Notes on GSC MIxS miscellaneous natural or artificial environment

[peterjc]

#277 added the thapbi_pict ena-submit command for use with the TSV template for mapping your FASTQ files to your samples. Prior to that you must define the samples, and ideally follow one of the metadata sample checklists: https://www.ebi.ac.uk/ena/browser/checklists

Right now for our samples which are a mix of water, soil and plant derived, I am leaning to ERC000025 GSC MIxS miscellaneous natural or artificial environment: https://www.ebi.ac.uk/ena/browser/view/ERC000025

This has 11 mandatory fields, first these non-sample terms:

• project name, would be "Phyto-Threats" etc.
• sequencing method, would be Illumina
• investigation type, would be mimarks-survey for our field samples (and blanks?) or mimarks-specimen for our single isolate samples.

And then under collection event information:

• collection date, ISO8601 style
• geographic location (country and/or sea), e.g. "United Kingdom"
• geographic location (latitude), decimal degrees
• geographic location (longitude), decimal degrees
• miscellaneous environmental package, would be "miscellaneous natural or artificial environment"
• environment (biome), tricky...
  • Biomes are defined based on factors such as plant structures, leaf types, plant spacing, and other factors like climate. Biome should be treated as the descriptor of the broad ecological context of a sample. Examples include: desert, taiga, deciduous woodland, or coral reef. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO
  • is it too vague to use "terrestrial ecosystem" http://purl.obolibrary.org/obo/ENVO_01001790
  • would tree nurseries fall under "agricultural ecosystem" http://purl.obolibrary.org/obo/ENVO_00000077 or perhaps "woodland ecosystem" http://purl.obolibrary.org/obo/ENVO_01001245
  • see also "botanical garden" http://purl.obolibrary.org/obo/ENVO_00010624
• environment (feature), tricky... especially for our root/plant samples
  • Environmental feature level includes geographic environmental features. Compared to biome, feature is a descriptor of the more local environment. Examples include: harbor, cliff, or lake. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO
  • Maybe "agricultural ecosystem" http://purl.obolibrary.org/obo/ENVO_00000077 as a default, or "cultivated environment" http://purl.obolibrary.org/obo/ENVO_01000311
  • "manufactured product" http://purl.obolibrary.org/obo/ENVO_00003074 for equipment?
  • "borehole" http://purl.obolibrary.org/obo/ENVO_00002226
  • "ditch" http://purl.obolibrary.org/obo/ENVO_00000037
  • "pond" http://purl.obolibrary.org/obo/ENVO_00000033
  • "stream" http://purl.obolibrary.org/obo/ENVO_00000023
• environment (material), this should be fine based on our existing metadata:
  • The environmental material level refers to the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Environmental material terms are generally mass nouns. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO
  • "soil" http://purl.obolibrary.org/obo/ENVO_00001998
  • "water" http://purl.obolibrary.org/obo/CHEBI_15377 or "liquid water" http://purl.obolibrary.org/obo/ENVO_00002006
  • "root matter" http://purl.obolibrary.org/obo/ENVO_01000349
  • "plant matter" http://purl.obolibrary.org/obo/ENVO_01001121

[peterjc]

Using ERC000020 GSC MIxS plant associated would have the same mandatory fields.

[peterjc]

Sadly from skimming ENA entries using ERC000025, the three environment fields are something of a mixed bag. The good news is we can probably just put something generic there a more precise term can't be found.