diff --git a/mpxv/yale/v3/info.yml b/mpxv/yale/v3/info.yml index b36e012..697d8e7 100644 --- a/mpxv/yale/v3/info.yml +++ b/mpxv/yale/v3/info.yml @@ -2,7 +2,8 @@ schema_version: 0.9.0 name: yale-v3 organism: mpxv developers: -- person_name: Chantal B.F. Vogels +- type: Person + name: Chantal B.F. Vogels orcid: 0000-0003-0027-6480 vendors: - organisation_name: IDT diff --git a/schema/primer_scheme.yml b/schema/primer_scheme.yml index f793e52..6f16378 100644 --- a/schema/primer_scheme.yml +++ b/schema/primer_scheme.yml @@ -1,7 +1,7 @@ id: https://github.com/pha4ge/primer-schemes/schemas/primer-scheme name: primer-scheme description: Data model for tiling PCR primer scheme definitions -version: 0.9.0 +version: 0.10.0 prefixes: linkml: https://w3id.org/linkml/ schema: http://schema.org/ @@ -17,69 +17,58 @@ default_range: string classes: PrimerScheme: tree_root: true - description: "A description of an amplicon primer scheme" - slots: - - schema_version - - name - - organism - - organism_aliases - - display_name - - primer_scheme_status - - aliases - - derived_from - - developers - - vendors - - amplicon_size - - notes - - citations - - primer_checksum - - reference_checksum - - repository_url + description: "Definition of a tiling amplicon PCR primer scheme" Vendor: class_uri: GENEPIO:0100674 - description: "Vendor of the primers described in the amplicon scheme or a kit containing these primers" + description: "Vendor of oligoneucleotide primers matching this primer scheme definition" mixins: - Organisation attributes: kit_name: slot_uri: GENEPIO:0100693 - description: "Vendor specific kit name for primer kit" + description: "Vendor-specific name for oligonucleotide primers matching this primer scheme definition" + + Developer: + abstract: true + attributes: + type: + designates_type: true + required: true + name: + description: "x" + url: + description: "x" - Entity: - Person: description: "A natural person" - is_a: Entity - slots: - - person_name - - orcid - + is_a: Developer + attributes: + orcid: + description: "ORCID ('Open Researcher and Contributor IDentifier')" + Organisation: description: "An organisation" - is_a: Entity - slots: - - organisation_name - - home_page + is_a: Developer slots: schema_version: required: true - description: The version of the schema used to create this scheme definition + description: "The version of the schema used to create this scheme definition" name: slot_uri: GENEPIO:0001456 required: true identifier: true - description: The canonical name of the primer scheme (lowercase) + description: "The canonical name of the primer scheme (lowercase)" pattern: "^[\\da-z0-9_.-]+$" display_name: - description: The human-friendly display name of the primer scheme + description: "The human-friendly display name of the primer scheme" organism: slot_uri: GENEPIO:0100682 required: true - description: The organism against which this primer scheme is targeted. Lowercase, e.g. sars-cov-2 + description: "the name of the target organism of this primer scheme definition" organism_aliases: - description: "Aliases for the organism that this primer scheme targets" + description: "Aliases for the name of the target organism of this primer scheme definition" multivalued: true aliases: slot_uri: GENEPIO:0100670 @@ -88,29 +77,26 @@ slots: inlined_as_list: true developers: slot_uri: GENEPIO:0100673 - description: Persons or organisations responsible for developing the primer scheme + description: "Persons and/or organisations responsible for developing this primer scheme" required: true multivalued: true inlined: true inlined_as_list: true - range: Entity - any_of: - - range: Person - - range: Organisation + range: Developer vendors: - description: "Vendors where one can purchase the primers described in the amplicon scheme or a kit containing these primers" + description: "Vendors supplying oligonucleotide primers matching this primer scheme definition" multivalued: true inlined_as_list: true range: Vendor amplicon_size: slot_uri: GENEPIO:0001449 - description: "The length (in base pairs) of an amplicon in the primer scheme" + description: "The length of amplicons described by this primer scheme in base pairs (bp)" range: integer minimum_value: 1 repository_url: slot_uri: GENEPIO:0100683 required: true - description: "Link to repository where primer scheme BED and reference files can be found" + description: "URL of canonical repository where primer scheme BED and reference files can be found" notes: description: "Notes about the amplicon primer scheme" slot_uri: GENEPIO:0100672 @@ -135,17 +121,10 @@ slots: derived_from: slot_uri: GENEPIO:0100671 description: "Canonical name of the primer scheme from which this scheme was derived" - person_name: - slot_uri: schema:name - required: true - description: "The name of a natural person" - orcid: - description: "ORCID ('Open Researcher and Contributor IDentifier') of a person" organisation_name: required: true - description: "The name of an organisation" home_page: - description: "A link to the home page of an organisation" + description: "Developer website URL (e.g. home page)" enums: PrimerSchemeStatus: