Ancient Extension
Version
The current version is: v0.0.3.
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.
A simplified current version of the metadata fields to be proposed to be included 'ancient' extension is rendered below.
For feedback, on the current proposals, please see the contact information on the homepage.
For the current release of the base MIxS checklists and other extensions, please see the GenSC and/or MIxS websites.
| Structured comment name | Item (rdfs:label) | Definition | Expected value | Value syntax | Example | Section | minas | Preferred unit | Occurence | MIXS ID | Modification Suggestion | Requires Further Discussion | Reason for further discussion |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| cultural_era | nan | The cultural era approximating the period in which the individual lived from https://chronontology.dainst.org/ or PeriodO. Specify when no value for 'sample_age' is present, or additionally to it. | Chronotology or PeriodO term; text | {termLabel} {[termID]}|{text} | Copper Age [Chronotology: NW6hofAScJSE] | investigation | X | nan | m | MIXS:XXXXXXX | Question: switch to free-text? Conditional to sample_age | Y | nan |
| dna_extraction_date | nan | The date when the nucleic acids was extracted from the sample material. In case no exact time is available, the date can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant | date | {timestamp} | 2015 | nucleic acid sequence source | M | year | 1 | MIXS:XXXXXXX | nan | N | nan |
| recovery_date | nan | Date of excavation or retrieval from burial or depositional context, if known | date | {timestamp} | 1930 | investigation | X | date | 1 | MIXS:XXXXXXX | nan | N | nan |
| sample_age | nan | The approximate date that individual was living and then died, or the sample was exposed to the surface. Typically inferred from archaeological material, or biological material associated with a sediment, with radiocarbon dating and other chronometric methods. Should be midpoint of calibrated radiocarbon age. | value from BP (1950) | {integer} | 123440 | investigation | X | cal BP | m | MIXS:XXXXXXX | nan | N | nan |
| sample_age_inference_methods | nan | The method used to infer the sample age. Method (14C, OLS, etc.) and associated information (lab code, etc). An enumerated list with age/depths model, corralative (relative dating), annual lamination, pollen records, diatom records, physical observation, etc. | enumeration | ??? | C14 | investigation | X | nan | m | MIXS:XXXXXXX | nan | Y | [JAFY/MS] How to define, very heterogenous, maybe split: method/lab code |
| site_type | nan | The type of site the sediment cores where taken. E.g. ocean, marine, freshwater, brackish, ice caves, caves. | text | {text} | cave | environment | E | nan | 1 | MIXS:XXXXXXX | nan | Y | [JAFY] can this be expanded to non-seidment like sites? Open air burials? Is there an overlap here with env_*_scale? Otherwise I think this would go to the environmental_packages |
| damage_treatment | nan | Indication of whether characteristic ancient DNA damage has been removed in a laboratory | enumeration | [none|partial-udg|full-udg|enriched|other] | none | sequencing | M | nan | 1 | MIXS:XXXXXXX | nan | N | [JAFY] what if people upload BAMs of merged multiple libraries |
| experimental_procedures | nan | Provide a DOI to refer to the paper where the procedure is explained in more details | PMID, DOI or URL | {PMID}|{DOI}|{URL} | nan | sequencing | X | nan | 1 | MIXS:XXXXXXX | nan | Y | [JAFY] What procedures does this refer to? Each paper will have many protocols to cite for extraction, library construction, reconditioning, etc. Duplicate of SOP? |
| lib_concentration | nan | Concentration of library in copies per µl, as inferred by qPCR. | integer | {integer} | 123000000 | sequencing | X | copies/µl | 1 | MIXS:XXXXXXX | nan | N | nan |
| lib_index_polymerase | nan | The name of polymerase enzyme used to index DNA libraries | text | {text} | Agilent PfuTurbo Cx HotStart | sequencing | X | nan | 1 | MIXS:XXXXXXX | nan | Y | [JAFY] Condition on what? And would including the SKU be useful to include too (as it's a more stable code) |
| lib_preparation_protocol | nan | Citation(s) for the DNA library preparation protocol | text | {text} | Meyer and Kircher, 2010 | sequencing | X | nan | 1 | MIXS:XXXXXXX | nan | Y | [JAFY] Condition on what? |
| lib_reamplification_polymerase | nan | The name of polymerase enzyme used for reamplifying DNA libraries | text | {text} | KAPA HiFi HotStart Uracil+ | sequencing | X | nan | 1 | MIXS:XXXXXXX | nan | Y | [JAFY] Condition on what? |
