Entity API Usage
This resource documents how to programmatically retrieve entity information housed in the SenNet Data Sharing Portal.
Our programmatic example will be written in Python and will utilize the requests library for all HTTP calls.
import requests
The domain base for the Entity API is https://entity.api.sennetconsortium.org and will prefix the various
endpoints. For a full list of Entity API endpoints, see
its Smart API.
domain_base = "https://entity.api.sennetconsortium.org"
Create a headers object with a single Content-Type property and value application/json for now.
headers = {
"Content-Type": "application/json"
}
Defining a reusable api_request function
Here we provide a simple function that can be reused for all GET or POST requests.
def api_request(endpoint, body = None, method = 'GET'):
query_url = f"{domain_base}{endpoint}"
entity_data = None
try:
if method.lower() == 'post':
response = requests.post(query_url, data=body, headers=headers)
else:
response = requests.get(query_url, headers=headers)
response_code = response.status_code
if response_code == 200:
entity_data = response.json()
else:
print(f"An error occurred {response_code}")
except Exception as err:
print(f"An unexpected error occurred: {err}")
return entity_data
Let’s also create a simple helper function for POST requests (so we do not need to keep passing POST string as the method by directly calling api_request).
def api_post_request(endpoint, body):
return api_request(endpoint, body, 'POST')
Below are some real world examples of how to retrieve specific entity information.
Given a Source with SenNet ID SNT722.BGFJ.623
Get Entity by ID:
The following code retrieves a speicifc entity by its ID (either SenNet ID or UUID) by making a call to the
/entities/<id>
endpoint.
uuid = "2f2a7af9951f50b399d76b5080486fe1"
entity_data = api_request(f"/entities/{uuid}")
We could similarly use the entity’s SenNet ID, and the results would remain the same.
sennet_id = "SNT722.BGFJ.623"
entity_data = api_request(f"/entities/{uuid}")
The response to any of these calls would look like:
{
"cedar_mapped_metadata": {
"Bedding": "1/4-inch pelleted cellulose",
"Cage Enhancements": "Nestlets",
"Date Of Birth Or Fertilization": "2021/9/9 12:00:00 AM",
"Date Of Death": "2023/10/24 12:00:00 AM",
"Diet": "Chow",
"Euthanization Method": "Inhaled anesthetic euthanasia",
"Is Deceased": "Yes",
"Is Embryo": "No",
"Light Cycle": "Standard/default",
"Local Lifespan Data": "25.5 month",
"Metadata Schema ID": "44662059-aa73-4756-a4a7-990489ca2f43",
"Rack Setup": "Ventilated",
"Room Health Status": "Pathogen free",
"Room Temperature": "23",
"Sex": "Male",
"Source ID": "SNT722.BGFJ.623",
"Strain": "C57BL6",
"Strain Rrid": "RRID:IMSR_JAX:000664",
"Water Source": "Hydropac individual pouch water"
},
"created_by_user_displayname": "Hester Doyle",
"created_by_user_email": "hester.doyle@yale.edu",
"created_by_user_sub": "0e5f9972-21ad-42e2-8aef-01a324a400a1",
"created_timestamp": 1698069424312,
"creation_action": "Create Source Activity",
"data_access_level": "public",
"entity_type": "Source",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"last_modified_timestamp": 1754746533320,
"last_modified_user_displayname": "Jungmin Nam",
"last_modified_user_email": "jungmin.nam@yale.edu",
"last_modified_user_sub": "6b297ad2-d33e-4534-8acf-3456e4611324",
"metadata": {
"bedding": "1/4-inch pelleted cellulose",
"cage_enhancements": "Nestlets",
"date_of_birth_or_fertilization": "2021/9/9 12:00:00 AM",
"date_of_death": "2023/10/24 12:00:00 AM",
"diet": "Chow",
"euthanization_method": "Inhaled anesthetic euthanasia",
"is_deceased": "Yes",
"is_embryo": "No",
"light_cycle": "Standard/default",
"local_lifespan_data": "25.5 month",
"metadata_schema_id": "44662059-aa73-4756-a4a7-990489ca2f43",
"rack_setup": "Ventilated",
"room_health_status": "Pathogen free",
"room_temperature": "23",
"sex": "Male",
"source_id": "SNT722.BGFJ.623",
"strain": "C57BL6",
"strain_rrid": "RRID:IMSR_JAX:000664",
"water_source": "Hydropac individual pouch water"
},
"protocol_url": "dx.doi.org/10.17504/protocols.io.kqdg3x8keg25/v2",
"sennet_id": "SNT722.BGFJ.623",
"source_type": "Mouse",
"uuid": "2f2a7af9951f50b399d76b5080486fe1"
}
Downloads & Tools
Get Entity’s Descendants:
When retrieving descendants of the Source there are two endpoints to consider. The /descendants/<id> (which we will
use in this example) returns all descendants downstream in the provenance chain. An alternative option is to use the
/children/<id> endpoint, which returns just the immediate descendants of the specified entity.
