Merge pull request #2 from pirovc/alpha1

Alpha1

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2021 pirovc.github.io
+Copyright (c) 2022 pirovc.github.io
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -2,7 +2,7 @@
 
 ![GRIMER](grimer/img/logo.png)
 
-GRIMER automates analysis and reports an offline and interactive dashboard integrating annotation, taxonomy and metadata to analyse microbiome studies and detect contamination.
+GRIMER perform analysis of microbiome data and generates a portable and interactive dashboard integrating annotation, taxonomy and metadata.
 
 ## Examples
 
@@ -22,19 +22,34 @@ grimer -h
 
 ## Usage
 
-### Basic
+### Tab-separated input table
 ```bash
-grimer -i input_table.tsv -m metadata.tsv -c config/default.yaml
+grimer -i input_table.tsv
+```
+
+### BIOM file
+```bash
+grimer -i myfile.biom
+```
+
+### Tab-separated input table with taxonomic annotated observations (e.g. sk__Bacteria;k__;p__Actinobacteria;c__Actinobacteria...)
+```bash
+grimer -i input_table.tsv -f ";"
+```
+
+### Tab-separated input table with metadata
+```bash
+grimer -i input_table.tsv -m metadata.tsv
 ```
 
 ### With taxonomy integration (ncbi)
 ```bash
-grimer -i input_table.tsv -m metadata.tsv -c config/default.yaml -t ncbi #optional -b taxdump.tar.gz
+grimer -i input_table.tsv -m metadata.tsv -t ncbi #optional -b taxdump.tar.gz
 ```
 
-### With DECONTAM and MGnify annotations
+### With configuration file to setup external tools, references and annotations
 ```bash
-grimer -i input_table.tsv -m metadata.tsv -c config/default.yaml -d -g
+grimer -i input_table.tsv -m metadata.tsv -t ncbi -c config/default.yaml -d -g
 ```
 
 ### List all options 
@@ -44,7 +59,7 @@ grimer -h
 
 ## Powered by
 
-[<img src="https://static.bokeh.org/branding/logos/bokeh-logo.png" width="100">](https://bokeh.org)
-[<img src="https://pandas.pydata.org/static/img/pandas.svg" width="100">](https://pandas.org)
-[<img src="https://www.scipy.org/_static/logo.png" width="100">](https://scipy.org)
-[<img src="http://scikit-bio.org/assets/logo.svg" width="100">](https://scikit-bio.org)
+[<img src="https://static.bokeh.org/branding/logos/bokeh-logo.png" height="60">](https://bokeh.org)
+[<img src="https://pandas.pydata.org/static/img/pandas.svg" height="40">](https://pandas.org)
+[<img src="https://raw.githubusercontent.com/scipy/scipy/master/doc/source/_static/logo.svg" height="40">](https://scipy.org)
+[<img src="http://scikit-bio.org/assets/logo.svg" height="40">](https://scikit-bio.org)

config/default.yaml

@@ -1,26 +1,15 @@
-sources:
-  contaminants:
-    "CC Bacteria": "sources/contaminants/cc_bacteria.yml"
-    "CC Viruses": "sources/contaminants/cc_viruses.yml"
-    "CC Eukaryota": "sources/contaminants/cc_eukaryota.yml"
-    # "Custom Contaminants 1": "path/contfile1.tsv"
-    # "Custom Contaminants 2": "path/contfile2.tsv"
-  references:
-    "Human-Related": "sources/references/human-related.yml"
-    "Skin": "sources/references/skin.yml"
-    "Oral": "sources/references/oral.yml"
-    # "Custom References 1": "path/reffile1.tsv"
-    # "Custom References 2": "path/reffile2.tsv"
-
-# samples:
-#   controls:
-#     "Positve Controls": "path/file1.tsv"
-#     "Negative Controls": "path/file1.tsv"
+references:
+  "Contaminants": "files/contaminants.yml"
+  "Human-related": "files/human-related.yml" 
+
+#controls:
+  # "Positve Controls": "path/file1.tsv"
+  # "Negative Controls": "path/file1.tsv"
 
