From 6e1a8b567ceb9b83d975377829dc1610f027621c Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Tue, 22 Oct 2024 11:54:42 +0100 Subject: [PATCH 01/10] Deleted many outdated human-readable content;deleted organoid --- .../differentiated_cell_line.md | 207 ---- .../gene_expression_alteration_protocol.md | 1070 ----------------- human_readable_schemas/organoid.md | 297 ----- json_schema/type/biomaterial/organoid.json | 221 ---- json_schema/versions.json | 1 - 5 files changed, 1796 deletions(-) delete mode 100644 human_readable_schemas/differentiated_cell_line.md delete mode 100644 human_readable_schemas/gene_expression_alteration_protocol.md delete mode 100644 human_readable_schemas/organoid.md delete mode 100644 json_schema/type/biomaterial/organoid.json diff --git a/human_readable_schemas/differentiated_cell_line.md b/human_readable_schemas/differentiated_cell_line.md deleted file mode 100644 index eee4450..0000000 --- a/human_readable_schemas/differentiated_cell_line.md +++ /dev/null @@ -1,207 +0,0 @@ -# Differentiated cell line - -- [1. Property `Differentiated cell line > label`](#label) -- [2. Property `Differentiated cell line > description`](#description) -- [3. Property `Differentiated cell line > culture_medium`](#culture_medium) -- [4. Property `Differentiated cell line > terminally_differentiated`](#terminally_differentiated) -- [5. Property `Differentiated cell line > model_system`](#model_system) -- [6. Property `Differentiated cell line > timepoint_value`](#timepoint_value) -- [7. Property `Differentiated cell line > timepoint_unit`](#timepoint_unit) - -**Title:** Differentiated cell line - -| | | -| ------------------------- | ------------------------------------------------------------------------- | -| **Type** | `object` | -| **Required** | No | -| **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | - -**Description:** Information about the differentiated cell line. - -| Property | Pattern | Type | Deprecated | Definition | Title/Description | -| ---------------------------------------------------------- | ------- | ---------------- | ---------- | ---------- | ------------------------------------ | -| + [label](#label ) | No | string | No | - | Differentiated cell line label | -| - [description](#description ) | No | string | No | - | Differentiated cell line description | -| - [culture_medium](#culture_medium ) | No | string | No | - | Culture medium | -| + [terminally_differentiated](#terminally_differentiated ) | No | enum (of string) | No | - | Terminally differentiated? | -| - [model_system](#model_system ) | No | string | No | - | Model system | -| + [timepoint_value](#timepoint_value ) | No | number | No | - | Timepoint value | -| + [timepoint_unit](#timepoint_unit ) | No | string | No | - | Timepoint unit | - -## 1. Property `Differentiated cell line > label` - -**Title:** Differentiated cell line label - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | Yes | -| **Format** | `regex` | - -**Description:** A unique label for the differentiated cell line. - -**Example:** - -```json -"kolf2_2j_knockout_1_trophoblast" -``` - -| Restrictions | | -| --------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------ | -| **Min length** | 1 | -| **Must match regular expression** | ```^[a-zA-Z0-9_]*$``` [Test](https://regex101.com/?regex=%5E%5Ba-zA-Z0-9_%5D%2A%24&testString=%22kolf2_2j_knockout_1_trophoblast%22) | - -## 2. Property `Differentiated cell line > description` - -**Title:** Differentiated cell line description - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -**Description:** A general description of the differentiated cell line. - -**Example:** - -```json -"KOLF2.2J derived knockout cell line, PAX6/STL2 DKO, differentiated into trophoblasts" -``` - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 3. Property `Differentiated cell line > culture_medium` - -**Title:** Culture medium - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -**Description:** The solid, liquid, or semi-solid medium used to support growth. - -**Examples:** - -```json -"RPMI 1640 + 2mM Glutamine + 10-20% FBS" -``` - -```json -"human placental cord serum" -``` - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 4. Property `Differentiated cell line > terminally_differentiated` - -**Title:** Terminally differentiated? - -| | | -| ------------ | ------------------ | -| **Type** | `enum (of string)` | -| **Required** | Yes | - -**Description:** Is the cell line terminally differentiated. - -**Examples:** - -```json -"no" -``` - -```json -"unknown" -``` - -```json -"yes" -``` - -Must be one of: -* "yes" -* "no" -* "unknown" - -## 5. Property `Differentiated cell line > model_system` - -**Title:** Model system - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -**Description:** To which model system this differentiated cell line has been derived into - -**Examples:** - -```json -"UBERON:0000006" -``` - -```json -"islet of Langerhans" -``` - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 6. Property `Differentiated cell line > timepoint_value` - -**Title:** Timepoint value - -| | | -| ------------ | -------- | -| **Type** | `number` | -| **Required** | Yes | - -**Description:** Value of the timepoint. - -**Examples:** - -```json -7.5 -``` - -```json -8 -``` - -```json -9.1 -``` - -## 7. Property `Differentiated cell line > timepoint_unit` - -**Title:** Timepoint unit - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | Yes | - -**Description:** Unit of the timepoint. - -**Examples:** - -```json -"UO:0000010" -``` - -```json -"second" -``` - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - ----------------------------------------------------------------------------------------------------------------------------- - -Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-09-06 at 15:22:35 +0000 \ No newline at end of file diff --git a/human_readable_schemas/gene_expression_alteration_protocol.md b/human_readable_schemas/gene_expression_alteration_protocol.md deleted file mode 100644 index 3a62f7b..0000000 --- a/human_readable_schemas/gene_expression_alteration_protocol.md +++ /dev/null @@ -1,1070 +0,0 @@ -# Expression alteration protocol - -- [1. Property `Expression alteration protocol > label`](#label) -- [2. Property `Expression alteration protocol > parent_protocol_id`](#parent_protocol_id) -- [3. Property `Expression alteration protocol > gene_edition`](#gene_edition) - - [3.1. Expression alteration protocol > gene_edition > Gene edition](#autogenerated_heading_2) - - [3.1.1. Property `Expression alteration protocol > gene_edition > Gene edition > allele_specific`](#gene_edition_items_allele_specific) - - [3.1.2. Property `Expression alteration protocol > gene_edition > Gene edition > target_gene_symbol`](#gene_edition_items_target_gene_symbol) - - [3.1.3. Property `Expression alteration protocol > gene_edition > Gene edition > target_gene_hgnc_id`](#gene_edition_items_target_gene_hgnc_id) - - [3.1.4. Property `Expression alteration protocol > gene_edition > Gene edition > targeted_genomic_region`](#gene_edition_items_targeted_genomic_region) - - [3.1.5. Property `Expression alteration protocol > gene_edition > Gene edition > expected_alteration_type`](#gene_edition_items_expected_alteration_type) - - [3.1.6. Property `Expression alteration protocol > gene_edition > Gene edition > editing_strategy`](#gene_edition_items_editing_strategy) - - [3.1.7. Property `Expression alteration protocol > gene_edition > Gene edition > altered_locus`](#gene_edition_items_altered_locus) - - [3.1.7.1. Expression alteration protocol > gene_edition > Gene edition > altered_locus > altered_locus items](#autogenerated_heading_3) - - [3.1.8. Property `Expression alteration protocol > gene_edition > Gene edition > guide_sequence`](#gene_edition_items_guide_sequence) - - [3.1.8.1. Expression alteration protocol > gene_edition > Gene edition > guide_sequence > guide_sequence items](#autogenerated_heading_4) -- [4. Property `Expression alteration protocol > variation_type`](#variation_type) -- [5. Property `Expression alteration protocol > coordinates`](#coordinates) -- [6. Property `Expression alteration protocol > allele_type`](#allele_type) -- [7. Property `Expression alteration protocol > alteration_size`](#alteration_size) - - [7.1. Expression alteration protocol > alteration_size > alteration_size items](#autogenerated_heading_5) -- [8. Property `Expression alteration protocol > culture_medium`](#culture_medium) - - [8.1. Expression alteration protocol > culture_medium > culture_medium items](#autogenerated_heading_6) -- [9. Property `Expression alteration protocol > nuclease`](#nuclease) - - [9.1. Expression alteration protocol > nuclease > nuclease items](#autogenerated_heading_7) -- [10. Property `Expression alteration protocol > guide_rna`](#guide_rna) - - [10.1. Property `Expression alteration protocol > guide_rna > first`](#guide_rna_first) - - [10.2. Property `Expression alteration protocol > guide_rna > second`](#guide_rna_second) -- [11. Property `Expression alteration protocol > ssodn`](#ssodn) - - [11.1. Property `Expression alteration protocol > ssodn > first`](#ssodn_first) - - [11.2. Property `Expression alteration protocol > ssodn > second`](#ssodn_second) -- [12. Property `Expression alteration protocol > pcr`](#pcr) - - [12.1. Expression alteration protocol > pcr > pcr items](#autogenerated_heading_8) - - [12.1.1. Property `Expression alteration protocol > pcr > pcr items > forward_primer`](#pcr_items_forward_primer) - - [12.1.2. Property `Expression alteration protocol > pcr > pcr items > reverse_primer`](#pcr_items_reverse_primer) - - [12.1.3. Property `Expression alteration protocol > pcr > pcr items > type`](#pcr_items_type) -- [13. Property `Expression alteration protocol > genotype`](#genotype) -- [14. Property `Expression alteration protocol > karyotype`](#karyotype) -- [15. Property `Expression alteration protocol > viability_method`](#viability_method) -- [16. Property `Expression alteration protocol > viability`](#viability) -- [17. Property `Expression alteration protocol > mycoplasma`](#mycoplasma) -- [18. Property `Expression alteration protocol > donor_plasmid`](#donor_plasmid) - - [18.1. Property `Expression alteration protocol > donor_plasmid > first_sequence`](#donor_plasmid_first_sequence) - - [18.2. Property `Expression alteration protocol > donor_plasmid > second_sequence`](#donor_plasmid_second_sequence) -- [19. Property `Expression alteration protocol > method`](#method) - - -**Title:** Expression alteration protocol - -| | | -| ------------------------- | ------------------------------------------------------------------------- | -| **Type** | `object` | -| **Required** | No | -| **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | - -**Description:** Information about the gene expression alteration protocol. - -| Property | Pattern | Type | Deprecated | Definition | Title/Description | -| -------------------------------------------- | ------- | ---------------- | ---------- | ---------- | -------------------------------------- | -| + [label](#label ) | No | string | No | - | Gene expression alteration protocol ID | -| - [parent_protocol_id](#parent_protocol_id ) | No | string | No | - | Parent protocol ID | -| - [gene_edition](#gene_edition ) | No | array of object | No | - | Gene edition | -| - [variation_type](#variation_type ) | No | string | No | - | Variation type | -| - [coordinates](#coordinates ) | No | string | No | - | Coordinates (GRCh38) | -| - [allele_type](#allele_type ) | No | enum (of string) | No | - | Allele type | -| - [alteration_size](#alteration_size ) | No | array of integer | No | - | Insertion/Deletion size | -| - [culture_medium](#culture_medium ) | No | array of string | No | - | Culture medium | -| - [nuclease](#nuclease ) | No | array of string | No | - | Nuclease | -| - [guide_rna](#guide_rna ) | No | object | No | - | - | -| - [ssodn](#ssodn ) | No | object | No | - | - | -| - [pcr](#pcr ) | No | array of object | No | - | - | -| - [genotype](#genotype ) | No | string | No | - | Genotype | -| - [karyotype](#karyotype ) | No | string | No | - | Karyotype | -| - [viability_method](#viability_method ) | No | string | No | - | Viability/Mycoplasma method | -| - [viability](#viability ) | No | string | No | - | Viability | -| - [mycoplasma](#mycoplasma ) | No | string | No | - | Mycoplasma | -| - [donor_plasmid](#donor_plasmid ) | No | object | No | - | - | -| + [method](#method ) | No | string | No | - | Expression alteration method | - -## 1. Property `Expression alteration protocol > label` - -**Title:** Gene expression alteration protocol ID - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | Yes | -| **Format** | `regex` | - -**Description:** A unique ID for the gene expression alteration protocol. - -**Examples:** - -```json -"JAXPE000E_MEIS1" -``` - -```json -"MSKKI119_MEF2C" -``` - -| Restrictions | | -| --------------------------------- | -------------------------------------------------------------------------------------------------------------------- | -| **Min length** | 1 | -| **Must match regular expression** | ```^[a-zA-Z0-9_]*$``` [Test](https://regex101.com/?regex=%5E%5Ba-zA-Z0-9_%5D%2A%24&testString=%22JAXPE000E_MEIS1%22) | - -## 2. Property `Expression alteration protocol > parent_protocol_id` - -**Title:** Parent protocol ID - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | -| **Format** | `regex` | - -**Description:** An ID for the parent gene expression alteration protocol. - -**Examples:** - -```json -"JAXPE000E_MEIS1" -``` - -```json -"MSKKI119_MEF2C" -``` - -| Restrictions | | -| --------------------------------- | -------------------------------------------------------------------------------------------------------------------- | -| **Min length** | 1 | -| **Must match regular expression** | ```^[a-zA-Z0-9_]*$``` [Test](https://regex101.com/?regex=%5E%5Ba-zA-Z0-9_%5D%2A%24&testString=%22JAXPE000E_MEIS1%22) | - -## 3. Property `Expression alteration protocol > gene_edition` - -**Title:** Gene edition - -| | | -| ------------ | ----------------- | -| **Type** | `array of object` | -| **Required** | No | - -**Description:** Information about an array of gene edition objects. - -| | Array restrictions | -| -------------------- | ------------------ | -| **Min items** | N/A | -| **Max items** | N/A | -| **Items unicity** | False | -| **Additional items** | False | -| **Tuple validation** | See below | - -| Each item of this array must be | Description | -| ----------------------------------- | ------------------------------------------------- | -| [Gene edition](#gene_edition_items) | Information about the gene edition in a protocol. | - -### 3.1. Expression alteration protocol > gene_edition > Gene edition - -**Title:** Gene edition - -| | | -| ------------------------- | ------------------------------------------------------------------------- | -| **Type** | `object` | -| **Required** | No | -| **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | - -**Description:** Information about the gene edition in a protocol. - -| Property | Pattern | Type | Deprecated | Definition | Title/Description | -| --------------------------------------------------------------------------- | ------- | ---------------- | ---------- | ---------- | ------------------------ | -| - [allele_specific](#gene_edition_items_allele_specific ) | No | boolean | No | - | Allele-specific? | -| - [target_gene_symbol](#gene_edition_items_target_gene_symbol ) | No | string | No | - | Target gene symbol | -| - [target_gene_hgnc_id](#gene_edition_items_target_gene_hgnc_id ) | No | string | No | - | HGNC ID | -| - [targeted_genomic_region](#gene_edition_items_targeted_genomic_region ) | No | enum (of string) | No | - | Targeted genomic region | -| - [expected_alteration_type](#gene_edition_items_expected_alteration_type ) | No | enum (of string) | No | - | Expected alteration type | -| - [editing_strategy](#gene_edition_items_editing_strategy ) | No | enum (of string) | No | - | Editing strategy | -| + [altered_locus](#gene_edition_items_altered_locus ) | No | array of string | No | - | Altered locus | -| - [guide_sequence](#gene_edition_items_guide_sequence ) | No | array of string | No | - | Guide sequence(s) | - -#### 3.1.1. Property `Expression alteration protocol > gene_edition > Gene edition > allele_specific` - -**Title:** Allele-specific? - -| | | -| ------------ | --------- | -| **Type** | `boolean` | -| **Required** | No | - -**Description:** Indicate if the technique used to modify expression of the gene is allele-specific. - -**Examples:** - -```json -false -``` - -```json -true -``` - -#### 3.1.2. Property `Expression alteration protocol > gene_edition > Gene edition > target_gene_symbol` - -**Title:** Target gene symbol - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -**Description:** Gene whose transcription was modified with this protocol. - -**Examples:** - -```json -"MEIS1" -``` - -```json -"PAX6" -``` - -```json -"OGG:3000005080" -``` - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -#### 3.1.3. Property `Expression alteration protocol > gene_edition > Gene edition > target_gene_hgnc_id` - -**Title:** HGNC ID - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -**Description:** HGNC gene identifier for the genes whose transcription was modified with this protocol. Please use HGNC gene identifiers. - -**Examples:** - -```json -"HGNC:7000" -``` - -```json -"HGNC:6761" -``` - -| Restrictions | | -| --------------------------------- | ------------------------------------------------------------------------------------------------------ | -| **Min length** | 1 | -| **Must match regular expression** | ```^HGNC:\d+$``` [Test](https://regex101.com/?regex=%5EHGNC%3A%5Cd%2B%24&testString=%22HGNC%3A7000%22) | - -#### 3.1.4. Property `Expression alteration protocol > gene_edition > Gene edition > targeted_genomic_region` - -**Title:** Targeted genomic region - -| | | -| ------------ | ------------------ | -| **Type** | `enum (of string)` | -| **Required** | No | - -**Description:** Type of region that is targeted by the gene expression