Merge branch 'master' into C14-Lebrasseur2024

.github/workflows/check_dataset.yml

@@ -3,6 +3,10 @@ name: check_dataset
 on:
   pull_request:
     branches: [master]
+    paths:
+      - "ancientmetagenome-environmental/**"
+      - "ancientmetagenome-hostassociated/**"
+      - "ancientsinglegenome-hostassociated/**"
 
 jobs:
   amdirt:

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project follows to [Calendar Versioning](https://calver.org/).
 #### Ancient Metagenome: Host Associated
 
 #### Ancient Single Genome: Host Associated
+- Added and Fixed C14 info for Warinner2014 10.1038/ng.2906 (added by @biancamariabonucci)
 
 - C14 Lebrasseur 2024 10.1093/ve/vead087 (added by @nihandilsad)
 

ancientsinglegenome-hostassociated/dates/ancientsinglegenome-hostassociated_dates.tsv

@@ -1,6 +1,7 @@
 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	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
+Spyrou2018	2018	10.1038/s41467-018-04550-9	RT5	PRJEB24296	ERS2106903	TRUE	TRUE	DNE	FALSE	supplement text	1	10.1038/s41467-018-04550-9	TRUE	MAMS	29430	AMS	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	supplement text	1	10.1038/s41467-018-04550-9	TRUE	MAMS	29431	AMS	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
+Warinner2014	2014	10.1038/ng.2906  G12	PRJNA216965	SRS473747,SRS473746,SRS473748,SRS473749,SRS473750	FALSE	FALSE	DNE	DNE	DNE	DNE	DNE	DNE	DNE	DNE	NA	DNE	DNE	DNE	unknown	NA	NA	NA	NA	NA	NA	DNE	DNE	DNE	DNE	DNE	DNE	NA	NA	NA	DNE	NA	DNE	DNE	DNE	NA	NA	NA	NA
 Lebrasseur2024	2024	10.1093/ve/vead087	UR17x29	PRJEB44430	ERS7256200	TRUE	TRUE	DNE	FALSE	main text	2	10.1038/s41586-021-04018-9	TRUE	UCIAMS	199248	AMS	TRUE	Collagen (ultrafiltered)	bone	3530	20	-99999	-99999	-99999	-99999	TRUE	IntCal20	OxCal	NR	NR	10.1017/S0033822200033865	3885	3719	-99999	cal BP	2	FALSE	DNE	DNE	NA	NA	NA	NA

ancientsinglegenome-hostassociated/dates/ancientsinglegenome-hostassociated_dates_schema.json

@@ -147,9 +147,9 @@
         "$id": "#/items/properties/reference_citation_depth",
         "type": "string",
         "title": "Reference Citation Depth?",
-        "pattern": "[1-3]|Unknown|NA",
+        "pattern": "[1-3]|Unknown|DNE",
         "description": "First place where the precise-radiocarbon date was recorded in the primary citation publication (i.e, the publication in ancientMetagenomeDir). 1 - main text > 2 - supplementary text > 3 - supplementary table.",
-        "examples": ["1", "2", "3", "Unknown", "NA"]
+        "examples": ["1", "2", "3", "Unknown", "DNE"]
       },
       "primary_secondary_reference_citation_doi": {
         "$id": "#/items/properties/primary_secondary_reference_citation_doi",

assets/enums/c14_calibrated_range_suffix.json

@@ -5,6 +5,8 @@
         "cal BC", 
         "cal CE", 
         "cal BCE", 
-        "cal BP"
+        "cal BP",
+        "cal BC/AD",
+        "cal BCE/CE"
     ]
-}
+}

assets/enums/c14_calibration_software.json

@@ -3,6 +3,8 @@
     "DNE",
     "NR",
     "OxCal",
-    "CalPal"
+    "CalPal",
+    "SwissCal",
+    "Calib"
   ]
 }

assets/enums/singlegenome_species.json

@@ -53,6 +53,9 @@
         "Mushuvirus mushu",
         "Streptococcus mutans",
         "Equid herpesvirus 4",
-        "Gallid alphaherpesvirus 2"
+        "Gallid alphaherpesvirus 2",
+        "Streptococcus pneumoniae",
+        "Yersinia enterocolitica",
+        "Erysipelothrix rhusiopathiae"
     ]
 }