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Refactor notebooks to be compliant with berkeley rollout #65

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merged 25 commits into from
Oct 17, 2024
Merged

Refactor notebooks to be compliant with berkeley rollout #65

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c87c5c8
Modified R NEON metadata notebook to berkeley schema
kheal Aug 1, 2024
99164b9
Update R bioscales metadata notebook to berkeley schema
kheal Aug 1, 2024
6f3c542
Update R taxonomy notebook for Berkeley refactor
kheal Aug 1, 2024
d9310df
fix bioscales notebook
brynnz22 Aug 26, 2024
5d68d4d
update Neon notebook
brynnz22 Aug 26, 2024
75db26c
fix taxaonomy notebook
brynnz22 Aug 26, 2024
7b13d5d
Remove omics processing from taxonomic R notebook
kheal Aug 27, 2024
930bc47
update NOM R notebook to Berkeley schema
bmeluch Sep 26, 2024
47b8212
berkeley api call updates
samobermiller Sep 30, 2024
b330039
change kernel and add todos
samobermiller Sep 30, 2024
0e5515f
add TODOs to R notebook urls
samobermiller Sep 30, 2024
0eaae1c
Merge branch 'main' into berkeley_refactor
brynnz22 Oct 1, 2024
d200a8c
Add step 8 narrative back in
brynnz22 Oct 1, 2024
a8979d5
remove dill reference
brynnz22 Oct 1, 2024
a3046c5
reran with changes from PR specifically changing names from omics pro…
samobermiller Oct 2, 2024
d088aab
fix omicsprocessing reference
bmeluch Oct 2, 2024
8eb4c49
Merge pull request #80 from microbiomedata/berkeley_nom
bmeluch Oct 2, 2024
2af6f9a
update Neon soil metadata python notebook
brynnz22 Oct 16, 2024
99c5a73
update R bioscales
brynnz22 Oct 16, 2024
f6e75bb
change url
brynnz22 Oct 16, 2024
952d159
rebase
brynnz22 Oct 16, 2024
07a4791
update nom py
brynnz22 Oct 16, 2024
b789ae9
update R nom notebook
brynnz22 Oct 16, 2024
2a535e4
Update nom_data.ipynb
samobermiller Oct 17, 2024
e3b168d
updated backticks on taxonomic notebook, section 8
samobermiller Oct 17, 2024
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94 changes: 53 additions & 41 deletions NEON_soil_metadata/R/NEON_data_exploration.ipynb
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904 changes: 452 additions & 452 deletions NEON_soil_metadata/python/neon_soil_metadata_visual_exploration.ipynb
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336 changes: 178 additions & 158 deletions NOM_visualizations/R/NOM_R_notebook.ipynb
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422 changes: 234 additions & 188 deletions NOM_visualizations/python/nom_data.ipynb
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51 changes: 29 additions & 22 deletions bioscales_biogeochemical_metadata/R/bioscales_metadata.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -77,20 +77,19 @@
"$ id \u001b[3m\u001b[90m<chr>\u001b[39m\u001b[23m \"nmdc:bsm-11-6zd5nb38\", \"nmdc:bsm-11-ahpvvb…\n",
"$ name \u001b[3m\u001b[90m<chr>\u001b[39m\u001b[23m \"Rhizosphere soil microbial communities fro…\n",
"$ description \u001b[3m\u001b[90m<chr>\u001b[39m\u001b[23m \"Rhizosphere soil microbial communities fro…\n",
