RESTful API

Programatically accessing MGnify data via the API (Application Programming Interface)

Author

Affiliation

Published

March 12, 2024

With the rapid expansion in the number of datasets deposited in MGnify, it has become increasingly important to provide programmatic access to the data for cross-database complex queries.

API Overview

Current version

Current API version is v1

Base URL

The base address to the API is https://www.ebi.ac.uk/metagenomics/api/latest/.

A GET request can be issued to the root endpoint to get all categories that the API supports.

curl -X GET "https://www.ebi.ac.uk/metagenomics/api/latest/"

There are several easy-to-use top-levels resources, such as studies, samples, runs, experiment-types, biomes, and annotations. For example https://www.ebi.ac.uk/metagenomics/api/latest/studies retrieves a list of all studies, while https://www.ebi.ac.uk/metagenomics/api/latest/studies/ERP009004 retrieves a single study, with the accession ERP009004. The samples contained within this study can be retrieved using the relationship URL: https://www.ebi.ac.uk/metagenomics/api/latest/studies/ERP009004/samples.

The Browsable API

The easiest way to discover the API’s capabilities is to open the interactive “Browsable API” in your web browser.

This interace is created automatically when you open an API endpoint from a program that supports HTML (i.e. your browser). If you were to request the same URL using e.g. curl, plain JSON would be returned. This means you can find the URL pattern for data you’re interested in interactively, then copy the URL into your scripts.

HTTP methods

API provides read-only access to all resources, that means only HTTP GET method can be used with exception of authentication endpoint.

Response

Links to a resource return a JSON object formatted data structure that contains the resource type (in this example studies), associated object identifier (id) and attributes. Where appropriate, relationships and links are provided to other resources, allowing complex queries to be constructed.

{
  "data": {
1      "type": "studies",
2      "id": "MGYS00002008",
3      "attributes": {
          "bioproject": "PRJEB22493",
          "samples-count": 136,
          "accession": "MGYS00002008",
          "secondary-accession": "ERP104174",
          "centre-name": "EMBL-EBI",
          "is-public": true,
          "public-release-date": null,
          "study-abstract": "The APY Third Party Annotation (TPA) assembly was derived from the primary whole genome shotgun (WGS) data set PRJEB1787. This project includes samples from the following biomes : Marine.",
          "study-name": "EMG produced TPA metagenomics assembly of the Shotgun Sequencing of Tara Oceans DNA samples corresponding to size fractions for  prokaryotes. (APY) data set",
          "data-origination": "SUBMITTED",
          "last-update": "2022-01-16T11:17:46"
      },
4      "relationships": {
          "downloads": {
              "links": {
                  "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002008/downloads"
              }
          },
          "biomes": {
              "links": {
                  "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002008/biomes"
              },
              "data": [
                  {
                      "type": "biomes",
                      "id": "root:Environmental:Aquatic:Marine:Oceanic",
                      "links": {
                          "self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Marine:Oceanic"
                      }
                  }
              ]
          },
          "studies": {
              "links": {
                  "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002008/studies"
              },
              "data": [
                  {
                      "type": "studies",
                      "id": "MGYS00000410",
                      "links": {
                          "self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000410"
                      }
                  },
                  {
                      "type": "studies",
                      "id": "MGYS00000492",
                      "links": {
                          "self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00000492"
                      }
                  },
                  {
                      "type": "studies",
                      "id": "MGYS00001482",
                      "links": {
                          "self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00001482"
                      }
                  }
              ]
          },
          "samples": {
              "links": {
                  "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002008/samples"
              }
          },
          "geocoordinates": {
              "links": {
                  "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002008/geocoordinates"
              }
          },
          "publications": {
              "links": {
                  "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002008/publications"
              },
          },
          "analyses": {
              "links": {
                  "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002008/analyses"
              },
          }
      },
      "links": {
          "self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002008"
      }
  }
}

1: The type of this data object
2: The id of this specific object
3: The attributes (i.e. properties) of this data object
4: The relationships this object has with others

Hypermedia

All resources may have one or more links properties referencing to other resources, to provide explicit URLs so that proper API clients don’t need to construct URLs on their own.

Note

It is highly recommended for API clients to use links for future upgrades of the API.

Pagination

As some queries can result in a large response, the API supports pagination, using a page number and size of results per page as query parameters. Request that return multiple items is paginated to 20 items by default, and can be increased up to 100:

curl -X GET "https://www.ebi.ac.uk/metagenomics/api/latest/studies?page_size=100"

Navigation through pages:

{
  "links": {
    "first": "https://www.ebi.ac.uk/metagenomics/api/latest/studies?page=1",
    "last": "https://www.ebi.ac.uk/metagenomics/api/latest/studies?page=63",
    "next": "https://www.ebi.ac.uk/metagenomics/api/latest/studies?page=26",
    "prev": "https://www.ebi.ac.uk/metagenomics/api/latest/studies?page=24"
  },
  "data": [ ],
  "meta": {
    "pagination": {
      "page": 25,
      "pages": 63,
      "count": 1255
    }
  }
}

Note

Some API endpoint use cursor-based pagination, because they come from a document database. The links object in responses provided the necesary cursors to fetch

For example, fetching Contigs for an analysis.

curl -X GET "https://www.ebi.ac.uk/metagenomics/api/v1/analyses/MGYA00585528/contigs"

Gives:

{
  "links": {
      "next": "https://www.ebi.ac.uk/metagenomics/api/v1/analyses/MGYA00585528/contigs?cursor=cD02MTUyMDU0Yzg5YTUzNWM2ZDQzYTY5MGI%3D",
      "prev": null
  },
  "data": [
      {
          "type": "analysis-job-contigs",
          "id": "6152054c89a535c6d43a68f3",
          "attributes": {
              "contig-id": "ERZ2310312.1-contig-1",
              "length": 20832,
              "coverage": 0.0,
              "analysis-id": "585528",
              "accession": "MGYA00585528",
              "pipeline-version": "5.0",
              "job-id": 585528,
              "has-cog": true,
              "has-kegg": true,
              "has-go": true,
              "has-pfam": true,
              "has-interpro": true,
              "has-antismash": false,
              "has-kegg-module": false
          }
      },
      "..."
  ],
  "meta": {
      "pagination": {
          "count": 105
      }
  }
}

Parameters

Lists of resources can be filtered and sorted by selected parameters, allowing the construction of more complex queries. For instance, in order to retrieve oceanographic samples from metagenomic studies taken at temperature less than 10C, the following query could be constructed https://www.ebi.ac.uk/metagenomics/api/latest/biomes/root:Environmental:Aquatic:Marine/samples?experiment_type=metagenomic&metadata_key=temperature&metadata_value_lte=10&ordering=accession

curl -X GET "https://www.ebi.ac.uk/metagenomics/api/latest/biomes/root:Environmental:Aquatic:Marine/samples?experiment_type=metagenomic&metadata_key=temperature&metadata_value_lte=10&ordering=accession"

The provision of such complex queries allows metadata to be combined with annotation for powerful data analysis and visualisation.

Customising queries: compound documents

The API response distinguishes between attributes and relationships, allowing customisation of the response by passing fields or including relations as parameters in the initial query.

Some relationship fields render the related data automatically, in cases where the count of related objects is known to always be small, and where this is an extremely common requirement.

For other relationships, adding ?include=<relationship field> to a query will result in the relationships response including a <relationship field>.data object, with a list of IDs of the related object. Provided these data arrays are non-empty, the response will also include a top-level included array, with the corresponding IDs and fully rendered data for the related objects. This format is known as a “Compound Document”.

Warning

The list of related objects is not paginated, and can be very expensive to query. Only a subset of relationships are available for inclusion in compound documents: these are based on common use cases and on queries that can be optimised so are less likely to run slowly or time out.

The supported ?include= relationships are discoverable using the “Browsable API” in your web browser.

For example:

curl -X GET "https://www.ebi.ac.uk/metagenomics/api/latest/studies/MGYS00002008?include=samples,biomes"

