Merge branch 'master' into C14Rasmussen2015

CHANGELOG.md

@@ -13,11 +13,15 @@ and this project follows to [Calendar Versioning](https://calver.org/).
 
 #### Ancient Single Genome: Host Associated
 
-- C14 Rasmussen 2015 10.1016/j.cell.2015.10.009 (added by @mlo89)
-- C14 Warinner2014 10.1038/ng.2906 (added by @biancamariabonucci)
+- Susat 2021 10.1016/j.celrep.2021.109278 (C14 added by @aidaanva)
+- C14 Austin 2022 10.1038/s42003-022-03890-z (added by @nihandilsad)
+- Added and Fixed C14 info for Warinner2014 10.1038/ng.2906 (added by @biancamariabonucci)
 - C14 Key2020 10.1038/s41559-020-1106-9 (added by @iseultj)
-
 - C14 deBarrosDamgaard2018 10.1038/s41586-018-0094-2 (added by @marcel-keller)
+- C14 Susat 2024 10.1038/s42003-024-06676-7 (added by @aidaanva)
+- C14 Warinner2014 10.1038/ng.2906 (added by @biancamariabonucci)
+- C14 Rasmussen 2015 10.1016/j.cell.2015.10.009 (added by @mlo89)
+
 
 #### Ancient Metagenome: Environmental
 

ancientsinglegenome-hostassociated/dates/ancientsinglegenome-hostassociated_dates.tsv

@@ -16,6 +16,10 @@ Key2020	2020	10.1038/s41559-020-1106-9	ETR001	PRJEB35216	ERS3967960	TRUE	TRUE	DN
 Key2020	2020	10.1038/s41559-020-1106-9	ETR001	PRJEB35216	ERS3967960	TRUE	TRUE	DNE	TRUE	supplement text	1	10.1038/s41559-020-1106-9	TRUE	MAMS	23339	AMS	NR	NR	tooth	1811	24	-99999	-99999	-99999	-99999	TRUE	NR	NR	DNE	NR	NR	1813	1618	NA	cal BP	2	FALSE	DNE	DNE	NA	NA	NA	NA
 deBarrosDamgaard2018	2018	10.1038/s41586-018-0094-2	DA101	PRJEB25891	ERS2367268	TRUE	TRUE	DNE	FALSE	supplement table	1	10.1038/s41586-018-0094-2	TRUE	UBA	31214	AMS	TRUE	Collagen (ultrafiltered)	unknown	1783	29	-16.3	-99999	12.6	3.15	TRUE	IntCal13	Calib	DNE	NR	10.1017/S0033822200013904	261	214	NA	cal AD	1	FALSE	FALSE	DNE	NA	NA	NA	NA
 deBarrosDamgaard2018	2018	10.1038/s41586-018-0094-2	DA147	PRJEB25891	ERS2367269	FALSE	FALSE	1450-1050	DNE	DNE	DNE	DNE	DNE	DNE	NA	DNE	DNE	DNE	unknown	NA	NA	NA	NA	NA	NA	TRUE	DNE	DNE	DNE	DNE	DNE	NA	NA	NA	DNE	NA	DNE	DNE	DNE	NA	NA	NA	NA
+Austin2022	2022	10.1038/s42003-022-03890-z	St.LI	PRJNA851947	SRS13524932	TRUE	FALSE	20	FALSE	main text	DNE	DNE	FALSE	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
+Susat2021	2021	10.1016/j.celrep.2021.109278	RV2039	PRJEB42185	ERS6638365	TRUE	TRUE	DNE	FALSE	main text	3	https://fu-berlin.primo.exlibrisgroup.com/permalink/49KOBV_FUB/1v1tp5h/alma9958233188402883	TRUE	KIA	46462	AMS	NR	NR	tooth	5049	33	-25.22	-99999	13.65	3.2	TRUE	IntCal13	OxCal	4	NR	10.1111/j.1475-4754.2008.00457.x	5300	5050	NA	cal BP	2	TRUE	TRUE	FRESHWATER	700	50	53	7
+Susat2024	2024	10.1038/s42003-024-06676-7	Warburg_1	PRJEB49648	ERS19529513	TRUE	TRUE	DNE	FALSE	supplement text	1	10.1038/s42003-024-06676-7	TRUE	KIA	55519	AMS	NR	NR	tooth	-99999	-99999	-99999	-99999	-99999	-99999	TRUE	IntCal20	OxCal	4.4.4	NR	10.1111/j.1475-4754.2008.00457.x	5291	4979	-99999	cal BP	2	FALSE	DNE	DNE	NA	NA	NA	NA
+Susat2024	2024	10.1038/s42003-024-06676-7	Warburg_2	PRJEB49648	ERS19529514	TRUE	TRUE	DNE	FALSE	supplement text	1	10.1038/s42003-024-06676-7	TRUE	KIA	56332	AMS	NR	NR	tooth	-99999	-99999	-99999	-99999	-99999	-99999	TRUE	IntCal20	OxCal	4.4.4	NR	10.1111/j.1475-4754.2008.00457.x	5265	4857	-99999	cal BP	2	FALSE	DNE	DNE	NA	NA	NA	NA
 Rasmussen2015	2015	10.1016/j.cell.2015.10.009	RISE00	PRJEB10885	ERS848971	TRUE	TRUE	4412	FALSE	supplement table	1	10.1016/j.cell.2015.10.009	TRUE	UBA	29064	AMS	NR	NR	bone	3969	32	-21.3	-99999	8.9	3.14	TRUE	IntCal13	OxCal	4.2	NR	10.1017/S0033822200033865	2575	2349	NA	cal BC	2	FALSE	DNE	DNE	NA	NA	NA	NA
 Rasmussen2015	2015	10.1016/j.cell.2015.10.009	RISE139	PRJEB10885	ERS848972	TRUE	TRUE	3979	FALSE	supplement table	1	10.1016/j.cell.2015.10.009	TRUE	Ua	44034	AMS	NR	NR	bone	3645	33	-99999	-99999	-99999	-99999	TRUE	IntCal13	OxCal	4.2	NR	10.1017/S0033822200033865	2135	1923	NA	cal BC	2	FALSE	DNE	DNE	NA	NA	NA	NA
 Rasmussen2015	2015	10.1016/j.cell.2015.10.009	RISE386*1	PRJEB10885	ERS848973	TRUE	TRUE	4113	TRUE	supplement table	1	10.1016/j.cell.2015.10.009	TRUE	OxA	30991	AMS	NR	NR	tooth	3740	33	-20.9	-99999	14.1	3.3	TRUE	IntCal13	OxCal	4.2	NR	10.1017/S0033822200033865	2277	2033	NA	cal BC	2	TRUE	FALSE	FRESHWATER	NA	-99999	-99999	-99999
@@ -24,3 +28,4 @@ Rasmussen2015	2015	10.1016/j.cell.2015.10.009	RISE397	PRJEB10885	ERS848974	TRUE
 Rasmussen2015	2015	10.1016/j.cell.2015.10.009	RISE505	PRJEB10885	ERS848975	TRUE	TRUE	3636	FALSE	supplement table	1	10.1016/j.cell.2015.10.009	TRUE	OxA	31216	AMS	NR	NR	tooth	3391	27	-18.8	-99999	11.4	3.3	TRUE	IntCal13	OxCal	4.2	NR	10.1017/S0033822200033865	1746	1626	NA	cal BC	2	FALSE	DNE	DNE	NA	NA	NA	NA
 Rasmussen2015	2015	10.1016/j.cell.2015.10.009	RISE509	PRJEB10885	ERS848976	TRUE	TRUE	4732-4744	FALSE	supplement table	1	10.1016/j.cell.2015.10.009	TRUE	OxA	31221	AMS	NR	NR	tooth	4186	27	-18.8	-99999	11.4	3.2	TRUE	IntCal13	OxCal	4.2	NR	10.1017/S0033822200033865	2887	2677	NA	cal BC	2	FALSE	DNE	DNE	NA	NA	NA	NA
 Rasmussen2015	2015	10.1016/j.cell.2015.10.009	RISE511	PRJEB10885	ERS848977	TRUE	TRUE	4732-4744	FALSE	supplement table	1	10.1016/j.cell.2015.10.009	TRUE	OxA	31568	AMS	NR	NR	tooth	4224	36	-18.6	-99999	10.4	3.3	TRUE	IntCal13	CalPal	4.2	NR	10.1017/S0033822200033865	2909	2679	NA	cal BC	2	FALSE	DNE	DNE	NA	NA	NA	NA
+

ancientsinglegenome-hostassociated/dates/ancientsinglegenome-hostassociated_dates_schema.json

@@ -333,7 +333,7 @@
       },
       "calibrated_range_sigma": {
         "$id": "#/items/properties/calibrated_range_sigma",
-        "type": [ "integer", "null" ],
+        "type": [ "number", "null" ],
         "title": "Calibrated range sigma",
         "description": "Confidence level of the reported calibrated age range, typically in 2 (95.4%) or 1 (68.2%) levels of significance (sigma).",
         "examples": [1, 2, -99999, "NA"]

assets/documentation/libraries/README.md

@@ -60,11 +60,12 @@ Library columns are as follows:
 ## data_publication_doi
 
 - Must correspond to the `publication_doi` of the publication in the
-  corresponding sample metadata table!
-- Publication DOI.
-- Or library permalink:
-  - e.g. [worldcat](https://www.worldcat.org/), [HAL](hal.archives-ouvertes.fr)
-    etc.
+corresponding sample metadata table!
+- Publication DOI. _Not_ the full URL, just the DOI
+  - e.g. 10.1038/ng.2906
+  - You can test it by adding it on to the end of https://doi.org/ and see if it resolves to the publication (e.g. https://doi.org/10.1038/ng.2906)
+- Or library permalink (full URL):
+  - e.g. [worldcat](https://www.worldcat.org/), [HAL](hal.archives-ouvertes.fr) etc.
 
