Adds Adipose tier2 fields

docs/jsonBrowser/required_fields.md

@@ -370,6 +370,8 @@ _There are no required properties in schema Disease profile_
 _There are no required properties in schema Reproductive history_
 ### Preservation and storage<a name='Preservation and storage'></a>
 _There are no required properties in schema Preservation and storage_
+### Lifestyle<a name='Lifestyle'></a>
+_There are no required properties in schema Lifestyle_
 ### Death<a name='Death'></a>
 Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example 
 --- | --- | --- | --- | --- | --- | --- 
@@ -378,6 +380,8 @@ cause_of_death | Conditions resulting in death. | string |  | Cause of death |
 _There are no required properties in schema Familial relationship_
 ### Medical history<a name='Medical history'></a>
 _There are no required properties in schema Medical history_
+### Blood test<a name='Blood test'></a>
+_There are no required properties in schema Blood test_
 ### Residence<a name='Residence'></a>
 _There are no required properties in schema Residence_
 ### Cell morphology<a name='Cell morphology'></a>

docs/jsonBrowser/type.md

@@ -130,6 +130,7 @@ spike_in_dilution | Dilution of spike-in. | integer | no |  | Spike-in dilution
 umi_barcode | Information about unique molecular identifier (UMI) barcodes. | object | no | [See module  barcode](module.md#barcode) | UMI barcode |  | 
 library_preamplification_method | The method used to amplify RNA prior to adaptor ligation. | object | no | [See module  library_amplification_ontology](module.md#library-amplification-ontology) | Library pre-amplification method |  | 
 cdna_library_amplification_method | The method used to amplify cDNA library prior to sequencing. | object | no | [See module  library_amplification_ontology](module.md#library-amplification-ontology) | cDNA library amplification method |  | 
+processing_time | Library preparation time in minutes. | string | no |  | Processing time |  | 20; 35; 60
 nominal_length | Average (insert) size of the fragments being sequenced. | integer | no |  | Nominal length |  | 250
 nominal_sdev | Standard deviation of the (insert) size of the fragments being sequenced. | integer | no |  | Nominal standard deviation |  | 30
 
@@ -225,6 +226,7 @@ schema_type | The type of the metadata schema entity. | string | yes |  |  | pro
 provenance | Provenance information provided by the system. | object | no | [See   provenance](.md#provenance) |  |  | 
 protocol_core | Core protocol-level information. | object | yes | [See core  protocol_core](core.md#protocol-core) | Protocol core |  | 
 method | Method used to collect the biomaterial. | object | yes | [See module  process_type_ontology](module.md#process-type-ontology) | Collection method |  | 
+biopsy_procedure | Type of biopsy procedure used in the sample collection. | string | no |  | Type of biopsy procedure | Bergstrom needle, Punch biopsy, Mercedes needle, dry aspiration, Mercedes needle, tumescent lidocaine “wet” aspiration | Bergstrom needle; Punch biopsy; Mercedes needle, dry aspiration; Mercedes needle, tumescent lidocaine “wet” aspiration
 reagents | A list of purchased reagents used in this protocol. | array | no | [See module  purchased_reagents](module.md#purchased-reagents) | Protocol reagents |  | 
 
 ## Differentiation protocol
@@ -352,10 +354,12 @@ organ_parts | A term for a specific part of the organ that the biomaterial came
 transplant_organ | Was the specimen collected after extraction for organ transplantation? | boolean | no |  | Transplant organ |  | yes; no
 diseases | Short description of known disease(s) of the specimen. | array | no | [See module  disease_ontology](module.md#disease-ontology) | Known disease(s) |  | 
 adjacent_diseases | Short description of the disease(s) adjacent to the specimen's collection site (e.g. breast cancer). | array | no | [See module  disease_ontology](module.md#disease-ontology) | Adjacent disease(s) |  | 
+experimental_condition | Case of the sample used in the experiment context, it should include a description of the experimental conditions of the study. If disease case, specify the disease that was studied. | string | no |  | Case Control definition |  | healthy control; disease control; MAFLD disease case; gestational diabetes case
 state_of_specimen | State of the specimen at the time of collection. | object | no | [See module  state_of_specimen](module.md#state-of-specimen) | State of specimen |  | 
 preservation_storage | Information about how a specimen was preserved and/or stored over a period of time. | object | no | [See module  preservation_storage](module.md#preservation-storage) | Preservation/Storage |  | 
 collection_time | When the biomaterial was collected. | string | no |  | Time of collection |  | 2016-01-21T00:00:00Z; 2016-03
 collection_institute | Institute where the biomaterial was collected on. | object | no | [See module  collection_institute](module.md#collection-institute) | Collection institute |  | 
+time_to_laboratory | Transit time in hours between tissue collection and tissue processing, meaning either storage in the laboratory or processing for sequencing. | string | no |  | Time to laboratory |  | 2; 5; 8
 purchased_specimen | Information about a purchased specimen. | object | no | [See module  purchased_reagents](module.md#purchased-reagents) | Purchased specimen |  | 
 
 ## Cell suspension
@@ -375,6 +379,7 @@ selected_cell_types | The cell type(s) selected to be present in the suspension.
 estimated_cell_count | Estimated number of cells in the suspension. | integer | no |  | Estimated cell count |  | 1; 2100
 plate_based_sequencing | Fields specific for plate-based sequencing experiments. | object | no | [See module  plate_based_sequencing](module.md#plate-based-sequencing) | Plate-based sequencing |  | 
 processing_institute | Institute where the biomaterial was processed. | string | no |  | Institute |  | Wellcome Sanger Institute; University of Zurich; University of Pennsylvania
+nuclei_yield | Number of nuclei sequenced per mg of tissue. | integer | no |  | Nuclei yield |  | 20; 32; 56
 
 ## Cell line
 _Information about the cell line or cell culture biomaterial._

json_schema/module/biomaterial/blood_test.json

@@ -0,0 +1,337 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema#",
+    "description": "Blood test results of the donor.",
+    "additionalProperties": false,
+    "minProperties": 1,
+    "title": "Blood test",
+    "name": "blood_test",
+    "type": "object",
+    "properties": {
+        "describedBy": {
+            "description": "The URL reference to the schema.",
+            "type": "string",
+            "pattern" : "^(http|https)://schema.(.*?)humancellatlas.org/module/biomaterial/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/blood_test"
+        },
+        "schema_version": {
+            "description": "The version number of the schema in major.minor.patch format.",
+            "type": "string",
+            "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$",
+            "example": "4.6.1"
+        },
+        "androstenedione": {
+            "description": "Androstenedione in the last blood test of the donor before collection.",
+            "type": "number",
+            "user_friendly": "Androstenedione",
+            "example": "0.7; 3.4; 2.41",
+            "bionetworks": ["adipose"]
+        },
+        "androstenedione_unit": {
+            "description": "Androstenedione unit.",
+            "type": "string",
+            "enum": [
+                "ng/dL",
+                "nmol/L"
+            ],
+            "user_friendly": "Androstenedione unit",
+            "example": "ng/dL; nmol/L",
+            "guidelines": "Should be one of: ng/dL; nmol/L",
+            "bionetworks": ["adipose"]
+        },
+        "dhea": {
+            "description": "Dehydroepiandrosterone (DHEA) in the last blood test of the donor before collection.",
+            "type": "number",
+            "user_friendly": "DHEA",
+            "example": "240; 3500; 1500",
+            "bionetworks": ["adipose"]
+        },
+        "dhea_unit": {
+            "description": "DHEA unit.",
+            "type": "string",
+            "enum": [
+                "ng/dL",
+                "nmol/L"
+            ],
+            "user_friendly": "DHEA unit",
+            "example": "ng/dL; nmol/L",
+            "guidelines": "Should be one of: ng/dL; nmol/L",
+            "bionetworks": ["adipose"]
+        },
+        "estrogen": {
+            "description": "Estrogen in the last blood test of the donor before collection.",
+            "type": "number",
+            "user_friendly": "Estrogen",
+            "example": "10; 150; 120",
+            "bionetworks": ["adipose"]
+        },
+        "estrogen_unit": {
+            "description": "Estrogen unit.",
+            "type": "string",
+            "enum": [
+                "pg/mL",
+                "pmol/L"
+            ],
+            "user_friendly": "Estrogen unit",
+            "example": "pg/mL; pmol/L",
+            "guidelines": "Should be one of: pg/mL; pmol/L",
+            "bionetworks": ["adipose"]
+        },
+        "fasting_glucose": {
+            "description": "Fasting glucose levels from the donor's last blood test after at least 8 hours of fasting, prior to the biopsy collection.",
+            "type": "number",
+            "user_friendly": "Fasting glucose",
+            "example": "70; 125; 90.2",
+            "bionetworks": ["adipose"]
+        },
+        "fasting_glucose_unit": {
+            "description": "Fasting glucose unit.",
+            "type": "string",
+            "enum": [
+                "mg/dL",
+                "mmol/L"
+            ],
+            "user_friendly": "Fasting glucose unit",
+            "example": "mg/dL; mmol/L",
+            "guidelines": "Should be one of: mg/dL; mmol/L",
+            "bionetworks": ["adipose"]
+        },
+        "fasting_insulin": {
+            "description": "Fasting insulin levels from the donor's last blood test after at least 8 hours of fasting, prior to the biopsy collection.",
+            "type": "number",
+            "user_friendly": "Fasting insulin",
+            "example": "2; 20; 14",
+            "bionetworks": ["adipose"]
+        },
+        "fasting_insulin_unit": {
+            "description": "Fasting insulin unit.",
+            "type": "string",
+            "enum": [
+                "μU/mL",
+                "pmol/L"
+            ],
+            "user_friendly": "Fasting insulin unit",
+            "example": "μU/mL; pmol/L",
+            "guidelines": "Should be one of: μU/mL; pmol/L",
+            "bionetworks": ["adipose"]
+        },
+        "free_fatty_acid": {
+            "description": "Free Fatty Acid (FFA) in the last blood test of the donor before collection.",
+            "type": "number",
+            "user_friendly": "FFA",
+            "example": "0.1; 0.6; 0.24",
+            "bionetworks": ["adipose"]
+        },
+        "free_fatty_acid_unit": {
+            "description": "Free Fatty Acid (FFA) unit.",
+            "type": "string",
+            "enum": [
+                "mmol/L"
+            ],
+            "user_friendly": "FFA unit",
+            "example": "mmol/L",
+            "guidelines": "Should be one of: mmol/L",
+            "bionetworks": ["adipose"]
+        },
+        "haematocrit": {
+            "description": "Percentage of red blood cells in whole blood from the donor's last blood test prior to biopsy collection.",
+            "type": "number",
+            "user_friendly": "Haematocrit",
+            "example": "36; 54; 45",
+            "bionetworks": ["adipose"]
+        },
+        "haematocrit_unit": {
+            "description": "Haematocrit unit.",
+            "type": "string",
+            "enum": [
+                "percentage (%)"
+            ],
+            "user_friendly": "Haematocrit unit",
+            "example": "%",
+            "guidelines": "Should be one of: %",
+            "bionetworks": ["adipose"]
+        },
+        "haemoglobin": {
+            "description": "Concentration of haemoglobin in whole blood from the donor's last blood test prior to biopsy collection.",
+            "type": "number",
+            "user_friendly": "Haemoglobin",
+            "example": "12; 17.5; 14.2",
+            "bionetworks": ["adipose"]
+        },
+        "haemoglobin_unit": {
+            "description": "Haemoglobin unit.",
+            "type": "string",
+            "enum": [
+                "g/dL",
+                "mmol/L"
+            ],
+            "user_friendly": "Haemoglobin unit",
+            "example": "g/dL; mmol/L",
+            "guidelines": "Should be one of: g/dL; mmol/L",
+            "bionetworks": ["adipose"]
+        },
+        "hba1c": {
+            "description": "Concentration of glycated hemoglobin (HbA1c) from the donor's last blood test prior to biopsy collection.",
+            "type": "number",
+            "user_friendly": "HbA1c",
+            "example": "42; 58; 53.3",
+            "bionetworks": ["adipose"]
+        },
+        "hba1c_unit": {
+            "description": "HbA1c unit.",
+            "type": "string",
+            "enum": [
+                "mmol/mol",
+                "%"
+            ],
+            "user_friendly": "HbA1c unit",
+            "example": "mmol/mol; %",
+            "guidelines": "Should be one of: mmol/mol; %",
+            "bionetworks": ["adipose"]
+        },
+        "hdl": {
+            "description": "High-density lipoprotein cholesterol (HDL) in the last blood test of the donor before collection.",
+            "type": "number",
+            "user_friendly": "HDL",
+            "example": "40; 60; 92",
+            "bionetworks": ["adipose"]
+        },
+        "hdl_unit": {
+            "description": "HDL unit.",
+            "type": "string",
+            "enum": [
+                "mg/dL",
+                "mmol/L"
+            ],
+            "user_friendly": "HDL unit",
+            "example": "mg/dL; mmol/L",
+            "guidelines": "Should be one of: mg/dL; mmol/L",
+            "bionetworks": ["adipose"]
+        },
+        "homa_ir": {
+            "description": "Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) in the last blood test of the donor before collection.",
+            "type": "number",
+            "user_friendly": "HOMA-IR",
+            "example": "0.4; 1.2; 0.94",
+            "bionetworks": ["adipose"]
+        },
+        "ldl": {
+            "description": "Low-density lipoprotein cholesterol (LDL) in the last blood test of the donor before collection.",
+            "type": "number",
+            "user_friendly": "LDL",
+            "example": "160; 133",
+            "bionetworks": ["adipose"]
+        },
+        "ldl_unit": {
+            "description": "LDL unit.",
+            "type": "string",
+            "enum": [
+                "mg/dL",
+                "mmol/L"
+            ],
+            "user_friendly": "LDL unit",
+            "example": "mg/dL; mmol/L",
+            "guidelines": "Should be one of: mg/dL; mmol/L",
+            "bionetworks": ["adipose"]
+        },
+        "platelet_count": {
+            "description": "Measurement of platelets per unit volume of blood from the donor's last blood test prior to biopsy collection",
+            "type": "number",
+            "user_friendly": "Platelet count",
+            "example": "240; 124; 110",
+            "bionetworks": ["adipose"]
+        },
+        "platelet_count_unit": {
+            "description": "Platelet count unit.",
+            "type": "string",
+            "enum": [
+                "10^9/L",
+                "cells/μL"
+            ],
+            "user_friendly": "Platelet count unit",
+            "example": "10^9/L; cells/μL",
+            "guidelines": "Should be one of: 10^9/L; cells/μL",
+            "bionetworks": ["adipose"]
+        },
+        "shbg": {
+            "description": "Sex hormone binding globulin (SHBG) in the last blood test of the donor before collection.",
+            "type": "number",
+            "user_friendly": "SHBG",
+            "example": "10; 140; 72",
+            "bionetworks": ["adipose"]
+        },
+        "shbg_unit": {
+            "description": "SHBG unit.",
+            "type": "string",
+            "enum": [
+                "nmol/L"
+            ],
+            "user_friendly": "SHBG unit",
+            "example": "nmol/L",
+            "guidelines": "Should be one of: nmol/L",
+            "bionetworks": ["adipose"]
+        },
+        "testosterone": {
+            "description": "Testosterone in the last blood test of the donor before collection.",
+            "type": "number",
+            "user_friendly": "Testosterone",
+            "example": "15; 1000; 420",
+            "bionetworks": ["adipose"]
+        },
+        "testosterone_unit": {
+            "description": "Testosterone unit.",
+            "type": "string",
+            "enum": [
+                "nmol/L",
+                "ng/dL"
+            ],
+            "user_friendly": "Testosterone unit",
+            "example": "nmol/L; ng/dL",
+            "guidelines": "Should be one of: nmol/L; ng/dL",
+            "bionetworks": ["adipose"]
+        },
+        "triglycerides": {
+            "description": "Triglycerides levels from the donor's last blood test after at least 9-12 hours of fasting, prior to the biopsy collection.",
+            "type": "number",
+            "user_friendly": "Triglycerides",
+            "example": "160; 133; 140",
+            "bionetworks": ["adipose"]
+        },
+        "triglycerides_unit": {
+            "description": "Triglycerides unit.",
+            "type": "string",
+            "enum": [
+                "mg/dL",
+                "mmol/L"
+            ],
+            "user_friendly": "Triglycerides unit",
+            "example": "mg/dL; mmol/L",
+            "guidelines": "Should be one of: mg/dL; mmol/L",
+            "bionetworks": ["adipose"]
+        },
+        "white_blood_cell_count": {
+            "description": "Measurement of total white blood cells per unit volume of blood from the donor's last blood test prior to biopsy collection.",
+            "type": "number",
+            "user_friendly": "White cell count",
+            "example": "4.5; 11; 9.24",
+            "bionetworks": ["adipose"]
+        },
+        "white_blood_cell_count_unit": {
+            "description": "White cell count unit.",
+            "type": "string",
+            "enum": [
+                "10^9/L",
+                "cells/μL"
+            ],
+            "user_friendly": "White cell count unit",
+            "example": "10^9/L; cells/μL",
+            "guidelines": "Should be one of: 10^9/L; cells/μL",
+            "bionetworks": ["adipose"]
+        },
+        "bloodtest_time_offset": {
+            "description": "Time between the test and the collection of the sample, in days.",
+            "type": "number",
+            "user_friendly": "Blood test time offset",
+            "example": "12; 42; 98",
+            "bionetworks": ["adipose"]
+        }
+    }
+}