C14 extension

.github/workflows/check_dataset.yml

@@ -55,6 +55,12 @@ jobs:
         run: |
           echo "## Ancient Metagenome Environmental" >> validation/validation_results_raw.txt
           amdirt validate -s -d -c -m ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries_schema.json &>> validation/validation_results_raw.txt
+      - name: RADIOCARBON DATES test ancient single genomes (e.g. pathogens)
+        if: always()
+        run: |
+          echo "# Radiocarbon Dates" >> validation/validation_results_raw.txt
+          echo "## Ancient Single Genome Host Associated" >> validation/validation_results_raw.txt
+          amdirt validate -s -d -c -m ancientsinglegenome-hostassociated/radiocarbondates/ancientsinglegenome-hostassociated_radiocarbondates.tsv ancientsinglegenome-hostassociated/radiocarbondates/ancientsinglegenome-hostassociated_radiocarbondates_schema.json &>>  validation/validation_results_raw.txt
       - name: cleanup validation results from streamlit warnings
         if: always()
         run: |

ancientsinglegenome-hostassociated/radiocarbondates/README.md

@@ -0,0 +1 @@
+../../assets/documentation/radiocarbondates/README.md

ancientsinglegenome-hostassociated/radiocarbondates/ancientsinglegenome-hostassociated_radiocarbondates.tsv

@@ -0,0 +1,5 @@
+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_13n	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