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Merge branch 'master' into Lebrasseur2024
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@alexhbnr
alexhbnr committed Jul 14, 2024
2 parents 5aee0a5 + 9b65763 commit 21fb153
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2 changes: 1 addition & 1 deletion .github/workflows/autofill.yml
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Expand Up @@ -38,7 +38,7 @@ jobs:
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install amdirt==1.5.0
pip install amdirt==1.6.1
pip install jsonschema==4.17.0
# Get context of PR...
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2 changes: 1 addition & 1 deletion .github/workflows/check_dataset.yml
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Expand Up @@ -16,7 +16,7 @@ jobs:
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install amdirt==1.5.0
pip install amdirt==1.6.1
pip install jsonschema==4.17.0
- name: Make validation results directory
run: mkdir validation/
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16 changes: 16 additions & 0 deletions .streamlit/config.toml
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[global]

# By default, Streamlit displays a warning when a user sets both a widget
# default value in the function defining the widget and a widget value via
# the widget's key in `st.session_state`.

# If you'd like to turn off this warning, set this to True.

# Default: false
disableWidgetStateDuplicationWarning = false

# If True, will show a warning when you run a Streamlit-enabled script
# via "python my_script.py".

# Default: true
showWarningOnDirectExecution = false
2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -13,6 +13,8 @@ and this project follows to [Calendar Versioning](https://calver.org/).

#### Ancient Single Genome: Host Associated

- Sun 2024 10.1038/s41467-024-47358-6 (added by @aidaanva)
- Urban 2024 10.1016/j.cub.2024.04.006 (added by @aidaanva)
- Lebrasseur 2024 10.1093/ve/vead087(added by @YuejiaoHuang)