"$ part_of \u001b[3m\u001b[90m<list>\u001b[39m\u001b[23m \"nmdc:sty-11-r2h77870\", \"nmdc:sty-11-r2h77…\n",
"$ env_broad_scale \u001b[3m\u001b[90m<df[,2]>\u001b[39m\u001b[23m <data.frame[26 x 2]>\n",
"$ env_local_scale \u001b[3m\u001b[90m<df[,2]>\u001b[39m\u001b[23m <data.frame[26 x 2]>\n",
"$ env_medium \u001b[3m\u001b[90m<df[,2]>\u001b[39m\u001b[23m <data.frame[26 x 2]>\n",
"$ host_taxid \u001b[3m\u001b[90m<df[,2]>\u001b[39m\u001b[23m <data.frame[26 x 2]>\n",
"$ env_broad_scale \u001b[3m\u001b[90m<df[,3]>\u001b[39m\u001b[23m <data.frame[26 x 3]>\n",
"$ env_local_scale \u001b[3m\u001b[90m<df[,3]>\u001b[39m\u001b[23m <data.frame[26 x 3]>\n",
"$ env_medium \u001b[3m\u001b[90m<df[,3]>\u001b[39m\u001b[23m <data.frame[26 x 3]>\n",
"$ host_taxid \u001b[3m\u001b[90m<df[,3]>\u001b[39m\u001b[23m <data.frame[26 x 3]>\n",
"$ collected_from \u001b[3m\u001b[90m<chr>\u001b[39m\u001b[23m \"nmdc:frsite-11-xckqtm38\", \"nmdc:frsite-…\n",
"$ type \u001b[3m\u001b[90m<chr>\u001b[39m\u001b[23m \"nmdc:Biosample\", \"nmdc:Biosample\", \"nmd…\n",
"$ img_identifiers \u001b[3m\u001b[90m<list>\u001b[39m\u001b[23m \"img.taxon:3300046665\", \"img.taxon:33000…\n",
"$ samp_name \u001b[3m\u001b[90m<chr>\u001b[39m\u001b[23m \"BESC-904-Co3_16_51 rhizosphere\", \"GW-95…\n",
"$ gold_biosample_identifiers \u001b[3m\u001b[90m<list>\u001b[39m\u001b[23m \"gold:Gb0291773\", \"gold:Gb0291786\", \"gold:G…\n",
"$ elev \u001b[3m\u001b[90m<dbl>\u001b[39m\u001b[23m 62, 1, 62, 62, 62, 1, 62, 62, 1, 62, 62, 62…\n",
"$ geo_loc_name \u001b[3m\u001b[90m<df[,1]>\u001b[39m\u001b[23m <data.frame[26 x 1]>\n",
"$ lat_lon \u001b[3m\u001b[90m<df[,3]>\u001b[39m\u001b[23m <data.frame[26 x 3]>\n",
"$ samp_taxon_id \u001b[3m\u001b[90m<df[,2]>\u001b[39m\u001b[23m <data.frame[26 x 2]>\n",
"$ geo_loc_name \u001b[3m\u001b[90m<df[,2]>\u001b[39m\u001b[23m <data.frame[26 x 2]>\n",
"$ lat_lon \u001b[3m\u001b[90m<df[,4]>\u001b[39m\u001b[23m <data.frame[26 x 4]>\n",
"$ samp_taxon_id \u001b[3m\u001b[90m<df[,3]>\u001b[39m\u001b[23m <data.frame[26 x 3]>\n",
"$ ecosystem \u001b[3m\u001b[90m<chr>\u001b[39m\u001b[23m \"Host-associated\", \"Host-associated\", \"Hos…\n",
"$ ecosystem_category \u001b[3m\u001b[90m<chr>\u001b[39m\u001b[23m \"Plants\", \"Plants\", \"Plants\", \"Plants\", \"Pl…\n",
"$ ecosystem_type \u001b[3m\u001b[90m<chr>\u001b[39m\u001b[23m \"Roots\", \"Roots\", \"Roots\", \"Roots\", \"Roots…\n",
Expand All @@ -103,20 +102,21 @@
"$ mod_date \u001b[3m\u001b[90m<chr>\u001b[39m\u001b[23m \"2021-05-03T00:00:00\", \"2021-05-03T00:00:00…\n",
"$ ncbi_taxonomy_name \u001b[3m\u001b[90m<chr>\u001b[39m\u001b[23m \"rhizosphere metagenome\", \"rhizosphere meta…\n",
"$ sample_collection_site \u001b[3m\u001b[90m<chr>\u001b[39m\u001b[23m \"Rhizosphere Soil\", \"Rhizosphere Soil\", \"Rh…\n",
"$ collection_date \u001b[3m\u001b[90m<df[,1]>\u001b[39m\u001b[23m <data.frame[26 x 1]>\n",
"$ depth \u001b[3m\u001b[90m<df[,3]>\u001b[39m\u001b[23m <data.frame[26 x 3]>\n",
"$ collection_date \u001b[3m\u001b[90m<df[,2]>\u001b[39m\u001b[23m <data.frame[26 x 2]>\n",
