Metadata API

The Brain Image Library (BIL) provides both a metadata API and web portal that uses the API to search and return metadata and links to datasets in BIL. The metadata API is extremely flexible and capable of full-text searching or individual metadata fields.

The metadata API has two primary user-facing endpoints:

query - the query endpoint will query the system and return a json document with matching entry. Queries use GET formatted URLs, which can be pasted in a web browser, utilized at the command-line through tools such as curl, or called programmatically. Query URLs take the form of:
/query/metadatadivision?metadataelement=querystring

retrieve - the retrieve endpoint will return the metadata as a json document for the given ids. Retrieve queries can be either GET formatted urls (for retrieving metadata for a single entry) or a POST request with a json payload. The json POST payload may be the results of an earlier query. The basic forms of the retrieve GET url are:

/retrieve?bildid=the_desired_id_to_retreive_metadata_for

For example:

https://api.brainimagelibrary.org/retrieve?bildid=ace-cot-pad

To make full programatic use of the Metadata API, we recommend that interested users first familiarize yourself with BIL's metadata model

Example Results

All successful queries will return a json file, that will all have the following json keys:

success -- true for successful queries
endpoint -- the endpoint used
message -- a user-friendly message, describing the status of the query
bildids -- a list of bil data ids that hold records that match the text used in the query

There will be other keys in the json payload, based on the metadata element and the search string. Here are a few examples:

Query:

https://api.brainimagelibrary.org/query/contributors?affiliation=Broad

	
{
          "success": "true",
          "endpoint": "Contributors/affiliation",
          "message": "GET success",
          "affiliation": "Broad",
          "bildids": [
                     "ace-big-pup",
                     "ace-big-pry",
                     "ace-big-pot",
                     "ace-big-pox",
                     "ace-big-pun"
          ]
        }

Query:

https://api.brainimagelibrary.org/query/image?gbytes=17.0

{
          "success": "true",
          "endpoint": "Image/gbytes",
          "message": "GET success",
          "gbytes": "17.0",
          "bildids": [
                     "act-zip",
                     "ace-bay-low",
                     "ace-aim-gum",
                     "ace-ask-row",
                     "ace-boo-dip"
          ]
        }

When one retreives an entry, the json payload returned will look like:

Query:

https://api.brainimagelibrary.org/retrieve?doi=https://doi.org/10.35077/rut

   {
    "success": "true",
    "endpoint": "Retrieve/doi",
    "message": "GET success",
    "doi": "https://doi.org/10.35077/rut",
    "retjson": [
        {
            "Metadata": "2.0",
            "Submission": {
                "sheet": "57",
                "collection": "1394",
                "submission_uuid": "96ba8210cceceeb7",
                "method": "ingest_1",
                "doi": "https://doi.org/10.35077/rut"
            },
            "Contributors": [
                {
                    "contributorname": "Allen Institute",
                    "creator": "Yes",
                    "contributortype": "ResearchGroup",
                    "nametype": "Organizational",
                    "nameidentifier": "",
                    "nameidentifierscheme": "",
                    "affiliation": "Allen Institute for Brain Science",
                    "affiliationidentifier": "https://ror.org/00dcv1019",
                    "affiliationidentifierscheme": "ROR"
                },
                {
                    "contributorname": "Bosiljka Tasic",
                    "creator": "No",
                    "contributortype": "ProjectLeader",
                    "nametype": "Personal",
                    "nameidentifier": "https://orcid.org/0000-0002-6861-4506",
                    "nameidentifierscheme": "ORCID",
                    "affiliation": "Allen Institute for Brain Science",
                    "affiliationidentifier": "https://ror.org/00dcv1019",
                    "affiliationidentifierscheme": "ROR"
                }
            ],
            "Funders": [
                {
                    "fundername": "National Institutes of Health",
                    "funding_reference_identifier": "https://ror.org/01cwqze88",
                    "funding_reference_identifier_type": "ROR",
                    "award_number": "1-RF-1MH121274-01",
                    "award_title": "Cell class- or type-specific viruses for brain-wide labeling and neural circuit examination"
                }
            ],
            "Publication": [],
            "Instrument": [
                {
                    "microscopetype": "Two Photon",
                    "microscopemanufacturerandmodel": "TissueVision TissueCyte 1000",
                    "objectivename": "Zeiss 20X Plan-Apochromat",
                    "objectiveimmersion": "Water",
                    "objectivena": "1.0",
                    "objectivemagnification": "20X",
                    "detectortype": "PMT",
                    "detectormodel": "Hamamatsu R3896",
                    "illuminationtypes": "",
                    "illuminationwavelength": "925nm",
                    "detectionwavelength": "447-593nm",
                    "sampletemperature": "20.0"
                }
            ],
            "Specimen": [
                {
                    "localid": "588181",
                    "species": "Mouse",
                    "ncbitaxonomy": "NCBI:txid10090",
                    "age": "58.0",
                    "ageunit": "Days",
                    "sex": "Female",
                    "genotype": "wt/wt",
                    "organlocalid": "1119684572.0",
                    "organname": "Brain",
                    "samplelocalid": "0539072223",
                    "atlas": "",
                    "locations": ""
                }
            ],
            "Dataset": [
                {
                    "bildirectory": "/bil/data/96/ba/96ba8210cceceeb7/0539072223",
                    "title": "588181",
                    "socialmedia": "",
                    "subject": "",
                    "subjectscheme": "",
                    "rights": "Allen Institute Terms of Use, Creative Commons Attribution 4.0 International",
                    "rightsuri": "https://alleninstitute.org/legal/terms-use/ , https://creativecommons.org/licenses/by/4.0/",
                    "rightsidentifier": "CC-BY-4.0",
                    "dataset_image": "https://alleninstitute.org/media/filer_public_thumbnails/filer_public/2e/6e/2e6e35a2-a82e-4e1c-af3d-4e95e43d3baf/logo_bs_header.png__220x220_q75_subsampling-2.jpg",
                    "generalmodality": "population imaging",
                    "technique": "enhancer virus labeling",
                    "other": "",
                    "abstract": "This is a series of serial two-photon images of whole mouse brain to characterize cell populations for the purpose of evaluating the specificity of newly created enhancer elements",
                    "methods": "",
                    "technicalinfo": "",
                    "doi": "https://doi.org/10.35077/rut",
                    "dataset_size": "None"
                }
            ],
            "Assets": [
                {
                    "bildid": "rut",
                    "bildoi": "https://doi.org/10.35077/rut",
                    "manifestfile": "https://download.brainimagelibrary.org/inventory/248f1b89-d78f-575c-88a4-32ad314a4a6e.json"
                }
            ],
            "Image": [
                {
                    "xaxis": "left-to-right",
                    "obliquexdim1": "",
                    "obliquexdim2": "",
                    "obliquexdim3": "",
                    "yaxis": "superior-to-inferior",
                    "obliqueydim1": "",
                    "obliqueydim2": "",
                    "obliqueydim3": "",
                    "zaxis": "posterior-to-anterior",
                    "obliquezdim1": "",
                    "obliquezdim2": "",
                    "obliquezdim3": "",
                    "landmarkname": "",
                    "landmarkx": "",
                    "landmarky": "",
                    "landmarkz": "",
                    "number": "1,2,3,red,green,blue",
                    "displaycolor": "(1.0,0.0,0.0),(0.0,1.0,0.0),(0.0,0.0,1.0)",
                    "representation": "neurite",
                    "flurophore": "CH1(background fluorescence)  CH2(GFP) CH3(background fluorescence)",
                    "stepsizex": "0.35",
                    "stepsizey": "0.35",
                    "stepsizez": "100.0",
                    "stepsizet": "",
                    "channels": "3.0",
                    "slices": "140.0",
                    "z": "1.0",
                    "xsize": "40000.0",
                    "ysize": "30000.0",
                    "zsize": "1.0",
                    "gbytes": "",
                    "files": "",
                    "dimensionorder": ""
                }
            ]
        }
    ]
    }

