From 84895d671303b182e4c3c83f06ba5029f567dfcd Mon Sep 17 00:00:00 2001 From: NuriaQueralt Date: Sun, 9 Jun 2024 15:48:08 +0200 Subject: [PATCH] Update documentation --- _sources/intro.md | 9 +- _sources/licenses.md | 5 + genindex.html | 3 +- intro.html | 19 +- licenses.html | 460 +++++++++++++++++++++++++++++++++ markdown-notebooks.html | 3 +- markdown.html | 3 +- metabolite_subsetting.html | 21 +- metabolite_subsetting_old.html | 3 +- mychapter.html | 3 +- notebooks.html | 5 +- notebooks_original.html | 5 +- objects.inv | Bin 477 -> 513 bytes search.html | 3 +- searchindex.js | 2 +- 15 files changed, 512 insertions(+), 32 deletions(-) create mode 100644 _sources/licenses.md create mode 100644 licenses.html diff --git a/_sources/intro.md b/_sources/intro.md index f8cdc73..1283e39 100644 --- a/_sources/intro.md +++ b/_sources/intro.md @@ -1,11 +1,8 @@ -# Welcome to your Jupyter Book +# Welcome to the BioHackathon 2023 - Metabolite subsetting Jupyter Book -This is a small sample book to give you a feel for how book content is -structured. -It shows off a few of the major file types, as well as some sample content. -It does not go in-depth into any particular topic - check out [the Jupyter Book documentation](https://jupyterbook.org) for more information. +This is a book devoted to showcase how to subset metabolite information from biomedical RDF resources - check out [DBCLS BioHackathon 2023](https://2023.biohackathon.org/) for more information. -Check out the content pages bundled with this sample book to see more. +Check out the content pages bundled with this book to see more. ```{tableofcontents} ``` diff --git a/_sources/licenses.md b/_sources/licenses.md new file mode 100644 index 0000000..4f943ff --- /dev/null +++ b/_sources/licenses.md @@ -0,0 +1,5 @@ +# Licenses +Project **Scripts** under this folder and recursive subfolders are licensed under the terms of the [MIT License](LICENSE). + + +Project **Data** under this folder and recursive subfolders are licensed under the terms of the [CC BY License](https://creativecommons.org/licenses/by/4.0/). diff --git a/genindex.html b/genindex.html index 88849c2..40be14e 100644 --- a/genindex.html +++ b/genindex.html @@ -149,12 +149,13 @@ diff --git a/intro.html b/intro.html index d7a03cb..9d1ccb1 100644 --- a/intro.html +++ b/intro.html @@ -9,7 +9,7 @@ - Welcome to your Jupyter Book — BioHackathon 2023 metabolite subsetting book + Welcome to the BioHackathon 2023 - Metabolite subsetting Jupyter Book — BioHackathon 2023 metabolite subsetting book @@ -151,12 +151,13 @@ @@ -338,7 +339,7 @@
-

Welcome to your Jupyter Book

+

Welcome to the BioHackathon 2023 - Metabolite subsetting Jupyter Book

@@ -352,16 +353,14 @@

Welcome to your Jupyter Book

-
-

Welcome to your Jupyter Book#

-

This is a small sample book to give you a feel for how book content is -structured. -It shows off a few of the major file types, as well as some sample content. -It does not go in-depth into any particular topic - check out the Jupyter Book documentation for more information.

-

Check out the content pages bundled with this sample book to see more.

+
+

Welcome to the BioHackathon 2023 - Metabolite subsetting Jupyter Book#

+

This is a book devoted to showcase how to subset metabolite information from biomedical RDF resources - check out DBCLS BioHackathon 2023 for more information.

+

Check out the content pages bundled with this book to see more.

diff --git a/licenses.html b/licenses.html new file mode 100644 index 0000000..08ad0a6 --- /dev/null +++ b/licenses.html @@ -0,0 +1,460 @@ + + + + + + + + + + + + Licenses — BioHackathon 2023 metabolite subsetting book + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+
+
+
+ + + Ctrl+K +
+
+ + + +
+
+ +
+ + + +
+ + + + +
+ +
+
+ + +
+
+
+ + +
+
+ + + + +
+ +
+ + + +
+ +
+
+ +
+
+ +
+ +
+ +
+ + +
+ +
+ +
+ + + + + +
+ + +
+ + + + + + +
+ + +
+ + + + + + + + + + + +
+ +
+ +
+
+ + + +
+

Licenses

+ +
+
+ +
+
+
+ + + + +
+ +
+

Licenses#

+

Project Scripts under this folder and recursive subfolders are licensed under the terms of the MIT License.

+

Project Data under this folder and recursive subfolders are licensed under the terms of the CC BY License.

+
+ + + + +
+ + + + + + +
+ + + + +
+
+ +
+ +
+ +

+By The BioHackathon Community +

+ +
+ +
+ +

+ + © Copyright 2022. +
+ +

+ +
+ +
+ +
+ +
+ +
+ +
+
+ + +
+
+
+ + + + + +
+
+ + \ No newline at end of file diff --git a/markdown-notebooks.html b/markdown-notebooks.html index 3c903ed..68c34ef 100644 --- a/markdown-notebooks.html +++ b/markdown-notebooks.html @@ -150,12 +150,13 @@
diff --git a/markdown.html b/markdown.html index 5aa3e28..9effa56 100644 --- a/markdown.html +++ b/markdown.html @@ -150,12 +150,13 @@
diff --git a/metabolite_subsetting.html b/metabolite_subsetting.html index 9cb3a9d..3194129 100644 --- a/metabolite_subsetting.html +++ b/metabolite_subsetting.html @@ -64,7 +64,8 @@ - + + @@ -151,12 +152,13 @@
@@ -438,12 +440,12 @@

Retrieving drug candidates based on activity metabolite similarity (UniProt, 
Requirement already satisfied: SPARQLWrapper in /home/nur/anaconda3/lib/python3.10/site-packages (2.0.0)
 Requirement already satisfied: rdflib>=6.1.1 in /home/nur/anaconda3/lib/python3.10/site-packages (from SPARQLWrapper) (6.3.2)
-Requirement already satisfied: pyparsing<4,>=2.1.0 in /home/nur/anaconda3/lib/python3.10/site-packages (from rdflib>=6.1.1->SPARQLWrapper) (3.0.9)
 Requirement already satisfied: isodate<0.7.0,>=0.6.0 in /home/nur/anaconda3/lib/python3.10/site-packages (from rdflib>=6.1.1->SPARQLWrapper) (0.6.1)
+Requirement already satisfied: pyparsing<4,>=2.1.0 in /home/nur/anaconda3/lib/python3.10/site-packages (from rdflib>=6.1.1->SPARQLWrapper) (3.0.9)
 Requirement already satisfied: six in /home/nur/anaconda3/lib/python3.10/site-packages (from isodate<0.7.0,>=0.6.0->rdflib>=6.1.1->SPARQLWrapper) (1.16.0)
-
/tmp/ipykernel_100073/2559832190.py:8: FutureWarning: Passing a negative integer is deprecated in version 1.0 and will not be supported in future version. Instead, use None to not limit the column width.
+
/tmp/ipykernel_202021/2559832190.py:8: FutureWarning: Passing a negative integer is deprecated in version 1.0 and will not be supported in future version. Instead, use None to not limit the column width.
   pd.set_option('display.max_colwidth', -1)
 

