BH16.12/DFAST
提供：TogoWiki
目次 |
概要
バクテリア アノテーション・DDBJ登録支援パイプラインDFASTの開発
DFAST: https://dfast.nig.ac.jp
谷沢・藤澤・山本・真島・李
TogoAnnotatorとの連携
- DFASTのアノテーション結果編集画面から、TogoAnnotatorへの問い合わせを実装
- TogoAnnotatorの推測結果から、最適な遺伝子名をユーザーが選択可能に。
参照データベース作成・更新作業の自動化
- Taxonomy RDF, Assembly RDFを利用してアノテーションリソース取得
- RefSeqからrefseq_category="reference genome"であるエントリを取得
- TogoGenome開発版エンドポイント利用 http://dev.togogenome.org/sparql-test
Phylumごとに"reference genome"の件数を取得
DEFINE sql:select-option "order"
PREFIX asm: <http://www.ncbi.nlm.nih.gov/assembly/>
PREFIX tax: <http://identifiers.org/taxonomy/>
PREFIX ddbjtax: <http://ddbj.nig.ac.jp/ontologies/taxonomy/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT ?phylum (count(?asmid) as ?count)
FROM <http://togogenome.org/graph/taxonomy>
FROM <http://togogenome.org/graph/assembly_report>
WHERE
{
VALUES ?taxon_root {tax:2} # 2 bacteria, 10239 virus, 2157 archaea
VALUES ?rank {ddbjtax:Phylum}
VALUES ?version_status {"latest"}.
VALUES ?category {"reference genome"}.
?taxon_root a ddbjtax:Taxon .
?taxon rdfs:subClassOf* ?taxon_root .
?taxon ddbjtax:rank ?rank .
?taxon2 rdfs:subClassOf* ?taxon .
?assembly asm:taxon ?taxon2 .
?assembly asm:refseq_category ?category .
?assembly asm:assembly_id ?asmid .
?taxon rdfs:label ?phylum .
FILTER (STRSTARTS(?asmid, "GCF")).
}
GROUP BY ?phylum ORDER BY ?phylum
"reference genome"のAssembly ID取得
DEFINE sql:select-option "order"
PREFIX asm: <http://www.ncbi.nlm.nih.gov/assembly/>
PREFIX tax: <http://identifiers.org/taxonomy/>
PREFIX ddbjtax: <http://ddbj.nig.ac.jp/ontologies/taxonomy/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT
(REPLACE(STR(?taxon), "http://identifiers.org/taxonomy/", "") as ?phylum_id)
(REPLACE(STR(?taxon2), "http://identifiers.org/taxonomy/", "") as ?taxonomy_id)
?phylum ?scientificname ?asmid ?version_status ?category
FROM <http://togogenome.org/graph/taxonomy>
FROM <http://togogenome.org/graph/assembly_report>
WHERE
{
VALUES ?taxon_root {tax:2} # 2 bacteria, 10239 virus, 2157 archaea
VALUES ?rank { ddbjtax:Phylum }
VALUES ?version_status {"latest"}.
VALUES ?category {"reference genome"}.
?taxon_root a ddbjtax:Taxon .
?taxon rdfs:subClassOf* ?taxon_root.
?taxon ddbjtax:rank ?rank.
?taxon2 rdfs:subClassOf* ?taxon.
?assembly asm:taxon ?taxon2 .
?assembly asm:refseq_category ?category .
?assembly asm:assembly_id ?asmid .
?taxon rdfs:label ?phylum .
?taxon2 ddbjtax:scientificName ?scientificname
FILTER (STRSTARTS(?asmid, "GCF")).
}
ORDER BY ?phylum
- UniprotへSparqlを利用して検索を行いデータ取得
Assembly ID を指定し、そこに含まれるタンパクのアノテーション情報をUniProtから取得
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX embl: <http://purl.uniprot.org/embl/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
SELECT (REPLACE(STR(?id),"http://purl.uniprot.org/uniprot/", "") as ?UPID)
(GROUP_CONCAT(STR(?review); separator = "~~~") as ?reviewed)
(GROUP_CONCAT(?recname; separator ="~~~") as ?recname)
(GROUP_CONCAT(?subname; separator ="~~~") as ?subname)
(GROUP_CONCAT(?gene; separator ="~~~") as ?gene)
(GROUP_CONCAT(?fragment; separator ="~~~") as ?fragment)
(GROUP_CONCAT(STR(?precursor); separator ="~~~") as ?precursor)
(GROUP_CONCAT(replace(STR(?dbref), "http://purl.uniprot.org/", ""); separator =", ") as ?protid)
(GROUP_CONCAT(?lt; separator =", ") as ?locustag)
(GROUP_CONCAT(?ecnum; separator =", ") as ?ec) (sample(?seq) as ?sequence)
WHERE
{
VALUES ?assemblyID { embl:GCA_000011365.1 }
?proteome rdfs:seeAlso ?assemblyID .
?proteome skos:narrower ?subproteome .
?id up:proteome ?subproteome .
?id a up:Protein .
{
?id up:reviewed ?review .
?id up:sequence / rdf:value ?seq .
OPTIONAL {?id up:encodedBy / skos:prefLabel ?gene .}
OPTIONAL {?id up:recommendedName / up:fullName ?recname .}
OPTIONAL {?id up:submittedName / up:fullName ?subname .}
OPTIONAL {?id up:sequence / up:fragment ?fragment .}
OPTIONAL {?id up:sequence / up:precursor ?precursor .}
} UNION {
{
VALUES ?dbtype { <http://purl.uniprot.org/database/RefSeq> <http://purl.uniprot.org/database/EMBL> }
?id rdfs:seeAlso ?dbref .
?dbref up:database ?dbtype .
} UNION {
?id up:encodedBy / up:locusName ?lt .
} UNION {
?id up:domain ?domain .
?domain up:recommendedName / up:ecName ?ecnum .
} UNION {
?id up:recommendedName / up:ecName ?ecnum .
}
}
} GROUP BY ?id"""
- 参照データベースを作成しβ版としてリリース
DDBJ登録フォーマット
- MSS登録フォーマットのヘッダー部分の表記方法
- DATATYPE、KEYWORDの表記
- [TODO] STANDARD_DRAFT/HI_QUALITY_DRAFTの選択 http://www.ddbj.nig.ac.jp/sub/keyword-e.htmll
- inferenceの記述形式を確認
