From 1a46c8a90c60ced4209731368b241aeaa9020dd5 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Thu, 12 Sep 2024 13:56:54 +0300 Subject: [PATCH 01/15] Add disease profile module with COPD fields --- docs/jsonBrowser/module.md | 160 +----------------- docs/jsonBrowser/required_fields.md | 41 +---- docs/jsonBrowser/type.md | 1 + .../module/biomaterial/disease_profile.json | 82 +++++++++ .../type/biomaterial/donor_organism.json | 6 + json_schema/update_log.csv | 2 + 6 files changed, 96 insertions(+), 196 deletions(-) create mode 100644 json_schema/module/biomaterial/disease_profile.json diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 34bf8f769..0834fbb8d 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -460,164 +460,10 @@ dlco_predicted_percent | Indicate the percentage of the predicted DLCO, based on kco | Indicate the transfer coefficient of the lung for carbon monoxide (KCO) in mmol/min/kPa/L if available. | number | no | | KCO | | 5; 6; 4.5 kco_predicted_percent | Indicate the percentage of the predicted KCO, based on patient demographics, if available. | number | no | | KCO percent of predicted | | 90; 98; 85 -## Preservation and storage -_Information relating to how a biomaterial was preserved and/or stored over a period of time._ +## Disease profile +_Information about specific diseases profile of the individual._ -Location: module/biomaterial/preservation_storage.json +Location: module/biomaterial/disease_profile.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 -_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 -_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 -_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_history | Estimated number of cigarettes smoked per day. | string | no | | Smoking history | | 20 cigarettes/day for 25 years, stopped 2000 -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 -_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 -_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 -_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 -_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 -_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 -_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 -_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 -_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 -_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'. - diff --git a/docs/jsonBrowser/required_fields.md b/docs/jsonBrowser/required_fields.md index 4f2ca17ed..b15d709c7 100644 --- a/docs/jsonBrowser/required_fields.md +++ b/docs/jsonBrowser/required_fields.md @@ -352,42 +352,5 @@ _There are no required properties in schema Human-specific_ _There are no required properties in schema Growth conditions_ ### Medical tests _There are no required properties in schema Medical tests_ -### Preservation and storage -_There are no required properties in schema Preservation and storage_ -### Death -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 -_There are no required properties in schema Familial relationship_ -### Medical history -_There are no required properties in schema Medical history_ -### Cell morphology -_There are no required properties in schema Cell morphology_ -### State of specimen -_There are no required properties in schema State of specimen_ -### Timecourse -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 -_There are no required properties in schema Mouse-specific_ -### Purchased reagents -_There are no required properties in schema Purchased reagents_ -### INSDC experiment -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 -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 -_There are no required properties in schema 10x-specific_ -### Plate-based sequencing -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 +### Disease profile +_There are no required properties in schema Disease profile_ diff --git a/docs/jsonBrowser/type.md b/docs/jsonBrowser/type.md index 1c02aed5e..632af46f8 100644 --- a/docs/jsonBrowser/type.md +++ b/docs/jsonBrowser/type.md @@ -434,6 +434,7 @@ diseases | Short description of known disease(s) of the organism. | array | no | death | Information about conditions of death of the organism. | object | no | [See module death](module.md#death) | Death conditions | | familial_relationships | Information about other organisms related to this organism. | array | no | [See module familial_relationship](module.md#familial-relationship) | Familial relationship | | medical_tests | Information about the medical tests of the organism. | object | no | [See module medical_tests](module.md#medical-tests) | Medical tests | | +disease_profile | Information about specific diseases profile of the individual. | object | no | [See module disease_profile](module.md#disease-profile) | Disease profile | | medical_history | Information about the medical history of the organism. | object | no | [See module medical_history](module.md#medical-history) | Medical history | | gestational_age | Gestational age of pregnancy in Gestational age units measured from the last menstrual period. | string | no | | Gestational age | | 22; 8-9 gestational_age_unit | The unit in which Gestational age is expressed. | object | no | [See module time_unit_ontology](module.md#time-unit-ontology) | Gestational age unit | | diff --git a/json_schema/module/biomaterial/disease_profile.json b/json_schema/module/biomaterial/disease_profile.json new file mode 100644 index 000000000..9a483dc7d --- /dev/null +++ b/json_schema/module/biomaterial/disease_profile.json @@ -0,0 +1,82 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "description": "Information about specific diseases profile of the individual.", + "additionalProperties": false, + "title": "Disease profile", + "name": "disease_profile", + "type": "object", + "minProperties": 1, + "properties": { + "describedBy": { + "description": "The URL reference to the schema.", + "type": "string", + "pattern" : "^(http|https)://schema.