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ccf-api-spec.yaml
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ccf-api-spec.yaml
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openapi: 3.0.0
servers:
- description: Mock Server
url: 'https://virtserver.swaggerhub.com/cns8/ccf/0.1.0'
info:
description: |
This API provides data for the CCF
[RUI](https://github.com/hubmapconsortium/ccf-3d-registration) and
[EUI](https://github.com/hubmapconsortium/ccf-ui)
[http://www.hubmap.org](http://www.hubmap.org)
version: 0.1.0
title: CCF RUI/EUI API
termsOfService: 'http://www.hubmap.org'
contact:
email: [email protected]
license:
name: Apache 2.0
url: 'http://www.apache.org/licenses/LICENSE-2.0.html'
tags:
- name: Primary Search
description: Primary Search Routes
- name: Primary Lookup
description: Primary Lookup Routes
- name: Secondary
description: Secondary Routes
paths:
/donors:
get:
tags:
- Primary Search
summary: Get Donors
operationId: getDonors
responses:
'200':
description: successful operation
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/Donor'
'400':
description: Invalid Id
'401':
description: User is not authorized to look for entities
'404':
description: not found
'/donors/{donor_id}':
get:
tags:
- Primary Lookup
summary: Get Donor
operationId: getDonor
parameters:
- name: donor_id
in: path
required: true
schema:
type: string
format: uuid
responses:
'200':
description: successful operation
content:
application/json:
schema:
$ref: '#/components/schemas/Donor'
'400':
description: Invalid Id
'401':
description: User is not authorized to look for entities
'404':
description: not found
/procedures:
get:
tags:
- Primary Search
summary: Get Procedures
operationId: getProcedures
responses:
'200':
description: successful operation
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/Procedure'
'400':
description: Invalid Id
'401':
description: User is not authorized to look for entities
'404':
description: not found
'/procedures/{procedure_id}':
get:
tags:
- Primary Lookup
summary: Get Procedure
operationId: getProcedure
parameters:
- name: procedure_id
in: path
required: true
schema:
type: string
format: uuid
responses:
'200':
description: successful operation
content:
application/json:
schema:
$ref: '#/components/schemas/Procedure'
links:
donor:
$ref: '#/components/links/GetDonorById'
'400':
description: Invalid Id
'401':
description: User is not authorized to look for entities
'404':
description: not found
/samples:
get:
tags:
- Primary Search
summary: Get Samples
operationId: getSamples
responses:
'200':
description: successful operation
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/Sample'
'400':
description: Invalid Id
'401':
description: User is not authorized to look for entities
'404':
description: not found
'/samples/{sample_id}':
get:
tags:
- Primary Lookup
summary: Get Sample
operationId: getSample
parameters:
- name: sample_id
in: path
required: true
schema:
type: string
format: uuid
responses:
'200':
description: successful operation
content:
application/json:
schema:
$ref: '#/components/schemas/Sample'
links:
donor:
$ref: '#/components/links/GetDonorById'
procedure:
$ref: '#/components/links/GetProcedureById'
superSample:
$ref: '#/components/links/GetSuperSampleById'
alignment:
$ref: '#/components/links/GetAlignmentById'
'400':
description: Invalid Id
'401':
description: User is not authorized to look for entities
'404':
description: not found
/alignments:
get:
tags:
- Primary Search
summary: Get Alignments
operationId: getAlignments
responses:
'200':
description: successful operation
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/Alignment'
'400':
description: Invalid Id
'401':
description: User is not authorized to look for entities
'404':
description: not found
'/alignments/{alignment_id}':
get:
tags:
- Primary Lookup
summary: Get Alignment
operationId: getAlignment
parameters:
- name: alignment_id
in: path
required: true
schema:
type: string
format: uuid
responses:
'200':
description: successful operation
content:
application/json:
schema:
$ref: '#/components/schemas/Alignment'
links:
referenceOrgan:
$ref: '#/components/links/GetReferenceOrganById'
'400':
description: Invalid Id
'401':
description: User is not authorized to look for entities
'404':
description: not found
/reference_organs:
get:
tags:
- Primary Search
summary: Get Reference Organs
operationId: getReferenceOrgans
responses:
'200':
description: successful operation
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/ReferenceOrgan'
'400':
description: Invalid Id
'401':
description: User is not authorized to look for entities
'404':
description: not found
'/reference_organs/{reference_organ_id}':
get:
tags:
- Primary Lookup
summary: Get Reference Organ
operationId: getReferenceOrgan
parameters:
- name: reference_organ_id
in: path
required: true
schema:
type: string
format: uuid
responses:
'200':
description: successful operation
content:
application/json:
schema:
$ref: '#/components/schemas/ReferenceOrgan'
'400':
description: Invalid Id
'401':
description: User is not authorized to look for entities
'404':
description: not found
/images:
get:
tags:
- Primary Search
summary: Get Images
operationId: getImages
responses:
'200':
description: successful operation
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/Image'
'400':
description: Invalid Id
'401':
description: User is not authorized to look for entities
'404':
description: not found
'/images/{image_id}':
get:
tags:
- Primary Lookup
summary: Get Image
operationId: getImage
parameters:
- name: image_id
in: path
required: true
schema:
type: string
format: uuid
responses:
'200':
description: successful operation
content:
application/json:
schema:
$ref: '#/components/schemas/Image'
links:
sample:
$ref: '#/components/links/GetSampleById'
'400':
description: Invalid Id
'401':
description: User is not authorized to look for entities
'404':
description: not found
/image-overlays:
get:
tags:
- Primary Search
summary: Get Image Overlays
operationId: getImageOverlays
responses:
'200':
description: successful operation
content:
application/json:
schema:
type: array
items:
$ref: '#/components/schemas/ImageOverlay'
'400':
description: Invalid Id
'401':
description: User is not authorized to look for entities
'404':
description: not found
'/image-overlays/{image_overlay_id}':
get:
tags:
- Primary Lookup
summary: Get Image Overlay
operationId: getImageOverlay
parameters:
- name: image_overlay_id
in: path
required: true
schema:
type: string
format: uuid
responses:
'200':
description: successful operation
content:
application/json:
schema:
$ref: '#/components/schemas/ImageOverlay'
links:
image:
$ref: '#/components/links/GetImageById'
'400':
description: Invalid Id
'401':
description: User is not authorized to look for entities
'404':
description: not found
'/image-data/{image_id}':
get:
tags:
- Secondary
summary: Get Image
operationId: getImageData
parameters:
- name: image_id
in: path
required: true
schema:
type: string
format: uuid
responses:
'200':
description: successful operation
content:
image/jpeg:
schema:
type: string
format: binary
'400':
description: Invalid image Id
'401':
description: User is not authorized to look for entities
'404':
description: Image not found
components:
links:
GetDonorById:
operationId: getDonor
parameters:
donor_id: '$response.body#/donorId'
GetProcedureById:
operationId: getProcedure
parameters:
procedure_id: '$response.body#/procedureId'
GetSampleById:
operationId: getSample
parameters:
sample_id: '$response.body#/sampleId'
GetSuperSampleById:
operationId: getSample
parameters:
sample_id: '$response.body#/superSampleId'
GetAlignmentById:
operationId: getAlignment
parameters:
alignment_id: '$response.body#/alignmentId'
GetReferenceOrganById:
operationId: getReferenceOrgan
parameters:
reference_organ_id: '$response.body#/referenceOrganId'
GetImageById:
operationId: getImage
parameters:
reference_organ_id: '$response.body#/imageId'
GetImageOverlayById:
operationId: getImageOverlay
parameters:
reference_organ_id: '$response.body#/imageOverlayId'
schemas:
Donor:
description: >-
Since very little data is guaranteed to be the same for a particular
donor across multiple clinical visits, we take the approach that the
donor is described only by an anonymized identifier (donor_id). All
other metadata for the donor is included in one of the metadata tables
described below and there is no “donor metadata” table.
type: object
required:
- id
properties:
id:
description: Unique donor id (anonymized)
type: string
format: uuid
example: d290f1ee-6c54-4b01-90e6-d701748f0851
Procedure:
description: >-
The procedure metadata describes the procedure or clinical visit that
produced the sample from a donor identified as donor_id. A “procedure”
produces a single “physical sample”. Note that a donor can have multiple
procedures, due to either multiple samples taken in a single visit or
samples taken during separate visits. The metadata for the donor can
vary from procedure to procedure. For example, a donor can have samples
taken on different dates and therefore have different donor ages
associated with the different samples.