uuid = "2f2a7af9951f50b399d76b5080486fe1"
entity_data = api_request(f"/descendants/{uuid}")
The response of this request would look like
[
{
"created_by_user_displayname": "Hester Doyle",
"created_by_user_email": "hester.doyle@yale.edu",
"created_by_user_sub": "0e5f9972-21ad-42e2-8aef-01a324a400a1",
"created_timestamp": 1698074603414,
"creation_action": "Create Sample Activity",
"data_access_level": "public",
"entity_type": "Sample",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"last_modified_timestamp": 1698074603414,
"last_modified_user_displayname": "Hester Doyle",
"last_modified_user_email": "hester.doyle@yale.edu",
"last_modified_user_sub": "0e5f9972-21ad-42e2-8aef-01a324a400a1",
"organ": "UBERON:0002106",
"organ_hierarchy": "Spleen",
"origin_samples": [
{
"created_by_user_displayname": "Hester Doyle",
"created_by_user_email": "hester.doyle@yale.edu",
"created_by_user_sub": "0e5f9972-21ad-42e2-8aef-01a324a400a1",
"created_timestamp": 1698074603414,
"creation_action": "Create Sample Activity",
"data_access_level": "public",
"entity_type": "Sample",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"last_modified_timestamp": 1698074603414,
"last_modified_user_displayname": "Hester Doyle",
"last_modified_user_email": "hester.doyle@yale.edu",
"last_modified_user_sub": "0e5f9972-21ad-42e2-8aef-01a324a400a1",
"organ": "UBERON:0002106",
"organ_hierarchy": "Spleen",
"protocol_url": "dx.doi.org/10.17504/protocols.io.kqdg3x8keg25/v2",
"sample_category": "Organ",
"sennet_id": "SNT666.XZGV.432",
"source": {
"created_by_user_displayname": "Hester Doyle",
"created_by_user_email": "hester.doyle@yale.edu",
"created_by_user_sub": "0e5f9972-21ad-42e2-8aef-01a324a400a1",
"created_timestamp": 1698069424312,
"creation_action": "Create Source Activity",
"data_access_level": "public",
"entity_type": "Source",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"last_modified_timestamp": 1754746533320,
"last_modified_user_displayname": "Jungmin Nam",
"last_modified_user_email": "jungmin.nam@yale.edu",
"last_modified_user_sub": "6b297ad2-d33e-4534-8acf-3456e4611324",
"metadata": {
"bedding": "1/4-inch pelleted cellulose",
"cage_enhancements": "Nestlets",
"date_of_birth_or_fertilization": "2021/9/9 12:00:00 AM",
"date_of_death": "2023/10/24 12:00:00 AM",
"diet": "Chow",
"euthanization_method": "Inhaled anesthetic euthanasia",
"is_deceased": "Yes",
"is_embryo": "No",
"light_cycle": "Standard/default",
"local_lifespan_data": "25.5 month",
"metadata_schema_id": "44662059-aa73-4756-a4a7-990489ca2f43",
"rack_setup": "Ventilated",
"room_health_status": "Pathogen free",
"room_temperature": "23",
"sex": "Male",
"source_id": "SNT722.BGFJ.623",
"strain": "C57BL6",
"strain_rrid": "RRID:IMSR_JAX:000664",
"water_source": "Hydropac individual pouch water"
},
"protocol_url": "dx.doi.org/10.17504/protocols.io.kqdg3x8keg25/v2",
"sennet_id": "SNT722.BGFJ.623",
"source_type": "Mouse",
"uuid": "2f2a7af9951f50b399d76b5080486fe1"
},
"uuid": "1c49b822f9a9341cfb2be080f08eb15f"
}
],
"protocol_url": "dx.doi.org/10.17504/protocols.io.kqdg3x8keg25/v2",
"sample_category": "Organ",
"sennet_id": "SNT666.XZGV.432",
"source": {
"created_by_user_displayname": "Hester Doyle",
"created_by_user_email": "hester.doyle@yale.edu",
"created_by_user_sub": "0e5f9972-21ad-42e2-8aef-01a324a400a1",
"created_timestamp": 1698069424312,
"creation_action": "Create Source Activity",
"data_access_level": "public",
"entity_type": "Source",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"last_modified_timestamp": 1754746533320,
"last_modified_user_displayname": "Jungmin Nam",
"last_modified_user_email": "jungmin.nam@yale.edu",
"last_modified_user_sub": "6b297ad2-d33e-4534-8acf-3456e4611324",
"metadata": {
"bedding": "1/4-inch pelleted cellulose",
"cage_enhancements": "Nestlets",
"date_of_birth_or_fertilization": "2021/9/9 12:00:00 AM",
"date_of_death": "2023/10/24 12:00:00 AM",
"diet": "Chow",
"euthanization_method": "Inhaled anesthetic euthanasia",
"is_deceased": "Yes",
"is_embryo": "No",