 external:
-  mgnify: "sources/mgnify/taxa_counts_top10.tsv"
+  mgnify: "files/mgnify.tsv"
   decontam:
-    threshold: 0.2 # [0-1]
+    threshold: 0.1 # [0-1] P* hyperparameter
     method: "frequency" # frequency, prevalence, combined
     # # frequency (default: use sum of counts)
     # frequency_file: "path/file1.txt"

sources/README.md → files/README.md

@@ -1,31 +1,33 @@
-# GRIMER Sources
+# GRIMER References and aux. files
 
-## File formats
-
-Contaminant and reference sources can be provided to grimer in two formats:
+## Reference file format
 
 1) File with a list (one per line) of taxonomic identifiers or taxonomic names
 
-2) Formatted .yml file:
+2) or formatted `.yml` file:
 
-	Description/Group 1:
-	  Description/Group 2:
-	     url: ""
-	     ids: []
+```yaml
+"General Description":
+  "Specific description":
+    url: "www.website.com?id={}" 
+    ids: [1,2,3]
+```
 
 The url can be a link to the entries listed on the id. Use the `{}` as a placeholder for the id. Example: `https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id={}`
 
 The files should be provided in the main configuration file for grimer as follows:
 
-	sources:
-	  contaminants:
-	    "CUSTOM CONTAMINANTS 1": "file.txt"
-	    "LAB CONT": "another_file.yml"
-	  references:
-	    "Human gut": "listofnames.txt"
-	    "XYZ": "another.yaml"
+```yaml
+references:
+  "Contaminants": "files/contaminants.yml"
+  "Human-related": "files/human-related.yml" 
+  "CUSTOM CONTAMINANTS": "file.txt"
+  "LAB RELATED BACTERIA": "another_file.yml"
+```
 
-## Contaminants
+### contaminants.yml
+
+Last update: 2021-04-01
 
  | Organism group | Genus | Species |
  |----------------|-------|---------|
@@ -49,20 +51,28 @@ The files should be provided in the main configuration file for grimer as follow
  | Viruses | 0 | 301 | 2019 Asplund, M. et al. |
  | Total (unique) | 201 | 625 | |
 
-## References
+### human-related.yml
+
+BacDive and eHOMD dump date: 2021-04-13
 
 ```bash
 scripts/bacdive_download.py
 scripts/ehomd_download.py
 ```
 
-BacDive and eHOMD dump date: 2021-04-13
+## MGnify
+
+The downloaded MGnify database file should be provided in the main configuration file for grimer as follows:
+
+    external:
+      mgnify: "files/mgnify.tsv"
+
+## mgnify.tsv
 
-## MGNify
+MGnify dump date: 2021-04-08 (latest study accession MGYS00005724)
 
 ```bash
 seq -f "MGYS%08g" 256 5724 | xargs -P 24 -I {} scripts/mgnify_download.py {} mgnify_dump_20210408/ > mgnify_dump_20210408.log 2>|1 |
 
-scripts/mgnify_extract.py -f mgnify_dump_20210408 -t 10 -o taxa_counts_top10.tsv
+scripts/mgnify_extract.py -f mgnify_dump_20210408 -t 10 -o files/mgnify.tsv
 ```
-MGnify dump date 2021-04-08 (latest study accession MGYS00005724)