"$ associated_studies \u001b[3m\u001b[90m<list>\u001b[39m\u001b[23m \"nmdc:sty-11-r2h77870\", \"nmdc:sty-11-r2h778…\n",
"$ depth \u001b[3m\u001b[90m<df[,4]>\u001b[39m\u001b[23m <data.frame[26 x 4]>\n",
"$ ph \u001b[3m\u001b[90m<dbl>\u001b[39m\u001b[23m NA, NA, NA, NA, NA, 5.41, 6.95, 6.23, 5.14,…\n",
"$ calcium \u001b[3m\u001b[90m<df[,3]>\u001b[39m\u001b[23m <data.frame[26 x 3]>\n",
"$ magnesium \u001b[3m\u001b[90m<df[,3]>\u001b[39m\u001b[23m <data.frame[26 x 3]>\n",
"$ potassium \u001b[3m\u001b[90m<df[,3]>\u001b[39m\u001b[23m <data.frame[26 x 3]>\n",
"$ tot_nitro \u001b[3m\u001b[90m<df[,3]>\u001b[39m\u001b[23m <data.frame[26 x 3]>\n",
"$ lbc_thirty \u001b[3m\u001b[90m<df[,3]>\u001b[39m\u001b[23m <data.frame[26 x 3]>\n",
"$ lbceq \u001b[3m\u001b[90m<df[,3]>\u001b[39m\u001b[23m <data.frame[26 x 3]>\n",
"$ manganese \u001b[3m\u001b[90m<df[,3]>\u001b[39m\u001b[23m <data.frame[26 x 3]>\n",
"$ zinc \u001b[3m\u001b[90m<df[,3]>\u001b[39m\u001b[23m <data.frame[26 x 3]>\n",
"$ ammonium_nitrogen \u001b[3m\u001b[90m<df[,3]>\u001b[39m\u001b[23m <data.frame[26 x 3]>\n",
"$ nitrate_nitrogen \u001b[3m\u001b[90m<df[,3]>\u001b[39m\u001b[23m <data.frame[26 x 3]>\n",
"$ nitrite_nitrogen \u001b[3m\u001b[90m<df[,3]>\u001b[39m\u001b[23m <data.frame[26 x 3]>\n"
"$ calcium \u001b[3m\u001b[90m<df[,4]>\u001b[39m\u001b[23m <data.frame[26 x 4]>\n",
"$ magnesium \u001b[3m\u001b[90m<df[,4]>\u001b[39m\u001b[23m <data.frame[26 x 4]>\n",
"$ potassium \u001b[3m\u001b[90m<df[,4]>\u001b[39m\u001b[23m <data.frame[26 x 4]>\n",
"$ tot_nitro \u001b[3m\u001b[90m<df[,4]>\u001b[39m\u001b[23m <data.frame[26 x 4]>\n",
"$ lbc_thirty \u001b[3m\u001b[90m<df[,4]>\u001b[39m\u001b[23m <data.frame[26 x 4]>\n",
"$ lbceq \u001b[3m\u001b[90m<df[,4]>\u001b[39m\u001b[23m <data.frame[26 x 4]>\n",
"$ manganese \u001b[3m\u001b[90m<df[,4]>\u001b[39m\u001b[23m <data.frame[26 x 4]>\n",
"$ zinc \u001b[3m\u001b[90m<df[,4]>\u001b[39m\u001b[23m <data.frame[26 x 4]>\n",
"$ ammonium_nitrogen \u001b[3m\u001b[90m<df[,4]>\u001b[39m\u001b[23m <data.frame[26 x 4]>\n",
"$ nitrate_nitrogen \u001b[3m\u001b[90m<df[,4]>\u001b[39m\u001b[23m <data.frame[26 x 4]>\n",
"$ nitrite_nitrogen \u001b[3m\u001b[90m<df[,4]>\u001b[39m\u001b[23m <data.frame[26 x 4]>\n"
]
}
],
Expand All @@ -128,7 +128,7 @@
"\n",
"# Set up query\n",
"per_page = 2000 # number of records to retrieve per page\n",
"filt = paste0(\"part_of:\", study_id) # filter to only get biosamples from the study of interest\n",
"filt = paste0(\"associated_studies:\", study_id) # filter to only get biosamples from the study of interest\n",
"get_more = TRUE # flag to indicate whether we need to get more records\n",
"page = 1 # page number to retrieve\n",
"while (get_more){\n",
Expand Down Expand Up @@ -352,6 +352,13 @@
"name": "R",
"pygments_lexer": "r",
"version": "4.3.1"
},
"widgets": {
"application/vnd.jupyter.widget-state+json": {
"state": {},
"version_major": 2,
"version_minor": 0
}
}
},
"nbformat": 4,
Expand Down
56 changes: 31 additions & 25 deletions bioscales_biogeochemical_metadata/python/bioscales.ipynb
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