"light_cycle": "Standard/default",
"local_lifespan_data": "25.5 month",
"metadata_schema_id": "44662059-aa73-4756-a4a7-990489ca2f43",
"rack_setup": "Ventilated",
"room_health_status": "Pathogen free",
"room_temperature": "23",
"sex": "Male",
"source_id": "SNT722.BGFJ.623",
"strain": "C57BL6",
"strain_rrid": "RRID:IMSR_JAX:000664",
"water_source": "Hydropac individual pouch water"
},
"protocol_url": "dx.doi.org/10.17504/protocols.io.kqdg3x8keg25/v2",
"sennet_id": "SNT722.BGFJ.623",
"source_type": "Mouse",
"uuid": "2f2a7af9951f50b399d76b5080486fe1"
},
"uuid": "1c49b822f9a9341cfb2be080f08eb15f"
},
{
"created_by_user_displayname": "Hester Doyle",
"created_by_user_email": "hester.doyle@yale.edu",
"created_by_user_sub": "0e5f9972-21ad-42e2-8aef-01a324a400a1",
"created_timestamp": 1698075340002,
"creation_action": "Create Sample Activity",
"data_access_level": "public",
"entity_type": "Sample",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"last_modified_timestamp": 1698075340002,
"last_modified_user_displayname": "Hester Doyle",
"last_modified_user_email": "hester.doyle@yale.edu",
"last_modified_user_sub": "0e5f9972-21ad-42e2-8aef-01a324a400a1",
"origin_samples": [
{
"created_by_user_displayname": "Hester Doyle",
"created_by_user_email": "hester.doyle@yale.edu",
"created_by_user_sub": "0e5f9972-21ad-42e2-8aef-01a324a400a1",
"created_timestamp": 1698074603414,
"creation_action": "Create Sample Activity",
"data_access_level": "public",
"entity_type": "Sample",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"last_modified_timestamp": 1698074603414,
"last_modified_user_displayname": "Hester Doyle",
"last_modified_user_email": "hester.doyle@yale.edu",
"last_modified_user_sub": "0e5f9972-21ad-42e2-8aef-01a324a400a1",
"organ": "UBERON:0002106",
"organ_hierarchy": "Spleen",
"protocol_url": "dx.doi.org/10.17504/protocols.io.kqdg3x8keg25/v2",
"sample_category": "Organ",
"sennet_id": "SNT666.XZGV.432",
"uuid": "1c49b822f9a9341cfb2be080f08eb15f"
}
],
"protocol_url": "dx.doi.org/10.17504/protocols.io.kqdg3x8keg25/v2",
"sample_category": "Block",
"sennet_id": "SNT664.KFZW.224",
"source": {
"created_by_user_displayname": "Hester Doyle",
"created_by_user_email": "hester.doyle@yale.edu",
"created_by_user_sub": "0e5f9972-21ad-42e2-8aef-01a324a400a1",
"created_timestamp": 1698069424312,
"creation_action": "Create Source Activity",
"data_access_level": "public",
"entity_type": "Source",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"last_modified_timestamp": 1754746533320,
"last_modified_user_displayname": "Jungmin Nam",
"last_modified_user_email": "jungmin.nam@yale.edu",
"last_modified_user_sub": "6b297ad2-d33e-4534-8acf-3456e4611324",
"metadata": {
"bedding": "1/4-inch pelleted cellulose",
"cage_enhancements": "Nestlets",
"date_of_birth_or_fertilization": "2021/9/9 12:00:00 AM",
"date_of_death": "2023/10/24 12:00:00 AM",
"diet": "Chow",
"euthanization_method": "Inhaled anesthetic euthanasia",
"is_deceased": "Yes",
"is_embryo": "No",
"light_cycle": "Standard/default",
"local_lifespan_data": "25.5 month",
"metadata_schema_id": "44662059-aa73-4756-a4a7-990489ca2f43",
"rack_setup": "Ventilated",
"room_health_status": "Pathogen free",
"room_temperature": "23",
"sex": "Male",
"source_id": "SNT722.BGFJ.623",
"strain": "C57BL6",
"strain_rrid": "RRID:IMSR_JAX:000664",
"water_source": "Hydropac individual pouch water"
},
"protocol_url": "dx.doi.org/10.17504/protocols.io.kqdg3x8keg25/v2",
"sennet_id": "SNT722.BGFJ.623",
"source_type": "Mouse",
"uuid": "2f2a7af9951f50b399d76b5080486fe1"
},
"uuid": "8208088865da724bbb55cae38632a88a"
},
{
"created_by_user_displayname": "Jungmin Nam",
"created_by_user_email": "jungmin.nam@yale.edu",
"created_by_user_sub": "6b297ad2-d33e-4534-8acf-3456e4611324",
"created_timestamp": 1725408148919,
"creation_action": "Create Sample Activity",
"data_access_level": "public",
"description": "fresh frozen",
"entity_type": "Sample",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"last_modified_timestamp": 1725408148919,