 

@@ -1035,8 +1037,17 @@ 
Other databases
       

         
previous

-        
Welcome to your Jupyter Book

+        
Welcome to the BioHackathon 2023 - Metabolite subsetting Jupyter Book

+      

+    
+    
+      

+        
next

+        
Licenses

       

+
diff --git a/metabolite_subsetting_old.html b/metabolite_subsetting_old.html index 25c8977..d939d79 100644 --- a/metabolite_subsetting_old.html +++ b/metabolite_subsetting_old.html @@ -150,12 +150,13 @@
diff --git a/mychapter.html b/mychapter.html index 91706fd..0a99076 100644 --- a/mychapter.html +++ b/mychapter.html @@ -150,12 +150,13 @@ diff --git a/notebooks.html b/notebooks.html index 129b1df..a5eae30 100644 --- a/notebooks.html +++ b/notebooks.html @@ -150,12 +150,13 @@ @@ -392,7 +393,7 @@

Code blocks and image outputs -
<contextlib.ExitStack at 0x7f11904e32b0>
+
<contextlib.ExitStack at 0x7fa04c9f32b0>
diff --git a/notebooks_original.html b/notebooks_original.html index 2c90d35..6e6fef5 100644 --- a/notebooks_original.html +++ b/notebooks_original.html @@ -152,12 +152,13 @@
@@ -408,7 +409,7 @@

