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dataset.schema.yaml
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dataset.schema.yaml
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additionalProperties: false
properties:
access_group:
description: TODO
ancestor_ids:
description: TODO
ancestors:
description: TODO
contains_human_genetic_sequences:
description: true if the data contains human gene sequence information, false
otherwise
create_timestamp:
description: The data/time when the entity was created
created_by_user_displayname:
description: The name of the person who registered/created the Entity.
created_by_user_email:
description: The email address of the person who registerd/created the Entity.
creation_action:
description: The action that created this this Entity
data_access_level:
description: The access control level for the entity
enum:
- consortium
- protected
- public
data_types:
description: 'TODO: An array of data/assay types contained in the Dataset.'
enum:
- AF
- ATACseq-bulk
- CODEX
- IMC
- LC-MS-untargeted
- Lightsheet
- MALDI-IMS-neg
- MALDI-IMS-pos
- MxIF
- PAS
- SNAREseq
- TMT-LC-MS
- Targeted-Shotgun-LC-MS
- WGS
- bulk-RNA
- codex_cytokit
- image_pyramid
- salmon_rnaseq_10x
- salmon_rnaseq_bulk
- salmon_rnaseq_sciseq
- salmon_rnaseq_snareseq
- scRNA-Seq-10x
- sc_atac_seq_sci
- sc_atac_seq_snare
- sciATACseq
- sciRNAseq
- seqFish
- seqFish_lab_processed
- snATACseq
- snRNAseq
descendant_ids:
description: TODO
descendants:
description: TODO
description:
description: A description of the Entity, hand entered into the UI
display_doi:
description: HuBMAP id generated at the same time as and associated directly with
the UUID for the Entity. This ID can be used when registering an object with
the DOI System.
donor:
additionalProperties: false
properties:
create_timestamp:
description: The data/time when the entity was created
created_by_user_displayname:
description: The name of the person who registered/created the Entity.
created_by_user_email:
description: The email address of the person who registerd/created the Entity.
creation_action:
description: The action that created this this Entity
data_access_level:
description: The access control level for the entity
enum:
- consortium
- protected
- public
description:
description: A description of the Entity, hand entered into the UI
display_doi:
description: HuBMAP id generated at the same time as and associated directly
with the UUID for the Entity. This ID can be used when registering an object
with the DOI System.
entity_type:
description: The entity type.
enum:
- Dataset
- Donor
- Sample
group_name:
description: The name of the lab/TMC/TTD/RTI where the Entity was registered.
group_uuid:
description: A UUID associated with the lab/TMC/TTD/RTI where the Entity was
registered.
hubmap_display_id:
description: 'HuBMAP id used internal to the Consortium, generated at the
same time as and associated directly with the UUID for the Entity. The
id is built on the the id from the parent object. Format explained here:
https://docs.google.com/document/d/1DjHgmqWF1VA5-3mfzLFNfabbzmc8KLSG9xWx1DDLlzo/'
lab_donor_id:
description: An donor id specific to the lab where the tissue was procured.
lab_name:
description: A lab specific label/name assigned to a donor by the lab during
registration of the donor.
last_modified_timestamp:
description: The date/time when the entity was last updatedl
metadata:
description: Metadata associated with the Entity. Formated in JSON. Donor
metadata is transformed from files uploaded into the Ingest UI. Sample
metadata will be transformed from files uploaded into the Ingest UI. Dataset
metadata will be transformed from the HIVE specified .tsv file provided
with data uploads and/or extraction from data or metadata files provided
in the data upload.
portal_metadata_upload_files:
description: An array of information about metadata files uploaded via the
Tissue Registration UI
portal_uploaded_image_files:
description: An array of information about image files uploaded during donor
or tissue registration via the Tissue Registration UI
protocol_url:
description: The url to the protocols.io instance describing donor selection
criteria, tissue procurement protocols and or data generation/derivation
details.
uuid:
description: The HuBMAP auto-generated UUID for the Entity
required:
- create_timestamp
- created_by_user_displayname
- created_by_user_email
- data_access_level
- entity_type
- group_name
- group_uuid
- last_modified_timestamp
- uuid
type: object
entity_type:
description: The entity type.
enum:
- Dataset
- Donor
- Sample
files:
description: An array of information about the files contained in the dataset.
group_name:
description: The name of the lab/TMC/TTD/RTI where the Entity was registered.
group_uuid:
description: A UUID associated with the lab/TMC/TTD/RTI where the Entity was registered.
last_modified_timestamp:
description: The date/time when the entity was last updatedl
metadata:
description: Metadata associated with the Entity. Formated in JSON. Donor metadata
is transformed from files uploaded into the Ingest UI. Sample metadata will
be transformed from files uploaded into the Ingest UI. Dataset metadata will
be transformed from the HIVE specified .tsv file provided with data uploads
and/or extraction from data or metadata files provided in the data upload.
