From dc08c07e720678fd7c7030b619e2221af250ad5f Mon Sep 17 00:00:00 2001 From: dgupta Date: Thu, 12 Mar 2026 13:51:03 +0000 Subject: [PATCH] Adding the BSDC00004 MICROBE checklist --- docker-compose.yml | 4 ++-- .../ena/ChecklistConverterController.java | 6 ++++++ src/main/resources/env/biosamples_schema.json | 12 ++++++++++++ 3 files changed, 20 insertions(+), 2 deletions(-) diff --git a/docker-compose.yml b/docker-compose.yml index 97ba40a..565fbce 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -12,7 +12,7 @@ services: build: . image: biosamples/json-schema-store:latest ports: - - 8085:8085 + - 8085:8080 links: - mongodb - validator @@ -23,4 +23,4 @@ services: # default: # ipam: # config: -# - subnet: 172.30.0.0/16 \ No newline at end of file +# - subnet: 172.30.0.0/16 diff --git a/src/main/java/uk/ac/ebi/biosamples/jsonschemastore/ena/ChecklistConverterController.java b/src/main/java/uk/ac/ebi/biosamples/jsonschemastore/ena/ChecklistConverterController.java index 407f394..07c386b 100644 --- a/src/main/java/uk/ac/ebi/biosamples/jsonschemastore/ena/ChecklistConverterController.java +++ b/src/main/java/uk/ac/ebi/biosamples/jsonschemastore/ena/ChecklistConverterController.java @@ -33,4 +33,10 @@ public ResponseEntity convertAndSaveAllEnaChecklistsAndBiosamplesSchema( String enaChecklists = checklistConverterService.persistEnaChecklists(); return new ResponseEntity<>(enaChecklists, HttpStatus.CREATED); } + + @GetMapping("/convert/biosamples") + public ResponseEntity convertAndSaveBiosamplesChecklistsFromFile() { + checklistConverterService.importBiosamplesSchema(); + return new ResponseEntity<>("BioSamples checklists imported from file", HttpStatus.CREATED); + } } diff --git a/src/main/resources/env/biosamples_schema.json b/src/main/resources/env/biosamples_schema.json index 4f36eee..cd9a887 100644 --- a/src/main/resources/env/biosamples_schema.json +++ b/src/main/resources/env/biosamples_schema.json @@ -35,6 +35,18 @@ "metaSchema" : "https://schemablocks.org/metaschemas/json-schema-draft-07/1.0.1", "schema" : "{\"$id\": \"https://www.ebi.ac.uk/biosamples/schemas/pha4ge-sars-cov-2/1.0.0\",\"$schema\": \"http://json-schema.org/draft-07/schema#\",\"title\": \"PHA4GE SARS-CoV-2 contextual data schema\",\"version\": \"1.0.0\",\"description\": \"https://github.com/pha4ge/SARS-CoV-2-Contextual-Data-Specification/blob/master/PHA4GE_SARS-CoV-2_Contextual_Data_Schema.json\",\"type\": \"object\",\"$async\": true,\"definitions\": {\"attribute_value\": {\"type\": \"object\",\"additionalProperties\": false,\"properties\": {\"text\": {\"type\": \"string\"},\"ontologyTerms\": {\"type\": \"array\",\"items\": { \"type\": \"string\",\"format\": \"uri\",\"isValidTerm\": true}},\"unit\": {\"description\": \"The unit associated with the attribute value\",\"type\": \"string\"}}},\"attribute_value_list\": {\"type\": \"array\",\"items\": {\"$ref\": \"#/definitions/attribute_value\"}} },\"properties\": {\"characteristics\": {\"description\": \"All the characteristics associated to the sample\",\"type\": \"object\",\"properties\": {\"specimen_collector_sample_id\": {\"description\": \"The user-defined name for the sample.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"bioproject_umbrella_accession\": {\"description\": \"The INSDC umbrella accession number of the BioProject to which the BioSample belongs.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"pattern\": \"^PRJ(N|E|D)([a-zA-Z]?)[0-9]+\"} }}},\"bioproject_accession\": {\"description\": \"The INSDC accession number of the BioProject(s) to which the BioSample belongs.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"pattern\": \"^PRJ(N|E|D)([a-zA-Z]?)[0-9]+\"} }}},\"biosample_accession\": {\"description\": \"The identifier assigned to a BioSample in INSDC archives.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"pattern\": \"^SAM(D|N|E([AG]?))[0-9]+\"} }}},\"sra_accession\": {\"description\": \"The Sequence Read Archive (SRA), European Nucleotide Archive (ENA) or DDBJ Sequence Read Archive (DRA) identifier linking raw read data, methodological metadata and quality control metrics submitted to the INSDC.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"pattern\": \"^(SRR|ERR|DRR)[0-9]+\"} }}},\"genbank_ena_ddbj_accession\": {\"description\": \"The GenBank/ENA/DDBJ identifier assigned to the sequence in the INSDC archives.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"pattern\": \"^([a-zA-Z]{2})\\\\d*.\\\\d{1}\"} }}},\"gisaid_accession\": {\"description\": \"The GISAID accession number assigned to the sequence.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"pattern\": \"^EPI_ISL_\\\\d*\"} }}},\"gisaid_virus_name\": {\"description\": \"The user-defined GISAID virus name assigned to the sequence.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"host_specimen_voucher\": {\"description\": \"Identifier for the physical specimen.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"sample_collected_by\": {\"description\": \"The name of the agency that collected the original sample.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"sample_collector_contact_email\": {\"description\": \"The email address of the contact responsible for follow-up regarding the sample.