sources/contaminants/cc_bacteria.yml → files/contaminants.yml

@@ -4,7 +4,7 @@
     ids: [407, 335058, 504481, 1747, 40324, 1033, 38304, 28037, 470, 29448, 1828, 92793, 75, 375, 180282, 851, 301302, 853, 816, 33870, 85698, 87883, 147207, 68909, 1043493, 293256, 1134405, 410, 321895, 432308, 1416628, 1314, 1343, 69359]
   "2018 Kirstahler, P. et al.":
     url: "http://doi.org/10.1038/s41598-018-22416-4"
-    ids: [1747, 40324, 470, 29448, 294, 1828, 39491, 40214, 28090, 134533, 108981, 202956, 239935, 28117, 28116, 818, 820, 161879, 33011, 80866, 853, 823, 821, 296, 303, 34073, 1050843, 1055192, 106648, 1075768, 1076, 1112209, 1131812, 1150298, 1159870, 1160721, 1198452, 1217692, 1276755, 1320556, 134534, 1353941, 136273, 1435036, 147645, 1492737, 1492738, 1497615, 1504823, 1509403, 1519439, 1538644, 1619232, 162426, 1646498, 165179, 1654716, 1665556, 1678129, 169292, 1706231, 1714344, 172088, 1736272, 1736280, 1736296, 1736316, 1736528, 1736532, 1740090, 1833, 1835254, 192843, 202952, 202954, 211589, 216465, 245, 246602, 246787, 247, 266749, 2702, 2736, 285, 28901, 29536, 310297, 310298, 33010, 34062, 346179, 362413, 362418, 370974, 38303, 387661, 40520, 418240, 46506, 47920, 503361, 50340, 52133, 529884, 53412, 55197, 55508, 5665, 64974, 70863, 75659, 756892, 76773, 80878, 80882, 86182, 96345, 986, 989370, 991, 99158]
+    ids: [1747, 40324, 470, 29448, 294, 1828, 39491, 40214, 28090, 134533, 108981, 202956, 239935, 28117, 28116, 818, 820, 161879, 33011, 80866, 853, 823, 821, 296, 303, 34073, 2559073, 1055192, 106648, 1075768, 1076, 1112209, 1131812, 1150298, 1159870, 1160721, 1198452, 1217692, 1276755, 1320556, 134534, 1353941, 136273, 1435036, 147645, 1492737, 1492738, 1497615, 1504823, 1509403, 1519439, 1538644, 1619232, 162426, 1646498, 165179, 1654716, 1665556, 1678129, 169292, 1706231, 1714344, 172088, 1736272, 1736280, 1736296, 1736316, 1736528, 1736532, 1740090, 1833, 1835254, 192843, 202952, 202954, 211589, 216465, 245, 246602, 246787, 247, 266749, 2702, 2736, 285, 28901, 29536, 310297, 310298, 33010, 34062, 346179, 362413, 362418, 370974, 38303, 387661, 40520, 418240, 46506, 47920, 503361, 50340, 52133, 529884, 53412, 55197, 55508, 5665, 64974, 70863, 75659, 756892, 76773, 80878, 80882, 86182, 96345, 986, 989370, 991, 99158]
   "2015 Jervis-Bardy, J. et al.":
     url: "http://doi.org/10.1186/s40168-015-0083-8"
     ids: [286, 48736, 59732, 335058, 41275, 28100, 34072]
@@ -44,3 +44,29 @@
   "2017 Salter, S.J. et al.":
     url: "http://doi.org/10.1371/journal.pntd.0005975"
     ids: [50709, 299566, 1375, 2040, 507, 31988, 165779, 161492, 150247, 92793, 374, 55080, 1696, 41275, 369926, 32008, 194, 2717, 75, 10, 59732, 1716, 37914, 231454, 423604, 212791, 117563, 963, 1004300, 682522, 1357, 149698, 906, 68287, 407, 33882, 1839, 528, 376469, 84567, 335058, 28100, 838, 286, 83618, 48736, 379, 1835, 45669, 22, 28453, 13687, 40323, 1054211, 13275, 33057, 157, 213484, 29465, 1827, 265, 1386]