alteration protocol. - -**Examples:** - -```json -"full coding region" -``` - -```json -"exon" -``` - -Must be one of: -* "exon" -* "intron" -* "promoter" -* "full coding region" -* "other" - -#### 3.1.5. Property `Expression alteration protocol > gene_edition > Gene edition > expected_alteration_type` - -**Title:** Expected alteration type - -| | | -| ------------ | ------------------ | -| **Type** | `enum (of string)` | -| **Required** | No | - -**Description:** How the expression for the gene(s) was altered. - -**Examples:** - -```json -"down-regulation" -``` - -```json -"up-regulation" -``` - -Must be one of: -* "down-regulation" -* "up-regulation" -* "silencing" - -#### 3.1.6. Property `Expression alteration protocol > gene_edition > Gene edition > editing_strategy` - -**Title:** Editing strategy - -| | | -| ------------ | ------------------ | -| **Type** | `enum (of string)` | -| **Required** | No | - -**Description:** Editing strategy followed in the CRISPR protocol. - -**Examples:** - -```json -"full coding length" -``` - -```json -"critical exon" -``` - -Must be one of: -* "full coding length" -* "critical exon" -* "termination codon" - -#### 3.1.7. Property `Expression alteration protocol > gene_edition > Gene edition > altered_locus` - -**Title:** Expression alteration method - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | Yes | - -**Description:** Method applied for alteration of the gene expression in the cell line. - -**Examples:** - -```json -"CRISPR/Cas9 method" -``` - -```json -"BAO:0010249" -``` - -```json -"gene knockdown by lentiviral shRNA transduction" -``` - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 9. Property `Expression alteration protocol > altered_locus` - -**Title:** Altered locus - -| | | -| ------------ | ----------------- | -| **Type** | `array of string` | -| **Required** | Yes | - -**Description:** Genomic coordiantes relative to GRCh38 of any genomic alterations made. - -**Examples:** - -```json -"chr2:66437727-66464411" -``` - -```json -"chr5:88751722-88752302" -``` - -| | Array restrictions | -| -------------------- | ------------------ | -| **Min items** | 1 | -| **Max items** | N/A | -| **Items unicity** | False | -| **Additional items** | False | -| **Tuple validation** | See below | - -| Each item of this array must be | Description | -| -------------------------------------------------------------- | ----------- | -| [altered_locus items](#gene_edition_items_altered_locus_items) | - | - -##### 3.1.7.1. Expression alteration protocol > gene_edition > Gene edition > altered_locus > altered_locus items - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -| Restrictions | | -| --------------------------------- | --------------------------------------------------------------------------------------------------------------- | -| **Min length** | 1 | -| **Must match regular expression** | ```^chr\d\d{0,1}:\d+-\d+$``` [Test](https://regex101.com/?regex=%5Echr%5Cd%5Cd%7B0%2C1%7D%3A%5Cd%2B-%5Cd%2B%24) | - -#### 3.1.8. Property `Expression alteration protocol > gene_edition > Gene edition > guide_sequence` - -**Title:** Guide sequence(s) - -| | | -| ------------ | ----------------- | -| **Type** | `array of string` | -| **Required** | No | - -**Description:** Full nucleotide sequence(s) of guide sequences. - -**Examples:** - -```json -"AAAGTCGATGTATCTTCTAC" -``` - -```json -"TTGGTGATAGACGATAGAGAAG" -``` - -| | Array restrictions | -| -------------------- | ------------------ | -| **Min items** | 1 | -| **Max items** | N/A | -| **Items unicity** | False | -| **Additional items** | False | -| **Tuple validation** | See below | - -| Each item of this array must be | Description | -| ---------------------------------------------------------------- | ----------- | -| [guide_sequence items](#gene_edition_items_guide_sequence_items) | - | - -##### 3.1.8.1. Expression alteration protocol > gene_edition > Gene edition > guide_sequence > guide_sequence items - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -| Restrictions | | -| --------------------------------- | ----------------------------------------------------------------------- | -| **Min length** | 1 | -| **Must match regular expression** | ```^[ACGT]+$``` [Test](https://regex101.com/?regex=%5E%5BACGT%5D%2B%24) | - -## 4. Property `Expression alteration protocol > variation_type` - -**Title:** Variation type - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -**Description:** Perturbation location in the gene (e.g. KO, PTC, CE). - -**Examples:** - -```json -"KO" -``` - -```json -"Double allele Knock-in" -``` - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 5. Property `Expression alteration protocol > coordinates` - -**Title:** Coordinates (GRCh38) - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | -| **Format** | `regex` | - -**Description:** Genomic coordinates for the variation type (Genome Reference Consortium Human Build 38) - -**Examples:** - -```json -"chr6:53127676-53145648" -``` - -```json -"chr3:27719425-27719444" -``` - -| Restrictions | | -| --------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------- | -| **Min length** | 1 | -| **Must match regular expression** | ```^chr\d{,2}:\d+-\d+$``` [Test](https://regex101.com/?regex=%5Echr%5Cd%7B%2C2%7D%3A%5Cd%2B-%5Cd%2B%24&testString=%22chr6%3A53127676-53145648%22) | - -## 6. Property `Expression alteration protocol > allele_type` - -**Title:** Allele type - -| | | -| ------------ | ------------------ | -| **Type** | `enum (of string)` | -| **Required** | No | - -**Description:** Whether the allele was deleted or inserted. - -**Examples:** - -```json -"deletion" -``` - -```json -"insertion" -``` - -Must be one of: -* "deletion" -* "insertion" - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 7. Property `Expression alteration protocol > alteration_size` - -**Title:** Insertion/Deletion size - -| | | -| ------------ | ------------------ | -| **Type** | `array of integer` | -| **Required** | No | - -**Description:** Size of the insertion or deletion in nucleotides. Use positive integers for insertions and negative integers for deletion. - -**Examples:** - -```json --17972 -``` - -```json -1664 -``` - -| | Array restrictions | -| -------------------- | ------------------ | -| **Min items** | 1 | -| **Max items** | N/A | -| **Items unicity** | False | -| **Additional items** | False | -| **Tuple validation** | See below | - -| Each item of this array must be | Description | -| ----------------------------------------------- | ----------- | -| [alteration_size items](#alteration_size_items) | - | - -### 7.1. Expression alteration protocol > alteration_size > alteration_size items - -| | | -| ------------ | --------- | -| **Type** | `integer` | -| **Required** | No | - -## 8. Property `Expression alteration protocol > culture_medium` - -**Title:** Culture medium - -| | | -| ------------ | ----------------- | -| **Type** | `array of string` | -| **Required** | No | - -**Description:** Culture medium for the clone. - -**Example:** - -```json -"StemFlex" -``` - -| | Array restrictions | -| -------------------- | ------------------ | -| **Min items** | 1 | -| **Max items** | N/A | -| **Items unicity** | False | -| **Additional items** | False | -| **Tuple validation** | See below | - -| Each item of this array must be | Description | -| --------------------------------------------- | ----------- | -| [culture_medium items](#culture_medium_items) | - | - -### 8.1. Expression alteration protocol > culture_medium > culture_medium items - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 9. Property `Expression alteration protocol > nuclease` - -**Title:** Nuclease - -| | | -| ------------ | ----------------- | -| **Type** | `array of string` | -| **Required** | No | - -**Description:** Nuclease used to generate the clone. - -**Example:** - -```json -"Cas9" -``` - -| | Array restrictions | -| -------------------- | ------------------ | -| **Min items** | 1 | -| **Max items** | N/A | -| **Items unicity** | False | -| **Additional items** | False | -| **Tuple validation** | See below | - -| Each item of this array must be | Description | -| --------------------------------- | ----------- | -| [nuclease items](#nuclease_items) | - | - -### 9.1. Expression alteration protocol > nuclease > nuclease items - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 10. Property `Expression alteration protocol > guide_rna` - -| | | -| ------------------------- | ------------------------------------------------------------------------- | -| **Type** | `object` | -| **Required** | No | -| **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | - -| Property | Pattern | Type | Deprecated | Definition | Title/Description | -| ------------------------------ | ------- | ------ | ---------- | ---------- | ----------------- | -| + [first](#guide_rna_first ) | No | string | No | - | Guide RNA 1 | -| - [second](#guide_rna_second ) | No | string | No | - | Guide RNA 2 | - -### 10.1. Property `Expression alteration protocol > guide_rna > first` - -**Title:** Guide RNA 1 - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | Yes | -| **Format** | `regex` | - -**Description:** Guide RNA 1 - -**Examples:** - -```json -"TGATAAGGTCAGGCCAGCCA" -``` - -```json -"TGGTTCCCACTGGATGAGAC" -``` - -| Restrictions | | -| --------------------------------- | ------------------------------------------------------------------------------------------------------------- | -| **Min length** | 1 | -| **Must match regular expression** | ```^[ACGT]+$``` [Test](https://regex101.com/?regex=%5E%5BACGT%5D%2B%24&testString=%22TGATAAGGTCAGGCCAGCCA%22) | - -### 10.2. Property `Expression alteration protocol > guide_rna > second` - -**Title:** Guide RNA 2 - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | -| **Format** | `regex` | - -**Description:** Guide RNA 2 - -**Example:** - -```json -"TAGTATTTCCACCCTCAGTA" -``` - -| Restrictions | | -| --------------------------------- | ------------------------------------------------------------------------------------------------------------- | -| **Min length** | 1 | -| **Must match regular expression** | ```^[ACGT]+$``` [Test](https://regex101.com/?regex=%5E%5BACGT%5D%2B%24&testString=%22TAGTATTTCCACCCTCAGTA%22) | - -## 11. Property `Expression alteration protocol > ssodn` - -| | | -| ------------------------- | ------------------------------------------------------------------------- | -| **Type** | `object` | -| **Required** | No | -| **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | - -| Property | Pattern | Type | Deprecated | Definition | Title/Description | -| -------------------------- | ------- | ------ | ---------- | ---------- | ----------------- | -| + [first](#ssodn_first ) | No | string | No | - | ssODN 1 | -| - [second](#ssodn_second ) | No | string | No | - | ssODN 2 | - -### 11.1. Property `Expression alteration protocol > ssodn > first` - -**Title:** ssODN 1 - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | Yes | -| **Format** | `regex` | - -**Description:** ssODN 1 - -**Example:** - -```json -"ACAAAATTCTCAAGCATTTCTGAGGGGAGTCGAATAGGTGAAAACCTTGHHTAAGGAATGGAAACCTGTCCCGTCTGGGGTGTGAAGTGCCCTCTGCTTT" -``` - -| Restrictions | | -| --------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| **Min length** | 1 | -| **Must match regular expression** | ```^[ACGT]+$``` [Test](https://regex101.com/?regex=%5E%5BACGT%5D%2B%24&testString=%22ACAAAATTCTCAAGCATTTCTGAGGGGAGTCGAATAGGTGAAAACCTTGHHTAAGGAATGGAAACCTGTCCCGTCTGGGGTGTGAAGTGCCCTCTGCTTT%22) | - -### 11.2. Property `Expression alteration protocol > ssodn > second` - -**Title:** ssODN 2 - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | -| **Format** | `regex` | - -**Description:** ssODN 2 - -**Example:** - -```json -"ACAAAATTCTCAAGCATTTCTGAGGGGAGTCGAATAGGTGAAAACCTTGHHTAAGGAATGGAAACCTGTCCCGTCTGGGGTGTGAAGTGCCCTCTGCTTT" -``` - -| Restrictions | | -| --------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| **Min length** | 1 | -| **Must match regular expression** | ```^[ACGT]+$``` [Test](https://regex101.com/?regex=%5E%5BACGT%5D%2B%24&testString=%22ACAAAATTCTCAAGCATTTCTGAGGGGAGTCGAATAGGTGAAAACCTTGHHTAAGGAATGGAAACCTGTCCCGTCTGGGGTGTGAAGTGCCCTCTGCTTT%22) | - -## 12. Property `Expression alteration protocol > pcr` - -| | | -| ------------ | ----------------- | -| **Type** | `array of object` | -| **Required** | No | - -| | Array restrictions | -| -------------------- | ------------------ | -| **Min items** | N/A | -| **Max items** | N/A | -| **Items unicity** | False | -| **Additional items** | False | -| **Tuple validation** | See below | - -| Each item of this array must be | Description | -| ------------------------------- | ----------- | -| [pcr items](#pcr_items) | - | - -### 12.1. Expression alteration protocol > pcr > pcr items - -| | | -| ------------------------- | ------------------------------------------------------------------------- | -| **Type** | `object` | -| **Required** | No | -| **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | - -| Property | Pattern | Type | Deprecated | Definition | Title/Description | -| ---------------------------------------------- | ------- | ------ | ---------- | ---------- | ------------------ | -| - [forward_primer](#pcr_items_forward_primer ) | No | string | No | - | PCR forward primer | -| - [reverse_primer](#pcr_items_reverse_primer ) | No | string | No | - | PCR reverse primer | -| - [type](#pcr_items_type ) | No | string | No | - | PCR type | - -#### 12.1.1. Property `Expression alteration protocol > pcr > pcr items > forward_primer` - -**Title:** PCR forward primer - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | -| **Format** | `regex` | - -**Description:** PCR forward primer sequence. - -| Restrictions | | -| --------------------------------- | ----------------------------------------------------------------------- | -| **Min length** | 1 | -| **Must match regular expression** | ```^[ACGT]+$``` [Test](https://regex101.com/?regex=%5E%5BACGT%5D%2B%24) | - -#### 12.1.2. Property `Expression alteration protocol > pcr > pcr items > reverse_primer` - -**Title:** PCR reverse primer - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | -| **Format** | `regex` | - -**Description:** PCR reverse primer sequence. - -| Restrictions | | -| --------------------------------- | ----------------------------------------------------------------------- | -| **Min length** | 1 | -| **Must match regular expression** | ```^[ACGT]+$``` [Test](https://regex101.com/?regex=%5E%5BACGT%5D%2B%24) | - -#### 12.1.3. Property `Expression alteration protocol > pcr > pcr items > type` - -**Title:** PCR type - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -**Description:** Type of PCR performed. If performed to amplify a gene, please indicate name (e.g. Neo, Puro) - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 13. Property `Expression alteration protocol > genotype` - -**Title:** Genotype - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -**Description:** Genotype (HOM, HET, NA). - -**Examples:** - -```json -"HOM" -``` - -```json -"Double allele Knock-in" -``` - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 14. Property `Expression alteration protocol > karyotype` - -**Title:** Karyotype - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -**Description:** Karyotyping information (If available). - -**Example:** - -```json -"not done" -``` - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 15. Property `Expression alteration protocol > viability_method` - -**Title:** Viability/Mycoplasma method - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -**Description:** Viability/Mycoplasma method. - -**Examples:** - -```json -"JAX (link/protocols.io)" -``` - -```json -"https://www.abmgood.com/pcr-mycoplasma-detection-kit-g238.html" -``` - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 16. Property `Expression alteration protocol > viability` - -**Title:** Viability - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -**Description:** Viability status. - -**Examples:** - -```json -"+++" -``` - -```json -"not done" -``` - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 17. Property `Expression alteration protocol > mycoplasma` - -**Title:** Mycoplasma - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -**Description:** Mycoplasma. - -**Example:** - -```json -"Negative" -``` - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 18. Property `Expression alteration protocol > donor_plasmid` - -| | | -| ------------------------- | ------------------------------------------------------------------------- | -| **Type** | `object` | -| **Required** | No | -| **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | - -| Property | Pattern | Type | Deprecated | Definition | Title/Description | -| ---------------------------------------------------- | ------- | ------ | ---------- | ---------- | ------------------------ | -| - [first_sequence](#donor_plasmid_first_sequence ) | No | string | No | - | Donor plasmid 1 sequence | -| - [second_sequence](#donor_plasmid_second_sequence ) | No | string | No | - | Donor plasmid 2 sequence | - -### 18.1. Property `Expression alteration protocol > donor_plasmid > first_sequence` - -**Title:** Donor plasmid 1 sequence - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | -| **Format** | `regex` | - -**Description:** Donor plasmid 1 sequence. - -**Examples:** - -```json -"TGATAAGGTCAGGCCAGCCA" -``` - -```json -"TGGTTCCCACTGGATGAGAC" -``` - -| Restrictions | | -| --------------------------------- | ------------------------------------------------------------------------------------------------------------- | -| **Min length** | 1 | -| **Must match regular expression** | ```^[ACGT]+$``` [Test](https://regex101.com/?regex=%5E%5BACGT%5D%2B%24&testString=%22TGATAAGGTCAGGCCAGCCA%22) | - -### 18.2. Property `Expression alteration protocol > donor_plasmid > second_sequence` - -**Title:** Donor plasmid 2 sequence - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | -| **Format** | `regex` | - -**Description:** Donor plasmid 2 sequence. - -**Example:** - -```json -"TAGTATTTCCACCCTCAGTA" -``` - -| Restrictions | | -| --------------------------------- | ------------------------------------------------------------------------------------------------------------- | -| **Min length** | 1 | -| **Must match regular expression** | ```^[ACGT]+$``` [Test](https://regex101.com/?regex=%5E%5BACGT%5D%2B%24&testString=%22TAGTATTTCCACCCTCAGTA%22) | - -## 19. Property `Expression alteration protocol > method` - -**Title:** Expression alteration method - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | Yes | - -**Description:** Method applied for alteration of the gene expression in the cell line. - -**Examples:** - -```json -"CRISPR/Cas9 method" -``` - -```json -"BAO:0010249" -``` - -```json -"gene knockdown by lentiviral shRNA transduction" -``` - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - ----------------------------------------------------------------------------------------------------------------------------- -Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-08-28 at 14:14:06 +0 \ No newline at end of file diff --git a/human_readable_schemas/organoid.md b/human_readable_schemas/organoid.md deleted file mode 100644 index 6201d31..0000000 --- a/human_readable_schemas/organoid.md +++ /dev/null @@ -1,297 +0,0 @@ -# Organoid - -- [1. Property `Organoid > label`](#label) -- [2. Property `Organoid > description`](#description) -- [3. Property `Organoid > model_system`](#model_system) -- [4. Property `Organoid > age_unit`](#age_unit) -- [5. Property `Organoid > age_value`](#age_value) -- [6. Property `Organoid > embedded_in_matrigel`](#embedded_in_matrigel) -- [7. Property `Organoid > growth_environment`](#growth_environment) -- [8. Property `Organoid > morphology`](#morphology) -- [9. Property `Organoid > size_value`](#size_value) -- [10. Property `Organoid > size_unit`](#size_unit) -- [11. Property `Organoid > stored_oxygen_levels`](#stored_oxygen_levels) - -**Title:** Organoid - -| | | -| ------------------------- | ------------------------------------------------------------------------- | -| **Type** | `object` | -| **Required** | No | -| **Additional properties** | [[Any type: allowed]](# "Additional Properties of any type are allowed.") | - -**Description:** Information about the organoid. - -| Property | Pattern | Type | Deprecated | Definition | Title/Description | -| ------------------------------------------------ | ------- | ------- | ---------- | ---------- | --------------------- | -| + [label](#label ) | No | string | No | - | Organoid label | -| - [description](#description ) | No | string | No | - | Organoid description | -| + [model_system](#model_system ) | No | string | No | - | Model system | -| - [age_unit](#age_unit ) | No | string | No | - | Age unit | -| - [age_value](#age_value ) | No | number | No | - | Organoid age | -| - [embedded_in_matrigel](#embedded_in_matrigel ) | No | boolean | No | - | Embeddded in matrigel | -| - [growth_environment](#growth_environment ) | No | string | No | - | Growth environment | -| - [morphology](#morphology ) | No | string | No | - | Organoid morphology | -| - [size_value](#size_value ) | No | number | No | - | Organoid size | -| - [size_unit](#size_unit ) | No | string | No | - | Size unit | -| - [stored_oxygen_levels](#stored_oxygen_levels ) | No | number | No | - | Stored oxygen level | - -## 1. Property `Organoid > label` - -**Title:** Organoid label - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | Yes | -| **Format** | `regex` | - -**Description:** A unique label for the organoid. No spaces allowed. - -**Example:** - -```json -"kolf2_2j_knockout_1" -``` - -| Restrictions | | -| --------------------------------- | ------------------------------------------------------------------------------------------------------------------------ | -| **Min length** | 1 | -| **Must match regular expression** | ```^[a-zA-Z0-9_]*$``` [Test](https://regex101.com/?regex=%5E%5Ba-zA-Z0-9_%5D%2A%24&testString=%22kolf2_2j_knockout_1%22) | - -## 2. Property `Organoid > description` - -**Title:** Organoid description - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -**Description:** A general description of the organoid. - -**Example:** - -```json -"Neuroectoderm organoid, derived from kolf2_2j DKO" -``` - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 3. Property `Organoid > model_system` - -**Title:** Model system - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | Yes | - -**Description:** To which model system this differentiated cell line has been derived into - -**Examples:** - -```json -"UBERON:0000006" -``` - -```json -"islet of Langerhans" -``` - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 4. Property `Organoid > age_unit` - -**Title:** Age unit - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -**Description:** Unit by which the age of the organoid was measured - -**Examples:** - -```json -"UO:0000033" -``` - -```json -"week" -``` - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 5. Property `Organoid > age_value` - -**Title:** Organoid age - -| | | -| ------------ | -------- | -| **Type** | `number` | -| **Required** | No | - -**Description:** Age of the organoid in Organoid age unit measured from when cell aggregates started differentiating to desired organoid model. - -**Examples:** - -```json -55 -``` - -```json -67 -``` - -## 6. Property `Organoid > embedded_in_matrigel` - -**Title:** Embeddded in matrigel - -| | | -| ------------ | --------- | -| **Type** | `boolean` | -| **Required** | No | - -**Description:** Whether the organoid is embedded in a matrigel. - -**Examples:** - -```json -false -``` - -```json -true -``` - -## 7. Property `Organoid > growth_environment` - -**Title:** Growth environment - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -**Description:** Growth environment in which the organoid is grown. - -**Examples:** - -```json -"adherent" -``` - -```json -"liquid suspension" -``` - -```json -"matrigel" -``` - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 8. Property `Organoid > morphology` - -**Title:** Organoid morphology - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -**Description:** General description of the organoid morphology. - -**Examples:** - -```json -"Epithelial monolayer with budding crypt-like domains" -``` - -```json -"Optic cup structure" -``` - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 9. Property `Organoid > size_value` - -**Title:** Organoid size - -| | | -| ------------ | -------- | -| **Type** | `number` | -| **Required** | No | - -**Description:** Size of the organoid in Organoid size unit. - -**Examples:** - -```json -4 -``` - -```json -5 -``` - -## 10. Property `Organoid > size_unit` - -**Title:** Size unit - -| | | -| ------------ | -------- | -| **Type** | `string` | -| **Required** | No | - -**Description:** Unit by which the size of the organoid was measured. - -**Examples:** - -```json -"UO:0000015" -``` - -```json -"millimeter" -``` - -| Restrictions | | -| -------------- | - | -| **Min length** | 1 | - -## 11. Property `Organoid > stored_oxygen_levels` - -**Title:** Stored oxygen level - -| | | -| ------------ | -------- | -| **Type** | `number` | -| **Required** | No | - -**Description:** Percent oxygen level organoid was stored in prior to sequencing. - -**Examples:** - -```json -75 -``` - -```json -80 -``` - ----------------------------------------------------------------------------------------------------------------------------- -Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-03 at 09:14:02 +0000 \ No newline at end of file diff --git a/json_schema/type/biomaterial/organoid.json b/json_schema/type/biomaterial/organoid.json deleted file mode 100644 index 303e634..0000000 --- a/json_schema/type/biomaterial/organoid.json +++ /dev/null @@ -1,221 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft/2019-09/schema", - "type": "object", - "description": "Information about the organoid.", - "unevaluatedProperties": false, - "title": "Organoid", - "name": "organoid", - "required": [ - "content" - ], - "allOf": [ - { - "type": "object", - "$ref": "system/document.json", - "$comment": "This loads the system needed properties outside the 'content' field. For implementation outside of MorPhiC, please ensure the system properties satisfy your implementation. These properties are not meant for the user to see.", - "properties": { - "accessions": { - "description": "An International Nucleotide Sequence Database Collaboration (INSDC) or BioSamples (BSD) sample accession.", - "title": "Sample accession", - "items": { - "anyOf": [ - { - "isValidIdentifier": { - "prefix": "biosample" - } - }, - { - "isValidIdentifier": { - "prefix": "insdc.sra" - } - } - ] - }, - "examples": [ - "SAMEA2397676", - "SRS000000" - ] - }, - "described_by": { - "pattern": "^.*/type/[0-9]+.[0-9]+.[0-9]+/biomaterial/organoid$" - }, - "schema_type": { - "const": "organoid", - "default": "organoid" - } - } - } - ], - "properties": { - "content": { - "type": "object", - "title": "Content", - "required": [ - "label", - "model_system" - ], - "dependentRequired": { - "age_value": [ - "age_unit" - ], - "age_unit": [ - "age_value" - ], - "size_value": [ - "size_unit" - ], - "size_unit": [ - "size_value" - ] - }, - "properties": { - "label": { - "type": "string", - "format": "regex", - "pattern": "^[a-zA-Z0-9_]*$", - "minLength": 1, - "description": "A unique label for the organoid. No spaces allowed.", - "title": "Organoid label", - "examples": [ - "kolf2_2j_knockout_1" - ] - }, - "description": { - "type": "string", - "minLength": 1, - "description": "A general description of the organoid.", - "title": "Organoid description", - "examples": [ - "Neuroectoderm organoid, derived from kolf2_2j DKO" - ] - }, - "model_system": { - "type": "string", - "minLength": 1, - "description": "To which model system this differentiated cell line has been derived into", - "title": "Model system", - "graphRestriction": { - "ontologies": [ - "obo:uberon" - ], - "classes": [ - "UBERON:0000465" - ], - "includeSelf": false, - "queryFields": [ - "obo_id", - "label" - ] - }, - "examples": [ - "UBERON:0000006", - "islet of Langerhans" - ] - }, - "age_unit": { - "type": "string", - "minLength": 1, - "description": "Unit by which the age of the organoid was measured", - "title": "Age unit", - "graphRestriction": { - "ontologies": [ - "obo:uo" - ], - "classes": [ - "UO:0000003" - ], - "includeSelf": false, - "queryFields": [ - "obo_id", - "label" - ] - }, - "examples": [ - "UO:0000033", - "week" - ] - }, - "age_value": { - "type": "number", - "description": "Age of the organoid in Organoid age unit measured from when cell aggregates started differentiating to desired organoid model.", - "title": "Organoid age", - "examples": [ - 55, - 67 - ] - }, - "embedded_in_matrigel": { - "type": "boolean", - "description": "Whether the organoid is embedded in a matrigel.", - "title": "Embeddded in matrigel", - "examples": [ - false, - true - ] - }, - "growth_environment": { - "type": "string", - "minLength": 1, - "description": "Growth environment in which the organoid is grown.", - "title": "Growth environment", - "examples": [ - "adherent", - "liquid suspension", - "matrigel" - ] - }, - "morphology": { - "type": "string", - "minLength": 1, - "description": "General description of the organoid morphology.", - "title": "Organoid morphology", - "examples": [ - "Epithelial monolayer with budding crypt-like domains", - "Optic cup structure" - ] - }, - "size_value": { - "type": "number", - "description": "Size of the organoid in Organoid size unit.", - "title": "Organoid size", - "examples": [ - 4, - 5 - ] - }, - "size_unit": { - "type": "string", - "minLength": 1, - "description": "Unit by which the size of the organoid was measured.", - "title": "Size unit", - "graphRestriction": { - "ontologies": [ - "obo:uo" - ], - "classes": [ - "UO:0000001" - ], - "includeSelf": false, - "queryFields": [ - "obo_id", - "label" - ] - }, - "examples": [ - "UO:0000015", - "millimeter" - ] - }, - "stored_oxygen_levels": { - "type": "number", - "description": "Percent oxygen level organoid was stored in prior to sequencing.", - "title": "Stored oxygen level", - "examples": [ - 75, - 80 - ] - } - } - } - } -} \ No newline at end of file diff --git a/json_schema/versions.json b/json_schema/versions.json index 074543a..7eb70bd 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -12,7 +12,6 @@ "clonal_cell_line": "1.0.0", "differentiated_product": "1.0.0", "library_preparation": "1.0.0", - "organoid": "1.0.0", "undifferentiated_product": "1.0.0" }, "file": { From df59af52d96d057761ab06a8202b9e314e769fdc Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Wed, 23 Oct 2024 11:40:16 +0100 Subject: [PATCH 02/10] Added/replaced fields. Fixes #77 --- .../type/biomaterial/differentiated_product.json | 8 ++++---- json_schema/type/biomaterial/library_preparation.json | 8 ++++---- json_schema/type/file/sequence_file.json | 11 +++++++++++ json_schema/versions.json | 8 ++++---- 4 files changed, 23 insertions(+), 12 deletions(-) diff --git a/json_schema/type/biomaterial/differentiated_product.json b/json_schema/type/biomaterial/differentiated_product.json index 45d6e3f..b866089 100644 --- a/json_schema/type/biomaterial/differentiated_product.json +++ b/json_schema/type/biomaterial/differentiated_product.json @@ -47,7 +47,7 @@ "required": [ "label", "differentiated_product_protocol_id", - "terminally_differentiated", + "final_timepoint", "timepoint_unit", "timepoint_value" ], @@ -85,10 +85,10 @@ "msk_pancreatic_diff_protocol" ] }, - "terminally_differentiated": { + "final_timepoint": { "type": "string", - "description": "Is the cell line terminally differentiated.", - "title": "Terminally differentiated?", + "description": "Is the product at its final differentiation stage in the experiment?", + "title": "Final time point", "enum": [ "yes", "no", diff --git a/json_schema/type/biomaterial/library_preparation.json b/json_schema/type/biomaterial/library_preparation.json index d01975c..8804243 100644 --- a/json_schema/type/biomaterial/library_preparation.json +++ b/json_schema/type/biomaterial/library_preparation.json @@ -212,19 +212,19 @@ "microliter" ] }, - "pcr_cycles": { + "cdna_pcr_cycles": { "type": "integer", "description": "The number of PCR cycles to amplify initial template material used as input for library preparation.", - "title": "Library PCR cycles", + "title": "Number of iterations of cDNA amplification", "examples": [ 10, 30 ] }, - "pcr_cycles_for_sample_index": { + "pcr_cycles_for_indexing": { "type": "integer", "description": "The number of PCR cycles to incorporate a single or dual sample index and sequencing adapters.", - "title": "Library PCR cycles for sample index", + "title": "Number of PCR cycles for indexing", "examples": [ 8, 10 diff --git a/json_schema/type/file/sequence_file.json b/json_schema/type/file/sequence_file.json index ea57ba6..f73799c 100644 --- a/json_schema/type/file/sequence_file.json +++ b/json_schema/type/file/sequence_file.json @@ -117,6 +117,17 @@ 51, 150 ] + }, + "run_id": { + "type": "string", + "format": "regex", + "pattern": "^(?!^0+$)[a-zA-Z0-9\\-_]+$", + "description": "A grouping variable to denote which sequence files were generated on the same sequencer run.", + "title": "Run ID", + "examples": [ + "1", + "HJKTJDSX7" + ] } } } diff --git a/json_schema/versions.json b/json_schema/versions.json index 7eb70bd..eb46eef 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -10,13 +10,13 @@ }, "biomaterial": { "clonal_cell_line": "1.0.0", - "differentiated_product": "1.0.0", - "library_preparation": "1.0.0", + "differentiated_product": "2.0.0", + "library_preparation": "2.0.0", "undifferentiated_product": "1.0.0" }, "file": { - "analysis_file": "1.0.0", - "sequence_file": "1.0.0" + "analysis_file": "2.0.0", + "sequence_file": "2.0.0" }, "protocol": { "expression_alteration": "1.0.0" From ac9a4783caa7e33c28f04705f38149b8c29670c6 Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Wed, 23 Oct 2024 12:00:45 +0100 Subject: [PATCH 03/10] fixed versions --- json_schema/versions.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/json_schema/versions.json b/json_schema/versions.json index eb46eef..7bd1e13 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -15,7 +15,7 @@ "undifferentiated_product": "1.0.0" }, "file": { - "analysis_file": "2.0.0", + "analysis_file": "1.0.0", "sequence_file": "2.0.0" }, "protocol": { From 7bab9e5ca8c6eef5a5ec84be7c158d7c709d411b Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Wed, 23 Oct 2024 12:16:33 +0100 Subject: [PATCH 04/10] fixed versions --- json_schema/versions.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/json_schema/versions.json b/json_schema/versions.json index 7bd1e13..0ae90e4 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -16,7 +16,7 @@ }, "file": { "analysis_file": "1.0.0", - "sequence_file": "2.0.0" + "sequence_file": "1.1.0" }, "protocol": { "expression_alteration": "1.0.0" From 3c8ca24837e9ecb8eb40aaefe20ffbf317d422fc Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Tue, 29 Oct 2024 09:29:10 +0000 Subject: [PATCH 05/10] Pushed latest schema updates --- human_readable_schemas/analysis_file.md | 3 +- human_readable_schemas/clonal_cell_line.md | 2 +- .../differentiated_product.md | 12 +++--- .../expression_alteration.md | 2 +- human_readable_schemas/library_preparation.md | 42 +++++++++---------- human_readable_schemas/sequence_file.md | 30 ++++++++++++- human_readable_schemas/study.md | 2 +- .../undifferentiated_product.md | 2 +- 8 files changed, 61 insertions(+), 34 deletions(-) diff --git a/human_readable_schemas/analysis_file.md b/human_readable_schemas/analysis_file.md index 2dd2da3..a0a7eb2 100644 --- a/human_readable_schemas/analysis_file.md +++ b/human_readable_schemas/analysis_file.md @@ -156,5 +156,4 @@ Must be one of: | **Min length** | 1 | ---------------------------------------------------------------------------------------------------------------------------- - -Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-03 at 09:14:02 +0000 \ No newline at end of file +Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-29 at 09:29:09 +0000 diff --git