(.*?)humancellatlas.org/module/biomaterial/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/medical_tests" + }, + "schema_version": { + "description": "The version number of the schema in major.minor.patch format.", + "type": "string", + "pattern": "^[0-9]{1,}.[0-9]{1,}.[0-9]{1,}$", + "example": "0.0.1" + }, + "copd_gold_stage": { + "user_friendly": "GOLD stage", + "description": "Indicating current GOLD stage (Global Initiative for Chronic Obstructive Lung Disease).", + "type": "integer", + "enum": [1, 2, 3, 4], + "example": "1; 2; 3; 4", + "bionetworks": ["lung"], + "guidelines": "Should be one of 1, 2, 3, 4" + }, + "copd_mmrc_grade": { + "user_friendly": "mMRC grade", + "description": "Indicate the Modified British Medical Research Council (mMRC) dyspnea scale grade.", + "type": "integer", + "enum": [0, 1, 2, 3, 4], + "example": "0, 1; 2; 3; 4", + "bionetworks": ["lung"], + "guidelines": "Should be one of 0, 1, 2, 3, 4" + }, + "copd_cat_score": { + "user_friendly": "CAT score", + "description": "Indicate the COPD Assessment Test (CAT) score.", + "type": "integer", + "minimum": 0, + "maximum": 40, + "example": "2; 5; 37", + "bionetworks": ["lung"], + "guidelines": "Should be between 0 and 40." + }, + "copd_gold_abe_assessment": { + "user_friendly": "GOLD ABE assessment", + "description": "Indicate the Global Initiative for Chronic Obstructive Lung Disease (GOLD) A, B, C, D assessment group if available.", + "type": "string", + "enum": ["A", "B", "E"], + "example": "A; B; E", + "bionetworks": ["lung"], + "guidelines": "Should be one of A, B, E" + + }, + "copd_phenotype": { + "user_friendly": "COPD phenotype", + "description": "Indicate the COPD disease phenotype(s) of donor. Please indicate all applicable phenotypes of donor.", + "type": "array", + "items": { + "type": "string", + "enum": ["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"] + }, + "example": "COPD with bronchitis; COPD with history of asthma; COPD with emphysema", + "bionetworks": ["lung"], + "guidelines": "Should be of: 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_emphysema_percentage": { + "user_friendly": "Percentage of emphysema", + "description": "Indicate the percentage of the lung that is affected by emphysema as judged based on non-invasive imaging, such as from a CT scan.", + "type": "number", + "maximum": 150, + "minimum": 0, + "bionetworks": ["lung"] + } + } +} \ No newline at end of file diff --git a/json_schema/type/biomaterial/donor_organism.json b/json_schema/type/biomaterial/donor_organism.json index f53e4f72e..8ba81c0f7 100644 --- a/json_schema/type/biomaterial/donor_organism.json +++ b/json_schema/type/biomaterial/donor_organism.json @@ -137,6 +137,12 @@ "$ref": "module/biomaterial/medical_tests.json", "user_friendly": "Medical tests" }, + "disease_profile": { + "description": "Information about specific diseases profile of the individual.", + "type": "object", + "$ref": "module/biomaterial/disease_profile.json", + "user_friendly": "Disease profile" + }, "medical_history": { "description": "Information about the medical history of the organism.", "type": "object", diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 3231ff199..1db5c04cb 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1 +1,3 @@ Schema,Change type,Change message,Version,Date +module/biomaterial/disease_profile,major,"Added new disease profile module with COPD fields. Fixes#1572",, +type/biomaterial/donor_organism,minor,"Added an optional disease profile field in the donor_organism. Fixes#1572" \ No newline at end of file From 1bbd4367038a2b5baa0c679cd2b28512d47fe7c8 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Thu, 12 Sep 2024 14:22:48 +0300 Subject: [PATCH 02/15] Fix removal from module.md --- docs/jsonBrowser/module.md | 167 +++++++++++++++++++++++++++++++++++++ 1 file changed, 167 insertions(+) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 0834fbb8d..86a115d56 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -467,3 +467,170 @@ 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 +_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 +_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 +_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 +_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_history | Estimated number of cigarettes smoked per day. | string | no | | Smoking history | | 20 cigarettes/day for 25 years, stopped 2000 +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 +_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 +_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 +_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 +_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 +_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 +_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 +_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 +_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 +_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'. From 32b94c3fc838e91e2b0cd638c25d088a1cf7815d Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Thu, 12 Sep 2024 14:23:48 +0300 Subject: [PATCH 03/15] Fix removal from required_fields.md --- docs/jsonBrowser/required_fields.md | 39 +++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/docs/jsonBrowser/required_fields.md b/docs/jsonBrowser/required_fields.md index b15d709c7..6052fb771 100644 --- a/docs/jsonBrowser/required_fields.md +++ b/docs/jsonBrowser/required_fields.md @@ -354,3 +354,42 @@ _There are no required properties in schema Growth conditions_ _There are no required properties in schema Medical tests_ ### Disease profile _There are no required properties in schema Disease profile_ +### Preservation and storage +_There are no required properties in schema Preservation and storage_ +### Death +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 +_There are no required properties in schema Familial relationship_ +### Medical history +_There are no required properties in schema Medical history_ +### Cell morphology +_There are no required properties in schema Cell morphology_ +### State of specimen +_There are no required properties in schema State of specimen_ +### Timecourse +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 +_There are no required properties in schema Mouse-specific_ +### Purchased reagents +_There are no required properties in schema Purchased reagents_ +### INSDC experiment +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 +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 +_There are no required properties in schema 10x-specific_ +### Plate-based sequencing +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 From 98c5a56e7eb4819bc712922293b374f312dc9db2 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 23 Sep 2024 13:42:45 +0100 Subject: [PATCH 04/15] Update json_schema/module/biomaterial/disease_profile.json Co-authored-by: idazucchi <45209056+idazucchi@users.noreply.github.com> --- json_schema/module/biomaterial/disease_profile.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/json_schema/module/biomaterial/disease_profile.json b/json_schema/module/biomaterial/disease_profile.json index 9a483dc7d..38118bb7b 100644 --- a/json_schema/module/biomaterial/disease_profile.json +++ b/json_schema/module/biomaterial/disease_profile.json @@ -10,7 +10,7 @@ "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]*?))/medical_tests" + "pattern" : "^(http|https)://schema.(.*?)humancellatlas.org/module/biomaterial/(([0-9]{1,}.[0-9]{1,}.[0-9]{1,})|([a-zA-Z]*?))/disease_profile" }, "schema_version": { "description": "The version number of the schema in major.minor.patch format.", From ee72039868f2029d6c3a95db0939c0ad3da1fcb7 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 23 Sep 2024 13:43:04 +0100 Subject: [PATCH 05/15] Update json_schema/module/biomaterial/disease_profile.json Co-authored-by: idazucchi <45209056+idazucchi@users.noreply.github.com> --- json_schema/module/biomaterial/disease_profile.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/json_schema/module/biomaterial/disease_profile.json b/json_schema/module/biomaterial/disease_profile.json index 38118bb7b..643dfa488 100644 --- a/json_schema/module/biomaterial/disease_profile.json +++ b/json_schema/module/biomaterial/disease_profile.json @@ -20,7 +20,7 @@ }, "copd_gold_stage": { "user_friendly": "GOLD stage", - "description": "Indicating current GOLD stage (Global Initiative for Chronic Obstructive Lung Disease).", + "description": "Indicate the current GOLD stage (Global Initiative for Chronic Obstructive Lung Disease).", "type": "integer", "enum": [1, 2, 3, 4], "example": "1; 2; 3; 4", From 775f2b8757a45749ef146476155ac2caf477b532 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 30 Sep 2024 13:30:47 +0100 Subject: [PATCH 06/15] Update json_schema/module/biomaterial/disease_profile.json Co-authored-by: ESapenaVentura <38617863+ESapenaVentura@users.noreply.github.com> --- json_schema/module/biomaterial/disease_profile.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/json_schema/module/biomaterial/disease_profile.json b/json_schema/module/biomaterial/disease_profile.json index 643dfa488..ceca67328 100644 --- a/json_schema/module/biomaterial/disease_profile.json +++ b/json_schema/module/biomaterial/disease_profile.json @@ -68,7 +68,7 @@ }, "example": "COPD with bronchitis; COPD with history of asthma; COPD with emphysema", "bionetworks": ["lung"], - "guidelines": "Should be of: 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" + "guidelines": "Should be one or more of: 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_emphysema_percentage": { "user_friendly": "Percentage of emphysema", From 278db8b1f990764f41441b05f73cb7eef5d123b2 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 30 Sep 2024 13:33:49 +0100 Subject: [PATCH 07/15] Initialise disease_profile in versions.json --- docs/jsonBrowser/module.md | 169 ---------------------------- docs/jsonBrowser/required_fields.md | 39 ------- json_schema/versions.json | 1 + 3 files changed, 1 insertion(+), 208 deletions(-) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 8eefbf26f..0834fbb8d 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -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 -_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 -_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 -_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 -_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 -_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 -_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 -_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 -_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 -_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 -_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 -_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 -_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 -_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'. diff --git a/docs/jsonBrowser/required_fields.md b/docs/jsonBrowser/required_fields.md index 6052fb771..b15d709c7 100644 --- a/docs/jsonBrowser/required_fields.md +++ b/docs/jsonBrowser/required_fields.md @@ -354,42 +354,3 @@ _There are no required properties in schema Growth conditions_ _There are no required properties in schema Medical tests_ ### Disease profile _There are no required properties in schema Disease profile_ -### Preservation and storage -_There are no required properties in schema Preservation and storage_ -### Death -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 -_There are no required properties in schema Familial relationship_ -### Medical history -_There are no required properties in schema Medical history_ -### Cell morphology -_There are no required properties in schema Cell morphology_ -### State of specimen -_There are no required properties in schema State of specimen_ -### Timecourse -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 -_There are no required properties in schema Mouse-specific_ -### Purchased reagents -_There are no required properties in schema Purchased reagents_ -### INSDC experiment -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 -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 -_There are no required properties in schema 10x-specific_ -### Plate-based sequencing -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 diff --git a/json_schema/versions.json b/json_schema/versions.json index 5cec5fd99..5947fe066 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -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", From 5bce7adf1b034112c051d27d2ba137297bfccd5f Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 30 Sep 2024 13:43:46 +0100 Subject: [PATCH 08/15] Revert removal of module.md --- docs/jsonBrowser/module.md | 169 +++++++++++++++++++++++++++++++++++++ 1 file changed, 169 insertions(+) diff --git a/docs/jsonBrowser/module.md b/docs/jsonBrowser/module.md index 0834fbb8d..8eefbf26f 100644 --- a/docs/jsonBrowser/module.md +++ b/docs/jsonBrowser/module.md @@ -467,3 +467,172 @@ 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 +_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 +_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 +_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 +_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 +_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 +_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 +_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 +_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 +_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 +_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 +_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 +_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 +_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'. From 366ee87a440f55e1eaee2883fdce868600816354 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 30 Sep 2024 13:46:13 +0100 Subject: [PATCH 09/15] @arschat Revert removal of required_fields.md --- docs/jsonBrowser/required_fields.md | 39 +++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) diff --git a/docs/jsonBrowser/required_fields.md b/docs/jsonBrowser/required_fields.md index b15d709c7..6052fb771 100644 --- a/docs/jsonBrowser/required_fields.md +++ b/docs/jsonBrowser/required_fields.md @@ -354,3 +354,42 @@ _There are no required properties in schema Growth conditions_ _There are no required properties in schema Medical tests_ ### Disease profile _There are no required properties in schema Disease profile_ +### Preservation and storage +_There are no required properties in schema Preservation and storage_ +### Death +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 +_There are no required properties in schema Familial relationship_ +### Medical history +_There are no required properties in schema Medical history_ +### Cell morphology +_There are no required properties in schema Cell morphology_ +### State of specimen +_There are no required properties in schema State of specimen_ +### Timecourse +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 +_There are no required properties in schema Mouse-specific_ +### Purchased reagents +_There are no required properties in schema Purchased reagents_ +### INSDC experiment +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 +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 +_There are no required properties in schema 10x-specific_ +### Plate-based sequencing +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 From 03fe256fe409bcd8e64e837888537c1b7d69c75b Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 30 Sep 2024 14:21:51 +0100 Subject: [PATCH 10/15] Ran release_prepare.py --- changelog.