Changes to the logsheets Jan 2025 version

[isanti]

Let's collect here all changes for the metadata logsheets. This will be a large task, and I would like to only do it once.

Reading from:
emo-bon/observatory-bpns-crate#31
and other relevant GH issues in each observatory RO-crate
and notes:
EMO_BON_metadata_instructions_updated.pdf
https://docs.google.com/document/d/1B1ZuuqN2rxDZZjpftpfHpvPVQ9cGUmpxlVdrdy4ccEk/edit?tab=t.0

Changes:

• remove unnecessary sheets

• add NAs properly

• observatory sheet

--data_owner: European Marine Biological Resource Centre
definition: the organization responsible for the curation, integrity, publication and use of generated data

--data_owner_edmoid: 5669
definition: EDMO id of the data owner organization

--data_contact_email: [email protected]
definition: data owner organization email

• sampling sheet

--seq_batch
definition: batch of EMO BON samples processed together for DNA extraction, sequencing, and data acquisition.
example: "batch 1", "batch 2"
This term is useful for managing the samples and instantly know where to find information from the next steps

-- source_mat_id
check if there
check if ascending normally (Data-> Column stats)
LOCK column

--noteworthy_env_cond check if this is added in all logsheets

--size_frac_low and size_frac_up check if values are correct

--replicate
check format (mostly for the blanks) should be:
1
2
3
4
blank_1
etc.

• measured sheet
  --color yellow all mandatory terms
  --redox is no longer mandatory
  change the definition and color

-- source_mat_id_orig
add it!

• definitions sheet

--SEDIMENT (but check if there for WATER and ARMS) add definitions for Tax_id Samp_description

--Term (column) name: source_material_id
Definition: Unique dentifier to each row/sample: it consists of the terms 1) Project (“EMOBON”) 2) Sampling Site ID; that is the Observatory ID (for example “SMN99”) supplemented with the sampling site indicator (“Wa” for water column, “So” for soft substrates and “Ha” for hard substrates) and 3) an iterator (1,2,3 etc). This is created via a google equation. To add this identifier to a new row, simply drag the value from the cell above. This column can only be filled by EMBRC.
Who is adding this information: EMBRC
 Term (column) name: source_material_id_orig
Definition: A unique identifier assigned to a material sample according to EMO BON Handbook as added by the sampling operators. This identifier is not quality controled but remains unchanged. This identifier consists of 5 terms: 1) Project (“EMOBON”) 2) Sampling Site ID; that is the Observatory ID (for example “SMN99”) supplemented with the sampling site indicator (“Wa” for water column, “So” for soft substrates and “Ha” for hard substrates) 3) Sampling Campaign Date formated as YYMMDD.For example “220315” would be the campaign on 15 March 2022. Especially for Hard substrates, both the deployment and retrieval dates have to be recorded formated as YYMMDD-YYMMDD 4) Size fraction (Wa: “3um” / “0.2um” / “20um” / “200um”) or organisms collected (So: “micro” for microorganisms, “meio” for meiobenthos and “macro” for macrobenthos) or ARMS fraction (Ha: “SF” for sessile fraction, “MF500” for motile fraction sieved through 0.5 mm, “MF100” for motile fraction sieved through 0.1 mm) 5) Replicate number (1-4). For labelling the negative control, this term will be replaced by the notation “blank”. All terms must be separated by "_".
Who is adding this information: sampling operators

--check the replicate definition (and added values)
"Indicates the replicate code of the material sample. For replicate 1, add "1", for replicate 2, add "2", etc. For blank samples, add "blank_1" for the first (even if there is never a second), and "blank_2" etc for subsequent blanks from the same event."
and the example change to "1, blank_1"

