From daeb5f57c250b0401f007b34a5059465a31aeb23 Mon Sep 17 00:00:00 2001 From: Eric Torstenson Date: Mon, 6 Apr 2026 17:12:44 -0500 Subject: [PATCH] Somewhat hierarchical platforms with meanings pointing to EFO --- .../schema/include_access_model.yaml | 576 ++++++++++-------- 1 file changed, 322 insertions(+), 254 deletions(-) diff --git a/src/include_access_model/schema/include_access_model.yaml b/src/include_access_model/schema/include_access_model.yaml index 27298c8..0570d1d 100644 --- a/src/include_access_model/schema/include_access_model.yaml +++ b/src/include_access_model/schema/include_access_model.yaml @@ -19,12 +19,13 @@ prefixes: ig2dac: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-code/ ig2dat: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/research-data-access-type/ ig2_biospecimen_availability: https://nih-ncpi.github.io/ncpi-fhir-ig-2/CodeSystem/biospecimen-availability/ - snomed_ct: http://snomed.info/id/ + snomed_ct: http://snomed.info/id/ MONDO: http://purl.obolibrary.org/obo/MONDO_ HP: http://purl.obolibrary.org/obo/HP_ mesh: http://id.nlm.nih.gov/mesh/ NCIT: http://purl.obolibrary.org/obo/NCIT_ PATO: http://purl.obolibrary.org/obo/PATO_ + EFO: http://www.ebi.ac.uk/efo default_prefix: includedcc default_range: string @@ -38,25 +39,25 @@ classes: title: Record abstract: true slots: - - external_id + - external_id Study: - title: Research Study - description: Study Metadata + title: Research Study + description: Study Metadata is_a: Record - slots: - #TODO: Split out core Study items and additional study metadata? + slots: + #TODO: Split out core Study items and additional study metadata? - study_id - - parent_study + - parent_study - study_title - study_code - study_short_name - program - funding_source - - principal_investigator + - principal_investigator - contact - study_description - website - # - dbgap : Should we call this out specifically or just use an external id? + # - dbgap : Should we call this out specifically or just use an external id? - publication - acknowledgments - citation_statement @@ -134,8 +135,9 @@ classes: - website Subject: title: Subject - description: This entity is the subject about which data or references are recorded. - This includes the idea of a human participant in a study, a cell line, an animal model, + description: + This entity is the subject about which data or references are recorded. + This includes the idea of a human participant in a study, a cell line, an animal model, or any other similar entity. is_a: Record slots: @@ -157,7 +159,7 @@ classes: - race - ethnicity - down_syndrome_status - - age_at_last_vital_status + - age_at_last_vital_status - vital_status - age_at_first_engagement slot_usage: @@ -165,9 +167,9 @@ classes: required: true identifier: true SubjectAssertion: - title: Subject Assertion + title: Subject Assertion description: Assertion about a particular Subject. May include Conditions, Measurements, etc. - is_a: Record + is_a: Record slots: - assertion_id - subject_id @@ -199,19 +201,19 @@ classes: required: true identifier: true Sample: - title: Sample + title: Sample description: A functionally equivalent specimen taken from a participant or processed from such a sample. is_a: Record - slots: + slots: - sample_id - - biospecimen_collection_id - - parent_sample_id + - biospecimen_collection_id + - parent_sample_id - sample_type - - processing - - availablity_status - - storage_method + - processing + - availablity_status + - storage_method - quantity_number - - quantity_unit + - quantity_unit slot_usage: sample_id: range: string @@ -222,14 +224,14 @@ classes: BiospecimenCollection: title: BiospecimenCollection description: A biospecimen collection event which yields one or more Samples. - is_a: Record - slots: + is_a: Record + slots: - biospecimen_collection_id - age_at_collection - - method - - site - - spatial_qualifier - - laterality + - method + - site + - spatial_qualifier + - laterality - encounter_id slot_usage: biospecimen_collection_id: @@ -239,13 +241,13 @@ classes: Aliquot: title: Aliquot description: A specific tube or amount of a biospecimen associated with a Sample. - is_a: Record - slots: + is_a: Record + slots: - aliquot_id - sample_id - availablity_status - quantity_number - - quantity_unit + - quantity_unit - concentration_number - concentration_unit slot_usage: @@ -255,7 +257,7 @@ classes: identifier: true Encounter: title: Participant Encounter - description: An event at which data was collected about a participant, + description: An event at which data was collected about a participant, an intervention was made, or information about a participant was recorded. is_a: Record slots: @@ -271,8 +273,8 @@ classes: identifier: true EncounterDefinition: title: Encounter Definition - description: A definition of an encounter type in this study, ie, - an event at which data was collected about a participant, + description: A definition