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"format\": \"email\"} }}},\"sample_collector_contact_address\": {\"description\": \"The mailing address of the agency submitting the sample.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"sequence_submitted_by\": {\"description\": \"The name of the agency that generated the sequence.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"sequence_submitter_contact_email\": {\"description\": \"The email address of the contact responsible for follow-up regarding the sequence.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"format\": \"email\"} }}},\"sequence_submitter_contact_address\": {\"description\": \"The mailing address of the agency submitting the sequence.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"sample_collection_date\": {\"description\": \"The date on which the sample was collected.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"format\": \"date\"} }}},\"sample_received_date\": {\"description\": \"The date on which the sample was received.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"format\": \"date\"} }}},\"geo_loc_name_country\": {\"description\": \"Country of origin of the sample.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"geo_loc_name_state_province_territory\": {\"description\": \"The state/province/territory of origin of the sample.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"geo_loc_name_county_region\": {\"description\": \"The county/region of origin of the sample.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"geo_loc_name_city\": {\"description\": \"The city of origin of the sample.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"geo_loc_latitude\": {\"description\": \"The latitude coordinates of the geographical location of sample collection.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"geo_loc_longitude\": {\"description\": \"The longitude coordinates of the geographical location of sample collection.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"organism\": {\"description\": \"Taxonomic name of the organism.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"isolate\": {\"description\": \"Identifier of the specific isolate.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"culture_collection\": {\"description\": \"The name of the source collection and unique culture identifier.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"purpose_of_sampling\": {\"description\": \"The reason that the sample was collected.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"purpose_of_sampling_details\": {\"description\": \"Further details pertaining to the reason the sample was collected.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"sample_plan_name\": {\"description\": \"The name of the sample plan implemented for sample collection.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"sample_collected_in_quarantine\": {\"description\": \"Whether the sample was collected from an individual in quarantine.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"anatomical_material\": {\"description\": \"A substance obtained from an anatomical part of an organism e.g. tissue, blood.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"anatomical_part\": {\"description\": \"An anatomical part of an organism e.g. oropharynx.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"body_product\": {\"description\": \"A substance excreted/secreted from an organism e.g. feces, urine, sweat.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"environmental_material\": {\"description\": \"A substance obtained from the natural or man-made environment e.g. soil, water, sewage, door handle, bed handrail, face mask.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"environmental_site\": {\"description\": \"An environmental location may describe a site in the natural or built environment e.g. hospital, wet market, bat cave.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"collection_device\": {\"description\": \"The instrument or container used to collect the sample e.g. swab.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"collection_method\": {\"description\": \"The process used to collect the sample e.g. phlebotomy, necropsy.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"collection_protocol\": {\"description\": \"The name and version of a particular protocol used for sampling.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"specimen_processing\": {\"description\": \"Any processing applied to the sample during or after receiving the sample.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"lab_host\": {\"description\": \"Name and description of the laboratory host used to propagate the source organism or material from which the sample was obtained.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"passage_number\": {\"description\": \"passage_number\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"pattern\": \"\\\\d+\"} }}},\"passage_method\": {\"description\": \"Description of how organism was passaged.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"biomaterial_extracted\": {\"description\": \"The biomaterial extracted from samples for the purpose of sequencing.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"data_abstraction_details\": {\"description\": \"A description of how any data elements were altered to preserve patient privacy.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"geo_loc_name_state_province_region\": {\"description\": \"State/province/region of origin of the sample.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"host_common_name\": {\"description\": \"The commonly used name of the host.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"host_scientific_name\": {\"description\": \"The taxonomic, or scientific name of the host.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"host_health_state\": {\"description\": \"Health status of the host at the time of sample collection.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"host_health_status_details\": {\"description\": \"Further details pertaining to the health or disease status of the host at time of collection.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"host_disease\": {\"description\": \"The name of the disease experienced by the host.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"host_disease_outcome\": {\"description\": \"Disease outcome in the host.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"host_age\": {\"description\": \"Age of host at the time of sampling.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"pattern\": \"\\\\d+-\\\\d+\"} }}},\"host_age_unit\": {\"description\": \"The units used to measure the host's age.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"host_age_bin\": {\"description\": \"The age category of the host at the time of sampling.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"pattern\": \"\\\\d+-\\\\d+\"} }}},\"host_gender\": {\"description\": \"The gender of the host at the time of sample collection.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"host_residence_geo_loc_name_country\": {\"description\": \"The country where the host resides.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"host_ethnicity\": {\"description\": \"The self-identified ethnicity(ies) of the host.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"host_subject_id\": {\"description\": \"A unique identifier by which each host can be referred to e.g. #131\",\"$ref\": \"#/definitions/attribute_value_list\"},\"symptom_onset_date\": {\"description\": \"The date on which the symptoms began or were first noted.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"format\": \"date\"} }}},\"signs_and_symptoms\": {\"description\": \"A perceived change in function or sensation, (loss, disturbance or appearance) indicative of a disease, reported by a patient.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"pre_existing_conditions_and_risk_factors\": {\"description\": \"Patient pre-existing conditions and risk factors.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"complications\": {\"description\": \"Patient medical complications that are believed to have occurred as a result of host disease.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"host_vaccination_status\": {\"description\": \"The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated).\",\"$ref\": \"#/definitions/attribute_value_list\"},\"vaccine_name\": {\"description\": \"The name of the vaccine.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"number_of_vaccine_doses_received\": {\"description\": \"The number of doses of the vaccine recived by the host.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"first_dose_vaccination_date\": {\"description\": \"The date the host was first vaccinated.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"format\": \"date\"} }}},\"last_dose_vacicnation_date\": {\"description\": \"The date the host received their last dose of vaccine.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"format\": \"date\"} }}},\"location_of_exposure_geo_loc_name_country\": {\"description\": \"The country where the host was likely exposed to the causative agent of the illness.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"destination_of_most_recent_travel_city\": {\"description\": \"The name of the city that was the destination of most recent travel.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"destination_of_most_recent_travel__state_province_territory\": {\"description\": \"The name of the province that was the destination of most recent travel.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"destination_of_most_recent_travel_country\": {\"description\": \"The name of the country that was the destination of most recent travel.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"most_recent_travel_departure_date\": {\"description\": \"The date of a person's most recent departure from their primary residence (at that time) on a journey to one or more other locations.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"format\": \"date\"} }}},\"most_recent_travel_return_date\": {\"description\": \"The date of a person's most recent return to some residence from a journey originating at that residence.