Note that if one retreives MULTIPLE entries via a PUT request, there will be multiple objects returned in the retjson array

Errors

When the API detects an error it will return a json message indicating the error. typical keys returned in the json payload include:

success - with an error, this will be false.
endpoint -- the endpoint used.
message -- a user-friendly message, describing why the error happened.

Here is an example (using CURL) if a POST was issued instead of GET:

Query:

	{
        "success": "false",
        "endpoint": "Contributors",
        "message": "POST method not allowed"
        }

Handling Partial Sucesss/ Partial Failure: This currently will only happen if one uses the /retreive endpoint with a post request. In such cases keys:

success -- this will be "true" NOT "false".
message -- will state that the POST was partially successful.
status -- (key,value)- will be "true" for ID's returned in "retjson", otherwise "false"
retjson -- will only contain metadata for the entries found.

Here is a brief example of what the beginning of the returned json document will look like:

     {
     "success": "true",
     "endpoint": "Retrieve",
     "message": "POST partially successful, some entries retreived",
     "status": {
          "act-zip": true,
          "ace-bay-low": true,
          "ace-aim-gum": false,
          "ace-ask-row": false,
          "ace-boo-dip": true
        },
     "retjson": [ ... ]
     }

Additional Examples

curl -k -X GET  'https://api.brainimagelibrary.org/query/fulltext?text=broad'
curl -k -X GET  'https://api.brainimagelibrary.org/query/funders?award_number=1-RF1-MH-124598-01'
curl -k -X GET  'https://api.brainimagelibrary.org/query/submission?doi=rut'
curl -k -X GET  'https://api.brainimagelibrary.org/query/contributors?affiliation=Broad'
curl -k -X GET  'https://api.brainimagelibrary.org/query/contributors?creator=Yes'
curl -k -X GET  'https://api.brainimagelibrary.org/query/instrument?microscopetype=upright'
curl -k -X GET  'https://api.brainimagelibrary.org/query/instrument?objectivename=olympus'
curl -k -X GET  'https://api.brainimagelibrary.org/query/specimen?localid=f024'
curl -k -X GET  'https://api.brainimagelibrary.org/query/specimen/linkage?xid=DO-FXXJ3038'
curl -k -X GET  'https://api.brainimagelibrary.org/query/specimen/linkage?type=cubie_tissue'
curl -k -X GET  'https://api.brainimagelibrary.org/query/specimen/linkage?relationship=slab'
curl -k -X GET  'https://api.brainimagelibrary.org/query/specimen/linkage?relationship=donor'
curl -k -X GET  'https://api.brainimagelibrary.org/query/specimen/linkage?class=xref'	
curl -k -X GET  'https://api.brainimagelibrary.org/query/dataset?title=mouse'
curl -k -X GET  'https://api.brainimagelibrary.org/query/image?gbytes=17.0'
curl -k -X GET  'https://api.brainimagelibrary.org/query/publication?relatedidentifier=doi'
	
curl -k -X GET  'https://api.brainimagelibrary.org/retrieve?bildid=rut'
curl -k -X GET  'https://api.brainimagelibrary.org/retrieve?doi=https://doi.org/10.35077/rut'