diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml index fefd91d1e..f2e1e031d 100644 --- a/kubernetes/loculus/values.yaml +++ b/kubernetes/loculus/values.yaml @@ -478,7 +478,7 @@ defaultOrganismConfig: &defaultOrganismConfig definition: The date on which the sample was received by the laboratory. guidance: Alternative if "sample_collection_date" is not available. Record the date the sample was received by the laboratory. Required granularity includes year, month and day. Before sharing this data, ensure this date is not considered identifiable information. If this date is considered identifiable, it is acceptable to add "jitter" to the received date by adding or subtracting calendar days. Do not change the received date in your original records. Alternatively, collection_date may be used as a substitute in the data you share. The date should be provided in ISO 8601 standard format "YYYY-MM-DD". example: '2020-03-20' - displayName: Sample Received Date + displayName: Sample received date type: date preprocessing: function: process_date @@ -556,42 +556,42 @@ defaultOrganismConfig: &defaultOrganismConfig definition: A material consumed and digested for nutritional value or enjoyment. guidance: This field includes animal feed. If applicable, select the standardized term and ontology ID for the anatomical material from the picklist provided. Multiple values can be provided, separated by a semi-colon. example: Feather meal [FOODON:00003927]; Bone meal [ENVO:02000054]; Chicken breast [FOODON:00002703] - displayName: Food Product + displayName: Food product header: Sampling - name: food_product_properties ontology_id: GENEPIO:0100445 definition: Any characteristic of the food product pertaining to its state, processing, a label claim, or implications for consumers. guidance: Provide any characteristics of the food product including whether it has been cooked, processed, preserved, any known information about its state (e.g. raw, ready-to-eat), any known information about its containment (e.g. canned), and any information about a label claim (e.g. organic, fat-free). example: Food (chopped) [FOODON:00002777]; Ready-to-eat (RTE) [FOODON:03316636] - displayName: Food Product Properties + displayName: Food product properties header: Sampling - name: specimen_processing ontology_id: GENEPIO:0100435 definition: The processing applied to samples post-collection, prior to further testing, characterization, or isolation procedures. guidance: Provide the sample processing information by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. example: Samples pooled [OBI:0600016] - displayName: Specimen Processing + displayName: Specimen processing header: Specimen processing - name: specimen_processing_details ontology_id: GENEPIO:0100311 definition: Detailed information regarding the processing applied to a sample during or after receiving the sample. guidance: Provide a free text description of any processing details applied to a sample. example: 25 swabs were pooled and further prepared as a single sample during library prep. - displayName: Specimen Processing Details + displayName: Specimen processing details header: Specimen processing - name: experimental_specimen_role_type ontology_id: GENEPIO:0100921 definition: The type of role that the sample represents in the experiment. guidance: Samples can play different types of roles in experiments. A sample under study in one experiment may act as a control or be a replicate of another sample in another experiment. This field is used to distinguish samples under study from controls, replicates, etc. If the sample acted as an experimental control or a replicate, select a role type from the picklist. If the sample was not a control, leave blank or select "Not Applicable". example: Positive experimental control [GENEPIO:0101018] - displayName: Experimental Specimen Role Type + displayName: Experimental specimen role type header: Specimen processing - name: host_age ontology_id: GENEPIO:0001392 definition: Age of host at the time of sampling. guidance: If known, provide age. Age-binning is also acceptable. example: "79" - displayName: Host Age + displayName: Host age type: int header: Host rangeSearch: true @@ -600,14 +600,14 @@ defaultOrganismConfig: &defaultOrganismConfig definition: The age category of the host at the time of sampling. guidance: Age bins in 10 year intervals have been provided. If a host's age cannot be specified due to provacy concerns, an age bin can be used as an alternative. example: 50 - 59 [GENEPIO:0100054] - displayName: Host Age Bin + displayName: Host age bin header: Host - name: host_gender ontology_id: GENEPIO:0001395 definition: The gender of the host at the time of sample collection. guidance: If known, select a value from the pick list. example: Male [NCIT:C46109] - displayName: Host Gender + displayName: Host gender header: Host ingest: ncbi_host_sex - name: host_origin_country @@ -615,7 +615,7 @@ defaultOrganismConfig: &defaultOrganismConfig definition: The country of origin of the host. guidance: If a sample is from a human or animal host that originated from outside of Canada, provide the the name of the country