type: object
required:
- id
properties:
id:
description: Unique procedure id
type: string
format: uuid
example: d290f1ee-6c54-4b01-90e6-d701748f0851
donor_id:
description: Unique donor id (anonymized)
type: string
format: uuid
example: d290f1ee-6c54-4b01-90e6-d701748f0851
provider:
description: Name of organization that was source of sample
type: string
example: TMC-Vanderbilt
procedure_date_time:
description: Date sample obtained
type: string
format: date-time
example: '2009-06-15T13:45:30'
age:
description: Donor age (in years) when sample obtained
type: integer
format: int32
minimum: 0
maximum: 150
example: 39
sex:
description: 'Donor sex when sample obtained Note: Not “gender”'
type: string
enum:
- male
- female
- other
- unknown
example: female
ethnicity:
description: >
Race or ethnicity, terms should be compatible with NIH guidance in
[NOT-OD-15-089](https://grants.nih.gov/grants/guide/notice-files/not-od-15-089.html)
type: string
enum:
- American Indian or Alaska Native
- Asian
- Black or African American
- Hispanic or Latino
- Native Hawaiian or Other Pacific Islander
- White
example: Asian
height:
description: Donor height (in centimeters) when sample obtained
type: number
format: float
example: 155.448
weight:
description: Donor weight (in kilograms) when sample obtained
type: number
format: float
example: 117.934
bmi:
description: |
Body mass index (in kg/m²) when sample obtained
(can be calculated from the height and body weight)
type: number
format: float
example: 37.3
comorbidities:
description: >
Comorbidities, and/or clinical indications and/or donor status
when sample obtained. Terms should be chosen from suitable
bio-ontologies.
type: array
items:
type: string
example:
- 'Obesity, type II diabetes'
notes:
description: |
Free text comments. This field can contain information that doesn’t
fit in other fields, comments, notes, exceptions etc.
type: string
example: This donor was part of the XX-YYY study.
Sample:
description: >-
The sample metadata describes a sample taken from a donor and also
describes any subsequent subsamples. For the initial sample, there will
be a procedure_id value. For subsamples, the procedure_id will be empty
and the supersample will be referenced by its sample_id in the field
super_sample_id field. (We need input from the TMCs and IEC on how they
will be tracking sample - subsample relationships.) The sample_id and
super_sample_id relationship can proceed down an arbitrary number of
levels. Samples can be referenced to a landmark such as a fiduciary
mark, to a clinically observable abnormality or the reference point
(usually the [0,0,0] point) in a reference image. In the case of a
reference image, fiduciary marks can be included in the image as well as
coarser descriptions based on regions of the organ. For example;
“capsule”, “cortex” or simply “upper” or “posterior”.
type: object
required:
- id
properties:
id:
description: Unique sample id
type: string
format: uuid
example: d290f1ee-6c54-4b01-90e6-d701748f0851
donor_id:
description: Unique donor id (anonymized)
type: string
format: uuid
example: d290f1ee-6c54-4b01-90e6-d701748f0851
procedure_id:
description: Unique procedure id
type: string
format: uuid
example: d290f1ee-6c54-4b01-90e6-d701748f0851
super_sample_id:
description: |
ID of the parent sample if this sample is a subsample.
Empty if this is an initial sample.
type: string
format: uuid
example: d290f1ee-6c54-4b01-90e6-d701748f0851
operator_orcid:
description: ID for operator that obtained the sample
type: string
example: 'https://orcid.org/0000-0002-1825-0097'
alignment_id:
description: >
ID of alignment information, if the sample has been placed using the
RUI
type: string
format: uuid
example: d290f1ee-6c54-4b01-90e6-d701748f0851
type_of_procedure:
description: |
Ontology term for the original clinical protocol, else
“subsample” if this is a sample derived from another sample.
type: string
example: Total Nephrectomy
indication_for_procedure:
description: Why the procedure was carried out
type: string
example: Renal tumor
laterality:
description: |
For bilateral organs such as the kidneys or lungs.
Empty for other organs such as heart.
type: string
enum:
- left
- right
- not applicable
- unknown
example: left
clinical_image:
description: |
Photo of the entire clinical sample prior to dissection.
May be a photo of a resected organ or an image
(x-ray, uCT, etc.) of the image in situ. Should be a URL to an
image suitable for display in a web browser (PNG, JPEG, GIF, etc).
type: string
format: url
example: >-
https://i.kym-cdn.com/entries/icons/original/000/005/608/nyan-cat-01-625x450.jpg
tissue_type:
description: Tissue or organ name as text or ontological term
type: string
example: kidney
sample_processing:
description: Sample handling and processing
type: string
example: Frozen
method_of_freezing:
description: Method used to freeze the sample
type: string
example: Dry Ice/Isopentane Slurry
embedding_media:
description: Embedding media used
type: string
example: CMC
sample_acquired_date_time:
description: Date sample collected
type: string
format: date-time
example: '2009-06-15T13:45:30'
sectioning_date_time:
description: Date sample sectioned
type: string
format: date-time
example: '2009-06-15T13:45:30'
notes:
description: |
Free text comments. This field can contain information that doesn’t
fit in other fields, comments, notes, exceptions etc.
type: string
example: This donor was part of the XX-YYY study.
