Docs related to Contextual DB

Contextual DB Schema definition file (db_schema_definitions/db_schema_definitions.xlsx)

Units and definitions align where possible with MIxS v5.0 (https://gensc.org/index.html)

Version history

4.2.0

Change summary

• Modified datatype for the following fields:

  • vegetation_total_cover from TEXT to NUMERIC
  • water_holding_capacity from TEXT to NUMERIC
  • tot_org_carb from TEXT to NUMERIC
  • sample_metadata_ingest_date from DATETIME to TEXT (changed to play nicely with BPA data format checks during ingest into AM portal)

• Modified units definition

  • conductivity from deci siemens per meter to decisiemens per meter
  • To meet BPA ingest standards some micro (μ) characters in Units column encoded with the legacy unicode (U+00B5) symbol have been replaced with the unicode (U+03BC) micro symbol.
  • Reported units with a direct 1:1 relationship were previously defined in the Units column (e.g., mg/m3 or μg/L), are now represented with a single unit.
  • Reported units for collection_date has been modified to yyyy-mm-ddThh-mm-ssZ. An explanation of how samples without time stamps are defined has been added to the field definition.

4.1.0

Change summary

• Modified datatype for the following fields:

  • cadmium from TEXT to NUMERIC
  • cation_exchange_capacity from TEXT to NUMERIC
  • conductivity_aqueous from TEXT to NUMERIC
  • grazing_number from TEXT to NUMERIC

• Fixed broken link to Genomic Standards Consortium

4.0.0

Change summary

• Fields added to database schema:
  • bicarbonate
  • bicarbonate_meth
  • carbonate
  • carbonate_meth
• Fields deleted from database schema:
  • carbonate_bicarbonate
  • carbonate_bicarbonate_meth
• Field name changes:
  • synecochoccus to synechococcus
  • synecochoccus_meth to synechococcus_meth
• Other changes
  • Fixed typographical errors

3.2.0

Change summary

• Fields added to database schema:
  • collection_permit
  • hyperspectral_analysis
  • hyperspectral_analysis_meth
• Changes made to the following field definitions:
  • am_environment (definition expanded for clarity)
  • chlorophyll_c1 (previous definition reflected definition for chlorophyll_c1c2)
  • chlorophyll_c1_meth (previous definition reflected definition for chlorophyll_c1c2_meth)
  • chlorophyll_c1c2 (previous definition reflected definition for chlorophyll_c1)
  • chlorophyll_c1c2_meth (previous definition reflected definition for chlorophyll_c1_meth)
• Changed am_environment value from Soil and Marine to Marine for the fields:
  • sio2
  • sio2_meth

3.1.2

Change summary

• Fixed error with schema sheet version number
  • Schema sheet version number for release 3.1.1 was not updated (Released as 3.1.0). Updated to reflect current version.

3.1.1

Change summary

• Fixed error in rubidium_meth dType

3.1.0

Change summary

• Fields added to database schema:
  • cast_id
  • rosette_position
  • synonyms
• Added definitions to Field_Definition

3.0.1

Change summary

• Added: Air [ENVO_00002005] and associated definition to controlled_vocab_0

3.0.0

Change summary

• Added README sheet

  • Outlines the contents of the workbook
  • Defines version control terms
  • Defines sentery values used in the database

• Renamed version x.x.x sheet to Schema_x.x.x (e.g., Schema_3.0.0)

• Renamed Control_vocab sheet to Control_Vocab

  • Modified Control_Vocab sheet layout

• Fields added to database schema:

  • bleaching_meth
  • fouling_meth
  • grazing_meth
  • grazing_number_meth
  • host_abundance_mean_meth
  • host_abundance_meth
  • host_abundance_seaweed_mean_meth
  • host_length_meth
  • vegetation_dom_grasses_meth
  • vegetation_dom_shrubs_meth
  • vegetation_dom_trees_meth
  • vegetation_total_cover_meth

• Field name changes:

  • gravel_percent_meth changed to gravel_meth
  • length changed to host_length
  • tot_depth_water_meth changed to tot_depth_water_col_meth
  • tot_n_meth changed to tot_nitro_meth

• Definition additions and modifications

• Fixed typographical errors

2.0.2

Change summary

• Fixed typographical errors

2.0.1

Change summary

• Added Control_vocab sheet - Outlines the controlled vocabulary and its source
• Fixed typographical errors

2.0.0

Initial commit of contextual DB schema

• sheet name = x.x.x (e.g., 2.0.0). Containing the following information:
  • Field: Contextual metadata field
  • dType: Datatype used in the database schema
  • AM_enviro: Internal reference to distinguish common, terrestrial or non terrestrial metadata fields
  • Units_Definition: Long format definition of the units for the field
  • Units: Abbreviated units as they appear on the AM portal
  • Control_Vocab: Controlled vocabulary associated with the field
  • Field_Definition: Provides a definition for the field and where applicable its source

Tagging version for a release

Version: x.y.z (e.g. 2.1.3)

where x.y (2.1) represents version of the database z (3) represents revision version of the definition file