Code blocks and outputs
-
<contextlib.ExitStack at 0x7fb8afccc130>
+
<contextlib.ExitStack at 0x7f507171f1c0>
diff --git a/objects.inv b/objects.inv index a5c4d6fe8c8ae2250d678859bfb0de8bc2721c02..5a6317af10d4e462dbed1634bf213c5bdd3c2b6c 100644 GIT binary patch delta 406 zcmV;H0crl-1AzpPb$?S$PlG@Zz3;D>q+T&vZ#~w;RAWtJH6EJ@UsydS#_dYvbkhM7u+|b(_cF@ zq(66|^vwB-Du3z=U6_=X8oLi6uaZm_&DDmJ^q?0k(AJGy4THf0bTx4{{FBTte5ir7 zA**)ENPX5LRK3|f8AikYe1Rm2GEOqg$6Nm#=Hv=iWqe<}tua$8mHFEEPFp|nXh z7JAHU*1o=yJFK}$bEe1>$J34iucsSCzE##SbYf8&RS#I=e=hrO)T&mAZw{fQ(|&-$ Ab^rhX delta 369 zcmV-%0gnEG1lhL)=?#saPwKf#S&>5AbbGjarpKkQ@ciUE32F{yHIi zU|Cjymb!rN*lK@u;x?@$$2I}D^hcfsP!soFl73saa_bPA@UHGN)-b~wdyk{R@ZM=-9D zbuia(;8TsA4Ql@+^9!FUuy$x
  • - Welcome to your Jupyter Book + Welcome to the BioHackathon 2023 - Metabolite subsetting Jupyter Book
    • diff --git a/searchindex.js b/searchindex.js index 8e24a29..fc40bde 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["intro", "markdown", "markdown-notebooks", "metabolite_subsetting", "metabolite_subsetting_old", "mychapter", "notebooks", "notebooks_original"], "filenames": ["intro.md", "markdown.md", "markdown-notebooks.md", "metabolite_subsetting.ipynb", "metabolite_subsetting_old.md", "mychapter.md", "notebooks.ipynb", "notebooks_original.ipynb"], "titles": ["Welcome to your Jupyter Book", "Markdown Files", "Notebooks with MyST Markdown", "Retrieving metabolite information", "Retrieving metabolite information", "Here is my new chapter", "Jupyter Notebook files", "Content with notebooks"], "terms": {"thi": [0, 1, 2, 3, 4, 6, 7], "small": [0, 1, 3], "sampl": [0, 6, 7], "give": 0, "you": [0, 1, 2, 7], "feel": 0, "how": [0, 2, 3, 4, 6], "content": [0, 1, 2, 3, 4], "structur": [0, 1, 6], "It": [0, 1], "show": [0, 1, 2, 3, 6], "off": [0, 1, 2], "few": 0, "major": 0, "file": [0, 2, 3], "type": [0, 3, 4], "well": [0, 3, 6, 7], "some": [0, 1, 6, 7], "doe": 0, "go": [0, 3], "depth": 0, "ani": [0, 2, 3, 6], "particular": [0, 6], "topic": 0, "check": [0, 6, 7], "out": [0, 7], "document": [0, 1, 2, 7], "more": [0, 2, 3, 4, 7], "inform": [0, 2, 6, 7], "page": [0, 1, 2, 6], "bundl": 0, "see": [0, 1, 2, 6, 7], "markdown": 6, "notebook": [1, 3], "myst": 6, "whether": 1, "write": [1, 2, 6], "your": [1, 2, 6, 7], "book": [1, 2, 6, 7], "s": [1, 2, 3, 6, 7], "jupyt": [1, 2, 7], "ipynb": 1, "regular": [1, 3], "md": [1, 2], "ll": [1, 6], "same": [1, 6], "flavor": 1, "call": [1, 3, 6], "simpl": 1, "help": [1, 3, 4, 6], "get": [1, 2, 3, 4], "start": [1, 2, 3], "syntax": [1, 3], "stand": 1, "markedli": 1, "text": [1, 2, 5, 6], "slight": 1, "variat": 1, "commonmark": [1, 6], "extens": 1, "allow": [1, 3], "sphinx": 1, "ecosystem": 1, "For": [1, 6, 7], "about": [1, 2, 3, 4, 6, 7], "overview": 1, "ar": [1, 2, 3, 4, 6], "two": [1, 2], "most": [1, 3, 6], "power": [1, 3], "tool": [1, 3, 4], "thei": [1, 3, 4, 6], "kind": 1, "like": [1, 2, 6], "function": [1, 3], "written": [1, 2], "markup": 1, "languag": 1, "both": [1, 3, 4], "serv": 1, "similar": 1, "purpos": 1, "one": 1, "line": [1, 2, 3, 6, 7], "wherea": 1, "span": 1, "mani": [1, 2, 6], "accept": 1, "differ": [1, 3], "input": 1, "do": [1, 6, 7], "those": [1, 3], "depend": [1, 6], "specif": [1, 3, 4], "being": 1, "here": [1, 3, 4, 6, 7], "note": [1, 6], "render": 1, "special": 1, "box": 1, "when": [1, 2, 6], "build": [1, 6], "an": [1, 3, 6], "inlin": 1, "refer": [1, 6], "can": [1, 2, 3, 4, 7], "also": [1, 2, 3, 4, 7], "cite": 1, "store": [1, 6], "bibtex": 1, "exampl": [1, 3, 6, 7], "follow": [1, 2, 3], "holdgraf_evidence_2014": 1, "hdhpk14": 1, "moreov": 1, "insert": 1, "bibliographi": 1, "The": [1, 2, 3, 4], "must": 1, "us": [1, 2, 3, 4, 6], "all": [1, 2, 3, 4, 6], "properli": 1, "bib": 1, "christoph": 1, "ramsai": 1, "holdgraf": 1, "wendi": 1, "de": 1, "heer": 1, "brian": 1, "n": [1, 6, 7], "paslei": 1, "robert": 1, "t": [1, 3, 4, 6, 7], "knight": 1, "evid": 1, "predict": [1, 3, 4], "code": [1, 2], "human": [1, 3, 4], "auditori": 1, "cortex": 1, "In": [1, 3, 4, 6], "intern": 1, "confer": 1, "cognit": 1, "neurosci": 1, "brisban": 1, "australia": 1, "2014": 1, "frontier": 1, "just": 1, "starter": 1, "lot": [1, 7], "jupyterbook": 1, "org": [1, 3], "let": 2, "base": 2, "detail": [2, 6], "instruct": 2, "With": [2, 3, 4], "defin": [2, 3], "direct": [2, 3], "so": [2, 6], "print": [2, 3], "2": [2, 3, 4, 6], "4": [2, 3, 6, 7], "built": [2, 6], "block": 2, "execut": [2, 3], "default": 2, "kernel": [2, 6], "output": [2, 3], "displai": [2, 3, 6], "rest": 2, "jupytext": 2, "convert": [2, 3, 6], "support": [2, 3, 6], "other": [2, 6], "thing": 2, "need": [2, 6], "understand": 2, "should": 2, "includ": [2, 3, 4, 7], "top": 2, "presenc": 2, "which": [2, 3, 4, 6], "That": 2, "If": [2, 6], "have": [2, 3, 4, 6], "d": [2, 6], "treat": 2, "run": 2, "command": [2, 6], "init": 2, "path": 2, "markdownfil": 2, "creat": [6, 7], "mean": 7, "As": 7, "emb": [6, 7], "imag": 7, "html": [6, 7], "etc": [3, 4, 7], "post": [3, 7], "add_": 7, "math": 7, "begin": 7, "align": 7, "mbox": 7, "la_": 7, "tex": 7, "end": [3, 7], "But": 7, "make": [3, 4, 7], "sure": 7, "escap": 7, "dollar": 7, "sign": [6, 7], "want": 7, "keep": [6, 7], "work": [3, 4, 6, 7], "guid": 7, "matplotlib": [6, 7], "from": [3, 4, 7], "import": [3, 4, 6, 7], "rcparam": [6, 7], "cycler": [6, 7], "pyplot": [6, 7], "plt": [6, 7], "numpi": [6, 7], "np": [3, 6, 7], "ion": [6, 