Sample Checklist Updates - June 2015
ENA are planning to update several sample metadata reporting checklists. Some of these changes have been carried out for harmonisation of attributes/fields between various checklist. Other changes were made to allow a standardised missing/null value reporting. All changes will come into effect as of 3rd August 2015.
ENA are planning to update several sample metadata reporting checklists. Programmatic submitters can see the detailed list of changes to be adopted into sample checklist XMLs in the table below. For submitters using the interactive Webin the below changes will be implemented into the Webin tool. Some of these changes have been carried out for harmonisation of attributes/fields between various checklist. Other changes were made to allow a standardised missing/null value reporting. More details on the missing value language can be found here.
All changes will come into effect as of 3rd August 2015.
| Checklist | Attribute/Field | Change |
|---|---|---|
| ENA default | country | becomes geographic location (country and/or sea) |
| geographic location (country and/or sea) | adopts INSDC country list CV including null value CV (not applicable, not collected, not provided, restricted access) | |
| geographic location (region and locality) | added; free text | |
| GMI pathogen | isolate | becomes mandatory |
| strain | becomes recommended | |
| serovar | becomes recommended | |
| collection_date | becomes collection date | |
| geographic location (country and/or sea) | adopts INSDC country list CV including null value CV (not applicable, not collected, not provided, restricted access) | |
| host_status | becomes host health state | |
| host_description | becomes host description | |
| host_subject_id | becomes host subject id | |
| host_disease_outcome | becomes host disease outcome | |
| host_disease_stage | becomes host disease stage | |
| isolation_source_host_associated | becomes isolation source host-associated | |
| isolation_source_non_host_associated | becomes isolation source non-host-associated | |
| host_health_state | becomes deprecated | |
| host health state | adopts null value CV (not applicable, not collected, not provided, restricted access) | |
| host sex | adopts CV (male, female, neuter, hermaphrodite, other) | |
| ENA default prokaryotic | isolate | becomes mandatory |
| strain | becomes recommended | |
| serovar | becomes recommended | |
| collection_date | becomes collection date | |
| country | becomes geographic location (country and/or sea) | |
| host_status | becomes host health state | |
| geographic location (country and/or sea) | adopts INSDC country list CV including null value CV (not applicable, not collected, not provided, restricted access) | |
| geographic location (region and locality) | added; free text | |
| host health state | adopts null value CV (not applicable, not collected, not provided, restricted access) | |
| ENA Influenza | geographic location (country and/or sea) | adopts null value CV (not applicable, not collected, not provided, restricted access) |
| host_description | becomes host description | |
| isolation_source_host_associated | becomes isolation source host-associated | |
| isolation_source_non_host_associated | becomes isolation source non-host-associated | |
| host health state | adopts null value CV (not applicable, not collected, not provided, restricted access) | |
| host sex | adopts null value CV (not applicable, not collected, not provided, restricted access) | |
| ALL MIxS checklists | geographic location (country and/or sea) | adopts null value CV (not applicable, not collected, not provided, restricted access) |
| investigation type | gets extended CV (metagenome, metatranscriptome, mimarks-survey) | |
| ALL except ENA default | added validation: regex for ISO8601 compliant date and time reporting |
