diff --git a/web/templates/ambr/schema.json b/web/templates/ambr/schema.json index ed9daefc..1210143c 100644 --- a/web/templates/ambr/schema.json +++ b/web/templates/ambr/schema.json @@ -2,7 +2,7 @@ "name": "AMBR", "description": "", "id": "https://example.com/AMBR", - "version": "2.1.1", + "version": "2.2.2", "prefixes": { "linkml": { "prefix_prefix": "linkml", @@ -19,6 +19,10 @@ "shex": { "prefix_prefix": "shex", "prefix_reference": "http://www.w3.org/ns/shex#" + }, + "schema": { + "prefix_prefix": "schema", + "prefix_reference": "http://schema.org/" } }, "default_prefix": "https://example.com/AMBR/", @@ -40,18 +44,27 @@ "string": { "name": "string", "description": "A character string", + "exact_mappings": [ + "schema:Text" + ], "base": "str", "uri": "xsd:string" }, "integer": { "name": "integer", "description": "An integer", + "exact_mappings": [ + "schema:Integer" + ], "base": "int", "uri": "xsd:integer" }, "boolean": { "name": "boolean", "description": "A binary (true or false) value", + "exact_mappings": [ + "schema:Boolean" + ], "base": "Bool", "uri": "xsd:boolean", "repr": "bool" @@ -59,18 +72,27 @@ "float": { "name": "float", "description": "A real number that conforms to the xsd:float specification", + "exact_mappings": [ + "schema:Float" + ], "base": "float", "uri": "xsd:float" }, "double": { "name": "double", "description": "A real number that conforms to the xsd:double specification", + "close_mappings": [ + "schema:Float" + ], "base": "float", "uri": "xsd:double" }, "decimal": { "name": "decimal", "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", + "broad_mappings": [ + "schema:Number" + ], "base": "Decimal", "uri": "xsd:decimal" }, @@ -80,6 +102,9 @@ "notes": [ "URI is dateTime because OWL reasoners do not work with straight date or time" ], + "exact_mappings": [ + "schema:Time" + ], "base": "XSDTime", "uri": "xsd:dateTime", "repr": "str" @@ -90,6 +115,9 @@ "notes": [ "URI is dateTime because OWL reasoners don't work with straight date or time" ], + "exact_mappings": [ + "schema:Date" + ], "base": "XSDDate", "uri": "xsd:date", "repr": "str" @@ -97,6 +125,9 @@ "datetime": { "name": "datetime", "description": "The combination of a date and time", + "exact_mappings": [ + "schema:DateTime" + ], "base": "XSDDateTime", "uri": "xsd:dateTime", "repr": "str" @@ -115,9 +146,28 @@ "uri": "xsd:anyURI", "repr": "str" }, + "curie": { + "name": "curie", + "conforms_to": "https://www.w3.org/TR/curie/", + "description": "a compact URI", + "comments": [ + "in RDF serializations this MUST be expanded to a URI", + "in non-RDF serializations MAY be serialized as the compact representation" + ], + "base": "Curie", + "uri": "xsd:string", + "repr": "str" + }, "uri": { "name": "uri", + "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", "description": "a complete URI", + "comments": [ + "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" + ], + "close_mappings": [ + "schema:URL" + ], "base": "URI", "uri": "xsd:anyURI", "repr": "str" @@ -1715,6 +1765,12 @@ "Marine broth agar (MBA)": { "text": "Marine broth agar (MBA)" }, + "Medium 10 agar (M10)": { + "text": "Medium 10 agar (M10)" + }, + "Medium DAMS5.8 simple": { + "text": "Medium DAMS5.8 simple" + }, "No salt lysogeny broth agar (NSLB)": { "text": "No salt lysogeny broth agar (NSLB)" }, @@ -2184,7 +2240,7 @@ }, "alternative isolate ID": { "name": "alternative isolate ID", - "description": "An alternative isolate_ID assigned to the isolate by another organization.", + "description": "An alternative isolate ID assigned to the isolate by another organization.", "title": "alternative isolate ID", "comments": [ "Provide the identifier that represents the site code, source and/or patient identifier, media type, strain identifier, colony number, growth condition and dilution factor as a single code. This value corresponds maps to the \"Label ID\" in the Alberta Microbiota Repository (AMBR) Master file." @@ -2240,10 +2296,10 @@ } ] }, - "sample_collection_project_name": { - "name": "sample_collection_project_name", + "sample collection project name": { + "name": "sample collection project name", "description": "The name of the project/initiative/program for which the sample was collected.", - "title": "sample_collection_project_name", + "title": "sample collection project name", "comments": [ "Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value." ], @@ -2779,6 +2835,7 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100583", + "required": true, "any_of": [ { "range": "taxonomic identification method menu" @@ -2802,6 +2859,7 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100584", + "required": true, "any_of": [ { "range": "taxonomic identification method details menu" @@ -2929,7 +2987,7 @@ "description": "The commonly used name of the host.", "title": "host (common name)", "comments": [ - "Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Hosts can be animals (including humans) and plants. Common name e.g. Human, Canola plant. If the sample was environmental, select \"Not Applicable\". Information for populating this field may be available in the \"Source of Isolation\" field in the Alberta Microbiota Repository (AMBR) Master file." + "Common name is required if there was a host. Both common anime and scientific name can be provided, if known. Use terms from the pick lists in the template. Hosts can be animals (including humans) and plants. Examples of common names are “Human” and “Canola plant”. Examples of scientific names are “Homo sapiens” and “Equus caballus”. If the sample was environmental, select \"Not Applicable\". Information for populating this field may be available in the \"Source of Isolation\" field in the Alberta Microbiota Repository (AMBR) Master file." ], "examples": [ { @@ -2938,6 +2996,7 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001386", + "required": true, "any_of": [ { "range": "host (common name) menu" @@ -3078,7 +3137,6 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0001445", - "multivalued": true, "any_of": [ { "range": "purpose of sequencing menu" @@ -3212,6 +3270,7 @@ ], "from_schema": "https://example.com/AMBR", "slot_uri": "GENEPIO:0100623", + "multivalued": true, "required": true, "any_of": [ { @@ -3551,8 +3610,8 @@ "rank": 4, "slot_group": "Sample collection and processing" }, - "sample_collection_project_name": { - "name": "sample_collection_project_name", + "sample collection project name": { + "name": "sample collection project name", "rank": 5, "slot_group": "Sample collection and processing" }, @@ -3863,7 +3922,7 @@ }, "alternative isolate ID": { "name": "alternative isolate ID", - "description": "An alternative isolate_ID assigned to the isolate by another organization.", + "description": "An alternative isolate ID assigned to the isolate by another organization.", "title": "alternative isolate ID", "from_schema": "https://example.com/AMBR", "rank": 2, @@ -3899,10 +3958,10 @@ "slot_group": "Sample collection and processing", "recommended": true }, - "sample_collection_project_name": { - "name": "sample_collection_project_name", + "sample collection project name": { + "name": "sample collection project name", "description": "The name of the project/initiative/program for which the sample was collected.", - "title": "sample_collection_project_name", + "title": "sample collection project name", "from_schema": "https://example.com/AMBR", "rank": 5, "slot_uri": "GENEPIO:0100429", @@ -4205,7 +4264,8 @@ "slot_uri": "GENEPIO:0100583", "alias": "taxonomic_identification_method", "owner": "AMBR", - "slot_group": "Strain and isolation information" + "slot_group": "Strain and isolation information", + "required": true }, "taxonomic identification method details": { "name": "taxonomic identification method details", @@ -4216,7 +4276,8 @@ "slot_uri": "GENEPIO:0100584", "alias": "taxonomic_identification_method_details", "owner": "AMBR", - "slot_group": "Strain and isolation information" + "slot_group": "Strain and isolation information", + "required": true }, "incubation temperature value": { "name": "incubation temperature value", @@ -4288,7 +4349,8 @@ "slot_uri": "GENEPIO:0001386", "alias": "host_(common_name)", "owner": "AMBR", - "slot_group": "Host Information" + "slot_group": "Host Information", + "required": true }, "host (scientific name)": { "name": "host (scientific name)", @@ -4366,7 +4428,6 @@ "from_schema": "https://example.com/AMBR", "rank": 43, "slot_uri": "GENEPIO:0001445", - "multivalued": true, "alias": "purpose_of_sequencing", "owner": "AMBR", "slot_group": "Sequencing" @@ -4438,6 +4499,7 @@ "from_schema": "https://example.com/AMBR", "rank": 49, "slot_uri": "GENEPIO:0100623", + "multivalued": true, "alias": "amplicon_pcr_primer_list", "owner": "AMBR", "slot_group": "Sequencing", diff --git a/web/templates/ambr/schema.yaml b/web/templates/ambr/schema.yaml index 0ec33308..50ca6b1a 100644 --- a/web/templates/ambr/schema.yaml +++ b/web/templates/ambr/schema.yaml @@ -1,7 +1,7 @@ id: https://example.com/AMBR name: AMBR description: '' -version: 2.1.1 +version: 2.2.2 imports: - linkml:types prefixes: @@ -25,7 +25,7 @@ classes: - alternative isolate ID - specimen collector sample ID - sample collected by - - sample_collection_project_name + - sample collection project name - sample collector contact email - sample collector contact address - sample collection date @@ -97,7 +97,7 @@ classes: sample collected by: rank: 4 slot_group: Sample collection and processing - sample_collection_project_name: + sample collection project name: rank: 5 slot_group: Sample collection and processing sample collector contact email: @@ -291,7 +291,7 @@ slots: alternative isolate ID: name: alternative isolate ID title: alternative isolate ID - description: An alternative isolate_ID assigned to the isolate by another organization. + description: An alternative isolate ID assigned to the isolate by another organization. comments: Provide the identifier that represents the site code, source and/or patient identifier, media type, strain identifier, colony number, growth condition and dilution factor as a single code. This value corresponds maps to the "Label @@ -330,9 +330,9 @@ slots: - range: WhitespaceMinimizedString - range: null value menu recommended: true - sample_collection_project_name: - name: sample_collection_project_name - title: sample_collection_project_name + sample collection project name: + name: sample collection project name + title: sample collection project name description: The name of the project/initiative/program for which the sample was collected. comments: Provide the name of the project and/or the project ID here. If the information @@ -700,6 +700,7 @@ slots: any_of: - range: taxonomic identification method menu - range: null value menu + required: true taxonomic identification method details: name: taxonomic identification method details title: taxonomic identification method details @@ -719,6 +720,7 @@ slots: any_of: - range: taxonomic identification method details menu - range: null value menu + required: true incubation temperature value: name: incubation temperature value title: incubation temperature value @@ -800,18 +802,21 @@ slots: name: host (common name) title: host (common name) description: The commonly used name of the host. - comments: Common name or scientific name are required if there was a host. Both - can be provided, if known. Use terms from the pick lists in the template. Hosts - can be animals (including humans) and plants. Common name e.g. Human, Canola - plant. If the sample was environmental, select "Not Applicable". Information - for populating this field may be available in the "Source of Isolation" field - in the Alberta Microbiota Repository (AMBR) Master file. + comments: "Common name is required if there was a host. Both common anime and\ + \ scientific name can be provided, if known. Use terms from the pick lists in\ + \ the template. Hosts can be animals (including humans) and plants. Examples\ + \ of common names are \u201CHuman\u201D and \u201CCanola plant\u201D. Examples\ + \ of scientific names are \u201CHomo sapiens\u201D and \u201CEquus caballus\u201D\ + . If the sample was environmental, select \"Not Applicable\". Information for\ + \ populating this field may be available in the \"Source of Isolation\" field\ + \ in the Alberta Microbiota Repository (AMBR) Master file." examples: - value: Human slot_uri: GENEPIO:0001386 any_of: - range: host (common name) menu - range: null value menu + required: true host (scientific name): name: host (scientific name) title: host (scientific name) @@ -913,7 +918,6 @@ slots: any_of: - range: purpose of sequencing menu - range: null value menu - multivalued: true purpose of sequencing details: name: purpose of sequencing details title: purpose of sequencing details @@ -990,6 +994,7 @@ slots: any_of: - range: amplicon pcr primer list menu - range: null value menu + multivalued: true required: true input file name: name: input file name @@ -2329,6 +2334,10 @@ enums: meaning: MICRO:0000558 Marine broth agar (MBA): text: Marine broth agar (MBA) + Medium 10 agar (M10): + text: Medium 10 agar (M10) + Medium DAMS5.8 simple: + text: Medium DAMS5.8 simple No salt lysogeny broth agar (NSLB): text: No salt lysogeny broth agar (NSLB) No salt lysogeny broth agar + 5-15% sucrose (NSLB + 5-15% sucrose): diff --git a/web/templates/ambr/schema_core.yaml b/web/templates/ambr/schema_core.yaml index 7975f291..b9402ee8 100644 --- a/web/templates/ambr/schema_core.yaml +++ b/web/templates/ambr/schema_core.yaml @@ -1,7 +1,7 @@ id: https://example.com/AMBR name: AMBR description: "" -version: 2.1.1 +version: 2.2.2 imports: - 'linkml:types' prefixes: diff --git a/web/templates/ambr/schema_enums.tsv b/web/templates/ambr/schema_enums.tsv index b8ac2d50..725133ba 100644 --- a/web/templates/ambr/schema_enums.tsv +++ b/web/templates/ambr/schema_enums.tsv @@ -403,6 +403,8 @@ isolation medium menu AMBR 1/10 869 AMBR M17 minimal medium (M17) MICRO:0000558 AMBR MacConkey agar (MCA) AMBR Marine broth agar (MBA) + AMBR Medium 10 agar (M10) + AMBR Medium DAMS5.8 simple AMBR No salt lysogeny broth agar (NSLB) AMBR No salt lysogeny broth agar + 5-15% sucrose (NSLB + 5-15% sucrose) MICRO:0000553 AMBR Nutrient agar diff --git a/web/templates/ambr/schema_slots.tsv b/web/templates/ambr/schema_slots.tsv index 4b05ef15..5bcf288e 100644 --- a/web/templates/ambr/schema_slots.tsv +++ b/web/templates/ambr/schema_slots.tsv @@ -1,11 +1,11 @@ class_name slot_group slot_uri title name