Skip to content

Import Material

Allows users to import a material by providing an external source to pull information from. This endpoint will populate all possible fields on the material with information from the given source.

Import a Dataset:

Request:

POST /materials/import/

Parameters:

Name Type Description
import_source string The source of resource being imported. Options include: ["SRA", "GEO", "PROTOCOLS_IO"].
accession int The accession code for the study representing the material, in the form "SRP123456" for SRA or "GSE123456" for GEO.
organization_id int The ID of the organization that this material will be owned by.
grant_id int The ID of the grant that this material will be associated with.

Note:

  • To import a material from SRA or GEO, set "import_source" to the corresponding value.
  • All parameters are required.
  • Authorization Protected
  • The user making the request must own the given grant and be a part of the given organization.

Response:

Content-Type application/json
200 OK

{
   "id":3,
   "category":"DATASET",
   "url":"https://www.ebi.ac.uk/ena/data/view/SRA464955",
   "pubmed_id":"28085667",
   "additional_metadata":{
      "accession_code":"SRA464955",
      "description":"Tails of the GFP positive embryos were amputated. Tails were placed on ice for 30min before tissue disociation. GFP positive cells were sorted by FACS. RNA was harvested from GFP positive cells using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2302) was used with 13 ng of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.",
      "platform":"Illumina HiSeq 2500",
      "technology":"Rna-Seq",
      "num_samples":9
   },
   "mta_attachment":"None",
   "title":"Proliferation-independent regulation of organ size by Notch signaling",
   "needs_irb":false,
   "needs_abstract":false,
   "imported":true,
   "shipping_requirements":"None",
   "import_source":"SRA",
   "contact_user":"c308f9ed-20d2-4be9-8e5f-0c33e60f0689",
   "organization":1,
   "organism":[
      "Danio rerio"
   ],
   "publication_title":"Proliferation-independent regulation of organ size by Fgf/Notch signaling.",
   "pre_print_doi":"None",
   "pre_print_title":"None",
   "citation":"None",
   "additional_info":"None",
   "embargo_date":"None",
   "grants":[
      1
   ]
}

Import a Protocol:

Request:

POST /materials/import/

Parameters:

Name Type Description
import_source string The source of resource being imported. Options include: ["SRA", "GEO", "PROTOCOLS_IO"].
protocol_doi int The DOI of the protocol in question. This can be taken from a protocol's page on protocols.io, and is in the form "dx.doi.org/10.17504/protocols.io.c4gytv"
organization_id int The ID of the organization that this material will be owned by.
grant_id int The ID of the grant that this material will be associated with.

Note:

  • To import a protocols.io material, import_source must be set to "PROTOCOLS_IO".
  • All parameters are required.
  • Authorization Protected
  • The user making the request must own the given grant and be a part of the given organization.

Response:

Content-Type application/json
200 OK

{
   "id":9,
   "category":"PROTOCOL",
   "url":"https://www.protocols.io/view/lysis-buffer-20-ml-c4gytv",
   "pubmed_id":"",
   "additional_metadata":{
      "protocol_name":"Lysis Buffer (20 mL)",
      "abstract":"Must be made fresh before experiment because of the Sucrose. For 20 mL solutions."
   },
   "mta_attachment":"None",
   "title":"Lysis Buffer (20 mL)",
   "needs_irb":false,
   "needs_abstract":false,
   "imported":true,
   "shipping_requirements":"None",
   "import_source":"PROTOCOLS_IO",
   "contact_user":"2fb65e45-bdee-49e3-b30e-9b7edfad5a97",
   "organization":16,
   "organisms":"None",
   "publication_title":"None",
   "pre_print_doi":"None",
   "pre_print_title":"None",
   "citation":"None",
   "additional_info":"None",
   "embargo_date":"None",
   "is_archived":false,
   "grants":[
      4
   ]
}