where the host originated by selecting a value from the template pick list. If the information is unknown or cannot be provided, leave blank or provide a null value. example: South Africa [GAZ:00001094] - displayName: Host Origin Country + displayName: Host origin country header: Host - name: host_disease ontology_id: GENEPIO:0001391 @@ -636,21 +636,21 @@ defaultOrganismConfig: &defaultOrganismConfig definition: Health status of the host at the time of sample collection. guidance: If known, select a value from the pick list. example: Asymptomatic [NCIT:C3833] - displayName: Host Health State + displayName: Host health state header: Host - name: host_health_outcome ontology_id: GENEPIO:0001390 definition: Disease outcome in the host. guidance: If known, select a value from the pick list. example: Recovered [NCIT:C49498] - displayName: Host Health Outcome + displayName: Host health outcome header: Host - name: travel_history ontology_id: GENEPIO:0001416 definition: Travel history in last six months. guidance: Specify the countries (and more granular locations if known) travelled in the last six months; can include multiple travels. Separate multiple travel events with a semicolon. Provide as free text. example: Canada, Vancouver; USA, Seattle; Italy, Milan - displayName: Travel History + displayName: Travel history header: Host - name: exposure_event ontology_id: GENEPIO:0001417 @@ -697,21 +697,21 @@ defaultOrganismConfig: &defaultOrganismConfig definition: The vaccination status of the host (fully vaccinated, partially vaccinated, or not vaccinated). guidance: Select the vaccination status of the host from the pick list. example: Fully Vaccinated [GENEPIO:0100100] - displayName: Host Vaccination Status + displayName: Host vaccination status header: Host - name: purpose_of_sequencing ontology_id: GENEPIO:0001445 definition: The reason that the sample was sequenced. guidance: 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. example: Baseline surveillance (random sampling) [GENEPIO:0100005] - displayName: Purpose Of Sequencing + displayName: Purpose of sequencing header: Sequencing - name: sequencing_date ontology_id: GENEPIO:0001447 definition: The date the sample was sequenced. guidance: Provide the sequencing date in ISO 8601 standard format "YYYY-MM-DD". example: "2021-04-26" - displayName: Sequencing Date + displayName: Sequencing date type: date preprocessing: function: process_date @@ -730,14 +730,14 @@ defaultOrganismConfig: &defaultOrganismConfig definition: The length of the amplicon generated by PCR amplification. guidance: Provide the amplicon size, including the units. example: 300bp - displayName: Amplicon Size + displayName: Amplicon size header: Sequencing - name: sequencing_instrument ontology_id: GENEPIO:0001452 definition: The model of the sequencing instrument used. guidance: Select the sequencing instrument from the pick list. example: Oxford Nanopore MinION [GENEPIO:0100142] - displayName: Sequencing Instrument + displayName: Sequencing instrument header: Sequencing - name: sequencing_protocol ontology_id: GENEPIO:0001454 @@ -751,28 +751,28 @@ defaultOrganismConfig: &defaultOrganismConfig definition: The overarching sequencing methodology that was used to determine the sequence of a biomaterial. guidance: 'Example Guidance: Provide the name of the DNA or RNA sequencing technology used in your study. If unsure refer to the protocol documentation, or provide a null value.' example: whole genome sequencing assay [OBI:0002117] - displayName: Sequencing Assay Type + displayName: Sequencing assay type header: Sequencing - name: sequenced_by_organization ontology_id: GENEPIO:0100416 definition: The name of the agency, organization or institution responsible for sequencing the isolate's genome. guidance: Provide the name of the agency, organization or institution that performed the sequencing in full (avoid abbreviations). If the information is unknown or cannot be provided, leave blank or provide a null value. example: Public Health Agency of Canada (PHAC) [GENEPIO:0100551] - displayName: Sequenced By + displayName: Sequenced by header: Sequencing - name: sequenced_by_contact_name ontology_id: GENEPIO:0100471 definition: The name or title of the contact responsible for follow-up regarding the sequence. guidance: 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. example: Enterics Lab Manager - displayName: Sequenced By Contact Name + displayName: Sequenced by - contact name header: Sequencing - name: sequenced_by_contact_email ontology_id: GENEPIO:0100422 definition: The email address of the contact responsible for follow-up regarding the sequence. guidance: 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. example: enterics@lab.ca - displayName: Sequenced By Contact Email + displayName: Sequenced by - contact email header: Sequencing - name: raw_sequence_data_processing_method ontology_id: GENEPIO:0001458 @@ -1018,7 +1018,7 @@ defaultOrganismConfig: &defaultOrganismConfig preprocessing: inputs: {input: nextclade.coverage} - name: versionComment - displayName: Version Comment + displayName: Version comment header: Submission details website: &website tableColumns: