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Initialise disease_profile in versions.json
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arschat committed Sep 30, 2024
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169 changes: 0 additions & 169 deletions docs/jsonBrowser/module.md
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Expand Up @@ -467,172 +467,3 @@ Location: module/biomaterial/disease_profile.json

Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | --- | ---
copd_gold_stage | Indicating current GOLD stage (Global Initiative for Chronic Obstructive Lung Disease). | integer | no | | GOLD stage | 1, 2, 3, 4 | 1; 2; 3; 4
copd_mmrc_grade | Indicate the Modified British Medical Research Council (mMRC) dyspnea scale grade. | integer | no | | mMRC grade | 0, 1, 2, 3, 4 | 0, 1; 2; 3; 4
copd_cat_score | Indicate the COPD Assessment Test (CAT) score. | integer | no | | CAT score | | 2; 5; 37
copd_gold_abe_assessment | Indicate the Global Initiative for Chronic Obstructive Lung Disease (GOLD) A, B, C, D assessment group if available. | string | no | | GOLD ABE assessment | A, B, E | A; B; E
copd_phenotype | Indicate the COPD disease phenotype(s) of donor. Please indicate all applicable phenotypes of donor. | array | no | | COPD phenotype | COPD not otherwise specified, COPD with emphysema, COPD with bronchitis, COPD with history of asthma, COPD with >300 eos in blood, COPD with allergy, COPD with Chronic Mucus Hypersecretion, COPD with frequent exacerbations | COPD with bronchitis; COPD with history of asthma; COPD with emphysema
copd_emphysema_percentage | Indicate the percentage of the lung that is affected by emphysema as judged based on non-invasive imaging, such as from a CT scan. | number | no | | Percentage of emphysema | | 30; 76; 92

## Preservation and storage<a name='Preservation and storage'></a>
_Information relating to how a biomaterial was preserved and/or stored over a period of time._

Location: module/biomaterial/preservation_storage.json

Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | --- | ---
storage_method | The method by which a biomaterial was stored after preservation or before another protocol was used. | string | no | | Storage method | ambient temperature, cut slide, fresh, frozen at -70C, frozen at -80C, frozen at -150C, frozen in liquid nitrogen, frozen in vapor phase, paraffin block, RNAlater at 4C, RNAlater at 25C, RNAlater at -20C | frozen in liquid nitrogen; fresh
storage_time | Length of time the biomaterial was stored for in Storage time units. | number | no | | Storage time | | 5
storage_time_unit | The unit in which Storage time is expressed. | object | no | [See module time_unit_ontology](module.md#time-unit-ontology) | Storage time unit | |
preservation_method | The method by which a biomaterial was preserved through the use of chemicals, cold, or other means to prevent or retard biological or physical deterioration. | string | no | | Preservation method | cryopreservation in liquid nitrogen (dead tissue), cryopreservation in dry ice (dead tissue), cryopreservation of live cells in liquid nitrogen, cryopreservation, other, formalin fixed, unbuffered, formalin fixed, buffered, formalin fixed and paraffin embedded, hypothermic preservation media at 2-8C, fresh | cryopreservation in liquid nitrogen (dead tissue); fresh

## Death<a name='Death'></a>
_Information relating to the death of an organism._

Location: module/biomaterial/death.json

Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | --- | ---
cause_of_death | Conditions resulting in death. | string | yes | | Cause of death | | Hypoxic brain damage; Sudden cardiac arrest
cold_perfused | Whether perfusion with cold fluid was used to help preserve tissues before heart stopped. | boolean | no | | Cold perfused | | Should be one of: yes, no.
days_on_ventilator | Number of days on ventilator before death occurred. | number | no | | Number of days on ventilator | | 4
hardy_scale | Value on 4-point Hardy scale cause of death classification. | integer | no | | Value on Hardy scale | | 0
time_of_death | Date and time when death was declared. | string | no | | Time of death | | 2016-01-21T00:00:00Z; 2016-03
organ_donation_death_type | Type of death preceding organ donation. | string | no | | Organ donation death type | Donation after circulatory death (DCD), Donation after brainstem death (DBD) | Should be one of: Donation after circulatory death (DCD), or Donation after brainstem death (DBD).
normothermic_regional_perfusion | Whether entire body was perfused with warm oxygenated blood. | string | no | | Normothermic regional perfusion | yes, no, unknown | Should be one of: yes, no, or unknown.