a/human_readable_schemas/clonal_cell_line.md b/human_readable_schemas/clonal_cell_line.md index 9121f8d..522a673 100644 --- a/human_readable_schemas/clonal_cell_line.md +++ b/human_readable_schemas/clonal_cell_line.md @@ -773,4 +773,4 @@ Must be one of: | **Min length** | 1 | ---------------------------------------------------------------------------------------------------------------------------- -Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-03 at 09:14:02 +0000 +Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-29 at 09:29:09 +0000 diff --git a/human_readable_schemas/differentiated_product.md b/human_readable_schemas/differentiated_product.md index d651f9d..dd6c86b 100644 --- a/human_readable_schemas/differentiated_product.md +++ b/human_readable_schemas/differentiated_product.md @@ -3,7 +3,7 @@ - [1. Property `Differentiated product > label`](#label) - [2. Property `Differentiated product > description`](#description) - [3. Property `Differentiated product > differentiated_product_protocol_id`](#differentiated_product_protocol_id) -- [4. Property `Differentiated product > terminally_differentiated`](#terminally_differentiated) +- [4. Property `Differentiated product > final_timepoint`](#final_timepoint) - [5. Property `Differentiated product > model_system`](#model_system) - [6. Property `Differentiated product > timepoint_value`](#timepoint_value) - [7. Property `Differentiated product > timepoint_unit`](#timepoint_unit) @@ -25,7 +25,7 @@ | + [label](#label ) | No | string | No | - | Differentiated product ID | | - [description](#description ) | No | string | No | - | Differentiated product description | | + [differentiated_product_protocol_id](#differentiated_product_protocol_id ) | No | string | No | - | Differentiated product protocol ID | -| + [terminally_differentiated](#terminally_differentiated ) | No | enum (of string) | No | - | Terminally differentiated? | +| + [final_timepoint](#final_timepoint ) | No | enum (of string) | No | - | Final time point | | - [model_system](#model_system ) | No | string | No | - | Model system | | + [timepoint_value](#timepoint_value ) | No | integer | No | - | Timepoint value | | + [timepoint_unit](#timepoint_unit ) | No | string | No | - | Timepoint unit | @@ -107,16 +107,16 @@ | **Min length** | 1 | | **Must match regular expression** | ```^[a-zA-Z0-9_]*$``` [Test](https://regex101.com/?regex=%5E%5Ba-zA-Z0-9_%5D%2A%24&testString=%22JAXPD002%22) | -## 4. Property `Differentiated product > terminally_differentiated` +## 4. Property `Differentiated product > final_timepoint` -**Title:** Terminally differentiated? +**Title:** Final time point | | | | ------------ | ------------------ | | **Type** | `enum (of string)` | | **Required** | Yes | -**Description:** Is the cell line terminally differentiated. +**Description:** Is the product at its final differentiation stage in the experiment? **Examples:** @@ -275,4 +275,4 @@ Must be one of: | **Min length** | 1 | ---------------------------------------------------------------------------------------------------------------------------- -Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-03 at 09:14:01 +0000 +Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-29 at 09:29:09 +0000 diff --git a/human_readable_schemas/expression_alteration.md b/human_readable_schemas/expression_alteration.md index f130c0e..a7eb95a 100644 --- a/human_readable_schemas/expression_alteration.md +++ b/human_readable_schemas/expression_alteration.md @@ -1061,4 +1061,4 @@ Must be one of: | **Min length** | 1 | ---------------------------------------------------------------------------------------------------------------------------- -Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-03 at 09:14:02 +0000 +Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-29 at 09:29:09 +0000 diff --git a/human_readable_schemas/library_preparation.md b/human_readable_schemas/library_preparation.md index d17b2b6..fdc4059 100644 --- a/human_readable_schemas/library_preparation.md +++ b/human_readable_schemas/library_preparation.md @@ -10,8 +10,8 @@ - [8. Property `Library preparation > concentration_unit`](#concentration_unit) - [9. Property `Library preparation > total_yield_value`](#total_yield_value) - [10. Property `Library preparation > total_yield_unit`](#total_yield_unit) -- [11. Property `Library preparation > pcr_cycles`](#pcr_cycles) -- [12. Property `Library preparation > pcr_cycles_for_sample_index`](#pcr_cycles_for_sample_index) +- [11. Property `Library preparation > cdna_pcr_cycles`](#cdna_pcr_cycles) +- [12. Property `Library preparation > pcr_cycles_for_indexing`](#pcr_cycles_for_indexing) **Title:** Library preparation @@ -23,20 +23,20 @@ **Description:** Information about the library preparation. -| Property | Pattern | Type | Deprecated | Definition | Title/Description | -| ---------------------------------------------------------------------- | ------- | ------- | ---------- | ---------- | ----------------------------------- | -| + [label](#label ) | No | string | No | - | Library preparation ID | -| - [description](#description ) | No | string | No | - | Library preparation description | -| + [library_preparation_protocol_id](#library_preparation_protocol_id ) | No | string | No | - | Library preparation protocol ID | -| - [average_fragment_size](#average_fragment_size ) | No | integer | No | - | Average fragment size | -| - [input_amount_value](#input_amount_value ) | No | number | No | - | Library input amount value | -| - [input_amount_unit](#input_amount_unit ) | No | string | No | - | Library input amount unit | -| - [concentration_value](#concentration_value ) | No | number | No | - | Library concentration value | -| - [concentration_unit](#concentration_unit ) | No | string | No | - | Library concentration unit | -| - [total_yield_value](#total_yield_value ) | No | number | No | - | Library final yield value | -| - [total_yield_unit](#total_yield_unit ) | No | string | No | - | Library final yield unit | -| - [pcr_cycles](#pcr_cycles ) | No | integer | No | - | Library PCR cycles | -| - [pcr_cycles_for_sample_index](#pcr_cycles_for_sample_index ) | No | integer | No | - | Library PCR cycles for sample index | +| Property | Pattern | Type | Deprecated | Definition | Title/Description | +| ---------------------------------------------------------------------- | ------- | ------- | ---------- | ---------- | ------------------------------------------ | +| + [label](#label ) | No | string | No | - | Library preparation ID | +| - [description](#description ) | No | string | No | - | Library preparation description | +| + [library_preparation_protocol_id](#library_preparation_protocol_id ) | No | string | No | - | Library preparation protocol ID | +| - [average_fragment_size](#average_fragment_size ) | No | integer | No | - | Average fragment size | +| - [input_amount_value](#input_amount_value ) | No | number | No | - | Library input amount value | +| - [input_amount_unit](#input_amount_unit ) | No | string | No | - | Library input amount unit | +| - [concentration_value](#concentration_value ) | No | number | No | - | Library concentration value | +| - [concentration_unit](#concentration_unit ) | No | string | No | - | Library concentration unit | +| - [total_yield_value](#total_yield_value ) | No | number | No | - | Library final yield value | +| - [total_yield_unit](#total_yield_unit ) | No | string | No | - | Library final yield unit | +| - [cdna_pcr_cycles](#cdna_pcr_cycles ) | No | integer | No | - | Number of iterations of cDNA amplification | +| - [pcr_cycles_for_indexing](#pcr_cycles_for_indexing ) | No | integer | No | - | Number of PCR cycles for indexing | ## 1. Property `Library preparation > label` @@ -292,9 +292,9 @@ | -------------- | - | | **Min length** | 1 | -## 11. Property `Library preparation > pcr_cycles` +## 11. Property `Library preparation > cdna_pcr_cycles` -**Title:** Library PCR cycles +**Title:** Number of iterations of cDNA amplification | | | | ------------ | --------- | @@ -313,9 +313,9 @@ 30 ``` -## 12. Property `Library preparation > pcr_cycles_for_sample_index` +## 12. Property `Library preparation > pcr_cycles_for_indexing` -**Title:** Library PCR cycles for sample index +**Title:** Number of PCR cycles for indexing | | | | ------------ | --------- | @@ -335,4 +335,4 @@ ``` ---------------------------------------------------------------------------------------------------------------------------- -Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-03 at 09:14:02 +0000 +Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-29 at 09:29:09 +0000 diff --git a/human_readable_schemas/sequence_file.md b/human_readable_schemas/sequence_file.md index 8c90666..50f7987 100644 --- a/human_readable_schemas/sequence_file.md +++ b/human_readable_schemas/sequence_file.md @@ -5,6 +5,7 @@ - [3. Property `Sequence file > lane_index`](#lane_index) - [4. Property `Sequence file > read_index`](#read_index) - [5. Property `Sequence file > read_length`](#read_length) +- [6. Property `Sequence file > run_id`](#run_id) **Title:** Sequence file @@ -23,6 +24,7 @@ | - [lane_index](#lane_index ) | No | integer | No | - | Lane index | | + [read_index](#read_index ) | No | enum (of string) | No | - | Read index | | - [read_length](#read_length ) | No | integer | No | - | Read length | +| - [run_id](#run_id ) | No | string | No | - | Run ID | ## 1. Property `Sequence file > label` @@ -150,5 +152,31 @@ Must be one of: 150 ``` +## 6. Property `Sequence file > run_id` + +**Title:** Run ID + +| | | +| ------------ | -------- | +| **Type** | `string` | +| **Required** | No | +| **Format** | `regex` | + +**Description:** A grouping variable to denote which sequence files were generated on the same sequencer run. + +**Examples:** + +```json +"1" +``` + +```json +"HJKTJDSX7" +``` + +| Restrictions | | +| --------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------ | +| **Must match regular expression** | ```^(?!