metAaRCive

This is the first release of metAaRCive, containing 1518 complete entries. metAaRCive: Overview metAaRCive is a resource of metadata for published ancient animal genomes, curated by members of AaRC. The resource is distributed as a tab-delimited text file metAaRCive.txt, with each row corresponding to a single genome/sample/individual. The individual-sheets folder contains files where the metAaRCive.txt has been split across individual files corresponding to rough taxonomical groupings of organisms. The raw folder holds a version of the resource that includes entries that did not pass validation, representing work-in-progress and will contain many formatting errors. The raw version is not recommended for most users, but is provided in case it might be useful to someone. Get involved To contribute to the resource, join our Element channel (see https://animal-adna.org/about/) and find the metadata working group. Summary of curated metadata Sheet Entries released Nuclear data Mitochondrial data Papers Entries raw bos 127 127 127 7 127 beluga 0 0 0 0 53 hippos 2 2 2 2 2 land_snails 2 2 2 2 2 canids 283 283 12 32 287 ovis 206 149 126 8 667 capra 145 145 79 11 145 ursus 0 0 0 0 50 elephantidae 50 50 50 7 311 cervinae 0 0 0 0 72 sus 354 354 0 4 354 felinae 172 172 1 7 172 rodent 52 39 52 2 52 nh_primates 15 4 15 8 15 columbidae 97 97 0 5 97 rhinocerotidae 0 0 0 0 72 sirenia 13 13 13 3 13 sturgeon 0 0 0 0 0 Summary 1518 1437 479 98 2491 Field definitions Field Description samp_name Sample name, the primary ID used in the DNA paper source_mat_id Any archaeology/museum ID(s) that exist for the sample sample_alt_lab_ids Optional: Any other sample aliases or IDs biosamples_accession BioSamples accession(s), can be more than one if incorrectly registered multiple times tissue_type Sampled tissue or element (Uberon ontology: https://www.ebi.ac.uk/ols4/ontologies/uberon) molecular_sex Genetically inferred sex molecular_sex_reference Reference/publication for molecular sex inference. If an unpublished inference: "AaRC curator" samp_taxon_common Sample taxon common name samp_taxon_ID NCBI taxonomy ID (https://www.ncbi.nlm.nih.gov/taxonomy), if one exists for the species specific_host The taxonomic (Latin) name of the host from which the tissue/DNA originated, to as low a level as possible. latitude Latitude where the sample was found longitude Longitude where the sample was found geo_loc_name geographic location (country and/or sea,region) site_name Name of archaelogical or natural site where remains were found. If there is no relevant site name, this can also be some geographical label, e.g. an island or village. If there are multiple names (including in multiple languages), can indicate these separated by "/" sample_age Point estimate, cal BP radiocarbon date if available, or other point estimate, relative to an age 0 at the year 1950. This should be a number directly usable in analyses. If a sample is more recent than 1950, give a negative number. If only a range is available, use the midpoint of the range. sample_age_upper Upper (older) end of date range sample_age_lower Lower (younger) end of date range sample_age_inference_methods The method used to infer the sample age c14_age Uncalibrated C14 age, BP c14_age_sd C14 standard deviation c14_lab_code C14 lab code sample_age_reference Reference/publication for age information sample_age_notes Optional: any potentially useful notes on the age of the samples nuclear_sequencing_platform What sequencing technology was used to generate nuclear data nuclear_library_strategy What library strategy was used to generate nuclear data, e.g. WGS or Targeted-Capture? nuclear_depth_of_coverage Depth of sequencing coverage of the nuclear genome, if shotgun sequencing nuclear_damage_treatment Indication of whether characteristic ancient DNA damage has been enzymatically or chemically removed in a laboratory nuclear_lib_strandedness The strandedness of the original template DNA molecules used for constructing the sequencing library nuclear_reference Reference/publication for nuclear genomic data mt_sequencing_platform What sequencing technology was used to generate mitochondrial data mt_library_strategy What library strategy was used to generate mitochondrial data, e.g. Targeted-Capture or AMPLICON (for PCR-based experiments). If there is a mitochondrial sequence obtained from WGS data, and that sequence is deposited with an accession number recorded in the field "mt_accession", then use "WGS" here in the "mt_library_strategy" field mt_targeted_region What region of the mitochondrial genome was targetted? mt_depth_of_coverage Depth of sequencing coverage of the mitochondrial genome mt_damage_treatment Indication of whether characteristic ancient DNA damage has been enzymatically or chemically removed in a laboratory mt_lib_strandedness The strandedness of the original template DNA molecules used for constructing the sequencing library mt_accession Accession number for assembled mitochondrial data (not raw reads) mt_reference Reference for mitochondrial data curator_comments Optional: Any general comments from the curator curated_by Listing of the people that curated this record, can be multiple. curation_complete Is this curation of this record complete? Contributors Anders Bergström, Kevin G. Daly, Deon de Jager, Marco De Martino, Marianne Dehasque, Jolijn Erven, Róisín Ferguson, Lohit Garikipati, Owen Goodchild, Germán Hernández-Alonso, Dani Kitaygorodskiy, Gisela Kopp, Juliana Larsdotter, Hannah Moots, George Popovici, Nikolaos Psonis, Lachie Scarsbrook, Mattias Sherman, Laura C. Viñas-Caron, He Yu, Zhihan Zhao