Alignment:
description: >-
Alignment metadata defines how the physical sample or section is
oriented relative to a reference 3D organ model. In general, this data
is generated by the Registration User Interface (RUI). We assume that
the reference objects are scaled to 1 unit = 1 millimeter. A reference
object file with a maximum dimension of 100 is assumed to mean the
maximum size is 100mm.
type: object
required:
- id
properties:
id:
description: UUID for each registration
type: string
format: uuid
example: d290f1ee-6c54-4b01-90e6-d701748f0851
alignment_operator_orcid:
description: ORCID of the person that did the alignment
type: string
example: 'https://orcid.org/0000-0002-1825-0097'
alignment_date_time:
description: Date and time the alignment was done
type: string
format: date-time
example: '2009-06-15T13:45:30'
reference_organ_id:
description: ID of the reference organ the sample was placed in
type: string
format: uuid
example: d290f1ee-6c54-4b01-90e6-d701748f0851
organ_object_size:
description: 'Dimensions (in millimeters) of entire organ, if available.'
allOf:
- description: Dimensions when orientation is unknown
type: object
properties:
L:
description: Length (lateral-medial axis)
type: number
format: float
W:
description: Width (anterior-posterior axis)
type: number
format: float
H:
description: Height (superior (head)-inferior (foot) axis)
type: number
format: float
example:
L: 19
W: 13
H: 7
- description: Dimensions when orientation is known
type: object
properties:
LM:
description: Length (lateral-medial axis)
type: number
format: float
AP:
description: Width (anterior-posterior axis)
type: number
format: float
SI:
description: Height (superior (head)-inferior (foot) axis)
type: number
format: float
example:
LM: 19
AP: 13
SI: 7
sample_position_center:
description: >
Sample’s center of volume position in the same coordinates as the
reference object.
Float, x,y,z list of coordinates.
allOf:
- $ref: '#/components/schemas/Point'
sample_object_rotation:
description: >-
Rotations of the sample object. Rotations must be done in the order
given:
x-rotation, y-rotation, z-rotation. Floating point numbers must be
in degrees.
allOf:
- $ref: '#/components/schemas/Point'
sample_object_dimensions:
description: >-
Dimensions of final sample. In the same units as the reference
object.
Float, x,y,z list of distances. These are the dimensions of the
square
prism selection region and not coordinates of the alignment.
Units are in millimeters.
allOf:
- $ref: '#/components/schemas/Point'
bounding_box_vertex_coordinates:
description: >-
List of (x,y,z) coordinates for the vertices of the selection box.
These
are after any rotations or translations and are generated directly
from
the alignment UI. In the same units as the reference object and
therefore
are in mm. Note: This data is preferred to giving the box’s
dimensions,
offsets and rotations.
Float, x,y,z list of list of vertex locations. For a rectangular
prism
there are 8 vertex locations. Note that if the image is pixel based
the
vertex positions do not necessarily fall on image lattice points.
type: array
items:
$ref: '#/components/schemas/Point'
bounding_shape:
description: >-
Shape of the selection box. Either a rectangular region (rectangular
prism)
or a cylindrical region for a needle biopsy.
type: string
enum:
- rectangular
- cylindrical
example: rectangular
alignment_screenshot:
description: >-
Screenshot of the alignment interface showing both the reference
organ and
the final positioning of the selection region. This is needed for
downstream validation. Should be a URL to an
image suitable for display in a web browser (PNG, JPEG, GIF, etc).
type: string
format: url
example: >-
https://i.kym-cdn.com/entries/icons/original/000/005/608/nyan-cat-01-625x450.jpg
base_section_plane:
description: >-
The coordinates of the face of the selection region (typically a
rectangular
region) that is the first section that will be taken. Subsequent
sections
will move from this face. For example, the rectangle highlighted in
red in
the image below. Float, x,y,z list of vertex locations. For a
rectangular
region there are 4 vertices.
type: array
items:
$ref: '#/components/schemas/Point'
reference_vertices:
description: >-
The coordinates of the three corners of the selection region used as
a
“dog ear” corner. This corner is used for subsequent alignment of
the
sample when it is analyzed or further sectioned. Float, x,y,z list
of vertex
locations. There are 3 vertices.
type: array
items:
$ref: '#/components/schemas/Point'
notes:
description: |
Free text comments. This field can contain information that doesn’t
fit in other fields, comments, notes, exceptions etc.
type: string
example: This donor was part of the XX-YYY study.
