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"
Defining a reusable get_data function
Here we provide a simple function that can be reused for all GET requests.
def get_data(endpoint):
query_url = f"{domain_base}{endpoint}"
entity_data = None
try:
response = requests.get(query_url)
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
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 = get_data(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 = get_data(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 = get_data(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",
"metadata_schema_id": "312f7be0-9aec-4cae-b942-a8864c0aa1ce",
"uniprot_accession_number": "P35461"
},
{
"antibody_concentration_unit": "",
"antibody_concentration_value": "",
"antibody_rrid": "AB_3254289",
"channel_id": "CD19",
"conjugated_cat_number": "",
"conjugated_tag": "",
"dilution_factor": "200",
"hgnc_symbol": "Not Applicable",
"lot_number": "B404569",
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"antibody_concentration_unit": "",
"antibody_concentration_value": "",
"antibody_rrid": "AB_3644269",
"channel_id": "CD24",
"conjugated_cat_number": "",
"conjugated_tag": "",
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"hgnc_symbol": "Not Applicable",
"lot_number": "1000000169",
"metadata_schema_id": "312f7be0-9aec-4cae-b942-a8864c0aa1ce",
"uniprot_accession_number": "P24807"
},
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"antibody_concentration_unit": "",
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"conjugated_cat_number": "",
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"lot_number": "B399274",
"metadata_schema_id": "312f7be0-9aec-4cae-b942-a8864c0aa1ce",
"uniprot_accession_number": "Q62230"
},
{
"antibody_concentration_unit": "ug/ml",
"antibody_concentration_value": "1032",
"antibody_rrid": "AB_3675507",
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"conjugated_cat_number": "5250018",
"conjugated_tag": "Atto550",
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"lot_number": "1072898",
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"antibody_concentration_unit": "",
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"lot_number": "B388259",
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"antibody_concentration_unit": "",
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"antibody_concentration_unit": "ug/ml",
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"antibody_concentration_unit": "",
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"channel_id": "IgD",
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"lot_number": "BX97932",
"metadata_schema_id": "312f7be0-9aec-4cae-b942-a8864c0aa1ce",
"uniprot_accession_number": "P01882"
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{
"antibody_concentration_unit": "",
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"channel_id": "TCRb",
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},
{
"antibody_concentration_unit": "",
"antibody_concentration_value": "",
"antibody_rrid": "AB_2895046",
"channel_id": "Ki67",
"conjugated_cat_number": "",
"conjugated_tag": "",
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"lot_number": "1000000313",
"metadata_schema_id": "312f7be0-9aec-4cae-b942-a8864c0aa1ce",
"uniprot_accession_number": "E9PVX6"
},
{
"antibody_concentration_unit": "",
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"antibody_rrid": "AB_3644277",
"channel_id": "IgM",
"conjugated_cat_number": "",
"conjugated_tag": "",
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"hgnc_symbol": "Not Applicable",
"lot_number": "B358628",
"metadata_schema_id": "312f7be0-9aec-4cae-b942-a8864c0aa1ce",
"uniprot_accession_number": "P01872"
},
{
"antibody_concentration_unit": "",
"antibody_concentration_value": "",
"antibody_rrid": "AB_3271529",
"channel_id": "CD11c",
"conjugated_cat_number": "",
"conjugated_tag": "",
"dilution_factor": "400",
"hgnc_symbol": "Not Applicable",
"lot_number": "B388264",
"metadata_schema_id": "312f7be0-9aec-4cae-b942-a8864c0aa1ce",
"uniprot_accession_number": "Q9QXH4"
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"antibody_concentration_unit": "",
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},
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"lot_number": "B396437",
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"uniprot_accession_number": "P06800"
},
{
"antibody_concentration_unit": "",
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"antibody_rrid": "AB_3271541",
"channel_id": "Ly6g",
"conjugated_cat_number": "",
"conjugated_tag": "",
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"hgnc_symbol": "Not Applicable",
"lot_number": "B381166",
"metadata_schema_id": "312f7be0-9aec-4cae-b942-a8864c0aa1ce",
"uniprot_accession_number": "P35461"
},
{
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"lot_number": "B397930",
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"lot_number": "1000000158",
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},
{
"antibody_concentration_unit": "",
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"antibody_rrid": "AB_3271535",
"channel_id": "CD71",
"conjugated_cat_number": "",
"conjugated_tag": "",
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"hgnc_symbol": "Not Applicable",
"lot_number": "B347017",
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"uniprot_accession_number": "Q62351"
},
{
"antibody_concentration_unit": "",
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"antibody_rrid": "AB_3271532",
"channel_id": "MHC II",
"conjugated_cat_number": "",
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"lot_number": "B360847",
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},
{
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},
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"lot_number": "B406310",
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},
{
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{
