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Merge pull request #1352 from SPAAM-community/c14-extension
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C14 extension - Change NA code to DNE (Does not Exist) for strings
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@aidaanva
aidaanva authored Feb 6, 2025
2 parents bb1777e + ce9e85e commit 57f6b6e
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8 changes: 4 additions & 4 deletions ancientsinglegenome-hostassociated/dates/ancientsinglegenome-hostassociated_dates.tsv
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project_name publication_year data_publication_doi sample_name archive_project archive_sample_accession date_information_present date_is_radiocarbon archaeological_historical_date multiple_dates reference_location reference_citation_depth primary_secondary_reference_citation_doi direct_dating radiocarbon_lab_code radiocarbon_lab_sample_id spectrometry_type pretreatment_reported pretreatment_type sample_material uncalibrated_date uncalibrated_uncertainty_plus_minus delta_13c carbon_perc delta_15n carbon_nitrogen_ratio calibration_reported calibration_curve calibration_software calibration_software_version calibration_software_settings calibration_software_citation_doi calibrated_range_lower calibrated_range_upper calibrated_range_median calibrated_range_suffix calibrated_range_sigma reservoir_offset_mentioned reservoir_offset_applied reservoir_offset_type reservoir_offset_reported reservoir_offset_reported_sd reservoir_aquatic_carbon_perc reservoir_aquatic_carbon_perc_sd
AndradesValtuena2017 2017 10.1016/j.cub.2017.10.025 1343UnTal85 PRJEB19335 ERS1892067 TRUE TRUE NA FALSE main text 2 10.1371/journal.pone.0139705 TRUE MAMS 18949 AMS NR NR tooth 3819 24 -20.5 47.5 -99999 3.3 TRUE IntCal13 OxCal v4.2.24 default 10.1017/S0033822200033865 4346 4098 4203 cal BP 2 TRUE FALSE NA NA NA NA NA
AndradesValtuena2017 2017 10.1016/j.cub.2017.10.025 6Post PRJEB19335 ERS1892066 TRUE TRUE NA FALSE main text 2 10.1371/journal.pone.0139705 TRUE MAMS 18955 AMS NR NR tooth 3574 19 -20.7 49 -99999 3.3 TRUE IntCal13 OxCal v4.2.24 default 10.1017/S0033822200033865 3957 3832 3873 cal BP 2 TRUE FALSE NA NA NA NA NA
Spyrou2018 2018 10.1038/s41467-018-04550-9 RT5 PRJEB24296 ERS2106903 TRUE TRUE NA FALSE main text 1 10.1038/s41467-018-04550-9 TRUE MAMS 29430 NR NR NR tooth 3517 27 -99999 -99999 -99999 -99999 TRUE NR NR NR NR NR 3868 3704 3789 cal BP 2 FALSE NA NA NA NA NA NA
Spyrou2018 2018 10.1038/s41467-018-04550-9 RT6 PRJEB24296 ERS2106904 TRUE TRUE NA FALSE main text 1 10.1038/s41467-018-04550-9 TRUE MAMS 29431 NR NR NR tooth 3499 25 -99999 -99999 -99999 -99999 TRUE NR NR NR NR NR 3842 3696 -99999 cal BP 2 FALSE NA NA NA NA NA NA
AndradesValtuena2017 2017 10.1016/j.cub.2017.10.025 1343UnTal85 PRJEB19335 ERS1892067 TRUE TRUE DNE FALSE main text 2 10.1371/journal.pone.0139705 TRUE MAMS 18949 AMS NR NR tooth 3819 24 -20.5 47.5 -99999 3.3 TRUE IntCal13 OxCal v4.2.24 default 10.1017/S0033822200033865 4346 4098 4203 cal BP 2 TRUE FALSE DNE NA NA NA NA
AndradesValtuena2017 2017 10.1016/j.cub.2017.10.025 6Post PRJEB19335 ERS1892066 TRUE TRUE DNE FALSE main text 2 10.1371/journal.pone.0139705 TRUE MAMS 18955 AMS NR NR tooth 3574 19 -20.7 49 -99999 3.3 TRUE IntCal13 OxCal v4.2.24 default 10.1017/S0033822200033865 3957 3832 3873 cal BP 2 TRUE FALSE DNE NA NA NA NA
Spyrou2018 2018 10.1038/s41467-018-04550-9 RT5 PRJEB24296 ERS2106903 TRUE TRUE DNE FALSE main text 1 10.1038/s41467-018-04550-9 TRUE MAMS 29430 NR NR NR tooth 3517 27 -99999 -99999 -99999 -99999 TRUE NR NR NR NR NR 3868 3704 3789 cal BP 2 FALSE DNE DNE NA NA NA NA
Spyrou2018 2018 10.1038/s41467-018-04550-9 RT6 PRJEB24296 ERS2106904 TRUE TRUE DNE FALSE main text 1 10.1038/s41467-018-04550-9 TRUE MAMS 29431 NR NR NR tooth 3499 25 -99999 -99999 -99999 -99999 TRUE NR NR NR NR NR 3842 3696 -99999 cal BP 2 FALSE DNE DNE NA NA NA NA
65 changes: 33 additions & 32 deletions ...entsinglegenome-hostassociated/dates/ancientsinglegenome-hostassociated_dates_schema.json
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Expand Up @@ -115,33 +115,33 @@
"$id": "#/items/properties/date_is_radiocarbon",
"type": "string",
