提取给定节点的所有父节点

Question

我正在尝试使用 EBI-RDF sparql endpoint, I was based on two 类似的问题来提取每个给定 GO Id（一个节点）的所有父节点来制定查询，这里有两个例子说明了这个问题：

biological_process (GO:0008150)
           |__ metabolic process (GO:0008152)
                           |__ methylation (GO:0032259)

在此示例中，使用以下查询：

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 dc: <http://purl.org/dc/elements/1.1/>
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX dbpedia2: <http://dbpedia.org/property/>
PREFIX dbpedia: <http://dbpedia.org/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>

PREFIX obo: <http://purl.obolibrary.org/obo/>

SELECT (count(?mid) as ?depth)
       (group_concat(distinct ?midId ; separator = " / ") AS ?treePath) 
FROM <http://rdf.ebi.ac.uk/dataset/go> 
WHERE {
    obo:GO_0032259 rdfs:subClassOf* ?mid .
    ?mid rdfs:subClassOf* ?class .
    ?mid <http://www.geneontology.org/formats/oboInOwl#id> ?midId.
}
GROUP BY ?treePath
ORDER BY ?depth

我毫无问题地得到了想要的结果：

c |              treePath
--|-------------------------------------
6 | GO:0008150 / GO:0008152 / GO:0032259

但是当术语存在于多个分支中时（例如GO:0007267），如下例，之前的方法不起作用：

示例 2 (Link to the structure)

biological_process (GO:0008150)
           |__ cellular_process (GO:0009987)
           |           |__ cell communication (GO:0007154)
           |                       |__ cell-cell signaling (GO:0007267)
           |
           |__ signaling (GO:0023052)
                      |__ cell-cell signaling (GO:0007267)

结果：

c |                            treePath
--|---------------------------------------------------------------
15| GO:0007154 / GO:0007267 / GO:0008150 / GO:0009987 / GO:0023052

我想得到的是：

GO:0008150 / GO:0009987 / GO:0007154 / GO:0007267
GO:0008150 / GO:0023052 / GO:0007267

我的理解是，在引擎盖下我正在计算每个级别的深度并使用它来构建路径，当我们有一个仅属于一个分支的元素时，这工作正常。

SELECT (count(?mid) as ?depth) ?midId
FROM <http://rdf.ebi.ac.uk/dataset/go> 
WHERE {
    obo:GO_0032259 rdfs:subClassOf* ?mid .
    ?mid rdfs:subClassOf* ?class .
    ?mid <http://www.geneontology.org/formats/oboInOwl#id> ?midId.
}
GROUP BY ?midId
ORDER BY ?depth

结果：

depth |   midId
------|------------
1     | GO:0008150
2     | GO:0008152
3     | GO:0032259

在第二个例子中，事情被遗漏了，我不明白为什么，无论如何我确定问题的一部分是具有相同 depth/level 的术语，但我不知道不知道怎么解决。

depth |   midId
------|------------
2     | GO:0008150
2     | GO:0009987
2     | GO:0023052
3     | GO:0007154
6     | GO:0007267

Answer 1

感谢@AKSW，我找到了一个使用 HyperGraphQL (a GraphQL 接口在 Web 上查询和提供链接数据的不错的解决方案。

我会在这里留下详细的答案，它可能会对某人有所帮助。

我下载并设置了 HyperGraphQL download page

将其链接到 this tutorial

中所述的 EBI Sparql 端点

我使用的config.json文件：

{
    "name": "ebi-hgql",
    "schema": "ebischema.graphql",
    "server": {
        "port": 8081,
        "graphql": "/graphql",
        "graphiql": "/graphiql"
    },
    "services": [
        {
            "id": "ebi-sparql",
            "type": "SPARQLEndpointService",
            "url": "http://www.ebi.ac.uk/rdf/services/sparql",
            "graph": "http://rdf.ebi.ac.uk/dataset/go",
            "user": "",
            "password": ""
        }
    ]
}

这是我的 ebischema.graphql 文件的样子（因为我只需要 Class、id、label 和 subClassOf）：

type __Context {
    Class:          _@href(iri: "http://www.w3.org/2002/07/owl#Class")
    id:             _@href(iri: "http://www.geneontology.org/formats/oboInOwl#id")
    label:          _@href(iri: "http://www.w3.org/2000/01/rdf-schema#label")
    subClassOf:     _@href(iri: "http://www.w3.org/2000/01/rdf-schema#subClassOf")
}

type Class @service(id:"ebi-sparql") {
    id: [String] @service(id:"ebi-sparql")
    label: [String] @service(id:"ebi-sparql")
    subClassOf: [Class] @service(id:"ebi-sparql")
}

我开始测试一些简单的查询，但不断得到空响应； this issue 的答案解决了我的问题。

最后我构建了获取树的查询

使用这个查询：

{
  Class_GET_BY_ID(uris:[
    "http://purl.obolibrary.org/obo/GO_0032259",
    "http://purl.obolibrary.org/obo/GO_0007267"]) {
    id
    label
    subClassOf {
      id
      label
      subClassOf {
        id
        label
      }
    }
  }
}

我得到了一些有趣的结果：

{
  "extensions": {},
  "data": {
    "@context": {
      "_type": "@type",
      "_id": "@id",
      "id": "http://www.geneontology.org/formats/oboInOwl#id",
      "label": "http://www.w3.org/2000/01/rdf-schema#label",
      "Class_GET_BY_ID": "http://hypergraphql.org/query/Class_GET_BY_ID",
      "subClassOf": "http://www.w3.org/2000/01/rdf-schema#subClassOf"
    },
    "Class_GET_BY_ID": [
      {
        "id": [
          "GO:0032259"
        ],
        "label": [
          "methylation"
        ],
        "subClassOf": [
          {
            "id": [
              "GO:0008152"
            ],
            "label": [
              "metabolic process"
            ],
            "subClassOf": [
              {
                "id": [
                  "GO:0008150"
                ],
                "label": [
                  "biological_process"
                ]
              }
            ]
          }
        ]
      },
      {
        "id": [
          "GO:0007267"
        ],
        "label": [
          "cell-cell signaling"
        ],
        "subClassOf": [
          {
            "id": [
              "GO:0007154"
            ],
            "label": [
              "cell communication"
            ],
            "subClassOf": [
              {
                "id": [
                  "GO:0009987"
                ],
                "label": [
                  "cellular process"
                ]
              }
            ]
          },
          {
            "id": [
              "GO:0023052"
            ],
            "label": [
              "signaling"
            ],
            "subClassOf": [
              {
                "id": [
                  "GO:0008150"
                ],
                "label": [
                  "biological_process"
                ]
              }
            ]
          }
        ]
      }
    ]
  },
  "errors": []
}

编辑

这正是我想要的，但我注意到我不能像这样添加另一个子级别：

{
  Class_GET_BY_ID(uris:[
    "http://purl.obolibrary.org/obo/GO_0032259",
    "http://purl.obolibrary.org/obo/GO_0007267"]) {
    id
    label
    subClassOf {
      id
      label
      subClassOf {
        id
        label
        subClassOf {  # <--- 4th sublevel
          id
          label
        }
      }
    }
  }
}

我创建了一个新问题：Endpoint returned Content-Type: text/html which is not recognized for SELECT queries

提取给定节点的所有父节点

Extract all parents of a given node

tree

ontology

sparql

virtuoso