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/changelog.md b/changelog.md index 5ceb6d723..876c26dc9 100644 --- a/changelog.md +++ b/changelog.md @@ -7,6 +7,14 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http:// ## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging) +### [module/biomaterial/disease_profile.json - v1.0.0] - 2024-09-30 +### Added +Added new disease profile module with COPD fields. Fixes#1572 + +### [type/biomaterial/donor_organism.json - v16.3.0] - 2024-09-30 +### Added +Added an optional disease profile field in the donor_organism. Fixes#1572 + ## [Released](https://github.com/HumanCellAtlas/metadata-schema/) ### [system/file_descriptor.json - v2.1.0] - 2024-09-24 From a1c7f937e795e2bcd6020059c9e982fe007deaa0 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 30 Sep 2024 14:22:44 +0100 Subject: [PATCH 11/15] Ran release_prepare.py --- json_schema/update_log.csv | 2 -- 1 file changed, 2 deletions(-) diff --git a/json_schema/update_log.csv b/json_schema/update_log.csv index 1db5c04cb..3231ff199 100644 --- a/json_schema/update_log.csv +++ b/json_schema/update_log.csv @@ -1,3 +1 @@ Schema,Change type,Change message,Version,Date -module/biomaterial/disease_profile,major,"Added new disease profile module with COPD fields. Fixes#1572",, -type/biomaterial/donor_organism,minor,"Added an optional disease profile field in the donor_organism. Fixes#1572" \ No newline at end of file From 57a8e3d36a3edb790065f6d72a63bda79be668b1 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 30 Sep 2024 14:23:40 +0100 Subject: [PATCH 12/15] Ran release_prepare.py --- json_schema/versions.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/json_schema/versions.json b/json_schema/versions.json index 5947fe066..e1db370b7 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -1,5 +1,5 @@ { - "last_update_date": "2024-09-24T15:16:27Z", + "last_update_date": "2024-09-30T14:15:52Z", "version_numbers": { "core": { "biomaterial": { @@ -22,12 +22,12 @@ "biomaterial": { "cell_morphology": "6.1.7", "death": "5.5.1", + "disease_profile": "1.0.0", "familial_relationship": "6.0.3", "growth_conditions": "6.4.2", "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", @@ -93,7 +93,7 @@ "biomaterial": { "cell_line": "16.0.0", "cell_suspension": "14.0.0", - "donor_organism": "16.2.0", + "donor_organism": "16.3.0", "imaged_specimen": "3.5.0", "organoid": "11.5.0", "specimen_from_organism": "10.9.0" @@ -139,4 +139,4 @@ } } } -} \ No newline at end of file +} From 95121da9eae488ed26ff93a5d0a902252aa4e77c Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 30 Sep 2024 15:07:04 +0100 Subject: [PATCH 13/15] Update required_fields.md From 87daac67ce645c214caa68fe9c2927e9b38a8693 Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 30 Sep 2024 15:10:13 +0100 Subject: [PATCH 14/15] Release from staging to master 2024-09-30. --- changelog.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/changelog.md b/changelog.md index 876c26dc9..0f08774f1 100644 --- a/changelog.md +++ b/changelog.md @@ -7,6 +7,8 @@ and (starting with v4.0.0) this project adheres to [Semantic Versioning](http:// ## [Unreleased](https://github.com/HumanCellAtlas/metadata-schema/tree/staging) +## [Released](https://github.com/HumanCellAtlas/metadata-schema/) + ### [module/biomaterial/disease_profile.json - v1.0.0] - 2024-09-30 ### Added Added new disease profile module with COPD fields. Fixes#1572 @@ -15,8 +17,6 @@ Added new disease profile module with COPD fields. Fixes#1572 ### Added Added an optional disease profile field in the donor_organism. Fixes#1572 -## [Released](https://github.com/HumanCellAtlas/metadata-schema/) - ### [system/file_descriptor.json - v2.1.0] - 2024-09-24 ### Added Added 'drs_uri' property to file_descriptor From 4e12db9ad00577f7cf4e0402cd2dca1ac057dcca Mon Sep 17 00:00:00 2001 From: Arsenios Chatzigeorgiou <49944135+arschat@users.noreply.github.com> Date: Mon, 30 Sep 2024 15:20:18 +0100 Subject: [PATCH 15/15] Update capitalisation in disease_profile --- docs/jsonBrowser/required_fields.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/jsonBrowser/required_fields.md b/docs/jsonBrowser/required_fields.md index 6052fb771..7ba742bae 100644 --- a/docs/jsonBrowser/required_fields.md +++ b/docs/jsonBrowser/required_fields.md @@ -353,7 +353,7 @@ _There are no required properties in schema Growth conditions_ ### Medical tests _There are no required properties in schema Medical tests_ ### Disease profile -_There are no required properties in schema Disease profile_ +_There are no required properties in schema disease profile_ ### Preservation and storage _There are no required properties in schema Preservation and storage_ ### Death