## Familial relationship<a name='Familial relationship'></a>
_Information about other organisms that this organism is related to._

Location: module/biomaterial/familial_relationship.json

Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | --- | ---
parent | The individual's parent. | string | no | | Parent | |
child | The individual's child. | string | no | | Child | |
sibling | The individual's sibling. | string | no | | Sibling | |

## Medical history<a name='Medical history'></a>
_Information about the medical history of a donor._

Location: module/biomaterial/medical_history.json

Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | --- | ---
alcohol_history | Estimated amount of alcohol consumed per day. | string | no | | Alcohol history | | 3-6 alcohol units/day; 1 drink per day
medication | Medications the individual was taking at time of biomaterial collection. | string | no | | Medications | | Naproxen 500mg/day; Citalopram 20mg/day
smoking_status | Whether the individual is actively, was formerly or never consumed smoking tobacco products like cigarettes, cigars, pipe etc. | string | no | | Smoking status | active, former, never | Should be one of: active, former, never.
smoking_pack_years | Estimated number of packs (20 cigarettes) smoked per day multiplied by the number of years the individual was smoking. | number | no | | Smoking pack years | | 4.55
years_since_smoking_cessation | If smoking status is 'former', specify the number of years since smoking cessation. | integer | no | | Years since smoking cessation | | 12
nutritional_state | Nutritional state of individual at time of biomaterial collection. | string | no | | Nutritional state | normal, fasting, feeding tube removed | Should be one of: normal, fasting, or feeding tube removed.
test_results | Results from medical tests performed on the individual. | string | no | | Test results | | lipid panel shows normal level of LDL (124 mg/dL); HIV, HBV, HCV: Negative
treatment | Treatments the individual has undergone prior to biomaterial collection. | string | no | | Treatments | | Patient treated with antibiotics for a urinary tract infection; Patient treated with chemotherapy (Epirubicin, cisplatin, capecitabine) to treat stomach cancer

## Cell morphology<a name='Cell morphology'></a>
_Information relating to pathological and morphological features of cells._

Location: module/biomaterial/cell_morphology.json

Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | --- | ---
cell_morphology | General description of the morphology of cells. | string | no | | Cell morphology | | adherent cells; form single layer colonies
cell_size | Size of cells in Cell size unit. | string | no | | Cell size | | 15; 20-30
cell_size_unit | The unit in which the Cell size is expressed. | object | no | [See module length_unit_ontology](module.md#length-unit-ontology) | Cell size unit | |
percent_cell_viability | Percent of cells determined to be viable. | number | no | | Percent cell viability | | 98.7
cell_viability_method | The method by which cell viability was determined. | string | no | | Cell viability method | | Fluorescein diacetate hydrolysis; ATP test
cell_viability_result | Result of the cell viability test. | string | no | | Cell viability result | pass, fail | Should be one of: pass, fail
percent_necrosis | Percent of cells identified to be necrotic. | number | no | | Percent necrotic cells | | 10