range range_2 identifier multivalued required recommended minimum_value maximum_value pattern structured_pattern description comments examples AMBR GENEPIO:0001122 Database Identifiers Database Identifiers GENEPIO:0100456 isolate ID WhitespaceMinimizedString TRUE The user-defined identifier for the isolate, as provided by the laboratory that originally isolated the isolate. Provide the identifier created by the lab for the organism after isolation. This value maps to the "Strain ID#" in the Alberta Microbiota Repository (AMBR) Master file. SA01 - Database Identifiers GENEPIO:0100457 alternative isolate ID WhitespaceMinimizedString TRUE An alternative isolate_ID assigned to the isolate by another organization. Provide the identifier that represents the site code, source and/or patient identifier, media type, strain identifier, colony number, growth condition and dilution factor as a single code. This value corresponds maps to the "Label ID" in the Alberta Microbiota Repository (AMBR) Master file. 3411301 + Database Identifiers GENEPIO:0100457 alternative isolate ID WhitespaceMinimizedString TRUE An alternative isolate ID assigned to the isolate by another organization. Provide the identifier that represents the site code, source and/or patient identifier, media type, strain identifier, colony number, growth condition and dilution factor as a single code. This value corresponds maps to the "Label ID" in the Alberta Microbiota Repository (AMBR) Master file. 3411301 Database Identifiers GENEPIO:0001123 specimen collector sample ID WhitespaceMinimizedString TRUE The user-defined name for the sample. Provide the sample ID provided by the original sample collector. This value is different from the "isolate_ID" as it represents the original material sampled rather than the organism that was isolated from the sampled material. This identifier may or may not be available. Lake_Louise_Water23 GENEPIO:0001150 Sample collection and processing Sample collection and processing GENEPIO:0001153 sample collected by WhitespaceMinimizedString null value menu TRUE The name of the agency that collected the original sample. The name of the institution of the original sample collector should be written out in full, (no abbreviations, with minor exceptions) and be consistent across multiple submissions e.g. University of Calgary, Alberta Health Services. The sample collector specified is at the discretion of the data provider (i.e. may be hospital, provincial public health lab, or other). University of Calgary - Sample collection and processing GENEPIO:0100429 sample_collection_project_name WhitespaceMinimizedString TRUE The name of the project/initiative/program for which the sample was collected. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. Children's Hospital biofilm study (A3-701-01) + Sample collection and processing GENEPIO:0100429 sample collection project name WhitespaceMinimizedString TRUE The name of the project/initiative/program for which the sample was collected. Provide the name of the project and/or the project ID here. If the information is unknown or cannot be provided, leave blank or provide a null value. Children's Hospital biofilm study (A3-701-01) Sample collection and processing GENEPIO:0001156 sample collector contact email WhitespaceMinimizedString ^\S+@\S+\.\S+$ The email address of the contact responsible for follow-up regarding the sample. The email address can represent a specific individual or lab e.g. johnnyblogs@lab.ca, or RespLab@lab.ca RespLab@lab.ca Sample collection and processing GENEPIO:0001158 sample collector contact address WhitespaceMinimizedString The mailing address of the agency submitting the sample. The mailing address should be in the format: Street number and name, City, Province/Territory, Postal Code, Country 655 Lab St, Vancouver, British Columbia, V5N 2A2, Canada Sample collection and processing GENEPIO:0001174 sample collection date date null value menu TRUE 2019-10-01 {today} The date on which the sample was collected. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-03-16 @@ -30,15 +30,15 @@ AMBR GENEPIO:0001122 Database Identifiers Sample collection and processing GENEPIO:0100311 specimen processing details WhitespaceMinimizedString Detailed information regarding the processing applied to a sample during or after receiving the sample. Provide a free text description of any processing details applied to a sample. Information about replicates may be available in the "Top-hit taxon (taxa)" or "Trimmed Ribosomal Sequence" fields if there are multiple values for the same "Strain ID#" in the Alberta Microbiota Repository (AMBR) Master file. Multiple amplicons generated for isolate SA32 using different primer sets GENEPIO:0100453 Strain and isolation information Strain and isolation information GENEPIO:0100455 strain WhitespaceMinimizedString null value menu TRUE The strain identifier. Provide the strain of the isolate. This value maps to the "Strain" in the Alberta Microbiota Repository (AMBR) Master file. CL10 - Strain and isolation information GENEPIO:0100583 taxonomic identification method taxonomic identification method menu null value menu The type of planned process by which an organismal entity is associated with a taxon or taxa. Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. For the AMBR Project, the "16S ribosomal gene sequencing assay" value will be the most appropriate. If the information is unknown or cannot be provided, leave blank or provide a null value. 16S ribosomal gene sequencing assay - Strain and isolation information GENEPIO:0100584 taxonomic identification method details taxonomic identification method details menu null value menu The details of the process used to determine the taxonomic identification of an organism. Provide the criteria used for 16S sequencing taxonomic determination by selection a value from the pick list. These criteria are specific to the AMBR project and so do not correspond with standardized criteria in any ontology. The pick list is strictly for providing consistency in records rather than implementing community data standards. If another method was used for the taxonomic determination, leave blank. This value maps to the information stored in the "ID Category*" field in the Alberta Microbiota Repository (AMBR) Master file. Species-level ID: >99.3% identity and unambiguous match to one type (T) sequence in a curated database + Strain and isolation information GENEPIO:0100583 taxonomic identification method taxonomic identification method menu null value menu TRUE The type of planned process by which an organismal entity is associated with a taxon or taxa. Provide the type of method used to determine the taxonomic identity of the organism by selecting a value from the pick list. For the AMBR Project, the "16S ribosomal gene sequencing assay" value will be the most appropriate. If the information is unknown or cannot be provided, leave blank or provide a null value. 16S ribosomal gene sequencing assay + Strain and isolation information GENEPIO:0100584 taxonomic identification method details taxonomic identification method details menu null value menu TRUE The details of the process used to determine the taxonomic identification of an organism. Provide the criteria used for 16S sequencing taxonomic determination by selection a value from the pick list. These criteria are specific to the AMBR project and so do not correspond with standardized criteria in any ontology. The pick list is strictly for providing consistency in records rather than implementing community data standards. If another method was used for the taxonomic determination, leave blank. This value maps to the information stored in the "ID Category*" field in the Alberta Microbiota Repository (AMBR) Master file. Species-level ID: >99.3% identity and unambiguous match to one type (T) sequence in a curated database Strain and isolation information GENEPIO:0100617 incubation temperature value WhitespaceMinimizedString null value menu TRUE An environmental datum specifying the temperature at which an organism or organisms were incubated for the purposes of growth on or in a particular medium. Provide the temperature at which the isolate was isolated. This value maps to the information stored in the "Incubation temperature" field in the Alberta Microbiota Repository (AMBR) Master file. 37 Strain and isolation information GENEPIO:0100618 incubation temperature unit incubation temperature unit menu null value menu TRUE An environmental datum specifying the temperature unit at which an organism or organisms were incubated for the purposes of growth on or in a particular medium. Select the temperature unit from the pick list. This value maps to the information stored in the "Incubation temperature" field in the Alberta Microbiota Repository (AMBR) Master file. Degree Celsius Strain and isolation information GENEPIO:0002107 isolation medium isolation medium menu null value menu TRUE An isolation medium is a culture medium which has the disposition to encourage growth of particular bacteria to the exclusion of others in the same growth environment. Select the isolation medium from the pick list. This value maps to the information stored in the "Incubation media" field in the Alberta Microbiota Repository (AMBR) Master file. Brain heart infusion (BHI) Strain and isolation information GENEPIO:0100619 isolate storage location WhitespaceMinimizedString TRUE An isolate datum specifying the location of where an isolate is stored e.g. in a particular freezer, on a particular shelf Enter the freezer storage location of the isolate as the "freezer number-shelf