name:
description: The name of a dataset as entered into the Ingest UI
origin_sample:
additionalProperties: false
properties:
create_timestamp:
description: The data/time when the entity was created
created_by_user_displayname:
description: The name of the person who registered/created the Entity.
created_by_user_email:
description: The email address of the person who registerd/created the Entity.
creation_action:
description: The action that created this this Entity
data_access_level:
description: The access control level for the entity
enum:
- consortium
- protected
- public
description:
description: A description of the Entity, hand entered into the UI
display_doi:
description: HuBMAP id generated at the same time as and associated directly
with the UUID for the Entity. This ID can be used when registering an object
with the DOI System.
donor:
description: The ancestor Donor at the top of the provenance chain for the
Entity. This contains, in JSON, the full Entity information for the Donor.
entity_type:
description: The entity type.
enum:
- Dataset
- Donor
- Sample
group_name:
description: The name of the lab/TMC/TTD/RTI where the Entity was registered.
group_uuid:
description: A UUID associated with the lab/TMC/TTD/RTI where the Entity was
registered.
hubmap_display_id:
description: 'HuBMAP id used internal to the Consortium, generated at the
same time as and associated directly with the UUID for the Entity. The
id is built on the the id from the parent object. Format explained here:
https://docs.google.com/document/d/1DjHgmqWF1VA5-3mfzLFNfabbzmc8KLSG9xWx1DDLlzo/'
lab_tissue_sample_id:
description: An id specific to the lab where the tissue was processed.
last_modified_timestamp:
description: The date/time when the entity was last updatedl
metadata:
description: Metadata associated with the Entity. Formated in JSON. Donor
metadata is transformed from files uploaded into the Ingest UI. Sample
metadata will be transformed from files uploaded into the Ingest UI. Dataset
metadata will be transformed from the HIVE specified .tsv file provided
with data uploads and/or extraction from data or metadata files provided
in the data upload.
organ:
description: The organ type when specimen_type == organ.
enum:
- BL
- BR
- HT
- LB
- LI
- LK
- LL
- LV
- LY01
- LY02
- LY03
- LY04
- LY05
- LY06
- LY07
- LY08
- LY09
- LY10
- LY11
- LY12
- LY13
- LY14
- LY15
- LY16
- LY17
- LY18
- LY19
- LY20
- OT
- RB
- RK
- RL
- SI
- SP
- TH
- TR
- UR
organ_other:
description: If organ type == other, the organ name is specified in this field
origin_sample:
description: The tissue sample directly below Donor (should usually be an
organ) at the top of the provenance chain for the Entity. This conntains,
in JSON, the full Entity information for the Sample.
portal_metadata_upload_files:
description: An array of information about metadata files uploaded via the
Tissue Registration UI
portal_uploaded_image_files:
description: An array of information about image files uploaded during donor
or tissue registration via the Tissue Registration UI
protocol_url:
description: The url to the protocols.io instance describing donor selection
criteria, tissue procurement protocols and or data generation/derivation
details.
rui_location:
description: Location information of where the tissue sample came from in
the organ that the tissue was sourced from. Specified in JSON, as outputed
from the RUI tool.
specimen_type:
description: For Sample entities, the type of tissue specimen.
enum:
- atacseq
- biopsy
- blood
- cell_lysate
- clarity_hydrogel
- codex
- cryosections_curls_from_fresh_frozen_oct
- cryosections_curls_rnalater
- ffpe_block
- ffpe_slide
- fixed_frozen_section_slide
- fixed_tissue_piece
- flash_frozen_liquid_nitrogen
- formalin_fixed_oct_block
- fresh_frozen_oct_block
- fresh_frozen_section_slide
- fresh_frozen_tissue
- fresh_frozen_tissue_section
- fresh_tissue
- frozen_cell_pellet_buffy_coat
- gdna
- module
- nuclei
- nuclei_rnalater
- organ
- organ_piece
- other
- pbmc
- pfa_fixed_frozen_oct_block
- plasma
- protein
- ran_poly_a_enriched
- rna_total
- rnalater_treated_and_stored
- rnaseq
- scatacseq
- scrnaseq
- segment
- seqfish
- serum
- single_cell_cryopreserved
- snatacseq
- snrnaseq
- tissue_lysate
- wgs
specimen_type_other:
description: If specimen_type == other, the specimen type name is specified
in this field
uuid:
description: The HuBMAP auto-generated UUID for the Entity
visit:
description: The clinical visit specifier of when a piece of tissue was procured. This
is hand entered via the Tissue Registration UI at the time of tissue registration.
required:
- create_timestamp
- created_by_user_displayname
- created_by_user_email
- data_access_level
- entity_type
- group_name
- group_uuid
- last_modified_timestamp
- specimen_type
- uuid
type: object
source_sample:
items:
additionalProperties: false
properties:
create_timestamp:
description: The data/time when the entity was created
created_by_user_displayname:
description: The name of the person who registered/created the Entity.
created_by_user_email:
description: The email address of the person who registerd/created the Entity.