of an encounter type in this study, ie, + an event at which data was collected about a participant, an intervention was made, or information about a participant was recorded. This may be something planned by a study or a type of data collection. #TODO: These are metadata and may not need the same Record basis. @@ -291,7 +293,7 @@ classes: multivalued: true ActivityDefinition: title: Activity Definition - description: A definition of an activity in this study, eg, + description: A definition of an activity in this study, eg, a biospecimen collection, intervention, survey, or assessment. #TODO: These are metadata and may not need the same Record basis. is_a: Record @@ -299,7 +301,7 @@ classes: - activity_definition_id - name - description - #TODO: Probably want an "expected data generated" slot, eg, + #TODO: Probably want an "expected data generated" slot, eg, #observation definitions or dd refs slot_usage: activity_definition_id: @@ -309,38 +311,38 @@ classes: File: title: File description: Required information for portal use. - is_a: Record - slots: - - study_id - - file_id - - subject_id # do we need both a subject and sample id in this table? + is_a: Record + slots: + - study_id + - file_id + - subject_id # do we need both a subject and sample id in this table? - sample_id - - s3_file_path # can name this url if more appropriate + - s3_file_path # can name this url if more appropriate - filename - size - format - - data_category + - data_category - data_type - format - size -#TODO: I'm not convinced this is the right strategy- access model vs operations + #TODO: I'm not convinced this is the right strategy- access model vs operations - staging_url - release_url - drs_uri - - hash + - hash slot_usage: - study_id: - required: true + study_id: + required: true file_id: range: string required: true identifier: true subject_id: - required: true + required: true multivalued: true sample_id: - required: true + required: true multivalued: true data_category: required: true @@ -365,25 +367,25 @@ classes: #TODO: Are these good elements for the core entity? - data_collection_start - data_collection_end - + slot_usage: dataset_id: range: string required: true identifier: true - file_id: + file_id: multivalued: true description: The list of files comprising this dataset. FileAdmin: # names are TBD; can change - idea is this is operational or file universe model title: File Admin description: File unvierse; contains all information about a file that may be needed for operational work - slots: - - study_id - - file_id - - subject_id # do we need both a subject and sample id in this table? + slots: + - study_id + - file_id + - subject_id # do we need both a subject and sample id in this table? - sample_id - - s3_file_path # can name this url if more appropriate - - file_category + - s3_file_path # can name this url if more appropriate + - file_category - size - s3_key - file_extension @@ -418,23 +420,23 @@ classes: - acl - is_released - is_registered - - repository + - repository - experimental_strategy - slot_usage: - study_id: - required: true - file_id: - required: true - identifier: true + slot_usage: + study_id: + required: true + file_id: + required: true + identifier: true FileAssay: title: File Assay - # for now group all types into one table; but we may want to split out since different - # assay types collect different types of information - # this is a basic model - description: A file produced by or associated with an assay - or data acquisition process including omics, imaging, + # for now group all types into one table; but we may want to split out since different + # assay types collect different types of information + # this is a basic model + description: A file produced by or associated with an assay + or data acquisition process including omics, imaging, actigraphy, and other experimental or observational data. slots: - file_id @@ -450,70 +452,70 @@ classes: - platform - workflow_name - workflow_version - - slot_usage: - file_id: - required: true - identifier: true - subject_id: - required: true - multivalued: true - sample_id: - required: true - multivalued: true - data_category: + + slot_usage: + file_id: + required: true + identifier: true + subject_id: + required: true + multivalued: true + sample_id: + required: true + multivalued: true + data_category: required: true - -slots: + +slots: study_id: title: Study ID description: INCLUDE Global ID for the study range: Study - multivalued: false + multivalued: false do_id: title: DOI description: Digital Object Identifier (DOI) for this Record. range: DOI - multivalued: false + multivalued: false subject_id: title: Study ID description: INCLUDE Global ID for the Subject range: Subject - multivalued: false + multivalued: false assertion_id: title: Assertion ID description: INCLUDE Global ID for the Assertion range: SubjectAssertion - multivalued: false - external_id: + multivalued: false + external_id: title: External Identifiers description: Other identifiers for this entity, eg, from the submitting study or in systems like dbGaP - required: false - range: uriorcurie - multivalued: true + required: false + range: uriorcurie + multivalued: true parent_study: title: Parent Study description: The parent study for this study, if it is a nested study. - required: false - range: Study + required: false + range: Study multivalued: false funding_source: - title: Funding Source + title: Funding Source description: The funding source(s) of the study. - required: false - range: string - multivalued: true - principal_investigator: - title: Principal Investigator + required: false + range: string + multivalued: true + principal_investigator: + title: Principal Investigator description: The Principal Investigator(s) responsible for the study. - required: true + required: true range: Investigator - multivalued: true - study_title: - description: Full Study Title - required: true - range: string - multivalued: false + multivalued: true + study_title: + description: Full Study Title + required: true + range: string + multivalued: false study_code: description: Unique identifier for the study (generally a short acronym) title: Study Code @@ -562,9 +564,9 @@ slots: contact: title: Contact Person description: The individual to contact with questions about this record. - required: true + required: true range: Investigator - multivalued: true + multivalued: true vbr: title: Virtual Biorepository description: Information about the study's Virtual Biorepository, if participating @@ -633,15 +635,15 @@ slots: description: Text use to reference this Record. range: string organism_type: - title: Organism Type + title: Organism Type description: Organism Type - required: false - range: uriorcurie - subject_type: - title: Subject Type + required: false + range: uriorcurie + subject_type: + title: Subject Type description: Type of entity this record represents - required: true - range: EnumSubjectType + required: true + range: EnumSubjectType sex: title: Sex description: Sex of Participant @@ -672,7 +674,7 @@ slots: ucum_code: d #Range -1 year to 89*365.25 (Privacy upper bound for ages over 89 years) minimum_value: -365 - maximum_value: 32507 + maximum_value: 32507 vital_status: title: Vital Status description: Whether participant is alive or dead @@ -697,7 +699,8 @@ slots: ucum_code: d age_at_event: title: Age at event - description: The age in days of the Subject at the time point which the assertion describes, + description: + The age in days of the Subject at the time point which the assertion describes, eg, age of onset or when a measurement was performed. range: integer unit: @@ -750,34 +753,34 @@ slots: title: Sample ID description: The unique identifier for this Sample. range: Sample - parent_sample_id: + parent_sample_id: title: Parent Sample ID description: Sample from which this sample is derived - range: Sample + range: Sample inlined: false - biospecimen_collection_id: + biospecimen_collection_id: title: Biospecimen Collection ID description: Unique identifier for this Biospecimen Collection. - range: BiospecimenCollection - aliquot_id: + range: BiospecimenCollection + aliquot_id: title: Aliquot ID description: Unique identifier for an Aliquot. - range: Aliquot + range: Aliquot sample_type: title: Sample Type - description: Type of material of which this Sample is comprised - required: true - range: uriorcurie + description: Type of material of which this Sample is comprised + required: true + range: uriorcurie processing: title: Sample Processing description: Processing that was applied to the Parent Sample or from the Biospecimen Collection that yielded this distinct sample - range: uriorcurie - multivalued: true - availablity_status: + range: uriorcurie + multivalued: true + availablity_status: title: Sample Availability description: Can this Sample be requested for further analysis? - range: EnumAvailabilityStatus - storage_method: + range: EnumAvailabilityStatus + storage_method: title: Sample Storage Method description: Sample storage method, eg, Frozen or with additives range: uriorcurie @@ -790,33 +793,33 @@ slots: title: Quantity Units description: The structured term defining the units of the quantity. range: Concept - concentration_number: + concentration_number: title: Concentration description: What is the concentration of the analyte in the Aliquot? - range: float - concentration_unit: + range: float + concentration_unit: title: Concentration Units description: Units associated with the concentration of the analyte in the Aliquot. - range: Concept + range: Concept age_at_collection: title: Age at Biospecimen Collection description: The age at which this biospecimen was collected in decimal years. - range: float + range: float unit: - ucum_code: a - method: - title: Biospecimen Collection Method + ucum_code: a + method: + title: Biospecimen Collection Method description: The approach used to collect the biospecimen. range: EnumSampleCollectionMethod - site: - title: Biospecimen Collection Site + site: + title: Biospecimen Collection Site description: The location of the specimen collection. range: EnumSite - spatial_qualifier: + spatial_qualifier: title: Spatial Qualifier description: Qualifier that further refine the specific location of biospecimen collection range: EnumSpatialQualifiers - laterality: + laterality: title: Location Laterality description: Laterality that further refine the specific location of biospecimen collection range: EnumLaterality @@ -860,8 +863,8 @@ slots: description: Size of the file, in Bytes. range: integer unit: - ucum_code: By - required: true + ucum_code: By + required: true staging_url: title: Staging Location description: URL for internal access to the data. May be temporary. @@ -870,8 +873,8 @@ slots: release_url: title: Release Location description: URL for controlled or open access to the data. - range: uriorcurie - required: false + range: uriorcurie + required: false drs_uri: title: DRS URI description: DRS location to access the data. @@ -906,7 +909,7 @@ slots: description: The date that data collection started. May include only a year. #TODO: We could re-evaluate these as dates, but that may be too implementation specific range: string - s3_file_path: + s3_file_path: title: S3 File Path description: The full s3 url of a file's location in aws range: string @@ -914,54 +917,54 @@ slots: is_released: title: Is Released description: A flag that notes whether a file has been released to the public - range: boolean + range: boolean required: true is_registered: title: Is Registered description: A flag that notes whether a file has been registered to a drs service range: boolean required: true - repository: + repository: title: Repository - description: The name of the drs service which files are registered to + description: The name of the drs service which files are registered to range: EnumRepository required: false - file_category: + file_category: title: File Category description: A high level classification of the file used for operations. range: string required: true - s3_key: + s3_key: title: S3 Key description: The unique identifier for an object within a bucket range: string required: true - file_extension: + file_extension: title: File Extension description: A 3-4 letter code at the end of a filename that identifies the file format. range: string required: true - data_transfer_id: + data_transfer_id: title: Data Transfer ID description: A jira ticket number associated with a file transfer request to production bucket range: string required: false - aws_account_id: + aws_account_id: title: AWS Account ID description: A 12-digit number that uniquely identifies a specific AWS account range: string required: true - account_name: + account_name: title: AWS Account Name description: A user-defined label used to define an AWS accoun. range: string required: true - account_alias: + account_alias: title: Account Alias description: A unique user-defined string that replaces the AWS Account ID in the IAM user sign-in URL range: string required: true - bucket_study_id: + bucket_study_id: title: Bucket Study ID description: The global study ID used to create the bucket range: string @@ -971,72 +974,72 @@ slots: description: Cloud storage container in AWS used to manage and store s3 objects range: string required: true - s3_created_at: + s3_created_at: title: S3 Created At description: Timestamp of when a file was uploaded to an s3 bucket. range: datetime required: true - s3_modified_at: + s3_modified_at: title: S3 Modified At description: Timestamp of when a file was modified in an s3 bucket. range: datetime required: true - intelligent_tiering_access_tier: + intelligent_tiering_access_tier: title: Intelligent Tiering Access Tier description: Storage access tier assigned by AWS intelliegnt tiering, indicating the current access frequency classification of the object range: string required: true - is_delete_marker: + is_delete_marker: title: Is Delete Marker description: A flag that notes whether a file has been deleted from s3 range: boolean required: true - is_latest: + is_latest: title: Is Latest description: Specifies whether an object version is the most recent version of that object range: boolean required: true - storage_class: + storage_class: title: Storage Class description: Storage tier of the object in AWS reflecting cost and access characteristics. range: string required: true - manifest_hash_value: + manifest_hash_value: title: Manifest Hash Value description: The provided hash value from external users to be validated against internal hash values range: string required: false - file_hash_validation_status: + file_hash_validation_status: title: File Hash Validation Status description: Notes whether hashes have been generated and verified against manifest hash values. range: string required: false - file_type: + file_type: title: File Type description: An internal type or classification of the files based on its operational usuage. range: string required: true - encryption_status: + encryption_status: title: Encryption Status description: Indicates whether the object in AWS is encrypted and the type of encryption applied. range: string required: true - is_multipart_uploaded: + is_multipart_uploaded: title: Is Multipart Uploaded description: Indicates whether the object was uploaded using a multipart upload process. range: string required: true - object_lock_level_hold_status: + object_lock_level_hold_status: title: Object Lock Level Hold Status description: Whether a legal hold is applied to prevent deletion of the object. range: string required: true - object_lock_mode: + object_lock_mode: title: Object Lock Mode description: Retention mode applied to the object that restricts deletion or modification. range: string required: true - replication_status: + replication_status: title: Replication Status description: Status of the object's replication to another storage location. range: string @@ -1046,55 +1049,51 @@ slots: description: Identifier for a specific version of the object range: string required: true - access_type: + access_type: title: Access Type description: Notes wheter a file is controlled, open, or registered-tier access range: EnumAccessType required: true - access_url: + access_url: title: Access URL description: HTTPS endpoint for accessing a file via a specific data repository service. range: string required: false - acl: + acl: title: ACL description: The object access control list. range: string required: true - experimental_strategy: + experimental_strategy: title: Experimental Strategy description: Method or assay used to generate the data range: EnumExperimentalStrategy required: true - assay_center: + assay_center: title: Assay Center description: The organization or center that generated the file range: EnumAssayCenter required: false - platform: + platform: title: Platform description: Instrument or platform family name - range: EnumPlatform + range: EnumPlatform required: true workflow_name: title: Workflow Name description: Processing tool that produced the file - range: string - required: false - workflow_version: + range: string + required: false + workflow_version: title: Workflow Version description: Version of the process tool that produced the file range: string required: false - object_lock_retain_until_date: + object_lock_retain_until_date: title: Object Lock Retain Until Date description: Specifies exact date and time when an object's Object Lock rentention period expires. range: datetime required: true - - - - enums: EnumProgram: @@ -1203,7 +1202,7 @@ enums: description: Categories of data which may be collected about participants. #TODO: Add meanings permissible_values: - #Should we have these two demo/clinical data categories? + #Should we have these two demo/clinical data categories? unharmonized_demographic_clinical_data: title: Unharmonized Demographic/Clinical Data harmonized_demographic_clinical_data: @@ -1237,15 +1236,16 @@ enums: title: Sleep Study EnumSubjectType: description: Types of Subject entities - permissible_values: - participant: + permissible_values: + participant: description: Study participant with consent, assent, or waiver of consent. non_participant: - description: An individual associated with a study who was not explictly consented, eg, the subject + description: + An individual associated with a study who was not explictly consented, eg, the subject of a reported family history. - cell_line: + cell_line: description: Cell Line - animal_model: + animal_model: description: Animal model group: description: A group of individuals or entities. @@ -1379,12 +1379,12 @@ enums: description: Is the biospecimen available for use? permissible_values: available: - title: Available - meaning: ig2_biospecimen_availability:available + title: Available + meaning: ig2_biospecimen_availability:available description: Biospecimen is Available - unavailable: - title: Unavailable - meaning: ig2_biospecimen_availability:unavailable + unavailable: + title: Unavailable + meaning: ig2_biospecimen_availability:unavailable description: Biospecimen is Unavailable EnumSampleCollectionMethod: description: The approach used to collect the biospecimen. [LOINC](https://loinc.org) is recommended. @@ -1392,12 +1392,12 @@ enums: description: The location of the specimen collection. [SNOMED Body Site](https://hl7.org/fhir/R4B/valueset-body-site.html) is recommended. EnumSpatialQualifiers: description: Any spatial/location qualifiers. - enum_uri: http://hl7.org/fhir/us/mcode/ValueSet/mcode-body-location-qualifier-vs + enum_uri: http://hl7.org/fhir/us/mcode/ValueSet/mcode-body-location-qualifier-vs reachable_from: source_ontology: bioregistry:snomedct source_nodes: - snomedct:106233006 - - snomedct:272424004 + - snomedct:272424004 - snomedct:51440002 - snomedct:399488007 - snomedct:24028007 @@ -1432,88 +1432,156 @@ enums: permissible_values: md5: title: MD5 - etag: + etag: title: ETag sha1: title: SHA-1 - EnumAccessType: - description: Types of file access levels. - permissible_values: - open: - title: Open Access - controlled: + EnumAccessType: + description: Types of file access levels. + permissible_values: + open: + title: Open Access + controlled: title: Controlled Access - registered: + registered: title: Registered-tier Access - EnumExperimentalStrategy: + EnumExperimentalStrategy: description: Types of sequencing methods. - permissible_values: + permissible_values: wgs: title: Whole Genome Sequencing - rnaseq: + rnaseq: title: RNA-Seq - wxs: + wxs: title: Whole Exome Sequencing - methlyation: + methlyation: title: Methylation - clr_wgs: + clr_wgs: title: Continuous Long Reads WGS - proteomics: - title: Proteomics - targeted_seq: + proteomics: + title: Proteomics + targeted_seq: title: Targeted Sequencing - ccs_wgs: + ccs_wgs: title: Circular Consensus Sequencing WGS - panel: + panel: title: Panel - ccs_rnaseq: + ccs_rnaseq: title: Circular Consensus Sequencing RNA-Se - ont_wgs: + ont_wgs: title: Oxford Nanopore Technologies WGS - clr_rnaseq: + clr_rnaseq: title: Continuous Long Reads RNA-Seq - EnumAssayCenter: + EnumAssayCenter: description: Organizations or centers producing raw or harmonized sequencing files. - permissible_values: - # can add more as needed - broad: - title: The Broad Institute - hudsonalpha: - title: HudsonAlpha Institute for Biotechnology - stjude: + permissible_values: + # can add more as needed + broad: + title: The Broad Institute + hudsonalpha: + title: HudsonAlpha Institute for Biotechnology + stjude: title: St. Jude - baylor: + baylor: title: Baylor College of Medicine - chop: + chop: title: The Children's Hospital of Philadelphia - other: + other: title: Other - unknown: + unknown: title: Unknown - EnumRepository: + EnumRepository: description: specific drs service used for registration - permissible_values: - cavatica: + permissible_values: + cavatica: title: Cavatica DRS - dcf: - title: NCI DCF - other: + dcf: + title: NCI DCF + other: title: Other - EnumPlatform: + EnumPlatform: description: names of instrument or platforms used for assay data generation - permissible_values: - illumina: + permissible_values: + illumina: title: Illumina - pacbio: - title: PacBio - ont: - title: ONT - illumina_epic: - title: Illumina Infinium HumanMethylationEPICv2 - other: - title: Other - unknown: + description: Illumina Platform + long_read: + description: Single-molecule sequencing technologies (PacBio, ONT). + unknown: title: Unknown - + description: Unknown platform + + # --- Illumina Sub-grouping --- + # High-Throughput / Production + novaseq_x: + is_a: illumina + title: NovaSeq X Series + description: Ultra-high throughput (NovaSeq X, X Plus). + meaning: EFO:EFO_0022840 + novaseq_6000: + title: NovaSeq 6000 + is_a: illumina + description: Standard high-throughput production platform. + meaning: EFO:EFO_0008637 + # Mid-to-Low Throughput + nextseq_1000: + title: NextSeq 1000 + is_a: illumina + description: Mid-range sequencing (P1, P2, P3 flowcells). + meaning: EFO:EFO_0010962 + nextseq_2000: + title: NextSeq 1000-2000 + is_a: illumina + description: Mid-range sequencing (P1, P2, P3 flowcells). + meaning: EFO:EFO_0010963 + nextseq_500: + title: NextSeq 500_550 + is_a: illumina + description: Older mid-range 2-channel systems. + meaning: EFO:EFO_0009173 + nextseq_550: + title: NextSeq 550 + is_a: illumina + description: Older mid-range 2-channel systems. + meaning: EFO:EFO_0008566 + miseq: + title: MiSeq Series + is_a: illumina + description: Benchtop low-throughput (MiSeq, MiSeqDx). + miniseq_iseq: + title: MiniSeq iSeq + is_a: illumina + description: Smallest entry-level sequencers. + + # Array + iscan_system: + is_a: illumina + description: Hardware for Infinium arrays (EPIC, GSA). + # --- PacBio (Pacific Biosciences) --- + pacbio_revio: + title: PacBio Revio + is_a: long_read + description: Current flagship high-throughput HiFi system. + pacbio_sequel_iie: + title: PacBio Sequel IIe + is_a: long_read + description: Reliable mid-to-high throughput HiFi system. + pacbio_onso: + title: PacBio Onso + is_a: long_read + description: Short-read SBB (Sequencing by Binding) platform from PacBio. + # --- ONT (Oxford Nanopore Technologies) --- + ont_promethion: + title: ONT PromethION + is_a: long_read + description: Ultra-high throughput scalable nanopore system. + ont_gridion: + title: ONT GridION + is_a: long_read + description: Benchtop nanopore system running up to 5 flow cells. + ont_minion: + title: ONT MiniION + is_a: long_read + description: Portable, pocket-sized nanopore sequencer.