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jfy133 authored Feb 7, 2025
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6 changes: 6 additions & 0 deletions .github/workflows/check_dataset.yml
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run: |
echo "## Ancient Metagenome Environmental" >> validation/validation_results_raw.txt
amdirt validate -s -d -c -m ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries_schema.json &>> validation/validation_results_raw.txt
- name: DATES ancient single genomes (e.g. pathogens)
if: always()
run: |
echo "# Dates" >> validation/validation_results_raw.txt
echo "## Ancient Single Genome Host Associated" >> validation/validation_results_raw.txt
amdirt validate -s -d -c -m ancientsinglegenome-hostassociated/dates/ancientsinglegenome-hostassociated_dates.tsv ancientsinglegenome-hostassociated/dates/ancientsinglegenome-hostassociated_dates_schema.json &>> validation/validation_results_raw.txt
- name: cleanup validation results from streamlit warnings
if: always()
run: |
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161 changes: 33 additions & 128 deletions README.md
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Expand Up @@ -21,22 +21,18 @@ development of the field of ancient metagenomics over time.

<!-- TOC -->

- [Description](#description)
- [Usage](#usage)
- [Citation](#citation)
- [Current Status](#current-status)
- [What is it about?](#what-is-it-about)
- [Samples](#samples)
- [Libraries](#libraries)
- [Interactive samples map](#interactive-samples-map)
- [Contributing](#contributing)
- [Contributing your own Publications](#contributing-your-own-publications)
- [Contributing previously published publications](#contributing-previously-published-publications)
- [Guidelines and Conventions](#guidelines-and-conventions)
- [Who can participate?](#who-can-participate)
- [How can you use it?](#how-can-you-use-it)
- [Citation](#citation)
- [Core Team](#core-team)

<!-- /TOC -->

## Description
## What is it about?

These lists contain information of ancient metagenomic samples such as publication, sample name, sample type,
geographic location, dates and DOIs and other accession numbers to raw data
Expand Down Expand Up @@ -74,50 +70,6 @@ to use the information in their own publications, as per the CC-BY 4.0 licence.
> "Pyu Cities" due to lack of interest from the community. It may be reinstated in
> the future.
## Usage

To download the latest _stable_ release of an AncientMetagenomeDir sample list:

1. Go to the AncientMetagenomeDir [Zenodo repository](https://doi.org/10.5281/zenodo.3980833)
2. Scroll down the page to the 'Files' section
3. Press the 'Download' button next to the `.zip` button
4. Once downloaded, unzip the archive by right-clicking and pressing e.g. decompress or extract
5. In the extracted folder, change into the sample list of interest, and open the `.tsv` file in a spreadsheet program (e.g. LibreOffice Calc, Microsoft Excel) or your programming language of choice (e.g. R)

To download the _bleeding edge_ AncientMetagenomeDir sample list:

1. Right click on one of the following URLs:
- Ancient single genome - host associated: [samples](https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv)
- Ancient metagenome - host associated: [samples](https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv)
- Ancient metagenome - environmental [samples](https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv)
- Ancient single genome - host associated: [libraries](https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv)
- Ancient metagenome - host associated: [libraries](https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv)
- Ancient metagenome - environmental [libraries](https://raw.githubusercontent.com/SPAAM-community/AncientMetagenomeDir/master/ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv)
2. Press 'Save Link as' and save. The file name should end in `.tsv`.
3. Open the resulting `.tsv` file in a spreadsheet program (e.g. LibreOffice Calc, Microsoft Excel) or your programming language of choice (e.g. R).

⚠️ these TSV files in the repository represent the cutting-edge version, and are subject to change, please use the files in the 'releases' section or Zenodo archive for when using for reproducible science!

✅ For some spreadsheet software copy>paste of the raw format directly into a spreadsheet of the \_contents\* of the links above can work, if not, follow instructions above.

## Citation

📖 For **general** use of the project, please use the publication citation below.

For a specific _release_ citation (e.g. the version used for analysis), go to [Releases](https://github.com/SPAAM-community/AncientMetagenomeDir/releases) and use the DOI in the badge of the given release's description, or check the corresponding [Zenodo entry](https://doi.org/10.5281/zenodo.3980833)

Alongside the Zenodo ID of the release version, please also cite:

Fellows Yates, J. A., Andrades Valtueña, A., Vågene, Å. J., Cribdon, B., Velsko, I. M., Borry, M., Bravo-Lopez, M. J., Fernandez-Guerra, A., Green, E. J., Ramachandran, S. L., Heintzman, P. D., Spyrou, M. A., Hübner, A., Gancz, A. S., Hider, J., Allshouse, A. F., Zaro, V., & Warinner, C. (2021). Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Scientific Data, 8(1), 31. DOI: [10.1038/s41597-021-00816-y](https://doi.org/10.1038/s41597-021-00816-y)

⚠️ You must also cite each paper you use data from, citing AncientMetagenomeDir is not sufficient on it's own!