"last_modified_user_displayname": "Jungmin Nam",
"last_modified_user_email": "jungmin.nam@yale.edu",
"last_modified_user_sub": "6b297ad2-d33e-4534-8acf-3456e4611324",
"origin_samples": [
{
"created_by_user_displayname": "Hester Doyle",
"created_by_user_email": "hester.doyle@yale.edu",
"created_by_user_sub": "0e5f9972-21ad-42e2-8aef-01a324a400a1",
"created_timestamp": 1698074603414,
"creation_action": "Create Sample Activity",
"data_access_level": "public",
"entity_type": "Sample",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"last_modified_timestamp": 1698074603414,
"last_modified_user_displayname": "Hester Doyle",
"last_modified_user_email": "hester.doyle@yale.edu",
"last_modified_user_sub": "0e5f9972-21ad-42e2-8aef-01a324a400a1",
"organ": "UBERON:0002106",
"organ_hierarchy": "Spleen",
"protocol_url": "dx.doi.org/10.17504/protocols.io.kqdg3x8keg25/v2",
"sample_category": "Organ",
"sennet_id": "SNT666.XZGV.432",
"uuid": "1c49b822f9a9341cfb2be080f08eb15f"
}
],
"protocol_url": "dx.doi.org/10.17504/protocols.io.kqdg3x8keg25/v2",
"sample_category": "Section",
"sennet_id": "SNT587.LHXH.846",
"source": {
"created_by_user_displayname": "Hester Doyle",
"created_by_user_email": "hester.doyle@yale.edu",
"created_by_user_sub": "0e5f9972-21ad-42e2-8aef-01a324a400a1",
"created_timestamp": 1698069424312,
"creation_action": "Create Source Activity",
"data_access_level": "public",
"entity_type": "Source",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"last_modified_timestamp": 1754746533320,
"last_modified_user_displayname": "Jungmin Nam",
"last_modified_user_email": "jungmin.nam@yale.edu",
"last_modified_user_sub": "6b297ad2-d33e-4534-8acf-3456e4611324",
"metadata": {
"bedding": "1/4-inch pelleted cellulose",
"cage_enhancements": "Nestlets",
"date_of_birth_or_fertilization": "2021/9/9 12:00:00 AM",
"date_of_death": "2023/10/24 12:00:00 AM",
"diet": "Chow",
"euthanization_method": "Inhaled anesthetic euthanasia",
"is_deceased": "Yes",
"is_embryo": "No",
"light_cycle": "Standard/default",
"local_lifespan_data": "25.5 month",
"metadata_schema_id": "44662059-aa73-4756-a4a7-990489ca2f43",
"rack_setup": "Ventilated",
"room_health_status": "Pathogen free",
"room_temperature": "23",
"sex": "Male",
"source_id": "SNT722.BGFJ.623",
"strain": "C57BL6",
"strain_rrid": "RRID:IMSR_JAX:000664",
"water_source": "Hydropac individual pouch water"
},
"protocol_url": "dx.doi.org/10.17504/protocols.io.kqdg3x8keg25/v2",
"sennet_id": "SNT722.BGFJ.623",
"source_type": "Mouse",
"uuid": "2f2a7af9951f50b399d76b5080486fe1"
},
"uuid": "fb1398a3f416df8f2fc97583796f29be"
},
{
"antibodies": [
{
"antibody_concentration_unit": "",
"antibody_concentration_value": "",
"antibody_rrid": "AB_3254603",
"channel_id": "CD31",
"conjugated_cat_number": "",
"conjugated_tag": "",
"dilution_factor": "200",
"hgnc_symbol": "Not Applicable",
"lot_number": "B406302",
"metadata_schema_id": "312f7be0-9aec-4cae-b942-a8864c0aa1ce",
"uniprot_accession_number": "Q08481"
},
{
"antibody_concentration_unit": "",
"antibody_concentration_value": "",
"antibody_rrid": "AB_3644273",
"channel_id": "CD90.2",
"conjugated_cat_number": "",
"conjugated_tag": "",
"dilution_factor": "200",
"hgnc_symbol": "Not Applicable",
"lot_number": "B406230",
"metadata_schema_id": "312f7be0-9aec-4cae-b942-a8864c0aa1ce",
"uniprot_accession_number": "P01831"
},
{
"antibody_concentration_unit": "",
"antibody_concentration_value": "",
"antibody_rrid": "AB_3271531",
"channel_id": "CD44",
"conjugated_cat_number": "",
"conjugated_tag": "",
"dilution_factor": "200",
"hgnc_symbol": "Not Applicable",
"lot_number": "B360593",
"metadata_schema_id": "312f7be0-9aec-4cae-b942-a8864c0aa1ce",
"uniprot_accession_number": "P15379"
},
{
"antibody_concentration_unit": "",
"antibody_concentration_value": "",
"antibody_rrid": "AB_3644275",
"channel_id": "Ter119",
"conjugated_cat_number": "",
"conjugated_tag": "",
"dilution_factor": "200",
"hgnc_symbol": "Not Applicable",
"lot_number": "B349936",
"metadata_schema_id": "312f7be0-9aec-4cae-b942-a8864c0aa1ce",