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"format\": \"date\"} }}},\"travel_history\": {\"description\": \"Travel history in last six months.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"exposure_event\": {\"description\": \"Event leading to exposure.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"exposure_contact_level\": {\"description\": \"The exposure transmission contact type.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"host_role\": {\"description\": \"The role of the host in relation to the exposure setting.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"exposure_setting\": {\"description\": \"The setting leading to exposure.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"exposure_details\": {\"description\": \"Additional host exposure information.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"prior_sars_cov_2_infection\": {\"description\": \"Whether there was prior SARS-CoV-2 infection.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"prior_sars_cov_2_infection_isolate\": {\"description\": \"The identifier of the isolate found in the prior SARS-CoV-2 infection.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"prior_sars_cov_2_infection_date\": {\"description\": \"The date of diagnosis of the prior SARS-CoV-2 infection.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"format\": \"date\"} }}},\"prior_sars_cov_2_antiviral_treatment\": {\"description\": \"Whether there was prior SARS-CoV-2 treatment with an antiviral agent.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"prior_sars_cov_2_antiviral_treatment_agent\": {\"description\": \"The name of the antiviral treatment agent administered during the prior SARS-CoV-2 infection.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"prior_sars_cov_2_antiviral_treatment_date\": {\"description\": \"The date treatment was first administered during the prior SARS-CoV-2 infection.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"format\": \"date\"} }}},\"purpose_of_sequencing\": {\"description\": \"The reason that the sample was sequenced.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"purpose_of_sequencing_details\": {\"description\": \"The description of why the sample was sequenced providing specific details.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"sequencing_date\": {\"description\": \"The date the sample was sequenced.\",\"type\": \"array\",\"items\": { \"type\": \"object\",\"properties\": {\"text\": {\"type\": \"string\",\"format\": \"date\"} }}},\"library_id\": {\"description\": \"The user-specified identifier for the library prepared for sequencing.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"amplicon_size\": {\"description\": \"The length of the amplicon generated by PCR amplification.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"library_preparation_kit\": {\"description\": \"The name of the DNA library preparation kit used to generate the library being sequenced.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"flow_cell_barcode\": {\"description\": \"The barcode of the flow cell used for sequencing.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"sequencing_instrument\": {\"description\": \"The model of the sequencing instrument used.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"sequencing_protocol_name\": {\"description\": \"The name and version number of the sequencing protocol used.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"sequencing_protocol\": {\"description\": \"The protocol used to generate the sequence.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"sequencing_kit_number\": {\"description\": \"The manufacturer's kit number.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"amplicon_pcr_primer_scheme\": {\"description\": \"The specifications of the primers (primer sequences, binding positions, fragment size generated etc) used to generate the amplicons to be sequenced.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"raw_sequence_data_processing_method\": {\"description\": \"The method used for raw data processing such as removing barcodes, adapter trimming, filtering etc.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"dehosting_method\": {\"description\": \"The method used to remove host reads from the pathogen sequence.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"consensus_sequence_name\": {\"description\": \"The name of the consensus sequence.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"consensus_sequence_filename\": {\"description\": \"The name of the consensus sequence file.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"consensus_sequence_filepath\": {\"description\": \"The filepath of the consesnsus sequence file.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"consensus_sequence_software_name\": {\"description\": \"The name of software used to generate the consensus sequence.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"consensus_sequence_software_version\": {\"description\": \"The version of the software used to generate the consensus sequence.