> ℹ️ The AncientMetagenomeDir community curates this data on a voluntary basis, and therefore
> provides no warranty or completeness or accuracy of the data. If in doubt, refer
> to the original publication of a given sample. Corrections are accepted, and thus later
> versions may have different values.
## Current Status

### Samples

Expand Down Expand Up @@ -148,83 +100,36 @@ Green: Environmental Metagenome,
Light Blue: Host Associated Metagenome,
Pink: Host Associated Single Genome

## Contributing

<p align="center">
<img src="assets/images/documentation/spaam-AncientMetagenomeDir_workflow.png" width=50% >
<p/>
## Who can participate?

This is a community project open to anyone. If you would like to get involved, you can
join our community on [archaeo.social](https://matrix.to/#/#ancientmetagenomedir:matrix.org).
A guide to join can be found [here](https://www.isbarch.org/chat).

## How can you use it?

Guides on how to use AncientMetagenomeDir can be found [here](docs/using/).

Guides on how to contribute to AncientMetagenomeDir can be found [here](docs/contributing/).

### Citation

📖 For **general** use of the project, please use the publication citation below.

For a specific _release_ citation (e.g. the version used for analysis), go to [Releases](https://github.com/SPAAM-community/AncientMetagenomeDir/releases) and use the DOI in the badge of the given release's description, or check the corresponding [Zenodo entry](https://doi.org/10.5281/zenodo.3980833)

Alongside the Zenodo ID of the release version, please also cite:

> Fellows Yates, J. A., Andrades Valtueña, A., Vågene, Å. J., Cribdon, B., Velsko, I. M., Borry, M., Bravo-Lopez, M. J., Fernandez-Guerra, A., Green, E. J., Ramachandran, S. L., Heintzman, P. D., Spyrou, M. A., Hübner, A., Gancz, A. S., Hider, J., Allshouse, A. F., Zaro, V., & Warinner, C. (2021). Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Scientific Data, 8(1), 31. DOI: [10.1038/s41597-021-00816-y](https://doi.org/10.1038/s41597-021-00816-y)
!> _WARNING_ You must also cite each paper you use data from, citing AncientMetagenomeDir is not sufficient on it's own!

> ℹ️ The AncientMetagenomeDir community curates this data on a voluntary basis, and therefore
> provides no warranty or completeness or accuracy of the data. If in doubt, refer
> to the original publication of a given sample. Corrections are accepted, and thus later
> versions may have different values.
If you are not familiar with Git(Hub), quick start step-by-step guides can be found in
the following (note these may be out of date):

- [Adding samples and libraries via pull request](https://github.com/SPAAM-community/AncientMetagenomeDir/wiki/Adding-metadata:-step-by-step-guide)
- Performing a pull request _review_ [here](https://hackmd.io/@jfy133/B156Z2mfP) or in PDF format [here](https://github.com/spaam-community/AncientMetagenomeDir/raw/master/assets/intro_to_ancientmetagenomedir_github_pull_request_review.pdf)

Samples must be from _published_ studies, and should only include _sample_ level
information. Preprints often have not made data avaliable at this point, and we make
the **assumption** that peer-review has correctly evaluated any submitted metagenome is
valid. Included papers should generally have uploaded their own data, however in certain
cases may see exceptions (such as retrieval of bacterial genomes from off-target reads from
human population studies). If unsure, please consult the AncientMetagenomeDir community on [slack](https://spaam-community.slack.com/channels/ancientmetagenomedir).

Samples must also have been accessible on public databases (e.g. [EBI
ENA](https://www.ebi.ac.uk/ena) or [NCBI
SRA](https://www.ncbi.nlm.nih.gov/sra)).

