Question

我可以使用带有此主体的/rest/data/import/upload/{repositoryID}/url方法将MonDO本体加载到GraphDB Free 9中：

{
  "context": "http://purl.obolibrary.org/obo/mondo.owl",
  "data": "https://github.com/monarch-initiative/mondo/releases/download/current/mondo.owl",
  "format": "RDF/XML"
}

我也可以通过Workbench加载它，但是不能以编程方式加载它： http://data.bioontology.org/ontologies/ICD9CM/submissions/17/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb

我将format行设置为“ Turtle”，得到202条响应，但是工作台未显示任何导入。好像有时我在工作台的导入页面上看到错误消息，但是我不知道要采取什么纠正措施。

例如，如果我故意通过工作台以错误的格式（RDF / XML）导入ICD9，那么我会看到

RDF解析错误：序言中不允许内容。 [第2行，第1栏]

Answer 1

curl 'http://localhost:7200/rest/data/import/upload/w2/url' -H 'Content-Type: application/json;charset=UTF-8' -H 'Accept: application/json, text/plain, */*' --data-binary '{"type":"url","name":"http://data.bioontology.org/ontologies/ICD9CM/submissions/17/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb","format":"text/turtle","data":"http://data.bioontology.org/ontologies/ICD9CM/submissions/17/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb","status":"NONE","message":"","context":"","replaceGraphs":[],"baseURI":null,"forceSerial":false,"timestamp":1534939094325,"parserSettings":{"preserveBNodeIds":false,"failOnUnknownDataTypes":false,"verifyDataTypeValues":false,"normalizeDataTypeValues":false,"failOnUnknownLanguageTags":false,"verifyLanguageTags":true,"normalizeLanguageTags":false,"verifyURISyntax":true,"verifyRelativeURIs":true,"stopOnError":true}}

GraphDB处理api密钥，但是您应该以up或“ format”：“ text / turtle”的方式提供文件格式。希望这会有所帮助。

Answer 2

curl 'http://localhost:7200/rest/data/import/upload/abc/url' -H 'Content-Type: application/json;charset=UTF-8' -H 'Accept: application/json, text/plain, */*' --data-binary '{"type":"url","name":"http://www.w3.org/TR/owl-guide/wine.rdf","format":"","data":"http://www.w3.org/TR/owl-guide/wine.rdf","status":"NONE","message":"","context":"","replaceGraphs":[],"baseURI":null,"forceSerial":false,"timestamp":1534939094325,"parserSettings":{"preserveBNodeIds":false,"failOnUnknownDataTypes":false,"verifyDataTypeValues":false,"normalizeDataTypeValues":false,"failOnUnknownLanguageTags":false,"verifyLanguageTags":true,"normalizeLanguageTags":false,"verifyURISyntax":true,"verifyRelativeURIs":true,"stopOnError":true}}'

哪里

abc-是存储库ID
http://www.w3.org/TR/owl-guide/wine.rdf-是要导入的URL
1534939094325-自纪元以来的当前时间戳（以bash为单位，等效于date +%s）

如果要执行定期更新，建议您将每个文件放在自己的图形中（使用"context":"<file's url>"），然后将其替换为"replaceGraphs":"<file's url>"。数据库将创建增量并仅更新更改的语句。

Answer 3

借助于Ontotext的Sava，我能够构造此最小的curl命令，从而成功地从NCBO BioPortal加载了ICD9CM Turtle文件。

curl -d \
'{"type":"url","format":"text/turtle","data":"http://data.bioontology.org/ontologies/ICD9CM/submissions/17/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb","context":"http://data.bioontology.org/ontologies/ICD9CM/"}' \
-H 'Content-Type: application/json;charset=UTF-8' \
-X POST http://localhost:7200/rest/data/import/upload/disease_diagnosis_dev/url

我遗漏了许多键，包括timestamp和所有parserSettings。
我使用的是- d ... -X POST卷曲样式而不是--data-binary样式

我并不是声称知道这些决定的所有后果。

这是我在R中的方法

library(httr)
post.endpoint <- "http://localhost:7200//rest/data/import/upload/disease_diagnosis_dev/url"
update.body <- '{
  "type":"url",
  "format":"text/turtle",
  "context": "http://purl.bioontology.org/ontology/ICD9CM/",
  "data": "http://data.bioontology.org/ontologies/ICD9CM/submissions/17/download?apikey=9cf735c3-a44a-404f-8b2f-c49d48b2b8b2"
}'

post.result <- POST(post.endpoint,
                    body = update.body,
                    content_type("application/json"))

无法通过GraphDB API从URL加载某些本体

3 个答案:

这是我在R中的方法