#### Ancient Metagenome: Environmental
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53 changes: 53 additions & 0 deletions ...entsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv
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40 changes: 39 additions & 1 deletion ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv
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Expand Up @@ -641,7 +641,7 @@ Hodgkins2023 2023 10.1038/s41467-023-41174-0 l’Observance in Marseille 43.296
Hodgkins2023 2023 10.1038/s41467-023-41174-0 Saints Màrtirs Just i Pastor, Barcelona 41.387 2.168 Spain Barcelona-3031-Tooth Homo sapiens 1400 10.1016/j.chom.2016.05.012 bacteria Clostridium tetani tooth chromosome ENA raw PRJEB13664 ERS1124787
Hodgkins2023 2023 10.1038/s41467-023-41174-0 Saint-Laurent-de-la-Cabrerisse 43.084 2.7 France SLC-France-Tooth Homo sapiens 1300 10.1073/pnas.1812865115 bacteria Clostridium tetani tooth chromosome ENA raw PRJEB24499 ERS2865271
Hodgkins2023 2023 10.1038/s41467-023-41174-0 Karlova, Tartu 58.371 26.732 Estonia Karolva-Tooth Homo sapiens 4200 10.1098/rspb.2019.1528 bacteria Clostridium tetani tooth chromosome ENA raw PRJEB32786 ERS3568107
Hodgkins2023 2023 10.1038/s41467-023-41174-0 Abusir el-Meleq, Middle Egypt 29.9 31.2 Egypt Abusir1655-Tooth Homo sapiens 3100 10.1038/ncomms15694 bacteria Clostridium tetani tooth chromosome ENA raw PRJEB33848 ERS3635957
Hodgkins2023 2023 10.1038/s41467-023-41174-0 Abusir el-Meleq, Middle Egypt 29.9 31.2 Egypt Abusir1655-Tooth Homo sapiens 3100 10.1038/ncomms15694 bacteria Clostridium tetani tooth chromosome ENA raw PRJEB33848 ERS3635957
Hodgkins2023 2023 10.1038/s41467-023-41174-0 Abusir el-Meleq, Middle Egypt 29.9 31.2 Egypt Abusir1595-Tooth Homo sapiens 2900 10.1038/ncomms15694 bacteria Clostridium tetani tooth chromosome ENA raw PRJEB33848 ERS3635963
Hodgkins2023 2023 10.1038/s41467-023-41174-0 Abusir el-Meleq, Middle Egypt 29.9 31.2 Egypt Abusir1668-Tooth Homo sapiens 2200 10.1038/ncomms15694 bacteria Clostridium tetani tooth chromosome ENA raw PRJEB33848 ERS3635986,ERS3636003
Hodgkins2023 2023 10.1038/s41467-023-41174-0 Abusir el-Meleq, Middle Egypt 29.9 31.2 Egypt Abusir1671-Tooth Homo sapiens 2100 10.1038/ncomms15694 bacteria Clostridium tetani tooth chromosome ENA raw PRJEB33848 ERS3636004
Expand All @@ -666,4 +666,42 @@ Rozwalak2024 2024 10.1038/s41467-023-44370-0 Cueva de los Muertos Chiquitos (Zap
Jackson2024 2024 10.1093/molbev/msae017 Killuragh 52.6 -8.33 Ireland KGH2-F Homo sapiens 3800 10.1093/molbev/msae017 bacteria Tannerella forsythia tooth chromosome ENA raw,reference_aligned PRJEB64128 ERS15977755
Jackson2024 2024 10.1093/molbev/msae017 Killuragh 52.6 -8.33 Ireland KGH2-B Homo sapiens 3800 10.1093/molbev/msae017 bacteria Streptococcus mutans tooth chromosome ENA raw,reference_aligned PRJEB64128 ERS15977754
Jackson2024 2024 10.1093/molbev/msae017 Killuragh 52.6 -8.33 Ireland KGH1-E Homo sapiens 3800 10.1093/molbev/msae017 bacteria Tannerella forsythia tooth chromosome ENA raw,reference_aligned PRJEB64128 ERS15977753
Urban2024 2024 10.1016/j.cub.2024.04.006 St. Mary Magdalene leprosarium, Winchester 51.059 -1.308 United Kingdom MMW_H50_1 Homo sapiens 600 10.1016/j.cub.2024.04.006 bacteria Mycobacterium leprae tooth chromosome SRA raw PRJNA1021938 SRS20486703
Urban2024 2024 10.1016/j.cub.2024.04.006 St. Mary Magdalene leprosarium, Winchester 51.059 -1.308 United Kingdom MMW_H80_1 Homo sapiens 900 10.1016/j.cub.2024.04.006 bacteria Mycobacterium leprae tooth chromosome SRA raw PRJNA1021938 SRS20486681
Urban2024 2024 10.1016/j.cub.2024.04.006 St. Mary Magdalene leprosarium, Winchester 51.059 -1.308 United Kingdom MMW_H94_1 Homo sapiens 700 10.1016/j.cub.2024.04.006 bacteria Mycobacterium leprae tooth chromosome SRA raw PRJNA1021938 SRS20486688
Urban2024 2024 10.1016/j.cub.2024.04.006 Staple Gardens, Winchester 51.064 -1.317 United Kingdom SGW_S3_1 Sciurus vulgaris 1000 10.1016/j.cub.2024.04.006 bacteria Mycobacterium leprae bone chromosome SRA raw PRJNA1021938 SRS20486690
Sun2024 2024 10.1038/s41467-024-47358-6 QuanErGou 43.65 92.16 China XBQM86 Homo sapiens 2900 10.1038/s41467-024-47358-6 virus Hepatitis B virus bone chromosome GSA reference_aligned PRJCA020853 SAMC3135916
Sun2024 2024 10.1038/s41467-024-47358-6 Tsagaan Del 45.79 112.96 Mongolia MY19 Homo sapiens 700 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135917
Sun2024 2024 10.1038/s41467-024-47358-6 XiHe 39.07 115.93 China XHM12 Homo sapiens 2400 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135918
Sun2024 2024 10.1038/s41467-024-47358-6 XiHe 39.07 115.93 China XHM16 Homo sapiens 2400 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135919
Sun2024 2024 10.1038/s41467-024-47358-6 XiHe 39.07 115.93 China XHM18 Homo sapiens 2400 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135920
Sun2024 2024 10.1038/s41467-024-47358-6 XiHe 39.07 115.93 China XHM23 Homo sapiens 2400 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135921
Sun2024 2024 10.1038/s41467-024-47358-6 XiHe 39.07 115.93 China XHM31 Homo sapiens 2400 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135922
Sun2024 2024 10.1038/s41467-024-47358-6 NanYang 39.07 115.93 China NYM8 Homo sapiens 2400 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135923
Sun2024 2024 10.1038/s41467-024-47358-6 Bayanbulag 42.37 105.21 Mongolia AT7 Homo sapiens 2200 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135924
Sun2024 2024 10.1038/s41467-024-47358-6 Bayanbulag 42.37 105.21 Mongolia AT19 Homo sapiens 2200 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135925
Sun2024 2024 10.1038/s41467-024-47358-6 Bayanbulag 42.37 105.21 Mongolia AT24 Homo sapiens 2200 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135926
Sun2024 2024 10.1038/s41467-024-47358-6 TaoJiaZhai 36.9 101.66 China TJZM25-2 Homo sapiens 1765 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135927
Sun2024 2024 10.1038/s41467-024-47358-6 QuanErGou 43.65 92.16 China XBQM47 Homo sapiens 2900 10.1038/s41467-024-47358-6 virus Hepatitis B virus bone chromosome GSA reference_aligned PRJCA020853 SAMC3135928
Sun2024 2024 10.1038/s41467-024-47358-6 Derestuj 50.6 106.12 Russia XN12 Homo sapiens 2100 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135929
Sun2024 2024 10.1038/s41467-024-47358-6 XingFuLinDai 34.35 108.95 China XFLDM173 Homo sapiens 800 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135930
Sun2024 2024 10.1038/s41467-024-47358-6 LongTouShan 43.07 118.48 China 91KLH18 Homo sapiens 2700 10.1038/s41467-020-16557-2 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135931
Sun2024 2024 10.1038/s41467-024-47358-6 FuLuTa 39.97 111.53 China FLTM18 Homo sapiens 2100 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135932
Sun2024 2024 10.1038/s41467-024-47358-6 FuLuTa 39.97 111.53 China FLTM48 Homo sapiens 2100 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135933
Sun2024 2024 10.1038/s41467-024-47358-6 FuLuTa 39.97 111.53 China FLTM97 Homo sapiens 2100 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135934
Sun2024 2024 10.1038/s41467-024-47358-6 FuLuTa 39.97 111.53 China FLTM101 Homo sapiens 2200 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135935
Sun2024 2024 10.1038/s41467-024-47358-6 NiuHeLiang 41.25 119.41 China 96NVZIM6 Homo sapiens 5000 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135946
Sun2024 2024 10.1038/s41467-024-47358-6 HengShui 35.5 111.58 China JHM2098 Homo sapiens 2500 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135947
Sun2024 2024 10.1038/s41467-024-47358-6 TianTaiJie 37.88 112.57 China SBSM101 Homo sapiens 1500 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135948
Sun2024 2024 10.1038/s41467-024-47358-6 HongHe 47.12 123.61 China HHM29 Homo sapiens 400 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135949
Sun2024 2024 10.1038/s41467-024-47358-6 JiangJiaLiang 40.13 114.02 China 98JJLM9 Homo sapiens 4100 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135936
Sun2024 2024 10.1038/s41467-024-47358-6 JiangJiaLiang 40.13 114.02 China 95JJLM34 Homo sapiens 4100 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135937
Sun2024 2024 10.1038/s41467-024-47358-6 JiangJiaLiang 40.13 114.02 China 95JJLM51 Homo sapiens 4100 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135938
Sun2024 2024 10.1038/s41467-024-47358-6 Tsagaan Del 45.79 112.96 Mongolia MY12 Homo sapiens 700 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135939
Sun2024 2024 10.1038/s41467-024-47358-6 Tsagaan Del 45.79 112.96 Mongolia MY17 Homo sapiens 700 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135940
Sun2024 2024 10.1038/s41467-024-47358-6 QiLangShan 41.06 113.01 China ZQM16 Homo sapiens 1600 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135941
Sun2024 2024 10.1038/s41467-024-47358-6 QuanErGou 43.65 92.16 China XBQM20 Homo sapiens 2900 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135942
Sun2024 2024 10.1038/s41467-024-47358-6 QuanErGou 43.65 92.16 China XBQM46 Homo sapiens 2900 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135943
Sun2024 2024 10.1038/s41467-024-47358-6 QuanErGou 43.65 92.16 China XBQM125 Homo sapiens 2900 10.1038/s41467-024-47358-6 virus Hepatitis B virus bone chromosome GSA reference_aligned PRJCA020853 SAMC3135944
Sun2024 2024 10.1038/s41467-024-47358-6 BeiFang 37.13 81.61 China 11KBM13 Homo sapiens 3400 10.1038/s41467-024-47358-6 virus Hepatitis B virus tooth chromosome GSA reference_aligned PRJCA020853 SAMC3135945
Lebrasseur2024 2024 10.1093/ve/vead087 Kamennyi Ambar 5 52.833 60.367 Russia UR17x29 Equus caballus 3800 10.1038/s41586-021-04018-9 virus Equid herpesvirus 4 bone chromosome ENA raw PRJEB44430 ERS7256200
3 changes: 2 additions & 1 deletion assets/enums/material.json
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"stomach",
"lung",
"skeleton",
"kidney stone"
"kidney stone",
"dentine"
]
}
4 changes: 3 additions & 1 deletion assets/enums/sample_host.json
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"Bovidae",
"Citrus aurantiifolia",
"Citrus medica",
"Lithobates pipiens"
"Lithobates pipiens",
"Equus caballus",
"Sciurus vulgaris"
]
}
3 changes: 2 additions & 1 deletion assets/enums/singlegenome_species.json
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"Xanthomonas citri pv. citri",
"Clostridium tetani",
"Mushuvirus mushu",
"Streptococcus mutans"
"Streptococcus mutans",
"Equid herpesvirus 4"
]
}
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