "Synechocystis sp. PCC 6803" . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:source> insdc:mol_type "genomic DNA" . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:gene.1> rdf:type insdc:Gene . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:gene.1> rdfs:subClassOf obo:SO_0000704 . # SO:gene <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:gene.1> obo:RO_0002162 <http://identifiers.org/taxonomy/1148> . # RO:in taxon <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:gene.1> rdfs:label "SGL_RS01875" . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:gene.1> skos:prefLabel "SGL_RS01875" . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:gene.1> insdc:locus_tag "SGL_RS01875" . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:gene.1> insdc:old_locus_tag "slr0611" . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:gene.1> obo:so_part_of <http://identifiers.org/insdc/NC_000911.1#sequence> . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:gene.1> insdc:location "join(3573271..3573470,1..772)" . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:gene.1> faldo:location <http://identifiers.org/insdc/NC_000911.1#region:1-3573470:1> . <http://identifiers.org/insdc/NC_000911.1#region:1-3573470:1> rdf:type faldo:Region . <http://identifiers.org/insdc/NC_000911.1#region:1-3573470:1> faldo:begin <http://identifiers.org/insdc/NC_000911.1#position:1:1> . <http://identifiers.org/insdc/NC_000911.1#region:1-3573470:1> faldo:end <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> . <http://identifiers.org/insdc/NC_000911.1#position:1:1> faldo:position 1 . <http://identifiers.org/insdc/NC_000911.1#position:1:1> faldo:reference <http://identifiers.org/insdc/NC_000911.1#sequence> . <http://identifiers.org/insdc/NC_000911.1#position:1:1> rdf:type faldo:ForwardStrandPosition . <http://identifiers.org/insdc/NC_000911.1#position:1:1> rdf:type faldo:ExactPosition . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> faldo:position 3573470 . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> faldo:reference <http://identifiers.org/insdc/NC_000911.1#sequence> . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> rdf:type faldo:ForwardStrandPosition . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> rdf:type faldo:ExactPosition . <urn:uuid:71d18150-ece2-467c-b20e-bce5fae79240> sio:SIO_000300 1 . # sio:has-value <urn:uuid:71d18150-ece2-467c-b20e-bce5fae79240> sio:SIO_000628 <http://identifiers.org/insdc/NC_000911.1#feature:3573271-3573470:1:exon> . # sio:refers-to <http://identifiers.org/insdc/NC_000911.1#feature:3573271-3573470:1:exon> rdf:type insdc:Exon . <http://identifiers.org/insdc/NC_000911.1#feature:3573271-3573470:1:exon> rdfs:subClassOf obo:SO_0000147 . # SO:exon <http://identifiers.org/insdc/NC_000911.1#feature:3573271-3573470:1:exon> faldo:location <http://identifiers.org/insdc/NC_000911.1#region:3573271-3573470:1> . <http://identifiers.org/insdc/NC_000911.1#region:3573271-3573470:1> rdf:type faldo:Region . <http://identifiers.org/insdc/NC_000911.1#region:3573271-3573470:1> faldo:begin <http://identifiers.org/insdc/NC_000911.1#position:3573271:1> . <http://identifiers.org/insdc/NC_000911.1#region:3573271-3573470:1> faldo:end <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> . <http://identifiers.org/insdc/NC_000911.1#position:3573271:1> faldo:position 3573271 . <http://identifiers.org/insdc/NC_000911.1#position:3573271:1> faldo:reference <http://identifiers.org/insdc/NC_000911.1#sequence> . <http://identifiers.org/insdc/NC_000911.1#position:3573271:1> rdf:type faldo:ForwardStrandPosition . <http://identifiers.org/insdc/NC_000911.1#position:3573271:1> rdf:type faldo:ExactPosition . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> faldo:position 3573470 . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> faldo:reference <http://identifiers.org/insdc/NC_000911.1#sequence> . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> rdf:type faldo:ForwardStrandPosition . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> rdf:type faldo:ExactPosition . <urn:uuid:b9dd7cbc-b072-4954-9e90-56e52ef0cf69> sio:SIO_000300 2 . # sio:has-value <urn:uuid:b9dd7cbc-b072-4954-9e90-56e52ef0cf69> sio:SIO_000628 <http://identifiers.org/insdc/NC_000911.1#feature:1-772:1:exon> . # sio:refers-to <http://identifiers.org/insdc/NC_000911.1#feature:1-772:1:exon> rdf:type insdc:Exon . <http://identifiers.org/insdc/NC_000911.1#feature:1-772:1:exon> rdfs:subClassOf obo:SO_0000147 . # SO:exon <http://identifiers.org/insdc/NC_000911.1#feature:1-772:1:exon> faldo:location <http://identifiers.org/insdc/NC_000911.1#region:1-772:1> . <http://identifiers.org/insdc/NC_000911.1#region:1-772:1> rdf:type faldo:Region . <http://identifiers.org/insdc/NC_000911.1#region:1-772:1> faldo:begin <http://identifiers.org/insdc/NC_000911.1#position:1:1> . <http://identifiers.org/insdc/NC_000911.1#region:1-772:1> faldo:end <http://identifiers.org/insdc/NC_000911.1#position:772:1> . <http://identifiers.org/insdc/NC_000911.1#position:1:1> faldo:position 1 . <http://identifiers.org/insdc/NC_000911.1#position:1:1> faldo:reference <http://identifiers.org/insdc/NC_000911.1#sequence> . <http://identifiers.org/insdc/NC_000911.1#position:1:1> rdf:type faldo:ForwardStrandPosition . <http://identifiers.org/insdc/NC_000911.1#position:1:1> rdf:type faldo:ExactPosition . <http://identifiers.org/insdc/NC_000911.1#position:772:1> faldo:position 772 . <http://identifiers.org/insdc/NC_000911.1#position:772:1> faldo:reference <http://identifiers.org/insdc/NC_000911.1#sequence> . <http://identifiers.org/insdc/NC_000911.1#position:772:1> rdf:type faldo:ForwardStrandPosition . <http://identifiers.org/insdc/NC_000911.1#position:772:1> rdf:type faldo:ExactPosition . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:gene.1> obo:so_has_part <http://identifiers.org/insdc/NC_000911.1#feature:3573271-3573470:1:exon>, <http://identifiers.org/insdc/NC_000911.1#feature:1-772:1:exon> . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:gene.1> sio:SIO_000974 <urn:uuid:71d18150-ece2-467c-b20e-bce5fae79240>, <urn:uuid:b9dd7cbc-b072-4954-9e90-56e52ef0cf69> . # sio:has-ordered-part <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> rdf:type insdc:Coding_Sequence . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> rdfs:subClassOf obo:SO_0000316 . # SO:CDS <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> obo:RO_0002162 <http://identifiers.org/taxonomy/1148> . # RO:in taxon <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> rdfs:label "SGL_RS01875" . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> skos:prefLabel "SGL_RS01875" . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> insdc:locus_tag "SGL_RS01875" . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> insdc:old_locus_tag "slr0611" . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> insdc:inference "EXISTENCE: similar to AA sequence:SwissProt:P72580.2" . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> insdc:note "Derived by automated computational analysis using gene prediction method: Protein Homology." . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> insdc:codon_start 1 . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> insdc:transl_table 11 . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> insdc:product "Prenyl transferase" . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> rdfs:seeAlso <http://identifiers.org/ncbiprotein/WP_010871207.1> . <http://identifiers.org/ncbiprotein/WP_010871207.1> rdfs:label "WP_010871207.1" . <http://identifiers.org/ncbiprotein/WP_010871207.1> rdf:type insdc:Protein . <http://identifiers.org/ncbiprotein/WP_010871207.1> sio:SIO_000068 <http://identifiers.org/ncbiprotein> . # sio:is-part-of <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> rdfs:seeAlso <http://identifiers.org/ncbigi/GI:499173620> . <http://identifiers.org/ncbigi/GI:499173620> rdfs:label "GI:499173620" . <http://identifiers.org/ncbigi/GI:499173620> rdf:type insdc:GI . <http://identifiers.org/ncbigi/GI:499173620> sio:SIO_000068 <http://identifiers.org/ncbigi> . # sio:is-part-of <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> sio:SIO_010081 <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:gene.1> . # sio:is-transcribed-from <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> rdfs:subClassOf obo:SO_0000673 . # SO:transcript <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:gene.1> rdfs:subClassOf obo:SO_0000010 . # SO:protein_coding <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> obo:so_part_of <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:gene.1> . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> insdc:location "join(3573271..3573470,1..772)" . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> faldo:location <http://identifiers.org/insdc/NC_000911.1#region:1-3573470:1> . <http://identifiers.org/insdc/NC_000911.1#region:1-3573470:1> rdf:type faldo:Region . <http://identifiers.org/insdc/NC_000911.1#region:1-3573470:1> faldo:begin <http://identifiers.org/insdc/NC_000911.1#position:1:1> . <http://identifiers.org/insdc/NC_000911.1#region:1-3573470:1> faldo:end <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> . <http://identifiers.org/insdc/NC_000911.1#position:1:1> faldo:position 1 . <http://identifiers.org/insdc/NC_000911.1#position:1:1> faldo:reference <http://identifiers.org/insdc/NC_000911.1#sequence> . <http://identifiers.org/insdc/NC_000911.1#position:1:1> rdf:type faldo:ForwardStrandPosition . <http://identifiers.org/insdc/NC_000911.1#position:1:1> rdf:type faldo:ExactPosition . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> faldo:position 3573470 . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> faldo:reference <http://identifiers.org/insdc/NC_000911.1#sequence> . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> rdf:type faldo:ForwardStrandPosition . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> rdf:type faldo:ExactPosition . <urn:uuid:36968b10-c862-4eaf-8086-403e5a26eea3> sio:SIO_000300 1 . # sio:has-value <urn:uuid:36968b10-c862-4eaf-8086-403e5a26eea3> sio:SIO_000628 <http://identifiers.org/insdc/NC_000911.1#feature:3573271-3573470:1:exon> . # sio:refers-to <http://identifiers.org/insdc/NC_000911.1#feature:3573271-3573470:1:exon> rdf:type insdc:Exon . <http://identifiers.org/insdc/NC_000911.1#feature:3573271-3573470:1:exon> rdfs:subClassOf obo:SO_0000147 . # SO:exon <http://identifiers.org/insdc/NC_000911.1#feature:3573271-3573470:1:exon> faldo:location <http://identifiers.org/insdc/NC_000911.1#region:3573271-3573470:1> . <http://identifiers.org/insdc/NC_000911.1#region:3573271-3573470:1> rdf:type faldo:Region . <http://identifiers.org/insdc/NC_000911.1#region:3573271-3573470:1> faldo:begin <http://identifiers.org/insdc/NC_000911.1#position:3573271:1> . <http://identifiers.org/insdc/NC_000911.1#region:3573271-3573470:1> faldo:end <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> . <http://identifiers.org/insdc/NC_000911.1#position:3573271:1> faldo:position 3573271 . <http://identifiers.org/insdc/NC_000911.1#position:3573271:1> faldo:reference <http://identifiers.org/insdc/NC_000911.1#sequence> . <http://identifiers.org/insdc/NC_000911.1#position:3573271:1> rdf:type faldo:ForwardStrandPosition . <http://identifiers.org/insdc/NC_000911.1#position:3573271:1> rdf:type faldo:ExactPosition . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> faldo:position 3573470 . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> faldo:reference <http://identifiers.org/insdc/NC_000911.1#sequence> . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> rdf:type faldo:ForwardStrandPosition . <http://identifiers.org/insdc/NC_000911.1#position:3573470:1> rdf:type faldo:ExactPosition . <urn:uuid:ede1f1e3-25d9-4058-a67d-a5963400abff> sio:SIO_000300 2 . # sio:has-value <urn:uuid:ede1f1e3-25d9-4058-a67d-a5963400abff> sio:SIO_000628 <http://identifiers.org/insdc/NC_000911.1#feature:1-772:1:exon> . # sio:refers-to <http://identifiers.org/insdc/NC_000911.1#feature:1-772:1:exon> rdf:type insdc:Exon . <http://identifiers.org/insdc/NC_000911.1#feature:1-772:1:exon> rdfs:subClassOf obo:SO_0000147 . # SO:exon <http://identifiers.org/insdc/NC_000911.1#feature:1-772:1:exon> faldo:location <http://identifiers.org/insdc/NC_000911.1#region:1-772:1> . <http://identifiers.org/insdc/NC_000911.1#region:1-772:1> rdf:type faldo:Region . <http://identifiers.org/insdc/NC_000911.1#region:1-772:1> faldo:begin <http://identifiers.org/insdc/NC_000911.1#position:1:1> . <http://identifiers.org/insdc/NC_000911.1#region:1-772:1> faldo:end <http://identifiers.org/insdc/NC_000911.1#position:772:1> . <http://identifiers.org/insdc/NC_000911.1#position:1:1> faldo:position 1 . <http://identifiers.org/insdc/NC_000911.1#position:1:1> faldo:reference <http://identifiers.org/insdc/NC_000911.1#sequence> . <http://identifiers.org/insdc/NC_000911.1#position:1:1> rdf:type faldo:ForwardStrandPosition . <http://identifiers.org/insdc/NC_000911.1#position:1:1> rdf:type faldo:ExactPosition . <http://identifiers.org/insdc/NC_000911.1#position:772:1> faldo:position 772 . <http://identifiers.org/insdc/NC_000911.1#position:772:1> faldo:reference <http://identifiers.org/insdc/NC_000911.1#sequence> . <http://identifiers.org/insdc/NC_000911.1#position:772:1> rdf:type faldo:ForwardStrandPosition . <http://identifiers.org/insdc/NC_000911.1#position:772:1> rdf:type faldo:ExactPosition . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> obo:so_has_part <http://identifiers.org/insdc/NC_000911.1#feature:3573271-3573470:1:exon>, <http://identifiers.org/insdc/NC_000911.1#feature:1-772:1:exon> . <http://identifiers.org/insdc/NC_000911.1#feature:1-3573470:1:CDS.1> sio:SIO_000974 <urn:uuid:36968b10-c862-4eaf-8086-403e5a26eea3>, <urn:uuid:ede1f1e3-25d9-4058-a67d-a5963400abff> . # sio:has-ordered-part <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:gene.2> rdf:type insdc:Gene . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:gene.2> rdfs:subClassOf obo:SO_0000704 . # SO:gene <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:gene.2> obo:RO_0002162 <http://identifiers.org/taxonomy/1148> . # RO:in taxon <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:gene.2> rdfs:label "SGL_RS01880" . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:gene.2> skos:prefLabel "SGL_RS01880" . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:gene.2> insdc:locus_tag "SGL_RS01880" . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:gene.2> insdc:old_locus_tag "slr0612" . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:gene.2> obo:so_part_of <http://identifiers.org/insdc/NC_000911.1#sequence> . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:gene.2> insdc:location "937..1494" . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:gene.2> faldo:location <http://identifiers.org/insdc/NC_000911.1#region:937-1494:1> . <http://identifiers.org/insdc/NC_000911.1#region:937-1494:1> rdf:type faldo:Region . <http://identifiers.org/insdc/NC_000911.1#region:937-1494:1> faldo:begin <http://identifiers.org/insdc/NC_000911.1#position:937:1> . <http://identifiers.org/insdc/NC_000911.1#region:937-1494:1> faldo:end <http://identifiers.org/insdc/NC_000911.1#position:1494:1> . <http://identifiers.org/insdc/NC_000911.1#position:937:1> faldo:position 937 . <http://identifiers.org/insdc/NC_000911.1#position:937:1> faldo:reference <http://identifiers.org/insdc/NC_000911.1#sequence> . <http://identifiers.org/insdc/NC_000911.1#position:937:1> rdf:type faldo:ForwardStrandPosition . <http://identifiers.org/insdc/NC_000911.1#position:937:1> rdf:type faldo:ExactPosition . <http://identifiers.org/insdc/NC_000911.1#position:1494:1> faldo:position 1494 . <http://identifiers.org/insdc/NC_000911.1#position:1494:1> faldo:reference <http://identifiers.org/insdc/NC_000911.1#sequence> . <http://identifiers.org/insdc/NC_000911.1#position:1494:1> rdf:type faldo:ForwardStrandPosition . <http://identifiers.org/insdc/NC_000911.1#position:1494:1> rdf:type faldo:ExactPosition . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:CDS.2> rdf:type insdc:Coding_Sequence . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:CDS.2> rdfs:subClassOf obo:SO_0000316 . # SO:CDS <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:CDS.2> obo:RO_0002162 <http://identifiers.org/taxonomy/1148> . # RO:in taxon <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:CDS.2> rdfs:label "SGL_RS01880" . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:CDS.2> skos:prefLabel "SGL_RS01880" . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:CDS.2> insdc:locus_tag "SGL_RS01880" . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:CDS.2> insdc:old_locus_tag "slr0612" . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:CDS.2> insdc:inference "EXISTENCE: similar to AA sequence:RefSeq:WP_010871208.1" . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:CDS.2> insdc:note "Uncharacterized RNA pseudouridine synthase slr0612; Derived by automated computational analysis using gene prediction method: Protein Homology." . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:CDS.2> insdc:codon_start 1 . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:CDS.2> insdc:transl_table 11 . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:CDS.2> insdc:product "hypothetical protein" . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:CDS.2> rdfs:seeAlso <http://identifiers.org/ncbiprotein/WP_010871208.1> . <http://identifiers.org/ncbiprotein/WP_010871208.1> rdfs:label "WP_010871208.1" . <http://identifiers.org/ncbiprotein/WP_010871208.1> rdf:type insdc:Protein . <http://identifiers.org/ncbiprotein/WP_010871208.1> sio:SIO_000068 <http://identifiers.org/ncbiprotein> . # sio:is-part-of <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:CDS.2> rdfs:seeAlso <http://identifiers.org/ncbigi/GI:499173621> . <http://identifiers.org/ncbigi/GI:499173621> rdfs:label "GI:499173621" . <http://identifiers.org/ncbigi/GI:499173621> rdf:type insdc:GI . <http://identifiers.org/ncbigi/GI:499173621> sio:SIO_000068 <http://identifiers.org/ncbigi> . # sio:is-part-of <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:CDS.2> sio:SIO_010081 <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:gene.2> . # sio:is-transcribed-from <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:CDS.2> rdfs:subClassOf obo:SO_0000673 . # SO:transcript <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:gene.2> rdfs:subClassOf obo:SO_0000010 . # SO:protein_coding <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:CDS.2> obo:so_part_of <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:gene.2> . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:CDS.2> insdc:location "937..1494" . <http://identifiers.org/insdc/NC_000911.1#feature:937-1494:1:CDS.2> faldo:location <http://identifiers.org/insdc/NC_000911.1#region:937-1494:1> . <http://identifiers.org/insdc/NC_000911.1#region:937-1494:1> rdf:type faldo:Region . <http://identifiers.org/insdc/NC_000911.1#region:937-1494:1> faldo:begin <http://identifiers.org/insdc/NC_000911.1#position:937:1> . <http://identifiers.org/insdc/NC_000911.1#region:937-1494:1> faldo:end <http://identifiers.org/insdc/NC_000911.1#position:1494:1> . <http://identifiers.org/insdc/NC_000911.1#position:937:1> faldo:position 937 . <http://identifiers.org/insdc/NC_000911.1#position:937:1> faldo:reference <http://identifiers.org/insdc/NC_000911.1#sequence> .
Biointerchange1.0データモデル図
Biointerchange1_rdf_sample.pdf
RefSeq/Genome-RDFとBiointerchange1.0/RDFのデータモデルの違い
- INSDC - GFVO オントロジー
- objectProperty, datatypePropertyの利用、dct:identifier -- gfvo:hasIdentifierなど
- .
- .
- .
今後の方針
- Genbank形式ファイルを作る or GFVOを利用したRefSeq-RDFと同等のデータモデルを設計し、コンバーター開発する
