MInAS Combinations
Warning
This can be considered a pre-alpha version, and has not been reviewed nor approved by the wider palaeogenomics community nor by the Genomics Standards Consortium.
Our current proposal for ancient DNA specific metadata fields can be found on GitHub under the dedicated repository. The schema file is under src/mixs/schema/.
Viewing current combinations
The best way to view and test the current schema is via the MInAS DataHarmonizer. Use the 'Template' dropdown menu to select the combination of your choice (see table below for guidance).
Description
A MIxS combination refers to a MIxS checklist of metadata terms (e.g. for a genome, metagenome, marker sequence) plus one or more sample type-specific metadata 'extensions'.
A MInAS combination consists of an existing MIxS combination plus the Ancient extension. Optionally this can also include the radiocarbon dating extension - however this is not yet at a sufficient state for inclusion.
The included combinations have been proposed by the MInAS development team to act as starting points for discussions. Not all types of ancient DNA research will currently be covered here, however the sub-fields should cover the vast majority of current research in the field. As the MInAS project develops, these default minimum-information submission combinations will be extended to include other areas.
The table below includes examples of which checklist would be used for which sample/sequence type. Note the table is only for guidance, and may not represent the latest state of the combinations.
Decision Tree
To help selecting the correct combination, we have developed a rough 'decision tree'. See an interactive (panning/scrolling) interactive version here.
Otherwise, see the examples in the table below.
Examples
| Full name | General Example | Explicit Example |
|---|---|---|
| MigsOrgHostAssociatedAncient | Ancient animal mitochondrial genome from a skeleton | Woolly mammoth mitochondrial genome from a femur for uploading to NCBI GenBank |
| MigsOrgHumanAssociatedAncient | Ancient human mitochondrial genome from a skeleton | Human mitochondrial genome from a tooth for uploading to NCBI GenBank |
| MiuvigHostAssociatedAncient | Ancient animal-derived virus genome from a skeleton | Avian Influenza genome reconstructed from a chicken bone for uploading to NCBI GenBank |
| MiuvigHumanAssociatedAncient | Ancient human-derived virus genome from a skeleton | Hepatitis B virus genome reconstructed from human tooth for uploading to NCBI GenBank |
| MimagHostAssociatedAncient | Ancient animal-derived metagenome-(de novo) assembled genome (MAG) from a tooth | Bacterial MAG from a pig tooth for uploading to MGnify |
| MimagHumanAssociatedAncient | General human-derived metagenome-(de novo) assembled genome (MAG) from a tooth | Bacterial MAG from a human femur for uploading to MGnify |
| MimagHumanOralAncient | Ancient human dental calculus-derived metagenome-(de novo) assembled genome (MAG) | Bacterial MAG from human dental calculus or tooth for uploading to MGnify |
| MimagHumanGutAncient | Human palaeofaeces-derived metagenome-(de novo) assembled genome (MAG) | Bacterial MAG from human paleofaeces for uploading to MGnify |
| MimagHumanSkinAncient | Human mummy skin-derived metagenome-(de novo) assembled genome (MAG) | Viral MAG from human mummy skin sample for uploading to MGnify |
| MimagSedimentAncient | Ancient sediment-derived metagenome-(de novo) assembled genome (MAG) | Bacteriophage MAG from a mid-depth lake sediment core for uploading to MGnify |
| MimagSoilAncient | Ancient soil-derived metagenome-(de novo) assembled genome (MAG) | Bacterial MAG from an upper-level cave sediment sample for uploading to MGnify |
| MimsHostAssociatedAncient | General skeleton-derived ancient DNA short-read sequences | Shotgun sequenced human femur for pathogen detection or reads of an Auroch femur |
| MimsHumanAssociatedAncient | Human skeleton-derived ancient DNA short-read sequences | Shotgun or 1240k captured reads from a tooth used for population genomics |
| MimsHumanOralAncient | Human tooth or dental calculus-derived ancient DNA short-read sequences | Shotgun or captured sequenced reads from a human tooth or dental calculus used for microbiome taxonomic profiling/pathogen screening/genome reconstruction |
| MimsHumanGutAncient | Human palaeofaeces-derived ancient DNA short-read sequences | Shotgun sequenced reads from human palaeofaeces later used for MAG reconstruction |
| MimsHumanSkinAncient | Human mummy skin-derived ancient DNA short-read sequences | Shotgun sequence reads from mummy skin sample for population-genomics analysis |
| MimsSedimentAncient | Sediment-derived ancient DNA short-read sequences | Shotgun sequenced or captured lake core reads for ecological taxonomic profiling |
| MimsSoilAncient | Soil-derived ancient DNA short-read sequences | Shotgun sequenced or captured cave core reads for ecological taxonomic profiling |
| MimsPlantAssociatedAncient | Plant-derived ancient DNA short-read sequences | Shotgun reads or chloroplast captured short reads for plant population analysis |
| MimsSymbiontAssociatedAncient | Parasite-derived ancient DNA short-read sequences | Shotgun sequenced or captured symbiont reads |