7], "contextlib": [6, 7], "exitstack": [6, 7], "0x7fad5e6fca00": [], "fix": [6, 7], "random": [6, 7], "state": [6, 7], "reproduc": [6, 7], "seed": [6, 7], "19680801": [6, 7], "10": [3, 6, 7], "data": [3, 4, 6, 7], "logspac": [6, 7], "0": [3, 6, 7], "1": [3, 4, 6, 7], "100": [6, 7], "randn": [6, 7], "ii": [6, 7], "rang": [6, 7], "arrai": [6, 7], "cmap": [6, 7], "cm": [6, 7], "coolwarm": [6, 7], "ax": [6, 7], "prop_cycl": [6, 7], "color": [6, 7], "linspac": [6, 7], "line2d": [6, 7], "custom_lin": [6, 7], "lw": [6, 7], "5": [3, 6, 7], "fig": [6, 7], "subplot": [6, 7], "figsiz": [6, 7], "plot": [6, 7], "legend": [6, 7], "cold": [6, 7], "medium": [6, 7], "hot": [6, 7], "There": [3, 4, 6, 7], "interact": 7, "link": [3, 4, 5, 6], "intro": [3, 4, 5], "he": 5, "retriev": 0, "metabolit": 0, "addit": [3, 4], "relat": [3, 4], "biomed": [3, 4], "knowledg": [3, 4], "graph": [3, 4], "gain": [3, 4], "describ": [3, 4], "learn": [3, 4], "sever": [3, 4], "applic": [3, 4], "repurpos": [3, 4], "biomark": [3, 4], "discoveri": [3, 4], "biohackathon": [3, 4], "we": [3, 4, 6], "investig": [3, 4], "focus": [3, 4], "case": [3, 4], "inborn": [3, 4], "error": [3, 4, 6], "metabol": [3, 4], "disord": [3, 4], "section": [3, 4, 6], "comprehens": [3, 4], "its": [3, 4], "natur": [3, 4], "product": [3, 4], "sparql": 3, "sib": 3, "anoth": 3, "bind": 3, "queri": [3, 4], "catalyt": [3, 4], "reaction": [3, 4], "39": 3, "40": 3, "http": 3, "known": [3, 4], "first": 3, "Then": [3, 4], "access": [3, 4], "id": [3, 4], "filter": 3, "endpoint": 3, "each": [3, 4], "sourc": [3, 4], "sy": 3, "os": 3, "time": 3, "m": [3, 6], "pip": 3, "instal": 3, "sparqlwrapp": 3, "json": 3, "panda": [3, 6], "pd": [3, 6], "alwai": 3, "full": 3, "column": [3, 6], "result": 3, "don": [3, 4], "truncat": 3, "set_opt": 3, "max_colwidth": 3, "wrapper": 3, "sparql_uniprot": 3, "tabl": 3, "def": 3, "pretty_print": 3, "transform": [3, 6], "datafram": [3, 6], "header": 3, "name": [3, 6], "kei": 3, "avail": 3, "entri": 3, "append": 3, "python": [3, 6], "list": [3, 4], "row": 3, "df": 3, "valu": 3, "none": 3, "els": 3, "return": 3, "requir": 3, "alreadi": 3, "satisfi": 3, "home": 3, "nur": 3, "anaconda3": 3, "lib": 3, "python3": 3, "site": [3, 6], "packag": [3, 6], "rdflib": 3, "6": [3, 6], "3": [3, 4, 6], "isod": 3, "7": [3, 6], "pypars": 3, "9": [3, 6], "six": 3, "16": 3, "tmp": 3, "ipykernel_99069": [], "2559832190": 3, "py": 3, "8": [3, 6], "futurewarn": 3, "pass": 3, "neg": 3, "integ": 3, "deprec": 3, "version": 3, "futur": 3, "instead": 3, "limit": 3, "width": 3, "rdf": 3, "query_human_enzym": 3, "prefix": 3, "xsd": 3, "www": 3, "w3": 3, "2001": 3, "xmlschema": 3, "wikibas": 3, "wikiba": 3, "se": 3, "ontolog": 3, "wdt": 3, "wikidata": 3, "prop": 3, "wd": 3, "entiti": 3, "vg": 3, "resourc": 3, "up": [3, 6], "purl": 3, "core": 3, "uniprotkb": 3, "uberon": 3, "obolibrari": 3, "obo": 3, "uo": 3, "taxon": 3, "taxonomi": 3, "sp": 3, "spinrdf": 3, "sko": 3, "2004": 3, "02": 3, "sio": 3, "semanticsci": 3, "sh": 3, "ns": 3, "shacl": 3, "schema": 3, "sachem": [3, 4], "bioinfo": 3, "uochb": 3, "ca": 3, "cz": 3, "v1": 3, "rh": 3, "db": 3, "2000": 3, "01": 3, "1999": 3, "22": 3, "pubm": 3, "ncbi": 3, "nlm": 3, "nih": 3, "gov": 3, "ps": 3, "statement": 3, "pq": 3, "qualifi": 3, "patent": 3, "epo": 3, "p": 3, "owl": 3, "2002": 3, "07": 3, "orthodbgroup": 3, "orthodb": 3, "odbgroup": 3, "orth": 3, "net": 3, "nextprot": 3, "mnx": 3, "metanetx": 3, "mnet": 3, "mesh": 3, "lscr": 3, "lipidmap": 3, "keyword": 3, "insdcschema": 3, "ddbj": 3, "nig": 3, "ac": 3, "jp": 3, "nucleotid": 3, "insdc": 3, "identifi": [3, 4], "glyconnect": 3, "glycan": 3, "bio": 3, "12": [3, 6], "glyco": 3, "genex": 3, "foaf": 3, "xmln": 3, "com": 3, "faldo": 3, "eunisspeci": 3, "euni": 3, "eea": 3, "europa": 3, "eu": 3, "speci": 3, "ensembltranscript": 3, "ebi": 3, "uk": 3, "ensembl": 3, "transcript": 3, "ensemblterm": 3, "term": 3, "ensemblprotein": 3, "protein": [3, 4], "ensemblexon": 3, "exon": 3, "ec": 3, "dcterm": 3, "dc": 3, "chebislash": 3, "chebi": [3, 4], "chebihash": 3, "cco": 3, "chembl": [3, 4], "busco": 3, "ezlab": 3, "bibo": 3, "alli": 3, "swisslipid": 3, "slm_": 3, "go_": 3, "eco": 3, "eco_": 3, "chebi_": 3, "select": 3, "distinct": 3, "where": 3, "annot": 3, "catalyticact": 3, "catalyzedreact": 3, "organ": 3, "9606": 3, "set": [3, 4], "against": 3, "format": [3, 6], "setqueri": 3, "setreturnformat": 3, "num_exampl": 3, "results_human_enzym": 3, "head": 3, "keyboardinterrupt": 3, "traceback": [3, 6], "recent": [3, 6], "last": [3, 6], "cell": 3, "1196": 3, "queryresult": 3, "self": 3, "1194": 3, "elif": 3, "_content_type_in_list": 3, "ct": 3, "_sparql_json": 3, "1195": 3, "_validate_format": 3, "requestedformat": 3, "_convertjson": 3, "1197": 3, "_rdf_xml": 3, "1198": 3, "1199": 3, "xml": 3, "rdfxml": 3, "1200": 3, "1059": 3, "1051": 3, "dict": 3, "1052": 3, "1053": 3, "method": 3, "overwritten": 3, "subclass": 3, "1054": 3, "convers": 3, "1057": 3, "rtype": 3, "1058": 3, "json_str": 3, "load": 3, "respons": 3, "read": 3, "decod": 3, "utf": 3, "1060": 3, "isinst": 3, "1061": 3, "client": 3, "460": 3, "httprespons": 3, "amt": 3, "457": 3, "b": [3, 6], "459": 3, "chunk": 3, "_read_chunk": 3, "462": 3, "463": 3, "length": 3, "464": 3, "clip": 3, "583": 3, "581": 3, "try": 3, "582": 3, "while": 3, "true": 3, "chunk_left": 3, "_get_chunk_left": 3, "584": 