+  "2018 Stinson, L.F. et al.":
+    url: "http://doi.org/10.3389/fmicb.2018.00270"
+    ids: [1696, 1716, 43668, 37914, 1269, 32207, 1743, 836, 838, 1016, 308865, 1386, 2755, 1279, 66831, 1350, 1578, 1301, 29465, 374, 407, 434, 165696, 13687, 283, 80865, 93681, 48736, 570, 713, 469, 212791, 286, 40323]
+  "2019 Stinson, L.F. et al.":
+    url: "http://doi.org/10.1111/lam.13091"
+    ids: [561, 335058, 407, 13687, 407, 374, 165696, 222, 1716, 547, 48736, 1004302, 1827, 1743, 1269, 204456, 106589, 1678]
+  "2002 Kulakov, L.A. et al.":
+    url: "http://doi.org/10.1128/AEM.68.4.1548-1555.2002"
+    ids: [329, 376, 239, 36773, 69392, 1785, 1409, 304, 28214, 294]
+"Common Viral contaminants":
+  "2019 Asplund, M. et al.":
+    url: "http://doi.org/10.1016/j.cmi.2019.04.028"
+    ids: [12071, 742919, 11103, 31647, 1678143, 10298, 10376, 10359, 11676, 129951, 10583, 31552, 10798, 11908, 585044, 518981, 1225745, 11620, 1891767, 493803, 11033, 159150, 35306, 68887, 11870, 11958, 11861, 11946, 11864, 363745, 363020, 242521, 11866, 11960, 31668, 31669, 31670, 11867, 11955, 11874, 11876, 11878, 11885, 36381, 11886, 11888, 269447, 269448, 11950, 11948, 1332312, 354090, 11884, 1352534, 1395610, 1395611, 1395612, 1395613, 1395614, 1395615, 1395616, 1395617, 1395618, 1395619, 1395620, 1341019, 11801, 11809, 1511763, 1394983, 697906, 1072204, 1148801, 1574422, 12104, 763552, 10264, 85708, 759804, 28344, 85506, 33747, 10345, 285986, 220638, 1154691, 185638, 1169627, 1045778, 185636, 72201, 345198, 176652, 1301280, 68347, 1618248, 1618254, 10288, 198112, 1454023, 1454024, 1454025, 1278278, 1278246, 1278252, 1278247, 1278248, 1278249, 1278250, 1278251, 399781, 1278255, 346932, 1278261, 1278263, 1278265, 1474867, 1379694, 1521385, 1521387, 1521389, 938081, 938082, 880162, 251749, 455370, 169864, 1379788, 1608440, 642253, 642255, 1224510, 1592207, 1592212, 1592083, 1592085, 1592086, 1592088, 1592093, 1592095, 1592096, 1592081, 1843761, 1519405, 1557033, 1608451, 664785, 1435438, 1170653, 40979, 12235, 12138, 11987, 51680, 12056, 146500, 554168, 212035, 1269028, 693272, 1420594, 1094892, 1128140, 1235314, 1128143, 1128151, 1128131, 1450746, 1461100, 181522, 1424633, 1010698, 1299317, 1450749, 1416631, 1128422, 1034806, 1592112, 1592113, 1592127, 938080, 1074214, 1519385, 1519387, 1519389, 1519390, 1519395, 1519396, 1519397, 186617, 1262072, 1407671, 743583, 340016, 745107, 745102, 745100, 1416009, 1187128, 889876, 760732, 1243183, 1229760, 1481186, 1505225, 1560342, 233894, 115987, 260149, 227470, 926067, 1127514, 1296654, 294382, 1486657, 1084719, 10756, 1486662, 1285382, 1497851, 1127515, 