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"breadth_of_coverage_value\": {\"description\": \"The percentage of the reference genome covered by the sequenced data, to a prescribed depth.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"depth_of_coverage_value\": {\"description\": \"The average number of reads representing a given nucleotide in the reconstructed sequence.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"depth_of_coverage_threshold\": {\"description\": \"The threshold used as a cut-off for the depth of coverage.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"r1_fastq_filename\": {\"description\": \"The user-specified filename of the r1 FASTQ file.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"r2_fastq_filename\": {\"description\": \"The user-specified filename of the r2 FASTQ file.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"r1_fastq_filepath\": {\"description\": \"The filepath of the r1 FASTQ file.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"r2_fastq_filepath\": {\"description\": \"The filepath of the r2 FASTQ file.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"fast5_filename\": {\"description\": \"The user-specified filename of the FAST5 file.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"fast5_filepath\": {\"description\": \"The filepath of the FAST5 file.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"number_of_base_pairs_sequenced\": {\"description\": \"The number of total base pairs generated by the sequencing process.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"consensus_genome_length\": {\"description\": \"Size of the assembled genome described as the number of base pairs.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"reference_genome_accession\": {\"description\": \"A persistent, unique identifier of a genome database entry.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"bioinformatics_protocol\": {\"description\": \"The name and version number of the bioinformatics protocol used.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"lineage_clade_name\": {\"description\": \"The name of the lineage or clade.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"lineage_clade_analysis_software_name\": {\"description\": \"The name of the software used to determine the lineage/clade.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"lineage_clade_analysis_software_version\": {\"description\": \"The version of the software used to determine the lineage/clade.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"variant_designation\": {\"description\": \"The variant classification of the lineage/clade i.e. variant, variant of concern.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"variant_evidence\": {\"description\": \"The evidence used to make the variant determination.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"gene_name_1\": {\"description\": \"The name of the gene used in the diagnostic RT-PCR test.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"diagnostic_pcr_protocol_1\": {\"description\": \"The name and version number of the protocol used for diagnostic marker amplification.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"diagnostic_pcr_ct_value_1\": {\"description\": \"The Ct value result from a diagnostic SARS-CoV-2 RT-PCR test.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"gene_name_2\": {\"description\": \"The name of the gene used in the diagnostic RT-PCR test.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"diagnostic_pcr_protocol_2\": {\"description\": \"The name and version number of the protocol used for diagnostic marker amplification.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"diagnostic_pcr_ct_value_2\": {\"description\": \"The cycle threshold (CT) value result from a diagnostic SARS-CoV-2 RT-PCR test.\",\"$ref\": \"#/definitions/attribute_value_list\"},\"authors\": {\"description\": \"Names of individuals contributing to the processes of sample collection, sequence generation, analysis, and data submission.\",\"$ref\": \"#/definitions/attribute_value_list\"}},\"required\": [\"specimen_collector_sample_id\",\"sample_collected_by\",\"sequence_submitted_by\",\"sample_collection_date\",\"geo_loc_name_country\",\"geo_loc_name_state_province_territory\",\"organism\",\"isolate\",\"geo_loc_name_state_province_region\",\"host_scientific_name\",\"host_disease\",\"sequencing_instrument\",\"consensus_sequence_software_name\",\"consensus_sequence_software_version\"],\"dependencies\": {\"environment parameter\":[\"environment parameter value\"],\"environment parameter value\":[\"environment parameter\"]},\"additionalProperties\": true} },\"required\": [\"name\",\"characteristics\"]}" }, + { + "id" : "BSDC00004:1.0.0", + "accession" : "BSDC00004", + "name" : "microbe-seed", + "version" : "1.0.0", + "title" : "MICROBE Seed Checklist", + "description" : "MICROBE Seed Checklist", + "domain" : "https://www.ebi.ac.uk/biosamples/schemas", + "authority" : "BIOSAMPLES", + "metaSchema" : "https://schemablocks.org/metaschemas/json-schema-draft-07/1.0.1", + "schema" : "{\"$schema\":\"https://json-schema.org/draft/2020-12/schema\",\"$id\":\"https://example.org/schemas/microbe-seed-checklist.schema.json\",\"title\":\"MICROBE