^0+$)[a-zA-Z0-9\-_]+$``` [Test](https://regex101.com/?regex=%5E%28%3F%21%5E0%2B%24%29%5Ba-zA-Z0-9%5C-_%5D%2B%24&testString=%221%22) | + ---------------------------------------------------------------------------------------------------------------------------- -Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-03 at 09:14:02 +0000 +Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-29 at 09:29:09 +0000 diff --git a/human_readable_schemas/study.md b/human_readable_schemas/study.md index f34fbe2..06b904d 100644 --- a/human_readable_schemas/study.md +++ b/human_readable_schemas/study.md @@ -712,4 +712,4 @@ Must be one of: | **Min length** | 1 | ---------------------------------------------------------------------------------------------------------------------------- -Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-03 at 09:14:02 +0000 \ No newline at end of file +Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-29 at 09:29:09 +0000 diff --git a/human_readable_schemas/undifferentiated_product.md b/human_readable_schemas/undifferentiated_product.md index 5f7023e..cddaa70 100644 --- a/human_readable_schemas/undifferentiated_product.md +++ b/human_readable_schemas/undifferentiated_product.md @@ -220,4 +220,4 @@ Must be one of: | **Min length** | 1 | ---------------------------------------------------------------------------------------------------------------------------- -Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-03 at 09:14:01 +0000 \ No newline at end of file +Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-29 at 09:29:09 +0000 From 27d2d3ec30b99bc239f2ce4443de5e830c80f59c Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Tue, 15 Oct 2024 15:58:13 +0100 Subject: [PATCH 06/10] fixed conflict --- json_schema/versions.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/json_schema/versions.json b/json_schema/versions.json index 0ae90e4..33ef2e9 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -1,5 +1,5 @@ { - "last_update_date": "2024-10-15T13:43:00Z", + "last_update_date": "2024-05-20T15:55:38Z", "version_numbers": { "system": { "document": "1.0.0" From 05ba8a9d81cc035dd7c38867a9b27b11b405b628 Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Tue, 15 Oct 2024 16:06:58 +0100 Subject: [PATCH 07/10] Bumped --- json_schema/versions.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/json_schema/versions.json b/json_schema/versions.json index 33ef2e9..8046837 100644 --- a/json_schema/versions.json +++ b/json_schema/versions.json @@ -1,5 +1,5 @@ { - "last_update_date": "2024-05-20T15:55:38Z", + "last_update_date": "2024-05-20T16:06:38Z", "version_numbers": { "system": { "document": "1.0.0" From 3914f238d2acf2799ef5c05a5e4b87194d4879f9 Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Tue, 15 Oct 2024 13:00:37 +0000 Subject: [PATCH 08/10] Pushed latest schema updates --- human_readable_schemas/analysis_file.md | 2 +- human_readable_schemas/clonal_cell_line.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/human_readable_schemas/analysis_file.md b/human_readable_schemas/analysis_file.md index a0a7eb2..ba21626 100644 --- a/human_readable_schemas/analysis_file.md +++ b/human_readable_schemas/analysis_file.md @@ -156,4 +156,4 @@ Must be one of: | **Min length** | 1 | ---------------------------------------------------------------------------------------------------------------------------- -Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-29 at 09:29:09 +0000 +Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-15 at 13:00:36 +0000 diff --git a/human_readable_schemas/clonal_cell_line.md b/human_readable_schemas/clonal_cell_line.md index 522a673..cceb4fc 100644 --- a/human_readable_schemas/clonal_cell_line.md +++ b/human_readable_schemas/clonal_cell_line.md @@ -773,4 +773,4 @@ Must be one of: | **Min length** | 1 | ---------------------------------------------------------------------------------------------------------------------------- -Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-29 at 09:29:09 +0000 +Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-15 at 13:00:36 +0000 From 70ac9a660cc97a3a84fcbbc7dea5c2df7090370c Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Tue, 29 Oct 2024 09:29:10 +0000 Subject: [PATCH 09/10] Pushed latest schema updates --- human_readable_schemas/analysis_file.md | 2 +- human_readable_schemas/clonal_cell_line.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/human_readable_schemas/analysis_file.md b/human_readable_schemas/analysis_file.md index ba21626..a0a7eb2 100644 --- a/human_readable_schemas/analysis_file.md +++ b/human_readable_schemas/analysis_file.md @@ -156,4 +156,4 @@ Must be one of: | **Min length** | 1 | ---------------------------------------------------------------------------------------------------------------------------- -Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-15 at 13:00:36 +0000 +Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-29 at 09:29:09 +0000 diff --git a/human_readable_schemas/clonal_cell_line.md b/human_readable_schemas/clonal_cell_line.md index cceb4fc..522a673 100644 --- a/human_readable_schemas/clonal_cell_line.md +++ b/human_readable_schemas/clonal_cell_line.md @@ -773,4 +773,4 @@ Must be one of: | **Min length** | 1 | ---------------------------------------------------------------------------------------------------------------------------- -Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-15 at 13:00:36 +0000 +Generated using [json-schema-for-humans](https://github.com/coveooss/json-schema-for-humans) on 2024-10-29 at 09:29:09 +0000 From c941eb1801daeeacd26eba64dbede0025434dbd3 Mon Sep 17 00:00:00 2001 From: ESapenaVentura Date: Tue, 29 Oct 2024 09:56:43 +0000 Subject: [PATCH 10/10] New test schema generated --- tests/test_schemas/differentiated_product.json | 8 ++++---- tests/test_schemas/library_preparation.json | 8 ++++---- tests/test_schemas/sequence_file.json | 11 +++++++++++ 3 files changed, 19 insertions(+), 8 deletions(-) diff --git a/tests/test_schemas/differentiated_product.json b/tests/test_schemas/differentiated_product.json index c857c11..d400825 100644 --- a/tests/test_schemas/differentiated_product.json +++ b/tests/test_schemas/differentiated_product.json @@ -118,7 +118,7 @@ "required": [ "label", "differentiated_product_protocol_id", - "terminally_differentiated", + "final_timepoint", "timepoint_unit", "timepoint_value" ], @@ -156,10 +156,10 @@ "msk_pancreatic_diff_protocol" ] }, - "terminally_differentiated": { + "final_timepoint": { "type": "string", - "description": "Is the cell line terminally differentiated.", - "title": "Terminally differentiated?", + "description": "Is the product at its final differentiation stage in the experiment?", + "title": "Final time point", "enum": [ "yes", "no", diff --git a/tests/test_schemas/library_preparation.json b/tests/test_schemas/library_preparation.json index b2b62ba..ae18349 100644 --- a/tests/test_schemas/library_preparation.json +++ b/tests/test_schemas/library_preparation.json @@ -283,19 +283,19 @@ "microliter" ] }, - "pcr_cycles": { + "cdna_pcr_cycles": { "type": "integer", "description": "The number of PCR cycles to amplify initial template material used as input for library preparation.", - "title": "Library PCR cycles", + "title": "Number of iterations of cDNA amplification", "examples": [ 10, 30 ] }, - "pcr_cycles_for_sample_index": { + "pcr_cycles_for_indexing": { "type": "integer", "description": "The number of PCR cycles to incorporate a single or dual sample index and sequencing adapters.", - "title": "Library PCR cycles for sample index", + "title": "Number of PCR cycles for indexing", "examples": [ 8, 10 diff --git a/tests/test_schemas/sequence_file.json b/tests/test_schemas/sequence_file.json index c9bc01d..ec8f0f4 100644 --- a/tests/test_schemas/sequence_file.json +++ b/tests/test_schemas/sequence_file.json @@ -188,6 +188,17 @@ 51, 150 ] + }, + "run_id": { + "type": "string", + "format": "regex", + "pattern": "^(?!^0+$)[a-zA-Z0-9\\-_]+$", + "description": "A grouping variable to denote which sequence files were generated on the same sequencer run.", + "title": "Run ID", + "examples": [ + "1", + "HJKTJDSX7" + ] } } }