145579, 263375, 764562, 1133292, 1133022, 242527, 260373, 279280, 644524, 242861, 1132026, 1357714, 1197951, 1327981, 1327976, 1327979, 1327992, 1328030, 1327990, 1327980, 1327972, 1327982, 1327995, 1327983, 1327970, 1327971, 756279, 1327977, 1327993, 1328029, 1327975, 1327974, 1327985, 756280, 756282, 1527524, 1540094, 1042123, 541865, 1567016, 765765, 1176422, 1327037, 1162295, 1141135, 1141136, 335924, 536444, 929832, 682650, 1137745, 536473, 749413, 1477406, 1048515, 1048516, 1048517, 1048520, 1048521, 1537091, 1264700, 1609634, 1455074, 414970, 10863, 10864, 1222338, 1147148, 1237364, 1414766, 1977402, 948870, 1524881, 10665, 10760, 1147094, 1429767, 925983, 925984, 1527519, 1527506, 1229753, 1540097, 1540098, 1054461, 1391223, 294631, 1325731, 908819, 1458858, 1458842, 90963, 1536592, 1527515, 551895, 1129191, 139872, 201847, 287412, 1262517, 754044, 1385658, 1176423, 889949, 446529, 1034128, 1056830, 1089119, 1486472, 1034111, 205879, 1340709, 1567475, 1472912, 1204539, 1399915, 1283076, 1283077, 1168479, 1168478, 440250, 400567, 994601, 1465639, 889956, 445700, 444862, 536454, 445688, 444861, 1229794, 1229793, 1229792, 1229791, 1229790, 1229789, 1229786, 1229787, 1229788, 1229784, 1229782, 376758, 1498188, 504501, 504553, 1235647, 1235648, 1235649, 1235650, 1235653, 1235654, 1235655, 1235656, 1235657, 877240, 754052, 1316739, 347326, 1235689, 31535, 757342, 582345, 1462581, 386793, 1204517, 347327, 1335230, 743813, 1348912, 1327964, 270673, 188350, 1541891, 169683, 998086, 1500757, 1458843, 1129146, 1279082, 1114179, 1548900, 1231048, 1548901, 1449437, 1548918, 1476390, 462590, 754048, 948071, 1481785, 1417599, 1131316, 691965, 136084, 754067, 1161935, 1173749, 1173761, 1173759, 1173762, 590739, 1406795, 1141134, 1204529, 1540099, 1168549, 866889, 1458859, 1458860, 1458861, 10761, 754060, 1524882, 1357423, 373126, 1150991, 1195080, 320843, 55510, 1434319, 320850, 369581, 537874, 1208587, 1566990, 10732, 490913, 1526550, 1340810, 756277, 753084, 753085, 756275, 1026955, 1340812, 238854, 555387, 754042, 444860, 981335, 469660, 215796, 1478972, 1385659, 926697, 336724, 278008, 1211417, 271647, 754075, 573173, 573174, 979525, 979534, 1529058, 1283071, 573176, 1589298, 1076759, 1461743, 1150989, 754058, 754051, 929835, 1414739, 754072, 1524880, 194802, 1168281, 1204514, 1188795, 331278]
+  "2015 Mukherjee, S. et al.":
+    url: "http://doi.org/10.1186/1944-3277-10-18"
+    ids: [10847]
+  "2015 Kjartansdóttir, K.R. et al.":
+    url: "https://doi.org/10.1073/pnas.1423756112"
+    ids: [322019]
+"Common Eukaryotic contaminants":
+  "PRJNA168":
+    url: "https://www.ncbi.nlm.nih.gov/genome/guide/human/"
+    ids: [9606]
+  "2016 Czurda, S. et al.":
+    url: "https://doi.org/10.1128/JCM.02112-15"
+    ids: [1895944, 76775, 5308]