## State of specimen<a name='State of specimen'></a>
_State of specimen at time of collection._

Location: module/biomaterial/state_of_specimen.json

Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | --- | ---
autolysis_score | State of tissue breakdown due to self-digestion. | string | no | | Autolysis score | none, mild, moderate | Should be one of: none, mild, or moderate.
gross_description | Color, size, and other aspects of specimen as visible to naked eye. | string | no | | Gross description | | focal wedge shaped region of tan-orange discoloration; cystic
gross_images | List of filenames of photographs of specimen without magnification. | array | no | | Gross image | | my_gross_image_file.jpg
ischemic_temperature | Whether specimen experienced warm or cold ischemia. | string | no | | Ischemic temperature | warm, cold | Should be one of: warm, or cold.
ischemic_time | Duration of time, in seconds, between when the specimen stopped receiving oxygen and when it was preserved or processed. | integer | no | | Ischemic time | | 7200
microscopic_description | How the specimen looks under the microscope and how it compares with normal cells. | string | no | | Microscopic description | | Mixture of different cell sizes apparent; Dead cells are quite faint on microscope
microscopic_images | List of filenames of photographs of specimen under microscope. | array | no | | Microscopic image | | my_microscopic_image_file.jpg
postmortem_interval | Duration of time between when death was declared and when the specimen was preserved or processed. | integer | no | | Post-mortem interval | | 2400

## Timecourse<a name='Timecourse'></a>
_Information relating to a timecourse._

Location: module/biomaterial/timecourse.json

Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | --- | ---
value | The numerical value in Timecourse unit associated with a time interval used in the experiment. | string | yes | | Timecourse value | | 2; 5.5-10.5
unit | The unit in which the Timecourse value is expressed. | object | yes | [See module time_unit_ontology](module.md#time-unit-ontology) | Timecourse unit | |
relevance | Relevance of the Timecourse value/unit to the experiment. | string | no | | Timecourse relevance | | Collection after tumor cells injected into the mammary gland; Time tissue underwent liberase digestion

## Mouse-specific<a name='Mouse-specific'></a>
_Information specific to an organism that is a mouse (Mus musculus)._

Location: module/biomaterial/mouse_specific.json

Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | --- | ---
strain | The name of the mouse strain. | array | no | [See module strain_ontology](module.md#strain-ontology) | Mouse strain | |

## Purchased reagents<a name='Purchased reagents'></a>
_Information describing purchased kits or reagents used in a protocol._

Location: module/process/purchased_reagents.json

Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | --- | ---
retail_name | The retail name of the kit/reagent. | string | no | | Retail name | | SureCell WTA 3' Library Prep Kit; CytoTune iPS 2.0 Sendai Reprogramming Kit
catalog_number | The catalog number of the kit/reagent. | string | no | | Catalog number | | 20014279
manufacturer | The manufacturer of the kit/reagent. | string | no | | Manufacturer | | Illumina; ThermoFisher Scientific
lot_number | The batch or lot number of the kit/reagent. | string | no | | Batch/lot number | | 10001A
expiry_date | The date of expiration for the kit/reagent. | string | no | | Expiry date | | 2018-01-31; 2018-01
kit_titer | Appropriate titer and volume recommendations found in kit/reagent Certificate of Analysis. | string | no | | Titer | | 3.0x10^7

## INSDC experiment<a name='INSDC experiment'></a>
_Information relating to an INSDC experiment._

Location: module/process/sequencing/insdc_experiment.json

Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | --- | ---
insdc_experiment_accession | An International Nucleotide Sequence Database Collaboration (INSDC) experiment accession. | string | yes | | INSDC experiment accession | | SRX0000000

## Barcode<a name='Barcode'></a>
_Information about barcodes used in a protocol._

Location: module/process/sequencing/barcode.json

Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | --- | ---
barcode_read | The read in which the barcode is found. | string | yes | | Barcode-containing read | Read 1, Read 2, Read 3, Read 4, i7 Index, i5 Index | Should be one of: Read 1, Read 2, i7 Index, or i5 Index.
barcode_offset | The 0-based offset of start of barcode in read. | integer | yes | | Barcode offset | | 0
barcode_length | Length of barcode in nucleotides. | integer | yes | | Barcode length | | 28
white_list_file | Name of file containing legitimate barcode sequences. | string | no | | White list barcode file | | barcode_whitelist_file.txt

## 10x-specific<a name='10x-specific'></a>
_Information specific to 10x experiments._

Location: module/process/sequencing/10x.json

Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | --- | ---
fastq_method | Method used for the generation of fastq files from bcl files. | string | no | | Fastq creation method | | Cellranger mkfastq; bcl2fastq2
fastq_method_version | Version of the program used for fastq generation. | string | no | | Fastq creation method version | | Cellranger 2.1.1; v2.20
pooled_channels | The number of channels pooled within a sequencing lane. | number | no | | Pooled channels | | 4
drop_uniformity | Whether drop uniformity was achieved as a result of visual inspection of emulsion after a 10x run. | boolean | no | | Drop uniformity | | Should be one of: yes, or no.

