JDS4 data: revision need

[knutet]

I have reviwed the JDS4 data output files and discovered the followign isuses to be resolved:

1. ENVIRON_COMPARTMENT: several contain data = Other (add to SAMPLE_REMARK). Shouldn't these be Freshwater?

2. SITE_CODE: Have you provided the RA_SITES sheet that uniquely identify the sites? If so, is there a separate file providing the details for this- see RAdb_import_template, sheet RA_SITES.

3. EXTRACTION_METHOD: Any information available for the extraction method? Values to choose from: Methanol extraction Dichloromethane extraction SPE Isolute Env+ SPE Strata X-CW SPE Oasis HLB FMOC Dichloromethane Not relevant No information/not reported SPE Strata X-AW Other (specify in SAMPLING_REMARK)

4. FRACTION_PROTOCOL_ID, EXTRACTION_PROTOCOL_ID and ANALYTICAL_PROTOCOL_ID: there are reference_ids, but have you provided the citation information in the sheet RA_USER_REFERENCES?

5. SUBSAMPLE: this refer to different biological/chemical samples from the same locality. When multiple samples exist have they been added as sequential sample numbers or the TOTAL number of samples? In case only one sample, use VALUE=1.

6. SAMPLE_ID_ORG: are there any unique identifiers used for the sample or the measurement done- this would tyoically be a reference ID to the data that we can use to trace back to the source data.

7. 3. FRACTION: should be from the following (it refers to whether any filtration or other way of manipulating the sample is performed): Its normally Total (no manipulation) or Aqueous (Aqueous fraction)

Not relevant No information/not reported Total Particles Colloidal LMM Anionic LMM Cationic LMM Aqueous Filtered_045 Free ions_045_Pred Inorganic_045_Pred Organic_045_Pred Cationic_045_Pred Anionic_045_Pred Free ions_Tot_Pred Inorganic_Tot_Pred Organic_Tot_Pred Cationic_Tot_Pred Anionic_Tot_Pred Conc_Biotic_Ligand Active ingredient Dissolved Formulation Labile (free metal ion) Unionized

8. DATA_TYPE_SUB (KET): Add unique categories to RAdb. Assigned to KET.

9. INCHIKEY_STANDARD: there are several compounds without a VALUE = NA in Standard_Inchikey. Can this be added?

10. MEASURED_FLAG: this column should contain indication whether <LOD OR <LOQ OR left empty (when value was above LOD and LOQ).

11. MEASURED_VALUE: this should only contain numeric values and if <LOD OR <LOQ, leave empty.

12. MEASURED_REFERENCE_ID: This field should cite the actual data used and refer to the unique identifier for the analysis (if such exists). If it does not exist, leave empty. If multiple sources, state the most relevant one as we cannot have 2 citations in current version. It now contain the value = 1,5.

13. ENTERED_DATE: the date of when data was added to db.

[kelseyng852]

1. ENVIRON_COMPARTMENT: several contain data = Other (add to SAMPLE_REMARK). Shouldn't these be Freshwater? Updated:

   • “Fresh water” for river water and groundwater samples
   • “Other (add to SAMPLE_REMARK)” for wastewater, biota and sediment samples

2. SITE_CODE: Have you provided the RA_SITES sheet that uniquely identify the sites? If so, is there a separate file providing the details for this- see RAdb_import_template, sheet RA_SITES. Updated:

   • The RA_SITES_EXT tab has been filled in at RAdb import template.xlsx

3. EXTRACTION_METHOD: Any information available for the extraction method? Values to choose from: Methanol extraction Dichloromethane extraction SPE Isolute Env+ SPE Strata X-CW SPE Oasis HLB FMOC Dichloromethane Not relevant No information/not reported SPE Strata X-AW Other (specify in SAMPLING_REMARK) Updated:

   • “SPE Oasis HLB” for wastewater, groundwater and river water samples
   • “Methanol extraction” for biota and sediment samples

4. FRACTION_PROTOCOL_ID, EXTRACTION_PROTOCOL_ID and ANALYTICAL_PROTOCOL_ID: there are reference_ids, but have you provided the citation information in the sheet RA_USER_REFERENCES? Updated:

   • “5” for FRACTION_PROTOCOL_ID and ANALYTICAL_PROTOCOL_ID
   • For EXTRACTION_PROTOCOL_ID, it depends on the sample matrix (“2” or “3” or “4” or “5”)

5. SUBSAMPLE: this refer to different biological/chemical samples from the same locality. When multiple samples exist have they been added as sequential sample numbers or the TOTAL number of samples? In case only one sample, use VALUE=1. Updated:

   • The input is the number of samples (multiple samples for biota samples, 1 sample each for sediment, wastewater, groundwater, and river water samples)

6. SAMPLE_ID_ORG: are there any unique identifiers used for the sample or the measurement done- this would tyoically be a reference ID to the data that we can use to trace back to the source data. Reply:

   • There is no such chemical-sample combination ID in the JDS4 data set

7. iii. FRACTION: should be from the following (it refers to whether any filtration or other way of manipulating the sample is performed): Its normally Total (no manipulation) or Aqueous (Aqueous fraction) Not relevant No information/not reported Total Particles Colloidal LMM Anionic LMM Cationic LMM Aqueous Filtered_045 Free ions_045_Pred Inorganic_045_Pred Organic_045_Pred Cationic_045_Pred Anionic_045_Pred Free ions_Tot_Pred Inorganic_Tot_Pred Organic_Tot_Pred Cationic_Tot_Pred Anionic_Tot_Pred Conc_Biotic_Ligand Active ingredient Dissolved Formulation Labile (free metal ion) Unionized Updated:

   • “Aqueous” for wastewater, groundwater and river water samples
   • “Total” for biota and sediment samples

8. DATA_TYPE_SUB (KET): Add unique categories to RAdb. Assigned to KET. Updated:

   • “KET” for all entries

9. INCHIKEY_STANDARD: there are several compounds without a VALUE = NA in Standard_Inchikey. Can this be added? Updated in:

   • STD INCHIKEY updated at: Source_file_JDS4_target_screening.xlsx
   • No VALUE = NA in INCHIKEY_STANDARD now

10. MEASURED_FLAG: this column should contain indication whether <LOD OR <LOQ OR left empty (when value was above LOD and LOQ). Updated:

    • “<LOD” for readings below LOD
    • “<LOQ” for readings below LOQ
    • Left blank otherwise

11. MEASURED_VALUE: this should only contain numeric values and if <LOD OR <LOQ, leave empty. Updated:

    • Left blank for readings below LOD & below LOQ

12. MEASURED_REFERENCE_ID: This field should cite the actual data used and refer to the unique identifier for the analysis (if such exists). If it does not exist, leave empty. If multiple sources, state the most relevant one as we cannot have 2 citations in current version. It now contain the value = 1,5. Updated:

    • “5” for all entries

13. ENTERED_DATE: the date of when data was added to db. Updated:

    • Left blank for all entries (depends on the date of importing data to db)

14. Additional updates:

    • ANALYTICAL_METHOD: “LCMS/MS” for all entries
    • DATA_TYPE: leave blank for all entries
    • SAMPLING_METHOD” “LVSPE” for wastewater, groundwater and river water samples
    • SAMPLE_MATRIX: “Groundwater” for groundwater samples
    • SAMPLE_REMARK: leave blank for groundwater samples