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"lot_number": "B406366",
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},
{
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"antibody_rrid": "AB_3271531",
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"lot_number": "B360593",
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}
],
"cedar_mapped_metadata": {
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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",
"Dataset Type": "PhenoCycler",
"Is Targeted": "Yes",
"Metadata Schema ID": "62af6829-743d-423e-a701-204710e56beb",
"Non Global Files": "",
"Nuclear Marker Or Stain": "DAPI",
"Number Of Antibodies": "35",
"Number Of Biomarker Imaging Rounds": "17",
"Number Of Channels": "3",
"Number Of Total Imaging Rounds": "19",
"Preparation Protocol DOI": "https://dx.doi.org/10.17504/protocols.io.8epv5jdbnl1b/v1",
"Source Storage Duration": "2 month",
"Time Since Acquisition Instrument Calibration": "5 day",
"Total Run Time": "22 hour"
},
"contacts": [
{
"affiliation": "Yale",
"display_name": "Jungmin Nam",
"email": "jungmin.nam@yale.edu",
"first_name": "Jungmin",
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"last_name": "Nam",
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"orcid": "0000-0002-6717-1328"
},
{
"affiliation": "Yale",
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"middle_name_or_initial": "",
"orcid": "0000-0001-7805-8059"
},
{
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"middle_name_or_initial": "Deep",
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}
],
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"contributors": [
{
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"first_name": "Jungmin",
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"orcid": "0000-0002-6717-1328"
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{
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{
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"orcid": "0000-0003-1631-7451"
},
{
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"last_name": "Youm",
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"orcid": "0000-0002-8098-8527"
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{
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}
],
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"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).",
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}
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"analyte_class": "Protein",
"antibodies_path": "extras/validated-SNT524_antibodies.tsv",
"cell_boundary_marker_or_stain": "Not applicable",
"contributors_path": "extras/validated-SNT524_contributors.tsv",
"dataset_type": "PhenoCycler",
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"nuclear_marker_or_stain": "DAPI",
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"preparation_protocol_doi": "https://dx.doi.org/10.17504/protocols.io.8epv5jdbnl1b/v1",
"source_storage_duration_unit": "month",
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"total_run_time_unit": "hour",
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},
"origin_samples": [
{
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"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"
}
],
"pipeline_message": "the process ran",
"provider_info": "FFPE Spleen Phenocycler Data",
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"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"
}
]
Downloads & Tools
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.
Here we provide a filter_data function to facilitate this.
def filter_data(endpoint, body):
query_url = f"{domain_base}{endpoint}"
entity_data = None
try:
response = requests.post(query_url, data=body) # notice the use of the post method, and passing additional data via the data param
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
In this method, notice the use of the post method, 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 = filter_data(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"
}
]
Downloads & Tools
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 = filter_data(f"/descendants/{uuid}", body)
That would yield:
[
"1c49b822f9a9341cfb2be080f08eb15f",
"8208088865da724bbb55cae38632a88a",
"fb1398a3f416df8f2fc97583796f29be",
"b2c290335c4d69f377fce7b71ae91db6",
"f9a36aa133fff9cb3e62c2e4ea885578"
]
Downloads & Tools
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 = filter_data(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 = filter_data(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 get_data method, let’s find out the
sources for our target dataset.
entity_data = get_data(f"/datasets/{uuid}/sources")
Downloads & Tools
Get Entity’s Organs
entity_data = get_data(f"/datasets/{uuid}/organs")
Downloads & Tools
Get Entity’s Samples
entity_data = get_data(f"/datasets/{uuid}/samples")
Downloads & Tools
Get Entity’s Ancestors
The /ancestors/<id> endpoint returns all ancestors upstream in the provenance chain.
entity_data = get_data(f"/ancestors/{uuid}")
Downloads & Tools
Get Entity’s Parents
The /parents/<id> endpoint gets the immediate ancestors of the specified entity.
entity_data = get_data(f"/parents/{uuid}")
Downloads & Tools
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
get_data function to reflect that making use of the headers param. (To retrieve an authorization token,
see this guide.)
headers = {
"Authorization": "Bearer COPIED_TOKEN_HERE",
"Content-Type": "application/json"
}
def get_data(endpoint):
query_url = f"{domain_base}{endpoint}"
entity_data = None
try:
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
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 = get_data(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.
Similarly, line 5 in our filter_data method above can be updated to:
response = requests.post(query_url, data=body, headers=headers)