Vocabularies

Introduction

Although the vocabularies are embedded, they're also available exposed to API users.

It should be noted that for a number of vocabularies, MBDB relies on external resources, so for general searching purposes you should use those directly rather than going through MBDB.

Retrieve vocabulary

The endpoint is:

https://mbdb.test.du.cesnet.cz/api/vocabularies/<vocabulary>/<vocabulary-id>

Where

<vocabulary> is one of affiliations, chemicals, grants, instruments, languages, organisms
<vocabulary-id> is the id of the vocabulary. Note that different vocabularies have different ID structures.

Example:

curl -k  \
  -H "Content-Type: application/json" \
  https://mbdb.test.du.cesnet.cz/api/vocabularies/organisms/taxid:562

Search vocabularies

Parameters

For all endpoints, the following search parameters are available:

Name	Description	Value options	Default value
q	The query string	string	`""`
l	layout	`list`	`list`
p	The page number	positive integer	`1`
s	The page size	positive integer	`10`
sort	The sorting order	`newest`, `title`, `oldest`, `bestmatch`	`title` if empty query, else `bestmatch`

Each parameter are set with = and parameters should be separated by &.

The endpoint is:

https://mbdb.test.du.cesnet.cz/api/vocabularies/<vocabulary>?

Where

<vocabulary> is one of affiliations, chemicals, grants, instruments, languages, organisms

Example:

curl -k  \
  -H "Content-Type: application/json" \
  https://mbdb.test.du.cesnet.cz/api/vocabularies/organisms?q="coli"&s=2

Using vocabulary items in API depositions

As each vocabulary item refers to a single global item (see Vocabularies), it is enough include the id of the item you want. The rest of the fields are fetched automatically and overwrites their corresponding fields if they are supplied.

Example

If the following (truncated) record is deposited:

{
  "metadata":{
    "general_parameters": {
      "funding_references": [
        {"id": "oa:corda__h2020::f219b1de6eeb4e5c5b2ad39010832d79"}
      ]
    }
  }
}

The following will be the resulting (truncated) record:

{
  "metadata":{
    "general_parameters": {
      "funding_references": [
        {
          "@v": "525aefc7-3183-457b-bf48-2c97c3aa4525::1",
          "funder_name": "European Commission",
          "grant_id": "101004806",
          "id": "oa:corda__h2020::f219b1de6eeb4e5c5b2ad39010832d79",
          "title": {
            "en": "MOlecular-Scale Biophysics Research Infrastructure"
          }
        }
      ]
    }
  }
}