MInAS ancient DNA MIxS extension
Specifications of the Ancient DNA extension of the Minimum Information about any Ancient Sequence (MInAS) standard project, generated using LinkML (https://linkml.io/linkml/). This file is released by the MInAS project for use by anyone handling ancient DNA data or information about biological sequences. This file is also used as an authoritative 'source of truth' to generate downstream artifacts of the extension, available here: https://github.com/MIxS-MInAS/extension-ancient/blob/main/src/mixs/schema/ancient.yml.
This reference documentation site is an automated rendering of the specifications of the mixs-minas schema, generated using LinkML (https://linkml.io/linkml/)
This page only includes MInAS metadata terms from the 'ancient' extension as well as the controlled vocabulary (enumerations) and categories (subsets) - it does not include the full standard.
How to use
How to use
Use the tables below or the search bar to find a metadata term (slot) of interest and open the dedicated page.
In each metadata term (slot) page you will find:
- Title
- Description
- Formatting properties
- Examples
- Additional annotations
- Raw source YAML the page was rendered from
Information
Name: mixs-minas
Slots
| Slot | Description |
|---|---|
| ancient_data | Data that comply with Extension Ancient |
| batch_ids | Identifiers for any form of batch or 'group' that the samples is associated w... |
| biocultural_label | Relevant biocultural labels defined by the local contexts project (https://lo... |
| capt_pcr_cyc_tot | Amplification cycles after capture enrichment total |
| capt_probe_desc | Description of target enrichment probe designs used (e |
| capt_probe_src_taxid | NCBI taxon ID(s) of all organisms included in the baits of a whole organelle ... |
| chrono_age_protocol | A description of or reference to the methods used to determine the earliest_c... |
| chrono_age_remarks | Notes or comments about the earliest_chrono_age and latest_chrono_age |
| context_retrieval_date | Date of excavation or retrieval from burial or depositional context, if known |
| cultural_era | The cultural era approximating to the period in which the archaeological rema... |
| damage_treatment | Indication of whether characteristic ancient DNA damage has been altered or r... |
| data_preproc_desc | Description of preprocessing performed on the reads in the sequencing data fi... |
| earliest_chrono_age | The maximum/earliest/oldest possible age of a specimen as determined by a dat... |
| earliest_chrono_sys | The reference system associated with the earliest_chrono_age |
| geological_epoch | The geological epoch approximating to the period within which the specimen or... |
| host_preserv_state | Description of the state of the sampled (ancient) organism/host as originally... |
| latest_chrono_age | The minimum/latest/youngest possible age of a specimen as determined by a dat... |
| latest_chrono_sys | The reference system associated with the latest_chrono_age |
| lib_gener_technique | The technique used to generate the library, i |
| lib_mid_desc | Index/barcode/primer configuration used during library building for sequencin... |
| lib_polymerase | The polymerase enzyme used for building nucleic acid libraries |
| lib_strandedness | The strandedness of the original template nucleic acid molecules used for con... |
| library_name | Any ID or name used for referring to a nucleic acid sequencing library associ... |
| nucl_acid_extr_date | The date when the nucleic acid extraction was started from the sample materia... |
| orig_site_lat | The latitude coordinate of the original geographical origin of the sample, e |
| orig_site_loc | The original geographical origin of the sample, when sampled outside its orig... |
| orig_site_lon | The longitude coordinate of the original geographical origin of the sample, e |
| orig_site_name | Designated name of the archaeological or ecological site, ancient settlement,... |
| palaeopath_status | Describe briefly any relevant palaeopathological or health-related observatio... |
| past_env_broad | Report information about the general ancient broad environmental system that ... |
| past_env_local | Report information about the smaller-scale environmental system of the local ... |
| permit_authority | Name of the authorit(ies) or institution(s) that granted sampling and analysi... |
| permit_date | Date on which a permit was granted |
| permit_id | A permit ID, code, or any form of identify provided by any authority (ethical... |
| permit_scope | Description of the original scope and permissions of the research on the gene... |
| prev_pubs | Any previous publications that report non-nucleic acid data from the same sam... |
| reads_removed_desc | Specify whether associated data was filtered in some form prior to upload, su... |
| reamp_pcr_cyc_tot | Number of amplification cycles after library indexing PCR |
| samp_alt_lab_ids | An alternative sample or material ID related to the sample not already covere... |
| samp_category | The type/category of a sample |
| samp_decont_pretreat | Protocols employed for sample surface decontamination of external modern nuc... |
| samp_preserv_treatm | Description of any treatment applied directly to samples for the specific pur... |
| sop | Standard operating procedures used to generate genomes, metagenomes or enviro... |
| sop_experimental | Provide a DOI or URL to refer to the paper where the field report, nucleic ac... |
| sop_lib_preparation | Citation(s) for the nucleic acid library preparation protocol |
| store_cond | Explain how and for how long the sample was stored before DNA extraction (for... |
| stratigraph_context | Associated stratigraphic context(s) that the sample was retrieved from, usual... |
Enumerations
| Enumeration | Description |
|---|---|
| BioCulturalLabelEnum | Options defining community expectations about the appropriate use of the sequ... |
| ChronoAgeProtocolEnum | Options for methods to determine the age at time of death of an organism or t... |
| ChronoAgeSysEnum | Options for specifying the chonometric age reference or timescale of a date |
| DamageTreatmentEnum | Options for types of molecular damage removal during library construction of ... |
| GeolEpochEnum | Chronometric epochs defined by the International Chronostratigraphic Chart (v... |
| LibStrandEnum | Options for the strandedness of the input 'template' DNA molecules used for D... |
| LibTypeEnum | Options for types of DNA that have been targeted for DNA library construction |
| SampCategoryEnum | Controlled vocabulary defining the category of a sample based on its experien... |
Subsets
| Subset | Description |
|---|---|
| CombinationClasses | MIxS combination classes that group related slots for specific sample types o... |
| Environment | MIxS terms related to the environmental context of the sample or specimen |
| Ethics | MIxS terms related to ethical considerations, permissions, and approvals asso... |
| Investigation | MIxS terms related to the overall investigation, study, or project associated... |
| NucleicAcidSequenceSource | MIxS terms related to the source of nucleic acids for sequencing, such as ext... |
| Sequencing | MIxS terms related to the sequencing stage of nucleic acid sequencing data ge... |