sources/references/oral.yml → files/human-related.yml

@@ -1,3 +1,16 @@
+"Human-related bacterial isolates from BacDive":
+  "Limbs":
+    url: "https://bacdive.dsmz.de/search?search=taxid:{}"
+    ids: [326522, 82380, 1701, 131110, 29388, 84698, 729, 69968, 28264, 200476, 58172, 490, 1280, 1290, 41276, 220685, 28449, 644, 1660, 147645, 1351, 90367, 391, 1717, 1720, 1314, 646, 29391, 732, 1365628, 90245, 495, 192066, 753, 1979962, 82633, 53363, 539, 37637, 37329, 755171, 29466, 291112, 614, 28090, 1402, 217204, 1509, 326523, 2014, 1303, 28038, 676, 105219, 13076, 66228, 504, 28189, 752, 108980, 1747, 1282, 1504, 33028, 303, 672, 28035, 1286, 485, 1311, 28188, 28132, 1328, 1506, 652, 29380, 760, 46124, 1379, 755172, 193461, 158822, 479, 68892, 479117, 33889, 670, 420404, 1305, 1697053, 71254, 310300, 47920, 669, 1245, 38289, 36740, 354351, 48296, 29318, 192, 38313, 180332, 135487, 33007, 287, 754, 29317, 1648, 1713, 1352, 550, 53437, 2054, 38284, 1667, 511, 1015, 40091, 59561, 411577, 587, 370622, 206506, 37326, 90239, 161902, 137732, 52132, 34105, 180588, 33968, 386414, 283734, 1891233, 478, 156979, 28125, 1529, 306, 123899, 220687, 620903, 1239307, 1348, 316, 28091, 178214, 84112, 44737, 487, 1536, 1273, 24, 630, 1034, 322095, 488730, 70348, 650, 43765, 43770, 39791, 115545, 150055, 411570, 196, 131111, 472, 38301, 51671, 292, 146827, 1785, 1977869, 40542, 29432, 28450, 1890675, 47312, 38875, 1710, 739, 47917, 33010, 1292, 169292, 158877, 1781, 400946, 501496, 488, 239, 361500, 470, 1430326, 29354, 82347, 65058, 714, 521520, 38303, 1513, 502790, 747, 1141657, 38304]
+  "Ear":
+    url: "https://bacdive.dsmz.de/search?search=taxid:{}"
+    ids: [1747, 2702, 1869190, 32002, 85698, 131111, 29388, 28037, 44750, 51671, 1353, 28264, 545, 292, 89093, 1872515, 1280, 511, 29379, 68766, 59561, 29321, 480, 1311, 285091, 727, 199591, 43263, 1313, 739, 760, 1661, 52769, 1421, 1314, 156979, 35703, 1898, 585, 87883, 90245, 123899, 306, 1895474, 670, 47770, 319939, 184870, 134375, 72557, 753, 663, 316, 1343, 217203, 267212, 678, 53364, 1014, 1776741, 93220, 1639, 666, 38313, 1652, 105219, 38287, 293, 33007, 287]
+  "Eye":
+    url: "https://bacdive.dsmz.de/search?search=taxid:{}"
+    ids: [40216, 28037, 1280, 490, 147645, 1351, 90367, 1824, 813, 1720, 38290, 29391, 732, 192066, 616, 161879, 753, 1304, 1655, 539, 37329, 28172, 161890, 90241, 504, 752, 253, 457921, 1871047, 1309, 154288, 280147, 485, 760, 46124, 1931, 1379, 29394, 1671023, 68892, 479, 1396, 1544416, 2035, 420404, 735, 47846, 666, 571, 2055, 1401, 1270, 34062, 545, 38284, 247, 498, 40091, 59561, 370622, 37326, 727, 945844, 1313, 180588, 1685, 1671022, 478, 1302, 134375, 477, 726, 47478, 197575, 207340, 38287, 650, 756689, 43765, 69392, 723, 72556, 187491, 472, 51671, 2047, 1177728, 46125, 29432, 480, 47312, 739, 134533, 740, 37330, 488, 1544413, 239, 483, 29354, 41202, 38304]
+  "Nose":
+    url: "https://bacdive.dsmz.de/search?search=taxid:{}"
