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dbi_dataset_table.md

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Dataset table (for DB interface) req. dbi_make_filter_code

  • 遅いので sparql クエリ分割
    • 必要な offset limit 分だけ別クエリで取得
    • javascript セクションで必要な sparql json 形式を返す
    • line count のときは unless でスキップ

Parameters

  • datasets (Opt.)
    • example: DS1631_1,DS1631_2,DS1631_3
  • species (Opt.)
    • example: TAX_9606
  • species_s (Opt.)
    • example: vertebrates,plants
  • sample_type (Opt.)
    • example: C16403
  • cell_line (Opt.)
  • organ (Opt.)
  • disease (Opt.)
  • disease_s (Opt.)
    • example: cancer
  • modification (Opt.)
    • example: UNIMOD_21
  • instrument_mode (Opt.)
    • example: JPO_006
  • instrument (Opt.)
  • project_keywords (Opt.)
    • example: iPS
  • dataset_keywords (Opt.)
    • example: CH2O,by trypsin
  • protein_keywords (not work)
  • excluded_datasets (Opt.)
    • example: DS1631_1,DS1631_2
  • excluded_proteins (not work)
  • order (Opt.)
    • default: dataset_id
  • desc (Opt.)
    • example: 1
  • limit (Opt.)
    • exmaple: 10
  • offset (Opt.)
    • example: 0
  • line_count
    • example 1

filter

async ({datasets, species, species_s, sample_type, cell_line, organ, disease, disease_s, modification, 
       instrument_mode, instrument, project_keywords, dataset_keywords, protein_keywords, excluded_datasets, excluded_proteins, 
       order, desc, limit, offset, line_count}) => {
  var sparqlet = (api, body) => {
    const options = {
      method: 'POST',
      body: body,
      headers: {
        'Accept': 'application/json',
        'Content-Type': 'application/x-www-form-urlencoded'
      }
    };
    var res = fetch(api, options).then(res=>res.json());
    return res;
  }
  var params = [];
  params.push("mode=dataset");		
  if(datasets) params.push("datasets=" + datasets);
  if(species) params.push("species=" + species);
  if(species_s) params.push("species_s=" + species_s);
  if(sample_type) params.push("sample_type=" + sample_type);
  if(cell_line) params.push("cell_line=" + cell_line );
  if(organ) params.push("organ=" + organ );
  if(disease) params.push("disease=" + disease );
  if(disease_s) params.push("disease_s=" + disease_s );
  if(modification) params.push("modification=" + modification );
  if(instrument) params.push("instrument=" + instrument );
  if(instrument_mode) params.push("instrument_mode=" + instrument_mode );
  if(project_keywords) params.push("dataset_keywords=" + project_keywords );
  if(dataset_keywords) params.push("dataset_keywords=" + dataset_keywords );
  if(protein_keywords) params.push("protein_keywords=" + protein_keywords );
  if(excluded_datasets) params.push("excluded_datasets=" + excluded_datasets );
  if(excluded_proteins) params.push("excluded_proteins=" + excluded_proteins );
  if(order) params.push("order=" + order );
  if(desc) params.push("desc=" + desc );
  if(limit) params.push("limit=" + limit );
  if(offset) params.push("offset=" + offset );
  
  var res = await sparqlet("dbi_make_filter_code", params.join("&"));
  res.select_line = "DISTINCT ?dataset_id ?project_id ?project_title ?project_date ?species_label ?protein_count ?spectrum_count";
  if(line_count){
    res.select_line = "(COUNT(DISTINCT ?dataset_id) AS ?line_count)";
    res.code_limit = "";
  }
  return res;
};

Endpoint

{{SPARQLIST_EP}}

dataset

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX jpo: <http://rdf.jpostdb.org/ontology/jpost.owl#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX unimod: <http://www.unimod.org/obo/unimod.obo#>
PREFIX uniprot: <http://purl.uniprot.org/core/>
PREFIX tax: <http://purl.bioontology.org/ontology/NCBITAXON/>
PREFIX owl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX : <http://rdf.jpostdb.org/entry/>
SELECT {{filter.select_line}}
WHERE {
{{filter.code_value}}
  ?dataset a jpo:Dataset ;
           dct:identifier ?dataset_id ;
           ^jpo:hasDataset ?project ;
           sio:SIO_000216 [ a jpo:NumOfLeadingProteins ;
                          sio:SIO_000300 ?protein_count ] ;
           sio:SIO_000216 [ a jpo:NumOfSpectra ;
                          sio:SIO_000300 ?spectrum_count ] ;
           jpo:hasProfile/jpo:hasSample/jpo:species/rdfs:seeAlso/skos:prefLabel ?species_label .
  FILTER (LANG(?species_label) = 'en') 
{{filter.code_dataset}}
}
{{filter.code_limit}}

query_code

({line_count, dataset, filter}) => {
  if (line_count) return 0;
  return {
    values: dataset.results.bindings.map(d => ":" + d.dataset_id.value).join(" "),
  }
}

info

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX jpo: <http://rdf.jpostdb.org/ontology/jpost.owl#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#>
PREFIX unimod: <http://www.unimod.org/obo/unimod.obo#>
PREFIX uniprot: <http://purl.uniprot.org/core/>
PREFIX tax: <http://purl.bioontology.org/ontology/NCBITAXON/>
PREFIX owl: <http://www.geneontology.org/formats/oboInOwl#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX : <http://rdf.jpostdb.org/entry/>
SELECT {{filter.select_line}}
WHERE {
  {{#unless line_count}}
  VALUES ?dataset { {{query_code.values}} }
  ?dataset a jpo:Dataset ;
           dct:identifier ?dataset_id .
  ?project jpo:hasDataset ?dataset ;
           dct:identifier ?project_id ;
           dct:title ?project_title ;
           dct:date ?project_date .
  {{/unless}}
}

dataset_items

({line_count, dataset, info}) => {
  if (line_count) return dataset;
  let ds2pro = {};
  info.results.bindings.forEach(d => {
    ds2pro[d.dataset_id.value] = {
      project_id : d.project_id ,
      project_title : d.project_title, 
      project_date : d.project_date 
    }
  });
  dataset.head.vars.push("project_id", "project_title", "project_date");
  for (let i = 0; i < dataset.results.bindings.length; i++) {
    const ds_id = dataset.results.bindings[i].dataset_id.value;
    if (ds2pro[ds_id]) {
      dataset.results.bindings[i].project_id = ds2pro[ds_id].project_id;
      dataset.results.bindings[i].project_title = ds2pro[ds_id].project_title;
      dataset.results.bindings[i].project_date = ds2pro[ds_id].project_date;
    }
  }
  return dataset;
}