Can't load some ontologies from URL via GraphDB API

Question

I can load the MonDO ontology into GraphDB Free 9 with the /rest/data/import/upload/{repositoryID}/url method with this body:

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

I can also load this via the Workbench, but not programatically: http://data.bioontology.org/ontologies/ICD9CM/submissions/17/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb

I set the format line to "Turtle" and I'm getting 202 responses, but the workbench doesn't show any import. It seems like some of the time I see error messages on the workbench's import page, but I don't understand what corrective action to take.

For example, if I intentionally import ICD9 via the workbench, with the wrong format (RDF/XML), then I see

RDF Parse Error: Content is not allowed in prolog. [line 2, column 1]

Sava Savov · Accepted Answer · 2019-11-29 08:25:32Z

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 handles api key but you should provide file format in the way up or "format":"text/turtle". Hope this helps.

answered Nov 29, 2019 at 8:25

Sava Savov

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2 Comments

Sava Savov Over a year ago

And also if in url part file format is known you should not write latter, GraphDB will recognize it.

Mark Miller Over a year ago

Can you provide a list of acceptable formats? I don't see them at graphdb.ontotext.com/free/devhub/workbench-rest-api/…. Can I trust iana.org/assignments/media-types/media-types.xhtml ? They don't list a type for BRF

Mark Miller · Accepted Answer · 2019-11-29 14:17:35Z

Thanks to Sava from Ontotext, I was able to construct this minimal curl command that successfully loads the ICD9CM Turtle file from the NCBO BioPortal.

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

I left out many of the keys, including the timestamp and all of the parserSettings.
I used the - d ... -X POST curl style instead of the --data-binary style

I don't claim to know all of the consequences of those decisions.

Here's my approach in R

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"))

TallTed · Accepted Answer · 2019-11-28 16:27:52Z

0

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}}'

where,

abc - is the repository id
http://www.w3.org/TR/owl-guide/wine.rdf - is the URL to import
1534939094325 - the current timestamp in seconds since epoch (in bash, equivalent to date +%s)

If you want to perform regular updates I advise you to put each file in its own graph (using the "context":"<file's url>") and then replace it with "replaceGraphs":"<file's url>". The database will create a delta and update only the changed statements.

edited Nov 28, 2019 at 16:27

TallTed

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answered Nov 28, 2019 at 16:19

Sava Savov

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3 Comments

Mark Miller Over a year ago

Can you provide a list of acceptable formats? I don't see them at graphdb.ontotext.com/free/devhub/workbench-rest-api/…

Sava Savov Over a year ago

The supported RDF formats are: 'ttl', 'rdf', 'rj', 'n3', 'nt', 'nq', 'trig', 'trix', 'brf', 'owl', 'jsonld', as well as their .gz versions and .zip archives.

Mark Miller Over a year ago

Thanks, I really appreciate all of your responses. Are you saying that I should pass "ttl" as the "format" argument, not "text/turtle"? I really want to see a list of the arguments that can be passed to that parameter. Is it in the documentation anywhere? The list you provided above looks like auto-recognized filename extensions.

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