| lib_type | library type | The type of library created. Amplicon based or non-amplicon based. Amplicon based, is a library that result in rather short DNA fragments while non-amplicon-based referres to non targeted approach. | enumeration | [shotgun|amplicon] | shotgun | sequencing | M | nan | 1 | MIXS:XXXXXXX | nan | Y | [JAFY] I'm not sure about the definition of amplicon here, it could be confusing - 'natural' aDNA is normally short, maybe need to rather change the definition to specify using primers targeting specific regions of the genome instead |
| neg_cont_status | negative control status | Specify whether the sample is a negative control or not. | negative control status | {boolean} | nan | investigation | X | nan | 1 | MIXS:XXXXXXX | nan | Y | [JAFY] Wouldn't this be mandatory if it's boolean? A sample is either a negative control or not ... Would this also potentially not apply to all other tables? [AFG/BM] The problem with negative controls is that they come from diff batches so becomes hard to control. (M). Issue: in paleometagenome less negative controls are used as there is a more reliance on damage patterns and this is not the case for sedaDNA where negative controls should be mandatory. |
| num_capture_reamp_cycles | nan | Number of amplification cycles after capture enrichment | number of amplification cycles | {integer} | 10 | sequencing | X | nan | 1 | MIXS:XXXXXXX | Condition: if performed | N | nan |
| num_reamp_cycles | number of reamplification cycles | Number of amplification cycles after library indexing PCR | number of amplification cycles | {integer} | 8 | sequencing | X | nan | 1 | MIXS:XXXXXXX | Condition: if performed | N | nan |
| preservational_treatment | preservation treatment | Description of any treatment applied to samples for the purpose of maximising collection preservation that may influence downstream DNA recovery or library construction, such as storage fluid or reconstructive glue | text | {text} | stored in formalin | nucleic acid sequence source | X | nan | 1 | MIXS:XXXXXXX | Condition: if present | N | nan |
| sample_alt_lab_ids | alternative sample IDs | Any alternate sample IDs used in by the research group publishing the paper or other groups. If known. | text | {text} | ABC_24 | investigation | X | nan | 1 | MIXS:XXXXXXX | nan | N | nan |
| samp_decontam_pretreat | sample decontamination pretreatment | Method(s) employed for surface decontamination of samples of external modern DNA; Treatment used on the samples. Depends on the sample type. More relevant for bones than environmental samples. E.g. buffers, EDTA, etc. | PMID, DOI or URL | {PMID}|{DOI}|{URL}|{text} | EDTA wash, 10.17504/protocols.io.bidyka7w | sequencing | X | nan | m | MIXS:XXXXXXX | nan | N | nan |
| prev_pubs | previous publications | Any publications that report data from the same body/skeleton/individual | text | {DOI}{URL}{PMID} | 10.1126/science.7761839 | investigation | X | nan | m | MIXS:XXXXXXX | nan | Y | [AG/PH] Just DNA data, or also contextual/archaeolgoical publications? |
| collection_context_name | context name where location was collected | Name of where sample originated and is typically stored. Typically will be 'owning institution' | text | {text} | Natural History London | environment | X | nan | 1 | MIXS:XXXXXXX | nan | Y | [AG/PH] e.g. Museum, community, field (want to avoid assumption that insitutuions instead of communities control samples) |
| ethical_authority | ethical authority | Name of the authority or institution that awarded sampling and analysis (e.g. human remains) and/or export permission (e.g. animal remains) | text | {text} | Federal Foreign Office (Germany) | investigation | X | nan | m | MIXS:XXXXXXX | nan | Y | [JAFY] What is the condition on? |
| ethical_date | date of ethical approval date | Date of award of ethical/export permission. The date can be right truncated i.e. all of these are valid times: 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant | date | {timestamp} | 2018-05-11T10:00:00+01:00; 2018-05-11 | investigation | X | nan | m | MIXS:XXXXXXX | nan | Y | [JAFY] What is the condition on? |
| ethical_id | ethical permit/approval ID | The permissions code or ID provided by the authority associated with approval of the analysis of this particular sample | text | {text} | DE-123-JK | investigation | X | nan | m | MIXS:XXXXXXX | nan | Y | [JAFY] What is the condition on? |
| storage_conditions | conditions of sample storage | General conditions in which the sample was stored in long-term collection storage, that may influenced DNA recovery or library construction. For example, specify temperature, humidity, presence of microbial overgrowth etc.. | text | {text} | Climate-controlled | environment | X | nan | 1 | MIXS:XXXXXXX | nan | N | nan |