"title": "Is Date Radiocarbon?",
"pattern": "TRUE|FALSE|NA|NR",
"pattern": "TRUE|FALSE|DNE|NR",
"description": "Whether a sample has a specific radiocarbon date reported (e.g. 1245, not 15th Century or similar)",
"examples": ["TRUE", "FALSE", "NR", "NA"]
"examples": ["TRUE", "FALSE", "NR", "DNE"]
},
"archaeological_historical_date": {
"$id": "#/items/properties/archaeological_historical_date",
"type": [ "string", "null"],
"type": [ "string"],
"title": "Archaeological or historical date range or singular date",
"pattern": "[0-9]+-*[0-9]+|NA",
"pattern": "[0-9]+-*[0-9]+|DNE",
"description": "Archaeological or historical date range or singular date. The unit of time is Before Present (before 1950, BP)",
"examples": ["500-550", "35", "NA"]
"examples": ["500-550", "35", "DNE"]
},
"multiple_dates": {
"$id": "#/items/properties/multiple_dates",
"type": "string",
"title": "Multiple Direct Dates Present?",
"pattern": "TRUE|FALSE|NA",
"pattern": "TRUE|FALSE|DNE",
"description": "Whether multiple (direct) dates are present for this sample; if so make multiple rows for the sample with one date per row.",
"examples": ["true", "false", "NA"]
"examples": ["true", "false", "DNE"]
},
"reference_location": {
"$id": "#/items/properties/reference_location",
"type": "string",
"title": "Location of Reference to Date",
"pattern": "main text|supplement text|supplement table|NA",
"pattern": "main text|supplement text|supplement table|DNE",
"description": "First place where the precise-radiocarbon date was recorded in the primary citation publication (i.e, the publication in ancientMetagenomeDir). main text > supplementary text > supplmentary table.",
"examples": ["main text", "supplement text", "supplement table", "NA"]
"examples": ["main text", "supplement text", "supplement table", "DNE"]
},
"reference_citation_depth": {
"$id": "#/items/properties/reference_citation_depth",
Expand All @@ -156,23 +156,23 @@
"type": "string",
"title": "Digital Object Identifier (DOI) of the publication that the uncalibrated date was originally reported.",
"description": "DOI of the primary or secondary reference (i.e. the DOI of the publication in which the date was original reported) or permalink",
"examples": ["10.1038/ng.2906", "https://www.jstor.org/stable/j.ctv270kvmk", "Unknown", "NA"]
"examples": ["10.1038/ng.2906", "https://www.jstor.org/stable/j.ctv270kvmk", "Unknown", "DNE"]
},
"direct_dating": {
"$id": "#/items/properties/direct_dating",
"type": "string",
"title": "Date Directly from Sample?",
"pattern": "TRUE|FALSE|NA|NR",
"pattern": "TRUE|FALSE|DNE|NR",
"description": "Whether the date of the ancient metagenomic sample was directly from the same skeleton (or similar), or whether inferred from other samples in the same context",
"examples": ["TRUE", "FALSE", "NA", "NR"]
"examples": ["TRUE", "FALSE", "DNE", "NR"]
},
"radiocarbon_lab_code": {
"$id": "#/items/properties/radiocarbon_lab_sample_id",
"type": "string",
"title": "Radiocarbon Lab Sample ID",
"$ref": "https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_lab_code.json",
"description": "Lab code of the date, from https://radiocarbon.webhost.uits.arizona.edu/sites/default/files/2025-01/Labs-2025_01_16.pdf NA is no date available, NR is date available but no lab code",
"examples": ["OxA", "ANAS", "Beta", "NR", "NA"]
"examples": ["OxA", "ANAS", "Beta", "NR", "DNE"]
},
"radiocarbon_lab_sample_id": {
"$id": "#/items/properties/radiocarbon_lab_sample_id",
Expand All @@ -187,15 +187,15 @@
"title": "Delta 13C measurement method.",
"$ref": "https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_spectometry_type.json",
"description": "Which spectrophotometry method was used to measure the delta carbon-13 value, either with Isotope Ratio Mass Spectrometer (IRMS) or Accelerated Mass Spectrometer (AMS).",
"examples": ["AMS", "IMRS", "NR", "NA"]
"examples": ["AMS", "IMRS", "NR", "DNE"]
},
"pretreatment_reported":{
"$id": "#/items/properties/pretreatment_reported",
"type": "string",
"title": "Is Preatreatmnet Reported?",
"pattern": "TRUE|FALSE|NR|NA",
"pattern": "TRUE|FALSE|NR|DNE",
"description": "Is a pretreatment reported?",
"examples": ["TRUE", "FALSE", "NA", "NR"]
"examples": ["TRUE", "FALSE", "DNE", "NR"]
},
"pretreatment_type":{