"uniprot_accession_number": "P14220"
},
{
"antibody_concentration_unit": "",
"antibody_concentration_value": "",
"antibody_rrid": "AB_3271528",
"channel_id": "CD3",
"conjugated_cat_number": "",
"conjugated_tag": "",
"dilution_factor": "400",
"hgnc_symbol": "Not Applicable",
"lot_number": "B388260",
"metadata_schema_id": "312f7be0-9aec-4cae-b942-a8864c0aa1ce",
"uniprot_accession_number": "P22646"
},
{
"antibody_concentration_unit": "",
"antibody_concentration_value": "",
"antibody_rrid": "AB_3271532",
"channel_id": "MHC II",
"conjugated_cat_number": "",
"conjugated_tag": "",
"dilution_factor": "400",
"hgnc_symbol": "Not Applicable",
"lot_number": "B360847",
"metadata_schema_id": "312f7be0-9aec-4cae-b942-a8864c0aa1ce",
"uniprot_accession_number": "P18468"
},
{
"antibody_concentration_unit": "",
"antibody_concentration_value": "",
"antibody_rrid": "AB_3644271",
"channel_id": "CD45",
"conjugated_cat_number": "",
"conjugated_tag": "",
"dilution_factor": "200",
"hgnc_symbol": "Not Applicable",
"lot_number": "1000000158",
"metadata_schema_id": "312f7be0-9aec-4cae-b942-a8864c0aa1ce",
"uniprot_accession_number": "P06800"
},
{
"antibody_concentration_unit": "",
"antibody_concentration_value": "",
"antibody_rrid": "AB_3271541",
"channel_id": "Ly6g",
"conjugated_cat_number": "",
"conjugated_tag": "",
"dilution_factor": "400",
"hgnc_symbol": "Not Applicable",
"lot_number": "B381166",
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"conjugated_cat_number": "",
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"antibody_concentration_unit": "ug/ml",
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"channel_id": "TCRb",
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"antibody_concentration_unit": "",
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"channel_id": "Ki67",
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"lot_number": "1000000313",
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"uniprot_accession_number": "E9PVX6"
},
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"antibody_concentration_unit": "",
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"uniprot_accession_number": "P01872"
},
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"antibody_concentration_unit": "",
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"channel_id": "CD11c",
"conjugated_cat_number": "",
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"lot_number": "B388264",
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"channel_id": "Ly6g",
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{
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}
],
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"Acquisition Instrument Vendor": "Akoya Biosciences",
"Analyte Class": "Protein",
"Antibodies Path": "extras/validated-SNT524_antibodies.tsv",
"Cell Boundary Marker Or Stain": "Not applicable",
"Contributors Path": "extras/validated-SNT524_contributors.tsv",
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"Preparation Protocol DOI": "https://dx.doi.org/10.17504/protocols.io.8epv5jdbnl1b/v1",
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"Total Run Time": "22 hour"
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"display_name": "Jungmin Nam",
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}
],
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"last_modified_user_sub": "6b297ad2-d33e-4534-8acf-3456e4611324",
"metadata": {
"bedding": "1/4-inch pelleted cellulose",
"cage_enhancements": "Nestlets",
"date_of_birth_or_fertilization": "2021/9/9 12:00:00 AM",
"date_of_death": "2023/10/24 12:00:00 AM",
"diet": "Chow",
"euthanization_method": "Inhaled anesthetic euthanasia",
"is_deceased": "Yes",
"is_embryo": "No",
"light_cycle": "Standard/default",
"local_lifespan_data": "25.5 month",
"metadata_schema_id": "44662059-aa73-4756-a4a7-990489ca2f43",
"rack_setup": "Ventilated",
"room_health_status": "Pathogen free",
"room_temperature": "23",
"sex": "Male",
"source_id": "SNT722.BGFJ.623",
"strain": "C57BL6",
"strain_rrid": "RRID:IMSR_JAX:000664",
"water_source": "Hydropac individual pouch water"
},
"protocol_url": "dx.doi.org/10.17504/protocols.io.kqdg3x8keg25/v2",
"sennet_id": "SNT722.BGFJ.623",
"source_type": "Mouse",
"uuid": "2f2a7af9951f50b399d76b5080486fe1"
}
],
"status": "Published",
"status_history": [
{
"change_timestamp": 1754923869475,
"changed_by_email": "sennet@sennetconsortium.org",
"status": "New"
},
{
"change_timestamp": 1754923910340,
"changed_by_email": "sennet@sennetconsortium.org",
"status": "Submitted"
},
{
"change_timestamp": 1754924048109,
"changed_by_email": "bhonick@andrew.cmu.edu",
"status": "Processing"
},
{
"change_timestamp": 1754924168277,
"changed_by_email": "sennet@sennetconsortium.org",
"status": "QA"
},
{
"change_timestamp": 1754943461890,
"changed_by_email": "MAS400@pitt.edu",
"status": "Published"
}
],
"uuid": "f9a36aa133fff9cb3e62c2e4ea885578"
}
]
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Filtering the results
All of the endpoints that support entity retrieval are issued using a GET request, however, most of these endpoints are accessible via a POST request.
This will allow you to define specific properties in the request body that are returned in the response rather than returning all properties.
We will now make use of our api_post_request which calls the api_request method.
In the api_request method, notice the use of the post method on line 6, and passing additional data via the data param.
Returning only basic entity properties
What if for the previous /descendants call we just want a list of the most basic information for the entities? We
could get those results by creating a request body with filter_properties. When this key exists in the request body,
certain properties will be returned by default, even if the list is empty [].
body = {
"filter_properties": []
}
uuid = "2f2a7af9951f50b399d76b5080486fe1"
entity_data = api_post_request(f"/descendants/{uuid}", body)
This call would yield:
[
{
"contains_human_genetic_sequences": false,
"data_access_level": "public",
"dataset_type": "PhenoCycler",
"entity_type": "Dataset",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"sennet_id": "SNT397.CRWK.458",
"status": "Published",
"uuid": "f9a36aa133fff9cb3e62c2e4ea885578"
},
{
"data_access_level": "public",
"entity_type": "Sample",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"sample_category": "Block",
"sennet_id": "SNT664.KFZW.224",
"uuid": "8208088865da724bbb55cae38632a88a"
},
{
"data_access_level": "public",
"entity_type": "Sample",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"sample_category": "Section",
"sennet_id": "SNT587.LHXH.846",
"uuid": "fb1398a3f416df8f2fc97583796f29be"
},
{
"contains_human_genetic_sequences": false,
"data_access_level": "public",
"dataset_type": "PhenoCycler",
"entity_type": "Dataset",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"sennet_id": "SNT854.VJMX.652",
"status": "Published",
"uuid": "b2c290335c4d69f377fce7b71ae91db6"
},
{
"data_access_level": "public",
"entity_type": "Sample",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"organ": "UBERON:0002106",
"sample_category": "Organ",
"sennet_id": "SNT666.XZGV.432",
"uuid": "1c49b822f9a9341cfb2be080f08eb15f"
}
]
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Returning only a list of UUIDs
If we only wanted the UUIDs in the response, we simply add the "uuid" property to the list. So our code would look like:
body = {
"filter_properties": ["uuid"]
}
uuid = "2f2a7af9951f50b399d76b5080486fe1"
entity_data = api_post_request(f"/descendants/{uuid}", body)
That would yield:
[
"1c49b822f9a9341cfb2be080f08eb15f",
"8208088865da724bbb55cae38632a88a",
"fb1398a3f416df8f2fc97583796f29be",
"b2c290335c4d69f377fce7b71ae91db6",
"f9a36aa133fff9cb3e62c2e4ea885578"
]
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Warning
Note that specifying any other single property in filter_properties besides uuid will always return other basic properties in the response.