creation_action:
description: The action that created this this Entity
data_access_level:
description: The access control level for the entity
enum:
- consortium
- protected
- public
description:
description: A description of the Entity, hand entered into the UI
display_doi:
description: HuBMAP id generated at the same time as and associated directly
with the UUID for the Entity. This ID can be used when registering an
object with the DOI System.
donor:
description: The ancestor Donor at the top of the provenance chain for the
Entity. This contains, in JSON, the full Entity information for the Donor.
entity_type:
description: The entity type.
enum:
- Dataset
- Donor
- Sample
group_name:
description: The name of the lab/TMC/TTD/RTI where the Entity was registered.
group_uuid:
description: A UUID associated with the lab/TMC/TTD/RTI where the Entity
was registered.
hubmap_display_id:
description: 'HuBMAP id used internal to the Consortium, generated at the
same time as and associated directly with the UUID for the Entity. The
id is built on the the id from the parent object. Format explained here:
https://docs.google.com/document/d/1DjHgmqWF1VA5-3mfzLFNfabbzmc8KLSG9xWx1DDLlzo/'
lab_tissue_sample_id:
description: An id specific to the lab where the tissue was processed.
last_modified_timestamp:
description: The date/time when the entity was last updatedl
metadata:
description: Metadata associated with the Entity. Formated in JSON. Donor
metadata is transformed from files uploaded into the Ingest UI. Sample
metadata will be transformed from files uploaded into the Ingest UI. Dataset
metadata will be transformed from the HIVE specified .tsv file provided
with data uploads and/or extraction from data or metadata files provided
in the data upload.
organ:
description: The organ type when specimen_type == organ.
enum:
- BL
- BR
- HT
- LB
- LI
- LK
- LL
- LV
- LY01
- LY02
- LY03
- LY04
- LY05
- LY06
- LY07
- LY08
- LY09
- LY10
- LY11
- LY12
- LY13
- LY14
- LY15
- LY16
- LY17
- LY18
- LY19
- LY20
- OT
- RB
- RK
- RL
- SI
- SP
- TH
- TR
- UR
organ_other:
description: If organ type == other, the organ name is specified in this
field
origin_sample:
description: The tissue sample directly below Donor (should usually be an
organ) at the top of the provenance chain for the Entity. This conntains,
in JSON, the full Entity information for the Sample.
portal_metadata_upload_files:
description: An array of information about metadata files uploaded via the
Tissue Registration UI
portal_uploaded_image_files:
description: An array of information about image files uploaded during donor
or tissue registration via the Tissue Registration UI
protocol_url:
description: The url to the protocols.io instance describing donor selection
criteria, tissue procurement protocols and or data generation/derivation
details.
rui_location:
description: Location information of where the tissue sample came from in
the organ that the tissue was sourced from. Specified in JSON, as outputed
from the RUI tool.
specimen_type:
description: For Sample entities, the type of tissue specimen.
enum:
- atacseq
- biopsy
- blood
- cell_lysate
- clarity_hydrogel
- codex
- cryosections_curls_from_fresh_frozen_oct
- cryosections_curls_rnalater
- ffpe_block
- ffpe_slide
- fixed_frozen_section_slide
- fixed_tissue_piece
- flash_frozen_liquid_nitrogen
- formalin_fixed_oct_block
- fresh_frozen_oct_block
- fresh_frozen_section_slide
- fresh_frozen_tissue
- fresh_frozen_tissue_section
- fresh_tissue
- frozen_cell_pellet_buffy_coat
- gdna
- module
- nuclei
- nuclei_rnalater
- organ
- organ_piece
- other
- pbmc
- pfa_fixed_frozen_oct_block
- plasma
- protein
- ran_poly_a_enriched
- rna_total
- rnalater_treated_and_stored
- rnaseq
- scatacseq
- scrnaseq
- segment
- seqfish
- serum
- single_cell_cryopreserved
- snatacseq
- snrnaseq
- tissue_lysate
- wgs
specimen_type_other:
description: If specimen_type == other, the specimen type name is specified
in this field
uuid:
description: The HuBMAP auto-generated UUID for the Entity
visit:
description: The clinical visit specifier of when a piece of tissue was
procured. This is hand entered via the Tissue Registration UI at the
time of tissue registration.
required:
- create_timestamp
- created_by_user_displayname
- created_by_user_email
- data_access_level
- entity_type
- group_name
- group_uuid
- last_modified_timestamp
- specimen_type
- uuid
type: object
type: array
status:
description: The status of a Dataset.
enum:
- Error
- Hold
- Invalid
- New
- Processing
- Published
- QA
- Withdrawn
uuid:
description: The HuBMAP auto-generated UUID for the Entity
required:
- contains_human_genetic_sequences
- create_timestamp
- created_by_user_displayname
- created_by_user_email
- data_access_level
- entity_type
- group_name
- group_uuid
- last_modified_timestamp
- uuid
- access_group
- ancestor_ids
- ancestors
- descendant_ids
- descendants
type: object