"$id": "#/items/properties/pretreatment_type",
Expand Down Expand Up @@ -260,47 +260,47 @@
"$id": "#/items/properties/calibration_reported",
"type": "string",
"title": "Is Calibration Reported?",
"pattern": "TRUE|FALSE|NA",
"pattern": "TRUE|FALSE|DNE",
"description": "Whether the date has additionally been calibrated.",
"examples": ["TRUE", "FALSE", "NA"]
"examples": ["TRUE", "FALSE", "DNE"]
},
"calibration_curve": {
"$id": "#/items/properties/calibration_curve",
"type": "string",
"$ref": "https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_curve.json",
"title": "Calibration Curve",
"description": "The tree-ring calibration curve used for calibration.",
"examples": ["IntCal20", "CalPal2007_HULU", "SHCal20", "Marine20", "NR", "NA"]
"examples": ["IntCal20", "CalPal2007_HULU", "SHCal20", "Marine20", "NR", "DNE"]
},
"calibration_software": {
"$id": "#/items/properties/calibration_software",
"type": "string",
"$ref": "https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_software.json",
"title": "Calibration Software",
"description": "Software used for radiocarbon calibration.",
"examples": ["OxCal", "CalPal", "NR", "NA"]
"examples": ["OxCal", "CalPal", "NR", "DNE"]
},
"calibration_software_version": {
"$id": "#/items/properties/calibration_software_version",
"type": "string",
"title": "Calibration Software",
"description": "Which version of the calibration software used, (set NR if not reported)",
"examples": ["v1.20", "0.35", "NR", "NA"]
"examples": ["v1.20", "0.35", "NR", "DNE"]
},
"calibration_software_settings": {
"$id": "#/items/properties/calibration_software_settings",
"type": "string",
"title": "Calibration Software settings",
"description": "Settings used with the calibration software, (set NR if not reported)",
"examples": ["default", "-m 10", "NR", "NA"]
"examples": ["default", "-m 10", "NR", "DNE"]
},
"calibration_software_citation_doi": {
"$id": "#/items/properties/calibration_software_citation_doi",
"type": "string",
"pattern": "^10.\\d{4,9}\\/[^,]+$|NR|NA",
"pattern": "^10.\\d{4,9}\\/[^,]+$|NR|DNE",
"title": "Digital Object Identifier (DOI) of the radiocarbon calibration software publication.",
"description": "A valid DOI code (not as an URL).",
"examples": ["10.1038/ng.2906", "NA"]
"examples": ["10.1038/ng.2906", "DNE"]
},
"calibrated_range_lower": {
"$id": "#/items/properties/calibrated_range_lower",
Expand Down Expand Up @@ -329,7 +329,7 @@
"$ref": "https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibrated_range_suffix.json",
"title": "Suffix of the calibrated date range",
"description": "The suffix of the calibrated date range",
"examples": ["cal BP", "NA"]
"examples": ["cal BP", "DNE"]
},
"calibrated_range_sigma": {
"$id": "#/items/properties/calibrated_range_sigma",
Expand All @@ -342,24 +342,25 @@
"$id": "#/items/properties/reservoir_offset_mentioned",
"type": "string",
"title": "Is Reservoir Offset Mentioned?",
"pattern": "TRUE|FALSE|NA",
"pattern": "TRUE|FALSE|DNE",
"description": "If radiocarbon C14 reservoir offset mentioned in any form. False here corresponds to not recorded (NR)",
"examples": ["TRUE", "FALSE", "NA"]
"examples": ["TRUE", "FALSE", "DNE"]
},
"reservoir_offset_applied": {
"$id": "#/items/properties/reservoir_offset_applied",
"type": ["boolean", "null"],
"type": ["string"],
"pattern": "TRUE|FALSE|DNE",
"title": "Is Reservoir Offset Applied?",
"description": "If an offset correction or recalibration has been reported to have been applied ",
"examples": ["TRUE", "FALSE", "NA"]
"examples": ["TRUE", "FALSE", "DNE"]
},
"reservoir_offset_type": {
"$id": "#/items/properties/reservoir_offset_type",
"type": ["string","null"],
"pattern": "FRESHWATER|MARINE|NR|NA",
"type": ["string"],
"$ref": "https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_reservoir_offset_type.json",
"title": "Is the reported Reservoir Effect of Marine or Freshwater nature?",
"description": "Specify if the reported reservoir effect is of marine or freshwater origin.",
"examples": ["FRESHWATER","MARINE","NR", "NA"]
"examples": ["FRESHWATER","MARINE","NR", "DNE"]
},
"reservoir_offset_reported": {
"$id": "#/items/properties/reservoir_offset_reported",
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