{
  "data": {
      "type": "studies",
      "id": "MGYS00002008",
      "attributes": {
          "..."
      },
      "relationships": {
          "samples": {
              "links": {
                  "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002008/samples"
              },
              "data": [
                  {
                      "type": "samples",
                      "id": "6173"
                  }
              ]
          },
          "..."
          "biomes": {
              "links": {
                  "related": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002008/biomes"
              },
              "data": [
                  {
                      "type": "biomes",
                      "id": "root:Environmental:Aquatic:Marine",
                      "links": {
                          "self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Marine"
                      }
                  }
              ]
          },
          "..."
      },
      "links": {
          "self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002008"
      }
  },
1  "included": [
      {
          "type": "biomes",
          "id": "root:Environmental:Aquatic:Marine",
          "attributes": {
              "samples-count": 183,
              "biome-name": "Marine",
              "lineage": "root:Environmental:Aquatic:Marine"
          },
          "relationships": {
              "samples": {
                  "links": {
                      "related": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Marine/samples"
                  }
              },
              "children": {
                  "links": {
                      "related": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Marine/children"
                  }
              },
              "genomes": {
                  "links": {
                      "related": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Marine/genomes"
                  }
              },
              "studies": {
                  "links": {
                      "related": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Marine/studies"
                  }
              }
          },
          "links": {
              "self": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Marine"
          }
      },
      {
          "type": "samples",
          "id": "ERS487899",
          "attributes": {
              "sample-metadata": [],
              "longitude": -6.5669,
              "biosample": "SAMEA2619376",
              "latitude": 36.5533,
              "accession": "ERS487899",
              "analysis-completed": "2015-03-17",
              "collection-date": "2009-09-15",
              "geo-loc-name": null,
              "sample-desc": "&quot;This sample (TARA_X000000263) was collected during the Tara Oceans expedition (2009-2013) at station TARA_004 (latitudeN=36.5533, longitudeE=-6.5669) on date/time=2009-09-15T11:30, using a PUMP (High Volume Peristaltic Pump).  The sample material (saline water (ENVO:00002010), including plankton (ENVO:xxxxxxxx)) was collected at a depth of 3-7 m, targeting a surface water layer (ENVO:00002042) in the marine biome (ENVO:00000447). The sample was size-fractionated (0.22-1.6 micrometres), and stored in liquid nitrogen for later detection of prokaryote nucleic acid sequences by pyrosequencing methods, and for later metagenomics analysis. This sample has replicate sample(s): TARA_X000000264.&quot;",
              "environment-biome": "marine biome (ENVO:00000447)",
              "environment-feature": "surface water layer (ENVO:00002042)",
              "environment-material": "&quot;saline water (ENVO:00002010), including plankton (ENVO:xxxxxxxx)&quot;",
              "sample-name": "TARA_X000000263",
              "sample-alias": "TARA_X000000263",
              "host-tax-id": null,
              "species": null,
              "last-update": "2019-09-25T16:24:35"
          },
          "relationships": {
              "runs": {
                  "links": {
                      "related": "https://www.ebi.ac.uk/metagenomics/api/v1/samples/ERS487899/runs"
                  }
              },
              "biome": {
                  "data": {
                      "type": "biomes",
                      "id": "root:Environmental:Aquatic:Marine"
                  },
                  "links": {
                      "related": "https://www.ebi.ac.uk/metagenomics/api/v1/biomes/root:Environmental:Aquatic:Marine"
                  }
              },
              "studies": {
                  "links": {
                      "related": "https://www.ebi.ac.uk/metagenomics/api/v1/samples/ERS487899/studies"
                  },
                  "data": [
                      {
                          "type": "studies",
                          "id": "MGYS00002008",
                          "links": {
                              "self": "https://www.ebi.ac.uk/metagenomics/api/v1/studies/MGYS00002008"
                          }
                      }
                  ]
              }
          },
          "links": {
              "self": "https://www.ebi.ac.uk/metagenomics/api/v1/samples/ERS487899"
          }
      }
  ]
}

1: The included data objects of this Compound Document

Datasets that cannot be made using a single Compound Document should be built up by making several requests to the API, using the URIs provided in the relationships.<related field>.links.related attributes.

Errors

There are three possible types of client errors on API calls:

400 Bad requests.
404 Not found.
403 Authentication failed.

Examples

Examples of using the API are provided in our MGnify Notebooks Server, which is available at notebooks.mgnify.org. See the dedicated documentation for that resource for more information.
You can also find our example notebooks and scripts on GitHub.
We also have short examples of how to fetch paginated data from the API into one big CSV/TSV file.

Interactive documentation

We have utilised an interactive documentation framework (Swagger UI) to visualise and simplify interaction with the API’s resources via an HTML interface. Detailed explanations of the purpose of all resources, along with many examples, are provided to guide end-users.

Documentation on how to use the endpoints is available at https://www.ebi.ac.uk/metagenomics/api/docs/.

Citation

BibTeX citation:

@online{2024,
  author = {, MGnify},
  title = {RESTful {API}},
  pages = {undefined},
  date = {2024-03-12},
  url = {https://docs.mgnify.org/src/docs/api.html},
  langid = {en}
}

For attribution, please cite this work as:

MGnify. 2024. “RESTful API.” March 12, 2024. https://docs.mgnify.org/src/docs/api.html.

API Overview

Current version

Base URL

The Browsable API

HTTP methods

Response

Hypermedia

Pagination

Parameters

Customising queries: compound documents

Errors

Cross Origin Resource Sharing

Examples

Interactive documentation

Citation