3, "585": 3, "break": 3, "566": 3, "564": 3, "_safe_read": 3, "toss": 3, "crlf": 3, "565": 3, "_read_next_chunk_s": 3, "567": 3, "except": [3, 6], "valueerror": 3, "568": 3, "rais": [3, 6], "incompleteread": 3, "526": 3, "524": 3, "525": 3, "next": 3, "size": 3, "fp": 3, "readlin": 3, "_maxlin": 3, "527": 3, "len": 3, "528": 3, "linetoolong": 3, "socket": 3, "705": 3, "socketio": 3, "readinto": 3, "703": 3, "704": 3, "_sock": 3, "recv_into": 3, "706": 3, "timeout": 3, "707": 3, "_timeout_occur": 3, "ssl": 3, "1307": 3, "sslsocket": 3, "buffer": 3, "nbyte": 3, "flag": 3, "1303": 3, "1304": 3, "1305": 3, "non": 3, "zero": 3, "1306": 3, "__class__": 3, "1308": 3, "1309": 3, "super": 3, "1163": 3, "1161": 3, "1162": 3, "_sslobj": 3, "1164": 3, "1165": 3, "particip": [3, 4], "13": 3, "involv": [3, 4], "pathwai": [3, 4], "reactant": [3, 4], "cross": [3, 4], "idsm": [3, 4], "expand": [3, 4], "compound": [3, 4], "three": [3, 4], "target": [3, 4], "sensibl": [3, 4], "unknown": [3, 4], "relev": [3, 4], "query_metabolit": 3, "servic": 3, "side": 3, "contain": [3, 6], "subclassof": 3, "results_metabolit": 3, "smallmolecul": 3, "b2rb89": 3, "17989": 3, "chebi_30616": 3, "genericpolypeptid": 3, "our": [3, 4], "user": [3, 4], "pdb": [3, 4], "imcd": [3, 4], "dataset": [3, 4], "recon": [3, 4], "model": [3, 4], "leiden": [3, 4], "rich": [3, 4], "author": 3, "jerven": 3, "bolleman": 3, "princip": 3, "softwar": 3, "engin": 3, "linkedin": 3, "feed": 3, "updat": 3, "7171566017431724033": 3, "trk": 3, "feed_main": 3, "card_soci": 3, "action": 3, "comment": 3, "et": 3, "al": 3, "combin": 3, "molecul": 3, "lnkd": 3, "e2jwcd2": 3, "e93pzuva": 3, "emde6cki": 3, "independ": 3, "ejxrwuh3": 3, "search": 3, "catalyz": 3, "substrat": 3, "ha": 3, "onli": [3, 6], "smile": 3, "represent": 3, "e83mrqmr": 3, "jervern": 3, "query_disease_enzymes_cholestan": 3, "omim": 3, "find": 3, "complet": 3, "skeleton": 3, "via": [3, 4], "czech": 3, "elixir": 3, "node": 3, "chemic": 3, "substructuresearch": 3, "h": 3, "c": [3, 6], "cc": 3, "ccc4cccc": 3, "12c": 3, "cccc": 3, "fact": 3, "map": [3, 6], "found": 3, "o": 3, "match": 3, "option": 3, "seealso": 3, "mim": 3, "results_disease_enzym": 3, "330": 3, "chebi_2288": 3, "235555": 3, "p51857": 3, "46632": 3, "chebi_2290": 3, "46640": 3, "chebi_16074": 3, "11524": 3, "hmdb": [3, 4], "larg": [3, 4], "amount": [3, 4], "complex": [3, 4], "tailor": [3, 4], "onc": [3, 4], "clear": [3, 4], "offer": [3, 4], "systemat": [3, 4], "wai": [3, 4], "subset": [3, 4], "join": [3, 4], "union": [3, 4], "role": [3, 4], "ask": [3, 4], "plant": [3, 4], "microbiom": [3, 4], "commun": [3, 4], "mainli": [3, 4], "sequenc": [3, 4], "phenom": [3, 4], "now": [3, 4], "kegg": [3, 4], "microb": [3, 4], "ms": [3, 4], "know": [3, 4], "much": [3, 4], "mayb": [3, 4], "standard": [3, 4], "usual": [3, 4], "obtain": [3, 4], "metabolom": [3, 4], "mass": [3, 4], "spectrometri": [3, 4], "gc": [3, 4], "lc": [3, 4], "ce": [3, 4], "tof": [3, 4], "metacyc": [3, 4], "would": [3, 4], "deepgo": [3, 4], "system": [3, 4], "enzym": 4, "rhea": 4, "ligand": 4, "dbcl": 4, "current": 6, "plain": 6, "still": 6, "automat": 6, "mostli": 6, "flavour": 6, "minor": 6, "modif": 6, "0x7fd377d4b2b0": [], "abov": 6, "captur": 6, "smoother": 6, "linez": 6, "layout": 6, "sidebar": 6, "web": 6, "download": 6, "thisvari": 6, "textbook": 6, "x": 6, "y": 6, "scatter": 6, "ab": 6, "fontsiz": 6, "20": 6, "transax": 6, "set_axis_off": 6, "quickli": 6, "without": 6, "clutter": 6, "hi": 6, "word": 6, "A": 6, "hide": 6, "materi": 6, "below": 6, "folium": 6, "retain": 6, "abl": 6, "standalon": 6, "javascript": 6, "underli": 6, "locat": 6, "45": 6, "372": 6, "121": 6, "6972": 6, "zoom_start": 6, "tile": 6, "stamen": 6, "terrain": 6, "marker": 6, "3288": 6, "6625": 6, "popup": 6, "mt": 6, "hood": 6, "meadow": 6, "icon": 6, "cloud": 6, "add_to": 6, "3311": 6, "7113": 6, "timberlin": 6, "lodg": 6, "green": 6, "3300": 6, "6823": 6, "red": 6, "info": 6, "modulenotfounderror": 6, "11": 6, "No": 6, "modul": 6, "becaus": 6, "menu": 6, "nice": 6, "And": 6, "mark": 6, "expect": 6, "ad": 6, "tag": 6, "them": 6, "this_will_error": 6, "take": 6, "advantag": 6, "gener": 6, "binder": 6, "connect": 6, "brows": 6, "0x7f66848bf3a0": [], "ipykernel_100073": 3, "0x7f11904e32b0": 6, "0x7fb8afccc130": 7}, "objects": {}, "objtypes": {}, "objnames": {}, "titleterms": {"welcom": 0, "your": 0, "jupyt": [0, 6], "book": 0, "markdown": [1, 2, 7], "file": [1, 6], "what": 1, "myst": [1, 2, 7], "sampl": 1, "role": 1, "direct": 1, "citat": 1, "learn": 1, "more": [1, 6], "notebook": [2, 6, 7], "an": 2, "exampl": 2, "cell": [2, 6], "creat": 2, "quickli": 2, "add": 2, "yaml": 2, "metadata": 2, "content": [6, 7], "code": [6, 7], "block": [6, 7], "output": [6, 7], "here": 5, "my": 5, "new": 5, "chapter": 5, "first": 5, "section": 5, "retriev": [3, 4], "metabolit": [3, 4], "inform": [3, 4], "uniprot": [3, 4], "explor": [3, 4], "genom": [3, 4], "druggabl": [3, 4], "drug": [3, 4], "candid": [3, 4], "base": [3, 4], "activ": [3, 4], "similar": [3, 4], "rhea": 3, "structur": [3, 4], "similarii": [3, 4], "dbcl": 3, "databas": [3, 4], "ligand": 3, "diseas": [3, 4], "patholog": [3, 4], "curat": [3, 4], "associ": [3, 4], "isoform": [3, 4], "enzym": 3, "interact": [3, 6], "cholestan": 3, "substructur": 3, "pubchem": [3, 4], "other": [3, 4], "imag": 6, "you": 6, "can": 