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kozo2 / rdf-doctor_output.txt
Created August 25, 2024 07:41
try rdf-doctor for MassBank.json [MassBank.ttl is converted from MassBank.json]
(base) knishida@anna:~$ rdf-doctor -i MassBank.ttl
25/08/2024 07:21:13 -- turtle:(not compressed)
PREFIX dcterms: <http://purl.org/dc/terms/>
PREFIX ns1: <http://schema.org/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX : <http://weso.es/shapes/>
:ChemicalSubstance [<https://massbank.eu/MassBank/>~] AND # 117732 instances. Instance example: 'https://massbank.eu/MassBank/RecordDisplay?id=MSBNK-HBM4EU-HB002846#ChemicalSubstance'
{
<http://www.w3.org/1999/02/22-rdf-syntax-ns#type> [ns1:ChemicalSubstance] ; # 100.0 % (117732 instances).
@kozo2
kozo2 / translations.md
Created August 19, 2024 15:46
https://community.crowdin.com/t/markdown-parser-problem-in-code-chunk/9557
source title teaching exercises
Rmd
Manipulation et analyse de données avec dplyr
75
75
@kozo2
kozo2 / source.md
Created August 19, 2024 15:43
https://community.crowdin.com/t/markdown-parser-problem-in-code-chunk/9557
source title teaching exercises
Rmd
Manipulating and analysing data with dplyr
75
75
@kozo2
kozo2 / MSBNK-RIKEN-PR010017.ttl
Last active April 19, 2024 07:36
@prefix : <http://example.org/rules/> .
@prefix chebi: <http://purl.obolibrary.org/obo/chebi/> .
@prefix ex: <http://example.org/> .
@prefix fnml: <http://semweb.mmlab.be/ns/fnml#> .
@prefix fno: <https://w3id.org/function/ontology#> .
@prefix idlab-fn: <http://example.com/idlab/function/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix ql: <http://semweb.mmlab.be/ns/ql#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@kozo2
kozo2 / error_in_fuseki.txt
Last active January 23, 2024 18:23
ChemFOnt version 1.0 OWL file import error
02:49:51 ERROR Fuseki :: [line: 70691, col: 99] {W002} <http://purl.obolibrary.org/obo/ChemFont.owl#Adrenal Gland> Code: 17/WHITESPACE in FRAGMENT: A single whitespace character. These match no grammar rules of URIs/IRIs.
@kozo2
kozo2 / docker-compose.yml
Created September 8, 2023 03:28
version: '3.9'
services:
R-notebook:
image: jupyter/r-notebook
ports:
- '8888:8888'
environment:
- JUPYTER_TOKEN=easy
- PASSWORD=easy
cytoscape-desktop:
@kozo2
kozo2 / RubyQuartoSlides.md
Last active August 28, 2023 04:11

  • Quartoとは?

    • 画像は quarto.org のスクリーンショット

  • Quartoの変換ができると何がうれしいのか？

  • Quartoはどのように使うものなのか？

    • コマンドラインラインツールとして使う。
    • 入力ipynbをpdfやword、ウェブサイトに変換できる

  • Quarto で ipynbをpdfやwordに変換できて何がうれしいのか？

    • 目次や図表へのクロスリファレンスを自動生成してくれる

  • クロスリファレンスとは何か？

@kozo2
kozo2 / pyopensci.md
Created August 18, 2023 08:07

Submitting Author: Kozo Nishida (@kozo2) All current maintainers: (@kozo2) Package Name: pywikipathways One-Line Description of Package: Python Client Package for the WikiPathways API Repository Link: https://github.com/kozo2/pywikipathways Version submitted: 0.0.2 Editor: TBD
Reviewer 1: TBD
Reviewer 2: TBD
Archive: TBD

@kozo2
kozo2 / msfexp_new.tsv
Created June 5, 2023 06:49
We can make this file beautiful and searchable if this error is corrected: It looks like row 3 should actually have 14 columns, instead of 13 in line 2.
File path File name Title MS1 count MSMS count PRECURSORMZ PRECURSORTYPE Structure rank Total score Databases Formula Ontology InChIKey SMILES
C:\Users\knishida\Desktop\MS-FINDER demo files\2-Deoxycytidine 5-diphosphate Trial 193 Neg.msp 2-Deoxycytidine 5-diphosphate Trial 193 Neg 2'-Deoxycytidine 5'-diphosphate; LC-ESI-QTOF; MS2; CE 0 8 386.015991 [M-H]- dCDP 8.0345 HMDB=HMDB0001245,ChEBI=CHEBI:28846;CHEBI:58593,SMPDB=PW_C000962,YMDB=YMDB00916,FooDB=FDB022510,BMDB=BMDB01245,ECMDB=ECMDB01245,PubChem=21122964;150855,PlantCyc=DCDP,BLEXP=BLEXPDB00000000623,COCONUT=CNP0142861 C9H15N3O10P2 Organic pyrophosphates FTDHDKPUHBLBTL-SHYZEUOFSA-N O=C1N=C(N)C=CN1C2OC(COP(=O)(O)OP(=O)(O)O)C(O)C2
C:\Users\knishida\Desktop\MS-FINDER demo files\2-Deoxycytidine 5-diphosphate Trial 193 Neg.msp 2-Deoxycytidine 5-diphosphate Trial 193 Neg 2'-Deoxycytidine 5'-diphosphate; LC-ESI-QTOF; MS2; CE 0 8 386.015991 [M-H]- UNPD122004 7.1501 UNPD=UNPD122004,COCONUT=CNP0270287 C9H15N3O10P2 Pyrimidine deoxyribonucleoside 3',5'-bisphosphates P
@kozo2
kozo2 / msfexp_old.tsv
Created June 5, 2023 06:32
We can make this file beautiful and searchable if this error is corrected: It looks like row 3 should actually have 78 columns, instead of 1 in line 2.
File path File name Title MS1 count MSMS count PRECURSORMZ PRECURSORTYPE Structure rank 1 Total score Databases Formula Ontology InChIKey SMILES Structure rank 2 Total score Databases Formula Ontology InChIKey SMILES Structure rank 3 Total score Databases Formula Ontology InChIKey SMILES Structure rank 4 Total score Databases Formula Ontology InChIKey SMILES Structure rank 5 Total score Databases Formula Ontology InChIKey SMILES Structure rank 6 Total score Databases Formula Ontology InChIKey SMILES Structure rank 7 Total score Databases Formula Ontology InChIKey SMILES Structure rank 8 Total score Databases Formula Ontology InChIKey SMILES Structure rank 9 Total score Databases Formula Ontology InChIKey SMILES Structure rank 10 Total score Databases Formula Ontology InChIKey SMILES
C:\Users\knishida\Desktop\MS-FINDER demo files\S-propylmercaptoglutathione.mat S-propylmercaptoglutathione Unknown 18 36 382.1105 [M+H]+
C:\Users\knishida\Des