ReferenceOrgan:
description: >-
The Reference Organ Metadata table describes the 3D models used as
reference organs. These models are used by both the RUI and EUI. We
specify the reference organs as annotated 3D OBJ files. Long term, this
specification may need to be extended if we reach the point where a
reference organ is derived from the donor supplying the sample. The OBJ
files have internal units of centimeters, and an origin ([0,0,0] point)
at the center of volume. The OBJ file’s y-axis if the body’s vertical
axis, x-axis the body’s left/right axis and the z-axis is the body’s
front/back axis.
type: object
required:
- id
properties:
id:
description: Unique ID for this reference organ
type: string
format: uuid
example: d290f1ee-6c54-4b01-90e6-d701748f0851
name:
description: Name of the organ
type: string
example: kidney
laterality:
description: |
For bilateral organs such as the kidneys or lungs.
Empty for other organs such as heart.
type: string
enum:
- left
- right
- not applicable
- unknown
example: left
donor_sex:
description: 'Donor sex when sample obtained Note: Not “gender”'
type: string
enum:
- male
- female
- other
- unknown
example: female
donor_height:
description: Donor height (in centimeters) when sample obtained
type: number
format: float
example: 155.448
donor_weight:
description: Donor weight (in kilograms) when sample obtained
type: number
format: float
example: 117.934
image_path:
description: Path and filename for the 3D obj file.
type: string
format: url
example: 'https://example.com/file.obj'
creation_date_time:
description: Date the reference organ was created and deposited
type: string
format: date-time
example: '2009-06-15T13:45:30'
creator_orcid:
description: ID for the person who created the reference organ
type: string
example: 'https://orcid.org/0000-0002-1825-0097'
notes:
description: |
Free text comments. This field can contain information that doesn’t
fit in other fields, comments, notes, exceptions etc.
type: string
example: >-
This reference was annotated as described in Jones et al., PNAS,
2017.
image_offset:
description: >-
Offsets needed to place the (0,0,0) point in the OBJ file into the
outline (possibly a 3D outline) of a body. The OBJ files (0,0,0)
point is at its center of volume. These offsets are normalized to
the donor’s height and refer to a lean individual. The reference
dimension is the body height, which is taken as 1. The left/right
and front/back displacements are of the same scale, and are relative
to the central median plane and central coronal plane, therefore the
y and z offsets can be positive or negative. (The x offset is always
>0 and less than or equal to 1.
Offsets needed to place the (0,0,0) point in the OBJ file into the
outline of a body. These are unitless.
Vertical position: normalized 0=heal, 1=top of head. Triple of
floats, unitless, in the order: vertical displacement, left/right
displacement, front/back displacement.
A left kidney would be at approximately: 0.64,-0.056,-0.039. A right
kidney would be at approximately: 0.64,0.056,-0.039.
allOf:
- $ref: '#/components/schemas/Point'
image_scaling:
description: >-
This value is the multiplier used to convert 1 unit in the OBJ file
into 1 millimeter. However, we assume all reference organ object
files are already scaled to 1 unit = 1 cm. Float,
millimeter/(unitless OBJ file unit)
type: number
format: float
example: 1
Image:
description: >-
Image metadata describes the characteristics of a particular image. In
some cases, we may have consecutive images/objects that have different
scaling and/or offsets. For example, the mass spec data may have a
resolution of several microns/pixels but be related to an adjacent
section, imaged via birefringence, that has 0.5 micron/pixel resolution,
and the MS data might have an x,y offset.
type: object
required:
- id
properties:
id:
description: Unique ID for this image
type: string
format: uuid
example: d290f1ee-6c54-4b01-90e6-d701748f0851
sample_id:
description: ID of sample that this image is derived from
type: string
format: uuid
example: d290f1ee-6c54-4b01-90e6-d701748f0851
operator_orcid:
description: ORCID id of operator
type: string
example: 'https://orcid.org/0000-0002-1825-0097'
technology_short_name:
description: >
Short name for the technology used to generate and/or process this
image
type: string