SPARQLthon26/CyanoBase
提供：TogoWiki
（版間での差分）
(→SPARQL更新) |
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asm:refseq_category ?category; | asm:refseq_category ?category; | ||
asm:asm_name ?name; | asm:asm_name ?name; | ||
| - | asm: | + | asm:assembly_id ?id; |
asm:assembly_level ?level; | asm:assembly_level ?level; | ||
asm:bioproject ?bioproject; | asm:bioproject ?bioproject; | ||
2016年12月13日 (火) 01:47時点における最新版
CyanoBase
NCBI assembly_reportsにおいてtaxonomy id = 1117以下のゲノムプロジェクトを取得するSPARQL
PREFIX asm: <http://www.ncbi.nlm.nih.gov/assembly/> select * #?predicate ?object FROM <http://togogenome.org/graph/taxonomy> FROM <http://togogenome.org/graph/assembly_report> WHERE { #?assembly ?predicate ?object. ?assembly asm:refseq_category ?category; asm:asm_name ?name; asm:assembly_id ?id; asm:assembly_level ?level; asm:bioproject ?bioproject; asm:bioproject_accession ?bioproject_accession; asm:biosample_accession ?biosample_accession; asm:gbrs_paired_asm ?gbrs_paired_asm; asm:genome_rep ?rep; asm:infraspecific_name ?infraspecific_name; asm:isolate ?isolate; asm:organism_name ?organism_name; asm:paired_asm_comp ?paired_asm_comp; asm:release_date ?release_date; asm:release_type ?release_type; asm:species_taxid ?species_taxid; asm:submitter ?submitter; asm:tax_id ?tax_id; asm:taxon ?taxon; asm:version_status ?version_status; asm:wgs_master ?wgs_master; rdfs:seeAlso ?link. values ?category {"representative genome"}. values ?version_status {"latest"}. #FILTER(?predicate != asm:sequnece) FILTER(?taxon_root = <http://identifiers.org/taxonomy/1117>). #FILTER(?taxon_root = <http://identifiers.org/taxonomy/1117>). #Cyanobacteria #FILTER(?taxon_root = <http://identifiers.org/taxonomy/147537>). #Saccharomycotina #FILTER(?taxon_root = <http://identifiers.org/taxonomy/147545>). #Eurotiomycetes #FILTER(?taxon_root = <http://identifiers.org/taxonomy/451866>). #Taphrinomycotina #FILTER(?taxon_root = <http://identifiers.org/taxonomy/3041>). #Chlorophyta #FILTER(?taxon_root = <http://identifiers.org/taxonomy/2763>). #Rhodophyta #FILTER(?taxon_root = <http://identifiers.org/taxonomy/33090>). #Viridiplantae ?lineage rdfs:subClassOf* ?taxon_root. FILTER(?lineage = ?taxon). #FILTER(?link = <http://www.ncbi.nlm.nih.gov/assembly/GCF_000009725.1>). #FILTER(?taxon = <http://identifiers.org/taxonomy/1148>). } #LIMIT 1000 #ORDER BY ?predicate
SPARQL更新
- OKBP先生による高速化＋複数tax_root対応のSPARQL
DEFINE sql:select-option "order"
PREFIX asm: <http://www.ncbi.nlm.nih.gov/assembly/>
PREFIX tax: <http://identifiers.org/taxonomy/>
select *
FROM <http://togogenome.org/graph/taxonomy>
FROM <http://togogenome.org/graph/assembly_report>
WHERE
{
values ?taxon_root { tax:1117 tax:147537 tax:147545 tax:451866 tax:3041 tax: 2763 tax:33090}
values ?category {"representative genome"}.
values ?version_status {"latest"}.
?taxon_root a <http://ddbj.nig.ac.jp/ontologies/taxonomy/Taxon> .
?taxon rdfs:subClassOf* ?taxon_root.
?assembly asm:taxon ?taxon;
asm:refseq_category ?category;
asm:asm_name ?name;
asm:assembly_id ?id;
asm:assembly_level ?level;
asm:bioproject ?bioproject;
asm:bioproject_accession ?bioproject_accession;
asm:biosample_accession ?biosample_accession;
asm:gbrs_paired_asm ?gbrs_paired_asm;
asm:genome_rep ?rep;
asm:infraspecific_name ?infraspecific_name;
asm:isolate ?isolate;
asm:organism_name ?organism_name;
asm:paired_asm_comp ?paired_asm_comp;
asm:release_date ?release_date;
asm:release_type ?release_type;
asm:species_taxid ?species_taxid;
asm:submitter ?submitter;
asm:tax_id ?tax_id;
asm:taxon ?taxon;
asm:version_status ?version_status;
asm:wgs_master ?wgs_master;
rdfs:seeAlso ?link.
}
- 20141112版でrefseq_categoryの記述が変更していた "representative-genome" → "representative genome", "reference-genome" → "reference genome"
- 20150203 asm:assembly_id → asm:assembly_accession に変更