## Plate-based sequencing<a name='Plate-based sequencing'></a>
_Information specific to plate-based sequencing experiments._

Location: module/process/sequencing/plate_based_sequencing.json

Property name | Description | Type | Required? | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | --- | ---
plate_label | A label or name for the plate on which the well is located. | string | yes | | Plate label | | 2217
well_label | A label or name for the well in which the cell is located. | string | no | | Well label | | A1
well_quality | Quality of well if imaged before sequencing. | string | no | | Well quality | OK, control, 2-cell well, control, empty well, low quality cell | Should be one of: 'OK', 'control, 2-cell well', 'control, empty well', or 'low quality cell'.
39 changes: 0 additions & 39 deletions docs/jsonBrowser/required_fields.md
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Expand Up @@ -354,42 +354,3 @@ _There are no required properties in schema Growth conditions_
_There are no required properties in schema Medical tests_
### Disease profile<a name='Disease profile'></a>
_There are no required properties in schema Disease profile_
### Preservation and storage<a name='Preservation and storage'></a>
_There are no required properties in schema Preservation and storage_
### Death<a name='Death'></a>
Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | ---
cause_of_death | Conditions resulting in death. | string | | Cause of death | | Hypoxic brain damage; Sudden cardiac arrest
### Familial relationship<a name='Familial relationship'></a>
_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_
### Cell morphology<a name='Cell morphology'></a>
_There are no required properties in schema Cell morphology_
### State of specimen<a name='State of specimen'></a>
_There are no required properties in schema State of specimen_
### Timecourse<a name='Timecourse'></a>
Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | ---
value | The numerical value in Timecourse unit associated with a time interval used in the experiment. | string | | Timecourse value | | 2; 5.5-10.5
unit | The unit in which the Timecourse value is expressed. | object | [See module time_unit_ontology](module.md#time-unit-ontology) | Timecourse unit | |
### Mouse-specific<a name='Mouse-specific'></a>
_There are no required properties in schema Mouse-specific_
### Purchased reagents<a name='Purchased reagents'></a>
_There are no required properties in schema Purchased reagents_
### INSDC experiment<a name='INSDC experiment'></a>
Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | ---
insdc_experiment_accession | An International Nucleotide Sequence Database Collaboration (INSDC) experiment accession. | string | | INSDC experiment accession | | SRX0000000
### Barcode<a name='Barcode'></a>
Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | ---
barcode_read | The read in which the barcode is found. | string | | Barcode-containing read | Read 1, Read 2, Read 3, Read 4, i7 Index, i5 Index | Should be one of: Read 1, Read 2, i7 Index, or i5 Index.
barcode_offset | The 0-based offset of start of barcode in read. | integer | | Barcode offset | | 0
barcode_length | Length of barcode in nucleotides. | integer | | Barcode length | | 28
### 10x-specific<a name='10x-specific'></a>
_There are no required properties in schema 10x-specific_
### Plate-based sequencing<a name='Plate-based sequencing'></a>
Property name | Description | Type | Object reference? | User friendly name | Allowed values | Example
--- | --- | --- | --- | --- | --- | ---
plate_label | A label or name for the plate on which the well is located. | string | | Plate label | | 2217
1 change: 1 addition & 0 deletions json_schema/versions.json
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Expand Up @@ -27,6 +27,7 @@
"human_specific": "1.0.11",
"medical_history": "6.0.0",
"medical_tests": "1.0.0",
"disease_profile": "0.0.0",
"mouse_specific": "1.0.8",
"preservation_storage": "6.1.1",
"state_of_specimen": "6.0.0",
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