6, "also": 6, "pop": 6, "out": 6, "side": 6, "remov": 6, "befor": 6, "publish": 6, "rich": 6, "from": 6, "featur": 6}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 6, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinxcontrib.bibtex": 9, "sphinx": 56}}) \ No newline at end of file +Search.setIndex({"docnames": ["intro", "licenses", "markdown", "markdown-notebooks", "metabolite_subsetting", "metabolite_subsetting_old", "mychapter", "notebooks", "notebooks_original"], "filenames": ["intro.md", "licenses.md", "markdown.md", "markdown-notebooks.md", "metabolite_subsetting.ipynb", "metabolite_subsetting_old.md", "mychapter.md", "notebooks.ipynb", "notebooks_original.ipynb"], "titles": ["Welcome to the BioHackathon 2023 - Metabolite subsetting Jupyter Book", "Licenses", "Markdown Files", "Notebooks with MyST Markdown", "Retrieving metabolite information", "Retrieving metabolite information", "Here is my new chapter", "Jupyter Notebook files", "Content with notebooks"], "terms": {"thi": [0, 1, 2, 3, 4, 5, 7, 8], "small": [2, 4], "sampl": [7, 8], "give": [], "you": [2, 3, 8], "feel": [], "how": [0, 3, 4, 5, 7], "content": [0, 2, 3, 4, 5], "structur": [2, 7], "It": 2, "show": [2, 3, 4, 7], "off": [2, 3], "few": [], "major": [], "file": [3, 4], "type": [4, 5], "well": [4, 7, 8], "some": [2, 7, 8], "doe": [], "go": 4, "depth": [], "ani": [3, 4, 7], "particular": 7, "topic": [], "check": [0, 7, 8], "out": [0, 8], "document": [2, 3, 8], "more": [0, 3, 4, 5, 8], "inform": [0, 3, 7, 8], "page": [0, 2, 3, 7], "bundl": 0, "see": [0, 2, 3, 7, 8], "markdown": 7, "notebook": [2, 4], "myst": 7, "whether": 2, "write": [2, 3, 7], "your": [2, 3, 7, 8], "book": [2, 3, 7, 8], "s": [2, 3, 4, 7, 8], "jupyt": [2, 3, 8], "ipynb": 2, "regular": [2, 4], "md": [2, 3], "ll": [2, 7], "same": [2, 7], "flavor": 2, "call": [2, 4, 7], "simpl": 2, "help": [2, 4, 5, 7], "get": [2, 3, 4, 5], "start": [2, 3, 4], "syntax": [2, 4], "stand": 2, "markedli": 2, "text": [2, 3, 6, 7], "slight": 2, "variat": 2, "commonmark": [2, 7], "extens": 2, "allow": [2, 4], "sphinx": 2, "ecosystem": 2, "For": [2, 7, 8], "about": [2, 3, 4, 5, 7, 8], "overview": 2, "ar": [1, 2, 3, 4, 5, 7], "two": [2, 3], "most": [2, 4, 7], "power": [2, 4], "tool": [2, 4, 5], "thei": [2, 4, 5, 7], "kind": 2, "like": [2, 3, 7], "function": [2, 4], "written": [2, 3], "markup": 2, "languag": 2, "both": [2, 4, 5], "serv": 2, "similar": 2, "purpos": 2, "one": 2, "line": [2, 3, 4, 7, 8], "wherea": 2, "span": 2, "mani": [2, 3, 7], "accept": 2, "differ": [2, 4], "input": 2, "do": [2, 7, 8], "those": [2, 4], "depend": [2, 7], "specif": [2, 4, 5], "being": 2, "here": [2, 4, 5, 7, 8], "note": [2, 7], "render": 2, "special": 2, "box": 2, "when": [2, 3, 7], "build": [2, 7], "an": [2, 4, 7], "inlin": 2, "refer": [2, 7], "can": [2, 3, 4, 5, 8], "also": [2, 3, 4, 5, 8], "cite": 2, "store": [2, 7], "bibtex": 2, "exampl": [2, 4, 7, 8], "follow": [2, 3, 4], "holdgraf_evidence_2014": 2, "hdhpk14": 2, "moreov": 2, "insert": 2, "bibliographi": 2, "The": [2, 3, 4, 5], "must": 2, "us": [2, 3, 4, 5, 7], "all": [2, 3, 4, 5, 7], "properli": 2, "bib": 2, "christoph": 2, "ramsai": 2, "holdgraf": 2, "wendi": 2, "de": 2, "heer": 2, "brian": 2, "n": [2, 7, 8], "paslei": 2, "robert": 2, "t": [2, 4, 5, 7, 8], "knight": 2, "evid": 2, "predict": [2, 4, 5], "code": [2, 3], "human": [2, 4, 5], "auditori": 2, "cortex": 2, "In": [2, 4, 5, 7], "intern": 2, "confer": 2, "cognit": 2, "neurosci": 2, "brisban": 2, "australia": 2, "2014": 2, "frontier": 2, "just": 2, "starter": 2, "lot": [2, 8], "jupyterbook": 2, "org": [2, 4], "let": 3, "base": 3, "detail": [3, 7], "instruct": 3, "With": [3, 4, 5], "defin": [3, 4], "direct": [3, 4], "so": [3, 7], "print": [3, 4], "2": [3, 4, 5, 7], "4": [3, 4, 7, 8], "built": [3, 7], "block": 3, "execut": [3, 4], "default": 3, "kernel": [3, 7], "output": [3, 4], "displai": [3, 4, 7], "rest": 3, "jupytext": 3, "convert": [3, 4, 7], "support": [3, 4, 7], "other": [3, 7], "thing": 3, "need": [3, 7], "understand": 3, "should": 3, "includ": [3, 4, 5, 8], "top": 3, "presenc": 3, "which": [3, 4, 5, 7], "That": 3, "If": [3, 7], "have": [3, 4, 5, 7], "d": [3, 7], "treat": 3, "run": 3, "command": [3, 7], "init": 3, "path": 3, "markdownfil": 3, "creat": [7, 8], "mean": 8, "As": 8, "emb": [7, 8], "imag": 8, "html": [7, 8], "etc": [4, 5, 8], "post": [4, 8], "add_": 8, "math": 8, "begin": 8, "align": 8, "mbox": 8, "la_": 8, "tex": 8, "end": [4, 8], "But": 8, "make": [4, 5, 8], "sure": 8, "escap": 8, "dollar": 8, "sign": [7, 8], "want": 8, "keep": [7, 8], "work": [4, 5, 7, 8], "guid": 8, "matplotlib": [7, 8], "from": [0, 4, 5, 8], "import": [4, 5, 7, 8], "rcparam": [7, 8], "cycler": [7, 8], "pyplot": [7, 8], "plt": [7, 8], "numpi": [7, 8], "np": [4, 7, 8], "ion": [7, 8], "contextlib": [7, 8], "exitstack": [7, 8], "0x7fad5e6fca00": [], "fix": [7, 8], "random": [7, 8], "state": [7, 8], "reproduc": [7, 8], "seed": [7, 8], "19680801": [7, 8], "10": [4, 7, 8], "data": [1, 4, 5, 7, 8], "logspac": [7, 8], "0": [4, 7, 8], "1": [4, 5, 7, 8], "100": [7, 8], "randn": [7, 8], "ii": [7, 8], "rang": [7, 8], "arrai": [7, 8], "cmap": [7, 8], "cm": [7, 8], "coolwarm": [7, 8], "ax": [7, 8], "prop_cycl": [7, 8], "color": [7, 8], "linspac": [7, 8], "line2d": [7, 8], "custom_lin": [7, 8], "lw": [7, 8], "5": [4, 7, 8], "fig": [7, 8], "subplot": [7, 8], "figsiz": [7, 