Returning custom properties
Let’s say along with basic properties, we’d also like protocol_url, description, last_modified_user_displayname but everything else out. Our code would look like:
body = {
"filter_properties": ["protocol_url", "description", "last_modified_user_displayname"]
}
uuid = "2f2a7af9951f50b399d76b5080486fe1"
entity_data = api_post_request(f"/descendants/{uuid}", body)
That would yield:
[
{
"contains_human_genetic_sequences": false,
"data_access_level": "public",
"dataset_type": "PhenoCycler",
"description": "Aging in the immune system is marked by various phenotypic changes of the immune cells across organs and a functional decline in their ability to combat disease and infection. At the Yale TMCs, we aim to characterize how senescence manifests in the lymphoid and non-lymphoid tissues, how it affects immune cell function, and the complex relationship between immune cells and senescence-associated secretory phenotype (SASP) producing senescence cells. To achieve this, we are using the Phenocycler-Fusion system and a customized immune-senescence panel to produce high-plex immunofluorescence images of young and aged immune tissues and cells. In this dataset, we present imaging data from formalin-fixed paraffin-embedded (FFPE) spleen tissues from a 7.5 month old and 25.5 month old wild-type C57BL6 mice, stained with 36 markers including eight markers for cell proliferation and senescence (Ki67, p16, 53BP1, p21, p53, gH2AX, LaminB1, Rb), various immune cell type markers, and two histone modification markers (H3K9me3, H3K27ac).",
"entity_type": "Dataset",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"last_modified_user_displayname": "Max Sibilla",
"sennet_id": "SNT397.CRWK.458",
"status": "Published",
"uuid": "f9a36aa133fff9cb3e62c2e4ea885578"
},
{
"data_access_level": "public",
"entity_type": "Sample",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"last_modified_user_displayname": "Hester Doyle",
"protocol_url": "dx.doi.org/10.17504/protocols.io.kqdg3x8keg25/v2",
"sample_category": "Block",
"sennet_id": "SNT664.KFZW.224",
"uuid": "8208088865da724bbb55cae38632a88a"
},
{
"data_access_level": "public",
"description": "fresh frozen",
"entity_type": "Sample",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"last_modified_user_displayname": "Jungmin Nam",
"protocol_url": "dx.doi.org/10.17504/protocols.io.kqdg3x8keg25/v2",
"sample_category": "Section",
"sennet_id": "SNT587.LHXH.846",
"uuid": "fb1398a3f416df8f2fc97583796f29be"
},
{
"contains_human_genetic_sequences": false,
"data_access_level": "public",
"dataset_type": "PhenoCycler",
"description": "Aging in the immune system is marked by various phenotypic changes of the immune cells across organs and a functional decline in their ability to combat disease and infection. At the Yale TMCs, we aim to characterize how senescence manifests in the lymphoid and non-lymphoid tissues, how it affects immune cell function, and the complex relationship between immune cells and senescence-associated secretory phenotype (SASP) producing senescence cells. To achieve this, we are using the Phenocycler-Fusion system and a customized immune-senescence panel to produce high-plex immunofluorescence images of young and aged immune tissues and cells. In this dataset, we present imaging data from fresh frozen (FF) spleen tissues from male 25.5 month old wild-type C57BL6 mice, stained with 20 markers consisting of immune cell type and cell proliferation markers that show the spatial distribution of various cell phenotypes in the spleen.",
"entity_type": "Dataset",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"last_modified_user_displayname": "Max Sibilla",
"sennet_id": "SNT854.VJMX.652",
"status": "Published",
"uuid": "b2c290335c4d69f377fce7b71ae91db6"
},
{
"data_access_level": "public",
"entity_type": "Sample",
"group_name": "TMC - Yale University - Dixit",
"group_uuid": "1350e2f9-23a9-11ed-a56b-4ffe8363feee",
"last_modified_user_displayname": "Hester Doyle",
"organ": "UBERON:0002106",
"protocol_url": "dx.doi.org/10.17504/protocols.io.kqdg3x8keg25/v2",
"sample_category": "Organ",
"sennet_id": "SNT666.XZGV.432",
"uuid": "1c49b822f9a9341cfb2be080f08eb15f"
}
]
Downloads & Tools
Pro tip
You can easily find out what property names are available for an entity by using the /entities/{id} endpoint.
Exclude certain properties
If instead of isolating certain properties to be returned you want to just exclude specific ones you can define those in filter_properties but also set "is_include": false to the request body:
body = {
"filter_properties": ["created_by_user_sub", "last_modified_user_sub", "group_uuid", "direct_ancestor", "source", "origin_samples"],
"is_include": false
}
entity_data = api_post_request(f"/descendants/{uuid}", body)
Downloads & Tools
Given a Dataset with SenNet ID SNT379.SJFD.828
uuid = "18c88ae2253ed9b4dabae35ad2c956ad" # remember we could use the value of the SenNet ID here, but it is more common to call the API via the UUID.
Get Entity’s Sources
In a similar fashion, we can call other common endpoints. Using the reusable api_request method, let’s find out the
sources for our target dataset.
entity_data = api_request(f"/datasets/{uuid}/sources")
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Get Entity’s Organs
entity_data = api_request(f"/datasets/{uuid}/organs")
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Get Entity’s Samples
entity_data = api_request(f"/datasets/{uuid}/samples")
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Get Entity’s Ancestors
The /ancestors/<id> endpoint returns all ancestors upstream in the provenance chain.
entity_data = api_request(f"/ancestors/{uuid}")
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Get Entity’s Parents
The /parents/<id> endpoint gets the immediate ancestors of the specified entity.
entity_data = api_request(f"/parents/{uuid}")
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Accessing restricted endpoints and data
In order to access restricted endpoints and data, you will need to pass a token in your request. Let’s update our headers object variable to include an Authorization key.
(To retrieve an authorization token, see this guide.)
headers = {
"Authorization": "Bearer COPIED_TOKEN_HERE",
"Content-Type": "application/json"
}
Get Entity’s Children:
The children are the nodes one level below the current node. To retrieve the children of an entity, we would request the
/children/<id> endpoint. This endpoint is restricted and requires a token.
uuid = "2f2a7af9951f50b399d76b5080486fe1"
entity_data = api_request(f"/children/{uuid}")
Downloads & Tools
Warning
You must pass a token in with your request for restricted endpoints. To retrieve an authorization token, see this guide.
Registering Entities
Registration of entities all require an authorization token in the API request and are sent as POST requests. In the next examples, we will make use of the helper method api_post_request to handle our registrations.
Did you know?
The SenNet Data Portal provides an intuitive user interface (UI) for registering Sources and Samples. For more information, see the Entitiy Registration docs.
Registering a Source:
First, prepare a payload with information about the Source to be registered. Then, send a POSTrequest to /entities/{entity_type} endpoint to register the new Source. Please note, the headers object sent with the request should include Authorization with your token.
source_info = {
"group_uuid":"57192604-18e0-11ed-b79b-972795fc9504",
"lab_source_id":"10/01/2025-a",
"source_type":"Mouse",
"protocol_url":"https://dx.doi.org/10.17504/protocols.io.0000",
"description":"Some optional lab notes."
}
entity_data = api_post_request(f"/entities/Source", source_info)
All properties but description are required. See the API docs for more information about properties associated with the Source entity.
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Registering a Sample:
First prepare a payload with information about the Sample to be registered. Then, send a POST request to /entities/{entity_type} endpoint to register the new Sample. Please note, the headers object sent with the request should include Authorization with your token.
sample_info = {
"group_uuid":"57192604-18e0-11ed-b79b-972795fc9504",
"direct_ancestor_uuid":"7f78680bf2d157586832176eab9a9022",
"sample_category":"Organ",
"organ":"UBERON:0000178",
"protocol_url":"https://dx.doi.org/10.17504/protocols.io.9nzhvf6",
"lab_tissue_sample_id":"10/10/2025-b",
"description":"Some optional lab notes."
}
entity_data = api_post_request(f"/entities/Sample", sample_info)
All properties but description are required. The organ property is required only when sample_category is set to Organ. See the API docs for more information about properties associated with the Sample entity.
Downloads & Tools
The process is similar for registering other single entity types. Via a POST request, simply issue a payload to /entities/{entity_type} where entity_type is the singular case insensitive name of the entity you are trying to register. Send a payload with the request using that entity’s associated properties. Please view the API documentation for information about these schemas.