Seed Checklist\",\"version\":\"1.0\",\"type\":\"object\",\"properties\":{\"project name\":{\"type\":\"string\",\"description\":\"Name of the project associated with the sample\"},\"sample name\":{\"type\":\"string\",\"description\":\"Unique name of the sample\"},\"sample type\":{\"type\":\"string\",\"description\":\"The type of the sample: soil, seed, or marine\"},\"assay\":{\"type\":\"string\",\"description\":\"List of assays performed on the sample\"},\"broad-scale environmental context\":{\"type\":\"string\",\"description\":\"Report the major environmental system the sample came from to provide general environmental context\"},\"center\":{\"type\":\"string\",\"description\":\"MICROBE center that analyzed this sample\"},\"checklist\":{\"type\":\"string\",\"description\":\"Selected checklist for validation\"},\"collection date\":{\"type\":\"string\",\"description\":\"The date the sample was collected with the intention of sequencing or an approved MIxS missing-value term\",\"pattern\":\"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)\"},\"intermediate storage during transport to lab temperature\":{\"type\":\"number\",\"unit\":\"°C\",\"description\":\"The temperature of the sample storage during transport to the lab\"},\"intermediate storage in the lab temperature \":{\"type\":\"number\",\"unit\":\"°C\",\"description\":\"The temperature of the sample storage when initially received in the lab\"},\"time to preservation (collection time point - start of preservation)\":{\"type\":\"number\",\"unit\":\"days\",\"description\":\"Duration between sample collection and sample preservation\"},\"cooling rate\":{\"type\":\"number\",\"unit\":\"°C/min\",\"description\":\"The cooling rate for the cryopreservation\"},\"freeze-free preservation medium\":{\"type\":\"string\",\"description\":\"The non-cryoprotectant preservation medium\"},\"cryoprotectant\":{\"type\":\"string\",\"description\":\"The cryoprotectant used for the cryopreservation\"},\"cultivation medium\":{\"type\":\"string\",\"description\":\"Material used to provide moisture, air, and support for seeds to germinate and develop into seedlings\"},\"cultivation temperature\":{\"type\":\"number\",\"unit\":\"°C\",\"description\":\"The temperature of the cultivation period\"},\"cultivation time\":{\"type\":\"number\",\"unit\":\"days\",\"description\":\"Duration of cultivation\"},\"soil component\":{\"type\":\"string\",\"description\":\"The component of the soil used\"},\"environmental medium\":{\"type\":\"string\",\"description\":\"Environmental material immediately surrounding the sample at the time of sampling\"},\"freezing method\":{\"type\":\"string\",\"description\":\"The method by which the sample is initially frozen as part of cryopreservation\"},\"freezing temperature\":{\"type\":\"number\",\"unit\":\"°C\",\"description\":\"The temperature at which the sample is frozen\"},\"geographic location (country and/or sea)\":{\"type\":\"string\",\"description\":\"Country or sea name\"},\"geographic location (latitude)\":{\"type\":\"number\",\"unit\":\"decimal degrees\",\"description\":\"Latitude in WGS84\"},\"geographic location (longitude)\":{\"type\":\"number\",\"unit\":\"decimal degrees\",\"description\":\"Longitude in WGS84\"},\"geographic location (region and locality)\":{\"type\":\"string\",\"description\":\"Specific region and locality description\"},\"host scientific name\":{\"type\":\"string\",\"description\":\"Scientific name of the natural host\"},\"local environmental context\":{\"type\":\"string\",\"description\":\"Local environmental influences surrounding the sample\"},\"organism\":{\"type\":\"string\",\"description\":\"Taxonomic name for the organism\"},\"preservation start date\":{\"type\":\"string\",\"description\":\"Start date of preservation or an approved MIxS missing-value term\",\"pattern\":\"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)\"},\"preservation finish date\":{\"type\":\"string\",\"description\":\"End date of preservation or an approved MIxS missing-value term\",\"pattern\":\"(^[12][0-9]{3}(-(0[1-9]|1[0-2])(-(0[1-9]|[12][0-9]|3[01])(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?(/[0-9]{4}(-[0-9]{2}(-[0-9]{2}(T[0-9]{2}:[0-9]{2}(:[0-9]{2})?Z?([+-][0-9]{1,2})?)?)?)?)?$)|(^not applicable$)|(^not collected$)|(^not provided$)|(^restricted access$)|(^missing: control sample$)|(^missing: sample group$)|(^missing: synthetic construct$)|(^missing: lab stock$)|(^missing: third party data$)|(^missing: data agreement established pre-2023$)|(^missing: endangered species$)|(^missing: human-identifiable$)|(^missing$)\"},\"preservation method\":{\"type\":\"string\",\"description\":\"Method used to preserve the sample\"},\"storage preservation temperature\":{\"type\":\"number\",\"unit\":\"°C\",\"description\":\"Temperature at which the sample is stored\"},\"targets\":{\"type\":\"string\",\"description\":\"Target genetic segments intended for sequencing\"},\"preservation duration\":{\"type\":\"integer\",\"unit\":\"days\",\"description\":\"Duration preserved\"}}}" + }, { "id" : "ERC000011:0.1", "accession" : "ERC000011",