8], "plot": [7, 8], "legend": [7, 8], "cold": [7, 8], "medium": [7, 8], "hot": [7, 8], "There": [4, 5, 7, 8], "interact": 8, "link": [4, 5, 6, 7], "intro": [4, 5, 6], "he": 6, "retriev": 0, "metabolit": [], "addit": [4, 5], "relat": [4, 5], "biomed": [0, 4, 5], "knowledg": [4, 5], "graph": [4, 5], "gain": [4, 5], "describ": [4, 5], "learn": [4, 5], "sever": [4, 5], "applic": [4, 5], "repurpos": [4, 5], "biomark": [4, 5], "discoveri": [4, 5], "biohackathon": [4, 5], "we": [4, 5, 7], "investig": [4, 5], "focus": [4, 5], "case": [4, 5], "inborn": [4, 5], "error": [4, 5, 7], "metabol": [4, 5], "disord": [4, 5], "section": [4, 5, 7], "comprehens": [4, 5], "its": [4, 5], "natur": [4, 5], "product": [4, 5], "sparql": 4, "sib": 4, "anoth": 4, "bind": 4, "queri": [4, 5], "catalyt": [4, 5], "reaction": [4, 5], "39": 4, "40": 4, "http": 4, "known": [4, 5], "first": 4, "Then": [4, 5], "access": [4, 5], "id": [4, 5], "filter": 4, "endpoint": 4, "each": [4, 5], "sourc": [4, 5], "sy": 4, "os": 4, "time": 4, "m": [4, 7], "pip": 4, "instal": 4, "sparqlwrapp": 4, "json": 4, "panda": [4, 7], "pd": [4, 7], "alwai": 4, "full": 4, "column": [4, 7], "result": 4, "don": [4, 5], "truncat": 4, "set_opt": 4, "max_colwidth": 4, "wrapper": 4, "sparql_uniprot": 4, "tabl": 4, "def": 4, "pretty_print": 4, "transform": [4, 7], "datafram": [4, 7], "header": 4, "name": [4, 7], "kei": 4, "avail": 4, "entri": 4, "append": 4, "python": [4, 7], "list": [4, 5], "row": 4, "df": 4, "valu": 4, "none": 4, "els": 4, "return": 4, "requir": 4, "alreadi": 4, "satisfi": 4, "home": 4, "nur": 4, "anaconda3": 4, "lib": 4, "python3": 4, "site": [4, 7], "packag": [4, 7], "rdflib": 4, "6": [4, 7], "3": [4, 5, 7], "isod": 4, "7": [4, 7], "pypars": 4, "9": [4, 7], "six": 4, "16": 4, "tmp": 4, "ipykernel_99069": [], "2559832190": 4, "py": 4, "8": [4, 7], "futurewarn": 4, "pass": 4, "neg": 4, "integ": 4, "deprec": 4, "version": 4, "futur": 4, "instead": 4, "limit": 4, "width": 4, "rdf": [0, 4], "query_human_enzym": 4, "prefix": 4, "xsd": 4, "www": 4, "w3": 4, "2001": 4, "xmlschema": 4, "wikibas": 4, "wikiba": 4, "se": 4, "ontolog": 4, "wdt": 4, "wikidata": 4, "prop": 4, "wd": 4, "entiti": 4, "vg": 4, "resourc": [0, 4], "up": [4, 7], "purl": 4, "core": 4, "uniprotkb": 4, "uberon": 4, "obolibrari": 4, "obo": 4, "uo": 4, "taxon": 4, "taxonomi": 4, "sp": 4, "spinrdf": 4, "sko": 4, "2004": 4, "02": 4, "sio": 4, "semanticsci": 4, "sh": 4, "ns": 4, "shacl": 4, "schema": 4, "sachem": [4, 5], "bioinfo": 4, "uochb": 4, "ca": 4, "cz": 4, "v1": 4, "rh": 4, "db": 4, "2000": 4, "01": 4, "1999": 4, "22": 4, "pubm": 4, "ncbi": 4, "nlm": 4, "nih": 4, "gov": 4, "ps": 4, "statement": 4, "pq": 4, "qualifi": 4, "patent": 4, "epo": 4, "p": 4, "owl": 4, "2002": 4, "07": 4, "orthodbgroup": 4, "orthodb": 4, "odbgroup": 4, "orth": 4, "net": 4, "nextprot": 4, "mnx": 4, "metanetx": 4, "mnet": 4, "mesh": 4, "lscr": 4, "lipidmap": 4, "keyword": 4, "insdcschema": 4, "ddbj": 4, "nig": 4, "ac": 4, "jp": 4, "nucleotid": 4, "insdc": 4, "identifi": [4, 5], "glyconnect": 4, "glycan": 4, "bio": 4, "12": [4, 7], "glyco": 4, "genex": 4, "foaf": 4, "xmln": 4, "com": 4, "faldo": 4, "eunisspeci": 4, "euni": 4, "eea": 4, "europa": 4, "eu": 4, "speci": 4, "ensembltranscript": 4, "ebi": 4, "uk": 4, "ensembl": 4, "transcript": 4, "ensemblterm": 4, "term": [1, 4], "ensemblprotein": 4, "protein": [4, 5], "ensemblexon": 4, "exon": 4, "ec": 4, "dcterm": 4, "dc": 4, "chebislash": 4, "chebi": [4, 5], "chebihash": 4, "cco": 4, "chembl": [4, 5], "busco": 4, "ezlab": 4, "bibo": 4, "alli": 4, "swisslipid": 4, "slm_": 4, "go_": 4, "eco": 4, "eco_": 4, "chebi_": 4, "select": 4, "distinct": 4, "where": 4, "annot": 4, "catalyticact": 4, "catalyzedreact": 4, "organ": 4, "9606": 4, "set": [4, 5], "against": 4, "format": [4, 7], "setqueri": 4, "setreturnformat": 4, "num_exampl": 4, "results_human_enzym": 4, "head": 4, "keyboardinterrupt": 4, "traceback": [4, 7], "recent": [4, 7], "last": [4, 7], "cell": 4, "1196": 4, "queryresult": 4, "self": 4, "1194": 4, "elif": 4, "_content_type_in_list": 4, "ct": 4, "_sparql_json": 4, "1195": 4, "_validate_format": 4, "requestedformat": 4, "_convertjson": 4, "1197": 4, "_rdf_xml": 4, "1198": 4, "1199": 4, "xml": 4, "rdfxml": 4, "1200": 4, "1059": 4, "1051": 4, "dict": 4, "1052": 4, "1053": 4, "method": 4, "overwritten": 4, "subclass": 4, "1054": 4, "convers": 4, "1057": 4, "rtype": 4, "1058": 4, "json_str": 4, "load": 4, "respons": 4, "read": 4, "decod": 4, "utf": 4, "1060": 4, "isinst": 4, "1061": 4, "client": 4, "460": 4, "httprespons": 4, "amt": 4, "457": 4, "b": [4, 7], "459": 4, "chunk": 4, "_read_chunk": 4, "462": 4, "463": 4, "length": 4, "464": 4, "clip": 4, "583": 4, "581": 4, "try": 4, "582": 4, "while": 4, "true": 4, "chunk_left": 4, "_get_chunk_left": 4, "584": 4, "585": 4, "break": 4, "566": 4, "564": 4, "_safe_read": 4, "toss": 4, "crlf": 4, "565": 4, "_read_next_chunk_s": 4, "567": 4, "except": [4, 7], "valueerror": 4, "568": 4, "rais": [4, 7], "incompleteread": 4, "526": 4, "524": 4, "525": 4, "next": 4, "size": 4, "fp": 4, "readlin": 4, "_maxlin": 4, "527": 4, "len": 4, "528": 4, "linetoolong": 4, "socket": 4, "705": 4, "socketio": 4, "readinto": 4, "703": 4, "704": 4, "_sock": 4, "recv_into": 4, "706": 4, "timeout": 4, "707": 4, "_timeout_occur": 4, "ssl": 4, "1307": 4, "sslsocket": 4, "buffer": 4, "nbyte": 4, "flag": 4, "1303": 4, "1304": 4, "1305": 4, "non": 4, "zero": 4, "1306": 4, "__class__": 4, "1308": 4, "1309": 4, "super": 4, "1163": 4, "1161": 4, "1162": 4, "_sslobj": 4, "1164": 4, "1165": 4, "particip": [4, 5], "13": 4, "involv": [4, 5], "pathwai": [4, 5], "reactant": [4, 5], "cross": [4, 5], "idsm": [4, 5], "expand": [4, 5], "compound": [4, 5], "three": [4, 5], "target": [4, 5], "sensibl": [4, 5], "unknown": [4, 5], "relev": [4, 5], "query_metabolit": 4, "servic": 4, "side": 4, "contain": [4, 7], "subclassof": 4, "results_metabolit": 4, "smallmolecul": 4, "b2rb89": 4, "17989": 4, "chebi_30616": 4, "genericpolypeptid": 4, "our": [4, 5], "user": [4, 5], "pdb": [4, 5], "imcd": [4, 5], "dataset": [4, 5], "recon": [4, 5], "model": [4, 5], "leiden": [4, 5], "rich": [4, 5], "author": 4, "jerven": 4, "bolleman": 4, "princip": 4, "softwar": 4, "engin": 4, "linkedin": 4, "feed": 4, "updat": 4, "7171566017431724033": 4, "trk": 4, "feed_main": 4, "card_soci": 4, "action": 4, "comment": 4, "et": 4, "al": 4, "combin": 4, "molecul": 4, "lnkd": 4, "e2jwcd2": 4, "e93pzuva": 4, "emde6cki": 4, "independ": 4, "ejxrwuh3": 4, "search": 4, "catalyz": 4, "substrat": 4, "ha": 4, "onli": [4, 7], "smile": 4, "represent": 4, "e83mrqmr": 4, "jervern": 4, "query_disease_enzymes_cholestan": 4, "omim": 4, "find": 4, "complet": 4, "skeleton": 4, "via": [4, 5], "czech": 4, "elixir": 4, "node": 4, "chemic": 4, "substructuresearch": 4, "h": 4, "c": [4, 7], "cc": [1, 4], "ccc4cccc": 4, "12c": 4, "cccc": 4, "fact": 4, "map": [4, 7], "found": 4, "o": 4, "match": 4, "option": 4, "seealso": 4, "mim": 4, "results_disease_enzym": 4, "330": 4, "chebi_2288": 4, "235555": 4, "p51857": 4, "46632": 4, "chebi_2290": 4, "46640": 4, "chebi_16074": 4, "11524": 4, "hmdb": [4, 5], "larg": [4, 5], "amount": [4, 5], "complex": [4, 5], "tailor": [4, 5], "onc": [4, 5], "clear": [4, 5], "offer": [4, 5], "systemat": [4, 5], "wai": [4, 5], "subset": [4, 5], "join": [4, 5], "union": [4, 5], "role": [4, 5], "ask": [4, 5], "plant": [4, 5], "microbiom": [4, 5], "commun": [4, 5], "mainli": [4, 5], "sequenc": [4, 5], "phenom": [4, 5], "now": [4, 5], "kegg": [4, 5], "microb": [4, 5], "ms": [4, 5], "know": [4, 5], "much": [4, 5], "mayb": [4, 5], "standard": [4, 5], "usual": [4, 5], "obtain": [4, 5], "metabolom": [4, 5], "mass": [4, 5], "spectrometri": [4, 5], "gc": [4, 5], "lc": [4, 5], "ce": [4, 5], "tof": [4, 5], "metacyc": [4, 5], "would": [4, 5], "deepgo": [4, 5], "system": [4, 5], "enzym": 5, "rhea": 5, "ligand": 5, "dbcl": [0, 5], "current": 7, "plain": 7, "still": 7, "automat": 7, "mostli": 7, "flavour": 7, "minor": 7, "modif": 7, "0x7fd377d4b2b0": [], "abov": 7, "captur": 7, "smoother": 7, "linez": 7, "layout": 7, "sidebar": 7, "web": 7, "download": 7, "thisvari": 7, "textbook": 7, "x": 7, "y": 7, "scatter": 7, "ab": 7, "fontsiz": 7, "20": 7, "transax": 7, "set_axis_off": 7, "quickli": 7, "without": 7, "clutter": 7, "hi": 7, "word": 7, "A": 7, "hide": 7, "materi": 7, "below": 7, "folium": 7, "retain": 7, "abl": 7, "standalon": 7, "javascript": 7, "underli": 7, "locat": 7, "45": 7, "372": 7, "121": 7, "6972": 7, "zoom_start": 7, "tile": 7, "stamen": 7, "terrain": 7, "marker": 7, "3288": 7, "6625": 7, "popup": 7, "mt": 7, "hood": 7, "meadow": 7, "icon": 7, "cloud": 7, "add_to": 7, "3311": 7, "7113": 7, "timberlin": 7, "lodg": 7, "green": 7, "3300": 7, "6823": 7, "red": 7, "info": 7, "modulenotfounderror": 7, "11": 7, "No": 7, "modul": 7, "becaus": 7, "menu": 7, "nice": 7, "And": 7, "mark": 7, "expect": 7, "ad": 7, "tag": 7, "them": 7, "this_will_error": 7, "take": 7, "advantag": 7, "gener": 7, "binder": 7, "connect": 7, "brows": 7, "0x7f66848bf3a0": [], "ipykernel_100073": [], "0x7f11904e32b0": [], "0x7fb8afccc130": [], "devot": 0, "showcas": 0, "licens": 0, "project": 1, "script": 1, "under": 1, "folder": 1, "recurs": 1, "subfold": 1, "mit": 1, "BY": 1, "ipykernel_202021": 4, "0x7fa04c9f32b0": 7, "0x7f507171f1c0": 8}, "objects": {}, "objtypes": {}, "objnames": {}, "titleterms": {"welcom": 0, "your": [], "jupyt": [0, 7], "book": 0, "markdown": [2, 3, 8], "file": [2, 7], "what": 2, "myst": [2, 3, 8], "sampl": 2, "role": 2, "direct": 2, "citat": 2, "learn": 2, "more": [2, 7], "notebook": [3, 7, 8], "an": 3, "exampl": 3, "cell": [3, 7], "creat": 3, "quickli": 3, "add": 3, "yaml": 3, "metadata": 3, "content": [7, 8], "code": [7, 8], "block": [7, 8], "output": [7, 8], "here": 6, "my": 6, "new": 6, "chapter": 6, "first": 6, "section": 6, "retriev": [4, 5], "metabolit": [0, 4, 5], "inform": [4, 5], "uniprot": [4, 5], "explor": [4, 5], "genom": [4, 5], "druggabl": [4, 5], "drug": [4, 5], "candid": [4, 5], "base": [4, 5], "activ": [4, 5], "similar": [4, 5], "rhea": 4, "structur": [4, 5], "similarii": [4, 5], "dbcl": 4, "databas": [4, 5], "ligand": 4, "diseas": [4, 5], "patholog": [4, 5], "curat": [4, 5], "associ": [4, 5], "isoform": [4, 5], "enzym": 4, "interact": [4, 7], "cholestan": 4, "substructur": 4, "pubchem": [4, 5], "other": [4, 5], "imag": 7, "you": 7, "can": 7, "also": 7, "pop": 7, "out": 7, "side": 7, "remov": 7, "befor": 7, "publish": 7, "rich": 7, "from": 7, "featur": 7, "biohackathon": 0, "2023": 0, "subset": 0, "licens": 1}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 6, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinxcontrib.bibtex": 9, "sphinx": 56}}) \ No newline at end of file