number-box number-unit number" e.g. FR1-R3-B1-S01. This value maps to the information stored in the "Spot code" in the Alberta Microbiota Repository (AMBR) Master file. FR1-R3-B1-S01 Strain and isolation information GENEPIO:0100620 cellular respiration type cellular respiration type menu null value menu TRUE An isolate datum specifying the type of cellular respiration process used by the organism. Select the respiration type from the pick list. This value maps to the information stored in the "Aerobic/Anaerobic" field in the Alberta Microbiota Repository (AMBR) Master file. Aerobic respiration GENEPIO:0001268 Host Information - Host Information GENEPIO:0001386 host (common name) host (common name) menu null value menu The commonly used name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Hosts can be animals (including humans) and plants. Common name e.g. Human, Canola plant. If the sample was environmental, select "Not Applicable". Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Human + Host Information GENEPIO:0001386 host (common name) host (common name) menu null value menu TRUE The commonly used name of the host. Common name is required if there was a host. Both common anime and scientific name can be provided, if known. Use terms from the pick lists in the template. Hosts can be animals (including humans) and plants. Examples of common names are “Human” and “Canola plant”. Examples of scientific names are “Homo sapiens” and “Equus caballus”. If the sample was environmental, select "Not Applicable". Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Human Host Information GENEPIO:0001387 host (scientific name) host (scientific name) menu null value menu The taxonomic, or scientific name of the host. Common name or scientific name are required if there was a host. Both can be provided, if known. Use terms from the pick lists in the template. Hosts can be animals (including humans) and plants. Common name e.g. Human, Canola plant. If the sample was environmental, select "Not Applicable". Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Homo sapiens Host Information GENEPIO:0001391 host disease host disease menu null value menu The name of the disease experienced by the host. If the sample was obtained from a host with a known disease, provide the name of the disease by seleting a value from the picklist. Information for populating this field may be available in the "Source of Isolation" field in the Alberta Microbiota Repository (AMBR) Master file. Cystic fibrosis GENEPIO:0001441 Sequencing @@ -46,13 +46,13 @@ AMBR GENEPIO:0001122 Database Identifiers Sequencing GENEPIO:0100470 sequenced by laboratory name WhitespaceMinimizedString The specific laboratory affiliation of the responsible for sequencing the isolate's genome. Provide the name of the specific laboratory that that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. For the AMBR Project, the value is most likely the "Harrison Lab". Harrison Lab Sequencing GENEPIO:0100471 sequenced by contact name WhitespaceMinimizedString The name or title of the contact responsible for follow-up regarding the sequence. Provide the name of an individual or their job title. As personnel turnover may render the contact's name obsolete, it is more prefereable to provide a job title for ensuring accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. Joe Harrison Sequencing GENEPIO:0100422 sequenced by contact email WhitespaceMinimizedString The email address of the contact responsible for follow-up regarding the sequence. Provide the email associated with the listed contact. As personnel turnover may render an individual's email obsolete, it is more prefereable to provide an address for a position or lab, to ensure accuracy of information and institutional memory. If the information is unknown or cannot be provided, leave blank or provide a null value. jjharris@ucalgary.ca - Sequencing GENEPIO:0001445 purpose of sequencing purpose of sequencing menu null value menu TRUE The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Research + Sequencing GENEPIO:0001445 purpose of sequencing purpose of sequencing menu null value menu The reason that the sample was sequenced. The reason why a sample was originally collected may differ from the reason why it was selected for sequencing. The reason a sample was sequenced may provide information about potential biases in sequencing strategy. Provide the purpose of sequencing from the picklist in the template. The reason for sample collection should be indicated in the "purpose of sampling" field. Research Sequencing GENEPIO:0001446 purpose of sequencing details WhitespaceMinimizedString null value menu The description of why the sample was sequenced providing specific details. Provide an expanded description of why the sample was sequenced using free text. This information can provide details about why the sample source might contain antibiotic potentiators. Screening for antibiotic potentiators in Cystic fibrosis disease contexts. Sequencing GENEPIO:0001447 sequencing date date null value menu {sample collection date} The date the sample was sequenced. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". 2020-06-22 Sequencing GENEPIO:0001448 library ID WhitespaceMinimizedString The user-specified identifier for the library prepared for sequencing. Provide the name of the run. This value maps to information in the "Sequencing Batch #" field Alberta Microbiota Repository (AMBR) Master file. 1876515_SA01_Plate 02 library ID Sequencing GENEPIO:0001452 sequencing instrument sequencing instrument menu null value menu TRUE TRUE The model of the sequencing instrument used. Select a sequencing instrument from the picklist provided in the template. Oxford Nanopore MinION Sequencing GENEPIO:0001453 sequencing protocol name WhitespaceMinimizedString TRUE The name and version number of the sequencing protocol used. Provide the name and version of the sequencing protocol e.g. 1D_DNA_MinION https://www.protocols.io/view/covid-19-artic-v3-illumina-library-construction-an-bibtkann - Sequencing GENEPIO:0100623 amplicon pcr primer list amplicon pcr primer list menu null value menu TRUE An information content entity specifying a list of primers used for amplicon sequencing. Select the primers used to generate the ribosomal 16S or 23S amplicon for sequencing from the pick list. This value maps to the information in the "Primers Used for sequencing" field Alberta Microbiota Repository (AMBR) Master file. 27F;1492R + Sequencing GENEPIO:0100623 amplicon pcr primer list amplicon pcr primer list menu null value menu TRUE TRUE An information content entity specifying a list of primers used for amplicon sequencing. Select the primers used to generate the ribosomal 16S or 23S amplicon for sequencing from the pick list. This value maps to the information in the "Primers Used for sequencing" field Alberta Microbiota Repository (AMBR) Master file. 27F;1492R GENEPIO:0001457 Bioinformatics and QC metrics Bioinformatics and QC metrics OBI:0002874 input file name WhitespaceMinimizedString The name of the file containing the sequence data to be analysed. Enter the file name of the target gene sequence to be analyzed. ambr_staph_ABC_123.fasta Bioinformatics and QC metrics OBI:0002885 reference accession WhitespaceMinimizedString null value menu TRUE An identifier that specifies an individual sequence record in a public sequence repository. Enter the EZBioCloud gene accession that most closely matches the sequence being analyzed. This value maps to the information in the "Accession No(s)." field in the Alberta Microbiota Repository (AMBR) Master file. FR821777 diff --git a/web/templates/canada_covid19/schema.json b/web/templates/canada_covid19/schema.json index 4b675ffa..0b3c947f 100644 --- a/web/templates/canada_covid19/schema.json +++ b/web/templates/canada_covid19/schema.json @@ -19,6 +19,10 @@ "shex": { "prefix_prefix": "shex", "prefix_reference": "http://www.w3.org/ns/shex#" + }, + "schema": { + "prefix_prefix": "schema", + "prefix_reference": "http://schema.org/" } }, "default_prefix": "https://example.com/CanCOGeN_Covid-19/", @@ -40,18 +44,27 @@ "string": { "name": "string", "description": "A character string", + "exact_mappings": [ + "schema:Text" + ], "base": "str", "uri": "xsd:string" }, "integer": { "name": "integer", "description": "An integer", + "exact_mappings": [ + "schema:Integer" + ], "base": "int", "uri": "xsd:integer" }, "boolean": { "name": "boolean", "description": "A binary (true or false) value", + "exact_mappings": [ + "schema:Boolean" + ], "base": "Bool", "uri": "xsd:boolean", "repr": "bool" @@ -59,18 +72,27 @@ "float": { "name": "float", "description": "A real number that conforms to the xsd:float specification", + "exact_mappings": [ + "schema:Float" + ], "base": "float", "uri": "xsd:float" }, "double": { "name": "double", "description": "A real number that conforms to the xsd:double specification", + "close_mappings": [ + "schema:Float" + ], "base": "float", "uri": "xsd:double" }, "decimal": { "name": "decimal", "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", + "broad_mappings": [ + "schema:Number" + ], "base": "Decimal", "uri": "xsd:decimal" }, @@ -80,6 +102,9 @@ "notes": [ "URI is dateTime because OWL reasoners do not work with straight date or time" ], + "exact_mappings": [ + "schema:Time" + ], "base": "XSDTime", "uri": "xsd:dateTime", "repr": "str" @@ -90,6 +115,9 @@ "notes": [ "URI is dateTime because OWL reasoners don't work with straight date or time" ], + "exact_mappings": [ + "schema:Date" + ], "base": "XSDDate", "uri": "xsd:date", "repr": "str" @@ -97,6 +125,9 @@ "datetime": { "name": "datetime", "description": "The combination of a date and time", + "exact_mappings": [ + "schema:DateTime" + ], "base": "XSDDateTime", "uri": "xsd:dateTime", "repr": "str" @@ -115,9 +146,28 @@ "uri": "xsd:anyURI", "repr": "str" }, + "curie": { + "name": "curie", + "conforms_to": "https://www.w3.org/TR/curie/", + "description": "a compact URI", + "comments": [ + "in RDF serializations this MUST be expanded to a URI", + "in non-RDF serializations MAY be serialized as the compact representation" + ], + "base": "Curie", + "uri": "xsd:string", + "repr": "str" + }, "uri": { "name": "uri", + "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", "description": "a complete URI", + "comments": [ + "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" + ], + "close_mappings": [ + "schema:URL" + ], "base": "URI", "uri": "xsd:anyURI", "repr": "str" diff --git a/web/templates/monkeypox/schema.json b/web/templates/monkeypox/schema.json index 03043c10..876a434f 100644 --- a/web/templates/monkeypox/schema.json +++ b/web/templates/monkeypox/schema.json @@ -2,7 +2,7 @@ "name": "Monkeypox", "description": "", "id": "https://example.com/monkeypox", - "version": "3.3.2", + "version": "3.3.3", "prefixes": { "linkml": { "prefix_prefix": "linkml", @@ -19,6 +19,10 @@ "shex": { "prefix_prefix": "shex", "prefix_reference": "http://www.w3.org/ns/shex#" + }, + "schema": { + "prefix_prefix": "schema", + "prefix_reference": "http://schema.org/" } }, "default_prefix": "https://example.com/monkeypox/", @@ -40,18 +44,27 @@ "string": { "name": "string", "description": "A character string", + "exact_mappings": [ + "schema:Text" + ], "base": "str", "uri": "xsd:string" }, "integer": { "name": "integer", "description": "An integer", + "exact_mappings": [ + "schema:Integer" + ], "base": "int", "uri": "xsd:integer" }, "boolean": { "name": "boolean", "description": "A binary (true or false) value", + "exact_mappings": [ + "schema:Boolean" + ], "base": "Bool", "uri": "xsd:boolean", "repr": "bool" @@ -59,18 +72,27 @@ "float": { "name": "float", "description": "A real number that conforms to the xsd:float specification", + "exact_mappings": [ + "schema:Float" + ], "base": "float", "uri": "xsd:float" }, "double": { "name": "double", "description": "A real number that conforms to the xsd:double specification", + "close_mappings": [ + "schema:Float" + ], "base": "float", "uri": "xsd:double" }, "decimal": { "name": "decimal", "description": "A real number with arbitrary precision that conforms to the xsd:decimal specification", + "broad_mappings": [ + "schema:Number" + ], "base": "Decimal", "uri": "xsd:decimal" }, @@ -80,6 +102,9 @@ "notes": [ "URI is dateTime because OWL reasoners do not work with straight date or time" ], + "exact_mappings": [ + "schema:Time" + ], "base": "XSDTime", "uri": "xsd:dateTime", "repr": "str" @@ -90,6 +115,9 @@ "notes": [ "URI is dateTime because OWL reasoners don't work with straight date or time" ], + "exact_mappings": [ + "schema:Date" + ], "base": "XSDDate", "uri": "xsd:date", "repr": "str" @@ -97,6 +125,9 @@ "datetime": { "name": "datetime", "description": "The combination of a date and time", + "exact_mappings": [ + "schema:DateTime" + ], "base": "XSDDateTime", "uri": "xsd:dateTime", "repr": "str" @@ -115,9 +146,28 @@ "uri": "xsd:anyURI", "repr": "str" }, + "curie": { + "name": "curie", + "conforms_to": "https://www.w3.org/TR/curie/", + "description": "a compact URI", + "comments": [ + "in RDF serializations this MUST be expanded to a URI", + "in non-RDF serializations MAY be serialized as the compact representation" + ], + "base": "Curie", + "uri": "xsd:string", + "repr": "str" + }, "uri": { "name": "uri", + "conforms_to": "https://www.ietf.org/rfc/rfc3987.txt", "description": "a complete URI", + "comments": [ + "in RDF serializations a slot with range of uri is treated as a literal or type xsd:anyURI unless it is an identifier or a reference to an identifier, in which case it is translated directly to a node" + ], + "close_mappings": [ + "schema:URL" + ], "base": "URI", "uri": "xsd:anyURI", "repr": "str" @@ -9270,7 +9320,7 @@ "annotations": { "version": { "tag": "version", - "value": "3.3.2" + "value": "3.3.3" } }, "description": "Canadian specification for Monkeypox clinical virus biosample data gathering", diff --git a/web/templates/monkeypox/schema.yaml b/web/templates/monkeypox/schema.yaml index 760a2255..c826a933 100644 --- a/web/templates/monkeypox/schema.yaml +++ b/web/templates/monkeypox/schema.yaml @@ -1,6 +1,6 @@ id: https://example.com/monkeypox name: Monkeypox -version: 3.3.2 +version: 3.3.3 description: '' imports: - linkml:types @@ -19,7 +19,7 @@ classes: is_a: dh_interface see_also: templates/monkeypox/SOP_Monkeypox.pdf annotations: - version: 3.3.2 + version: 3.3.3 slots: - specimen collector sample ID - Related specimen primary ID