 > ⚠️ Mandatory value
 
@@ -96,17 +97,11 @@ Library columns are as follows:
 
 ## archive_project
 
-- Must correspond to the `archive_project` of the publication in the
-  corresponding sample metadata table!
-- A project level accession code under which all libraries of a project are
-  assigned to.
+- Must correspond to the `archive_project` of the publication in the corresponding sample metadata table!
+- A project level accession code under which all libraries of a project are assigned to.
 - Specific examples:
-
-  - Archive: ENA/SRA/DDBJ: should be _primary_ accession code beginning with
-    `PRJ`. [Example](https://www.ebi.ac.uk/ena/browser/view/PRJNA438985).
-  - Archive: MG-RAST: should be accession code beginning with `mgp`.
-    [Example](https://www.mg-rast.org/mgmain.html?mgpage=project&project=mgp13354).
-
+  - Archive: ENA/SRA/DDBJ: should be _primary_ accession code beginning with `PRJ`. [Example](https://www.ebi.ac.uk/ena/browser/view/PRJNA438985).
+  - Archive: MG-RAST: should be accession code beginning with `mgp`. [Example](https://www.mg-rast.org/mgmain.html?mgpage=project&project=mgp13354).
 - Missing value: `Unknown`
 
 ## archive_sample_accession
@@ -177,6 +172,9 @@ Library columns are as follows:
   primary source protocol if referenced (e.g. if 'libraries prepared as described in Meyer
   and Kircher', use polymerase cited there. If you go down a citation chain,
   'as in X, as in Y, as in Z', specify `Unknown`.
+- Specific examples:
+  - [Kircher et al. (2012) Nucleic Acids Research](https://doi.org/10.1093/nar/gkr771): AmpliTaq Gold DNA
+  - [Meyer & Kircher (2010) Cold Spring Harbour Protocols](https://doi.org/10.1101/pdb.prot5448): Phusion Hot Start High-Fidelity DNA
 
 > ⚠️ Must follow categories specified in
 > `assets/enums/library_polymerase.json`
@@ -212,7 +210,7 @@ Library columns are as follows:
 ## instrument_model
 
 - Sequencing machine used for sequencing the library.
-- Follows [ENA categories](https://www.ebi.ac.uk/ena/portal/api/controlledVocab?field=instrument_model).
+- Follows [ENA categories](https://github.com/enasequence/webin-cli/blob/master/src/main/resources/uk/ac/ebi/ena/webin/cli/reads/instrument.properties).
 - In most cases for aDNA labs will be some form of Illumina platform.
 
 > ⚠️ If not described in the ENA table, or there is discrepency with the paper, specify: `unspecified`
@@ -287,7 +285,7 @@ Library columns are as follows:
 - Download link to raw data files.
 - Should start with `ftp`, `https`, or `http`.
 - Can be semi-colon separated list for paired-end sequenced runs.
-- Link must allow direct download of files via command-line utility e.g. with wget or curl. I.e., the link must send you directly to a file, not a gateway page.
+- Link must allow direct download of files via command-line utility e.g. with `wget` or `curl`. I.e., the link must send you directly to a file, not a gateway page.
 
 > ⚠️ Mandatory value
 
@@ -312,4 +310,5 @@ Library columns are as follows:
 - File sizes of corresponding download files in bytes.
 - This can be used to estimated HDD space that will be used after download.
 - Can be semi-colon separated list for paired-end data, and in some cases paired-end with singletons.
-- > ⚠️ Mandatory value
+
+> ⚠️ Mandatory value

assets/enums/c14_lab_code.json

@@ -277,6 +277,7 @@
     "UBAR",
     "UCD",
     "UCI",
+    "UCIAMS",
     "UCLA",
     "UCR",
     "UD",

assets/enums/sample_host.json

@@ -36,6 +36,8 @@
         "Lithobates pipiens",
         "Equus caballus",
         "Sciurus vulgaris",
-        "Gallus gallus"
+        "Gallus gallus",
+        "Gorilla gorilla",
+        "Pongo abelii"
     ]
 }

assets/enums/singlegenome_species.json

@@ -56,6 +56,7 @@
         "Gallid alphaherpesvirus 2",
         "Streptococcus pneumoniae",
         "Yersinia enterocolitica",
-        "Erysipelothrix rhusiopathiae"
+        "Erysipelothrix rhusiopathiae",
+        "Monkeypox virus"
     ]
 }