Harmonise MICROBE soil metadata

[ESapenaVentura]

Now that we have most of the metadata from the first sampling round, we would like to harmonise the available metadata according to the standards we are producing.

AI:

• [x] Gather all the soil sample metadata currently available in BSD
• [ ] Modify and document changes according to what has been discussed.
  • [ ] CABI
  • [ ] AIT
  • [ ] HMGU
  • [ ] DSMZ
• [x] Create a checklist based on ERC000022, including more mandatory fields
  • [ ] Decide where will it live

[ESapenaVentura]

Changes

Refactor values

• Collection date: Removed "T00....Z" ending to timestamps - If the information is not available, we don't need the full timestamp.
• analysis date: Removed "T00....Z" ending to timestamps
• preservation temperature: refactored values to "degree Celsius" from "degree celsius" to align with UO
• deleted sampleIdByYear field in HMGU samples
• adding ontologyTerms tag to soil type field, using ENVO for the ontology.
• adding ontologyTerms tag to time point field, using UO for the ontology
• refactor soil type value to lowercase, to align with ENVO terms.

Wrong fields (Probably artifacts in submission)

• deleted biome.1 field in HMGU samples
• deleted soil_type and moved data to soil type

Extra fields

• Deleted year and plot_id_bexis from HMGU samples (internal)

Timepoint harmonisation

Basically, with the timepoints, we want to capture a few things; namely:

• How many days since the original sample was taken until the assay started
• How many days has the cryopreservation protocol been applied

For that, we originally assigned 2 fields; collection date and time point. However, these don't prove to capture all the essential data: for example, the first point above can't be fully known. Other things, like the date that the assay finishes, can be inferred from the data; however, I think it's good practice to have them explicitly stated. For that purpose, I am going to harmonise this information by doing the following changes:

• Added assay start date; capture the exact day the assay starts
• Added assay finish date: capture the exact day the assay finishes/is expected to finish
• Unmodified time point: basically, assay finish date - assay start date, but explicitly stated.
• Unmodified collection date, which is actually a GSC-approved field

Preservation

Similar to the timepoints discussion, we have had other talks regarding temperatures for the whole assay; at the beginning, we were only capturing the freezing method and preservation temperature. However, after chatting with INRAE and CABI, we discovered that some fields were missing to capture the whole picture. With that in mind, I want to harmonise the sample metadata with the following fields:

• freezing method now to capture the method by using the ontologies provided with in NCIT
• Add freezing temperature, which would entail the temperature at which the sample was exposed with the method first. Learned from INRAE that they cool the samples in 2 steps: First they freeze them, to a certain temperature, until they're stabilised; once at that temperature (Usually -80), they can be preserved by further freezing in liquid nitrogen until -196 degrees.
• Add cooling rate, with either: the cooling rate (degrees celsius per minute) or uncontrolled (When the rate was not controlled)
• add preservation method and modify scope of preservation temperature, which is the method used to further freeze the sample during the assay.

[ESapenaVentura]

~On the preservation above:~ ~- [ ] Before updating, send a message to people involved in soil samples, asking about the changes.~

New plan in last comment below

[ESapenaVentura]

Contacted AIT regarding non-consistent timepoints. In the meantime, the curation is paused - I need their input to push the changes

[ESapenaVentura]

Full checklist modified below:

ERC000022_MICROBE_mod.json

List of changes:

New fields

These fields are all required

• "biome",
• "assay start date",
• "assay finish date",
• "cryoprotectant",
• "freezing temperature",
• "freezing method",
• "preservation temperature",
• "preservation_method",
• "cooling_rate",
• "time point"

Modified fields

• "soil type": Now validates against the ontology, instead of using an enum (Also, the enum is wrong; all soil types are capitalised and, in the ontology, they are not)

[ESapenaVentura]

Plan on metadata:

• [x] infer the timepoints and the new fields based on previous values and emails
• [x] Ask each centre to check their spreadsheets

[ESapenaVentura]

Sent the spreadsheets around (Forgot to update, whoops), waiting on responses. So far, we have received a response from AIT with a new question regarding if we should drop the analysis date now that we have the assay finish date field. We should probably discuss it in the DWG meeting

[ESapenaVentura]

Got another spreadsheet from Selma

[ESapenaVentura]

Got spreadsheets back from:

• CABI
• AIT
• DSMZ

Got a response from:

• HMGU

[ESapenaVentura]

Sieving

On our discussion reviewing Conny's metadata ,we noticed that sieving needs to be looked at

Units

Adding units from conny's metadata spreadsheet

[ESapenaVentura]

I am also adding lars' metadata from the T0 samples that needs to be added.

I have emailed Lars and sent him a merged spreadsheet with the already existing BioSamples metadata