--noteworthy_env_cond
If there were any noteworthy/special environmental conditions during the sampling event, please note down the most appropriate term from the Environmental Ontology. Some suggestions for terms are: marine algal bloom [ENVO:02500036], coral bleaching process [ENVO:01000852], glacial abrasion [ENVO:01000682], storm [ENVO:01000876], drought [ENVO:1000745], rain [ENVO:01001564], snow [ENVO:01000406], hail [ENVO:03400011], oil spill [ENVO:00002061], increased temperature [PATO:0001305], environmental pollution [ENVO:02500036], biofouling [ENVO:06105023]. Additional appropriate terms may be selected from here: https://ontobee.org/ontology/ENVO?iri=http://purl.obolibrary.org/obo/ENVO_01000203

--For all definitions of columns that are mandatory, add to the definition
"Write NA if you will not ever provide a value for this term. Write >Expected YY-MM< if you expect to be able to provide a value at a later date (it can be an estimate".
We do not need to add this to the definitions of the non-mandatory columns.

[isanti]

FYI @kmexter @cpavloud @melinalou
gather here any new changes/checks for the logsheets

[cpavloud]

I think we should also add the "valid until" column that we discussed here

[kmexter]

Indeed, potentially - we need to resolve that issue first, and then update accordingly here

[isanti]

freeze top row & first column in all

[isanti]

check failure
must be T or F
not Y or N

[isanti]

• definitions sheet
  noteworthy_env_cond
  If there were any noteworthy/special environmental conditions during the sampling event, please note down the most appropriate term from the Environmental Ontology. Some suggestions for terms are: marine algal bloom [ENVO:02500036], coral bleaching process [ENVO:01000852], glacial abrasion [ENVO:01000682], storm [ENVO:01000876], drought [ENVO:1000745], rain [ENVO:01001564], snow [ENVO:01000406], hail [ENVO:03400011], oil spill [ENVO:00002061], increased temperature [PATO:0001305], environmental pollution [ENVO:02500036], biofouling [ENVO:06105023]. Additional appropriate terms may be selected from here: https://ontobee.org/ontology/ENVO?iri=http://purl.obolibrary.org/obo/ENVO_01000203

[isanti]

more changes and checks for the ARMS log sheets here: emo-bon/observatory-profile#20

cymon's comment here: emo-bon/observatory-profile#38

katrina's comment here: emo-bon/observatory-profile#13

[isanti]

LOCK

• Sheet sampling
  last column
  column names (all sheets)
• Sheet measured
  first, second column (will be equations)
  column names (all sheets)
• Updated_definitions (change to definitions; remove old-sampling and definitions)
  entire sheet
  [email protected] & [email protected] & [email protected] &
  [email protected]

FREEZE

• Sheet observatory
  column names (all sheets)
• Sheet sampling
  first column
  column names (all sheets)
• Sheet measured
  the source_mat_id_orig column (will be equations)
  column names (all sheets)
• Sheet definitions
  column names (all sheets)

[melinalou]

check failure must be T or F not Y or N

I checked the logsheets now and they are ok, only one had Y instead of T, corrected.

[isanti]

who can work on the LOCKed entries? [email protected] & [email protected] & [email protected]

@cpavloud is this ok? should I also add the [email protected] as a safety net?

[isanti]

• Sheet sampling
  replicate
  check format (mostly for the blanks) should be:
  1
  2
  3
  4
  blank_1
  etc.

[cpavloud]

should I also add the [email protected] as a safety net?

It would be good, as an extra precaution.

[isanti]

• definitions
  For all definitions of columns that are mandatory, add to the definition
  "Write NA if you will not ever provide a value for this term. Write >Expected YY-MM< if you expect to be able to provide a value at a later date (it can be an estimate".
  We do not need to add this to the definitions of the non-mandatory columns.

[melinalou]

should I do this?:)

• definitions
  For all definitions of columns that are mandatory, add to the definition
  "Write NA if you will not ever provide a value for this term. Write >Expected YY-MM< if you expect to be able to provide a value at a later date (it can be an estimate".
  We do not need to add this to the definitions of the non-mandatory columns.

[cymon]

I'd simplify it to just add N/A when value is not available and they can add the value when it is available.

"Expected blah blah blah" and variations on that are not useful and need to be accounted for (evaluated) when QC'ing the data - N/A is just easier to deal with and we dont lose any relevant information.