+    ids: [59823, 72556, 131111, 1282, 28264, 38284, 1280, 520, 43990, 615, 727, 1328, 1313, 90367, 760, 181487, 29394, 478, 732, 40324, 33889, 306, 39950, 1304, 1673725, 65058, 74319, 1591, 90241, 105219, 504, 286802, 195105, 574]
 "Human-related bacterial isolates from BacDive":
   "Oral":
     url: "https://bacdive.dsmz.de/search?search=taxid:{}"
@@ -15,4 +28,17 @@
   "Nasal":
     url: "http://www.ehomd.org/?name=HOMD"
     ids: [553601, 406557, 497962, 1715211, 170187, 553573, 196620, 93062, 553594, 406559, 1008452, 1608882, 488223, 1203632, 857577, 727, 869269, 478, 553568, 760810, 1739522, 548470, 857573, 281310, 455227, 521004, 359787, 1095736, 374931, 1069623, 585203, 1715217, 497980, 585202, 1715123, 1069628, 553580, 1203562, 1834153, 1203627, 866630, 1415766, 553583, 158879, 760787, 548475, 453361, 406561, 451516, 869215, 553574, 553590, 282458, 1608898, 456482, 374928, 553592, 553588, 1069626, 452948, 480, 1130804, 1095746, 453362, 375177, 406556, 71421, 273036, 451515, 548474, 521005, 374930, 406560, 1035187, 1203619, 553565, 406562, 1095745, 1859695, 1069625, 857578, 585204, 1739317, 862964, 1340484, 681288, 1239793, 487213, 857581, 497963, 760791, 857574, 374933, 1739280, 869216, 406563, 453366, 574093, 516950, 1415765, 453363, 262727, 857575, 453364, 1203625, 548473, 1340485, 406558, 703339, 760746, 1340486, 656912, 189423, 1239792, 512767, 857572, 857579, 760834, 760861, 1203622, 585161, 1203557, 1203566, 373153, 1203559, 1095735, 1203561, 656913, 886289, 262728, 488221, 553571, 869309, 553577, 171101, 375432, 359786, 857576, 1236608, 1095737, 1121367, 375063, 888828, 374927, 1203624, 365659, 525381, 760809, 512769, 418127, 595501, 246201, 512566, 546342, 158878, 883103, 488222, 1008453, 857571, 1739254, 487214, 453365, 1739452, 90241, 553567, 28037, 512768, 553581, 426430, 553596, 93061, 935897, 450394, 282459, 561276, 374932, 862965]
-
+"Human-related bacterial isolates from BacDive":  
+  "Skin/Nail/Hair":
+    url: "https://bacdive.dsmz.de/search?search=taxid:{}"
+    ids: [1747, 106654, 1986155, 59823, 1869190, 1270, 71999, 1283, 1276, 131110, 1648, 1656, 472, 1352, 34062, 729, 29388, 2047, 28264, 1314, 1280, 1290, 672, 59561, 1780, 33918, 37326, 29432, 1286, 1891644, 74703, 90367, 1931, 33010, 1720, 1965292, 181487, 169292, 38290, 29506, 1622, 281920, 1292, 1781, 861, 1698, 1260, 2035, 202789, 521392, 470, 663, 29382, 1659, 1288, 37923, 1655, 45254, 1753, 1261, 38289, 36740, 1273, 1347368, 33034, 1347369, 1282, 66228, 132933, 43765, 287]
+"Top organisms form the human skin microbiome" :
+  "Bacteria":
+    url: "https://doi.org/10.1038/nrmicro.2017.157"
+    ids: [257758, 225324, 169292, 161879, 146827, 43765, 38304, 38287, 38286, 29466, 29388, 28037, 1747, 1305, 1303, 1290, 1282, 1270]
+  "Eukarya":
+    url: "https://doi.org/10.1038/nrmicro.2017.157"
+    ids: [2510778, 1047171, 379413, 119676, 117179, 76777, 76775, 76773, 44058, 41880, 36894, 34391, 31312, 5480, 5068, 3074, 2762]
+  "Viruses":
+    url: "https://doi.org/10.1038/nrmicro.2017.157"
+    ids: [185639, 746832, 10566, 493803, 10279, 746830, 746831, 46771]