> Important: we do not currently record _sequencing data_ information, due to
> different uploading strategies by different groups.
### Contributing your own Publications

Contributing a new publication's sample information consists of the following:

- check under the
[issues](https://github.com/spaam-community/AncientMetagenomeDir/issues) tab if
the paper is already listed (if not, make one!)
- check whether the issue has already been
[closed](https://github.com/spaam-community/AncientMetagenomeDir/issues?q=is%3Aissue+is%3Aclosed)
- if it listed, check to see if there is already a [pull
request](https://github.com/spaam-community/AncientMetagenomeDir/pulls)
linked to it
- assign yourself to the issue
- check if site/samples have been published before (i.e. to ensure the same
names are used for any new samples)
- making your own fork or branch of the repository
- update the given list (e.g. in spreadsheet program, R etc.)
- generally you will be copying direct from a publication's supplementary
information
- some columns have standard pre-defined categories, check a lists's README if
in doubt!
- if you need to add a category please request one by mentioning
@ancientmetagenomedir-coreteam in your PR, or update the enums in JSON files
under `assets/enums` yourself
- making a pull-request
- receive a review to check your additions follow current conventions
- have your PR merged
- close the issue

All contributions are attributed through Git's in-built recording of the author
of each commit and pull request. These will be displayed publically in the
future.

### Contributing previously published publications

In addition to researchers adding their own publications, we will also maintain
lists of published but not-yet-added studies using github issues.

Therefore researchers who wish to contribute who do not yet have their own
publications, can 'assign' themselves to specific 'issues' (papers), and reduce
the risk of duplicates.

Contribution of these publications follow as [above](#own-publications).

### Guidelines and Conventions

To ensure efficient and consistent searching, we include guidelines on how to
record and format information. Adherence to these guidelines is enforced by
'pull request' review by members of the SPAAM community and other contributors.
Furthermore, each category of metagenome will have their own 'special' fields,
which will be defined in each specific context.

## Core Team
The Core Team of AncientMetagenomeDir is responsible for the mantainance of the repository,
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../../assets/documentation/dates/README.md
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project_name publication_year data_publication_doi sample_name archive_project archive_sample_accession date_information_present date_is_radiocarbon archaeological_historical_date multiple_dates reference_location reference_citation_depth primary_secondary_reference_citation_doi direct_dating radiocarbon_lab_code radiocarbon_lab_sample_id spectrometry_type pretreatment_reported pretreatment_type sample_material uncalibrated_date uncalibrated_uncertainty_plus_minus delta_13c carbon_perc delta_15n carbon_nitrogen_ratio calibration_reported calibration_curve calibration_software calibration_software_version calibration_software_settings calibration_software_citation_doi calibrated_range_lower calibrated_range_upper calibrated_range_median calibrated_range_suffix calibrated_range_sigma reservoir_offset_mentioned reservoir_offset_applied reservoir_offset_type reservoir_offset_reported reservoir_offset_reported_sd reservoir_aquatic_carbon_perc reservoir_aquatic_carbon_perc_sd
AndradesValtuena2017 2017 10.1016/j.cub.2017.10.025 1343UnTal85 PRJEB19335 ERS1892067 TRUE TRUE DNE FALSE main text 2 10.1371/journal.pone.0139705 TRUE MAMS 18949 AMS NR NR tooth 3819 24 -20.5 47.5 -99999 3.3 TRUE IntCal13 OxCal v4.2.24 default 10.1017/S0033822200033865 4346 4098 4203 cal BP 2 TRUE FALSE DNE NA NA NA NA
AndradesValtuena2017 2017 10.1016/j.cub.2017.10.025 6Post PRJEB19335 ERS1892066 TRUE TRUE DNE FALSE main text 2 10.1371/journal.pone.0139705 TRUE MAMS 18955 AMS NR NR tooth 3574 19 -20.7 49 -99999 3.3 TRUE IntCal13 OxCal v4.2.24 default 10.1017/S0033822200033865 3957 3832 3873 cal BP 2 TRUE FALSE DNE NA NA NA NA
Spyrou2018 2018 10.1038/s41467-018-04550-9 RT5 PRJEB24296 ERS2106903 TRUE TRUE DNE FALSE supplement text 1 10.1038/s41467-018-04550-9 TRUE MAMS 29430 AMS NR NR tooth 3517 27 -99999 -99999 -99999 -99999 TRUE NR NR NR NR NR 3868 3704 3789 cal BP 2 FALSE DNE DNE NA NA NA NA

Spyrou2018 2018 10.1038/s41467-018-04550-9 RT6 PRJEB24296 ERS2106904 TRUE TRUE DNE FALSE supplement text 1 10.1038/s41467-018-04550-9 TRUE MAMS 29431 AMS NR NR tooth 3499 25 -99999 -99999 -99999 -99999 TRUE NR NR NR NR NR 3842 3696 -99999 cal BP 2 FALSE DNE DNE NA NA NA NA

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