PSICQUIC

glycovid_PSIQUIC

RDF schema

How to use

# query psicquic data by rest api
python query_all.py
# exppantion tsv by "|"
python mylib/expansion_tsv.py
# create ttl file from tsv
python create_ttl.py
# Create ShEx files of created RDF file by sheXer.
python shexer/main.py

Tree description

PSICQUIC
├── mylib
│   └── general_method.py      # Service list of psicquic
├── owl
├── resources
├── shexer                     # A sheXer script and ShEx files generated by sheXer to validate RDF data.
│   ├── main.py                # sheXer script.
│   └── shex_{time}.shex       # ShEx script generated by main.py.
├── sparql                     # Sample query with SPARQL and run SPARQL with Python
├── uri_list                   # List of interactor source database and the uri header
├── data                       # Tsv files which are ueried
├── expdata                    # Results of expantion queried tsv data
├── turtle                     # RDF files generated by create_ttl.py
├── create_ttl.py              # Create rdf files from queried data in data/ directroy.
└── query_all.py               # Query interaction datasets from PSICQUIC by REST API.

glycovid_PSICQUIC 仕様

• スキーマ

Flowchart Maker & Online Diagram Software

• db 一覧
  • BioGrid
  • bhf-ucl
  • ChEMBL
  • HPIDb
  • IntAct
  • IMEx
  • mentha
  • MPIDB
  • iRefIndex
  • MatrixDB
  • MINT
  • Reactome
  • Reactome-FIs
  • EBI-GOA-miRNA
  • UniProt
  • MBInfo
  • BindingDB
  • VirHostNet
  • #BAR
  • EBI-GOA-nonIntAct
  • tfact2gene
• クエリ内容

queryes = [
  "species:human" + " OR species:9606" + " OR taxidA:human" + " OR taxidA:9606" + " OR taxidB:human" + " OR taxidA:9606"
];
interactiontype_except_list = [
  'psi-mi:"MI:0217"(phosphorylation reaction)',
  'psi-mi:"MI:0203"(dephosphorylation reaction)',
  'psi-mi:"MI:1110"(predicted interaction)'
];

• MatrixDB とデータがつながる形でマッピング

Flowchart Maker & Online Diagram Software

@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix ns1: <http://purl.obolibrary.org/obo/> .
@prefix ns2: <http://rdf.glycoinfo.org/PSICQUIC/Ontology#> .
@prefix ns3: <http://www.biopax.org/release/biopax-level3.owl#> .
@prefix ns4: <http://semanticscience.org/resource/> .
@prefix ns5: <http://www.bioassayontology.org/bao#> .

<http://rdf.glycoinfo.org/matrixdb.association:chembl-target_CHEMBL2107838__uniprotkb_P35318%23PRO_0000000963> ns1:IAO_0000119 <http://rdf.glycoinfo.org/dbid/imex/IM-22908> ;
    ns1:INO_0000154 ns1:MI_0915 ;
    dc:identifier <http://rdf.glycoinfo.org/dbid/imex/IM-22908-12> ;
    dc:source ns1:MI_0469 ;
    ns2:has_interactor_A <http://rdf.glycoinfo.org/dbid/chembl.target/CHEMBL2107838> ;
    ns2:has_interactor_B <http://rdf.glycoinfo.org/dbid/uniprot/P35318%23PRO_0000000963> ;
    ns4:SIO_000253 <http://rdf.glycoinfo.org/dbid/taxonomy/9606> ;
    ns5:BAO_0002875 ns1:MI_0107 ;
    ns3:interactionType ns1:MI_0915 .

• subject: interactor_ab
  • https://identifiers.org/matrixdb.association:{databasea}{ida}__{database_b}{id_b}
  • 大文字は小文字に
  • 記号は-に変換(_)
• object
  • https://identifiers.org: 　 → 　　http://rdf.glycoinfo.org/dbid/
  • P39060-PRO_000005794 → P39060#PRO_000005794
  • chebi のデータはhttps://github.com/dbcls/togoid-config/blob/main/config/dataset.yamlに合わせる
• interaction_ab から interactorA/B へのプロパティ
  • ~~http://rdf.glycoinfo.org/ontology/interaction#has_interactor_A~~
  • http://rdf.glycoinfo.org/PSICQUIC/Ontology#has_interactor_A
• interaction id の class
  • ~~http://rdf.glycoinfo.org/ontology/interaction#InteractionId~~
  • http://rdf.glycoinfo.org/PSICQUIC/Ontology#InteractionId
• 基本的に URI は<http://rdf.glycoinfo.org/dbid/{db}/{id}>を使用する
  • https://identifiers.org/{db}/:　 → 　http://rdf.glycoinfo.org/dbid/{db}/
  • purl.obolibrary.org, bioregistry.org は例外的に使用する
• Host organism の URI について
  • taxonid: -1(in vitro)は<http://www.bioassayontosiyousuru.org/bao#BAO_0020008>を使用する
  • axohaid: -2(chemical synthesis)は<http://semanticscience.org/resource/SIO_000559>を使用する

  <...> <http://semanticscience.org/resource/SIO_000253> [ rdf:type <http://semanticscience.org/resource/SIO_000559> ] .
  

  <...> <http://semanticscience.org/resource/SIO_000253> [ rdf:type <http://www.bioassayontology.org/bao#BAO_0020008> ] .
  

• 除いたデータ
  • http://rdf\.glycoinfo\.org/dbid/pubmed/unassigned\d+
    • intact, imex, mentha
  • http://rdf\.glycoinfo\.org/dbid/reactome/REACT_\d{4}\.\d
    • mint
  • http://rdf\.glycoinfo\.org/dbid/uniprot/Missing-Uniprot-ID-for-[A-Z0-9]+
    • tfact2gene
  • http://rdf\.glycoinfo\.org/dbid/ensembl/Missing-Ensembl-Gene-ID-for-[-@A-Z0-9]+
    • tfact2gene

object list