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文献データベース Literature	Databases
• バイオサイエンス研究において、既存の知識としての
データベースの活用は欠かせない。本講義では、アメ
リカNIHの文献データベースPubMed、京都大学化学研
究所のKEGGデータベースなどの概略と実際の使用例
を紹介する。
• It	has	become	essential	to	use	literature	databases	as	
previously known	information	in	bioscience	studies.	This	
lecture	provides	the overview	and	some	actual	usage	
examples	of	some	databases	including PubMed	of	NIH	in	US,	
and	KEGG	of	Kyoto	University	Institute	for Chemical	Research.
12018/7/10
https://www.slideshare.net/maskot3/presentations
Short	Quiz	for	Today
• Choose	5	websites	and	
describe	their	usages.	
• Deadline:	The	end	of	
this	lecture.
1. Google
2. NCBI	PubMed
3. ExplorEnz
4. GO
5. GEO
6. PDBj
7. ChEBI
8. ChEMBL
9. ChemIDplus
10. PubChem
11. DBCLS
12. KEGG
22018/7/10
https://www.slideshare.net/maskot3/presentations
Google
• https://www.google.com
• Try	to	input	the	following	phrases	and	submit:
• ChemSys Kotera
• KEGG	Kotera (without	quotation	marks)
• ”KEGG	Kotera” (with	quotation	marks)
• KEGG	Kotera lang:en
• KEGG	Kotera site:genome.jp
• KEGG	Kotera site:uk
• KEGG	Kotera	filetype:pdf
32018/7/10
Google	Images
• https://images.google.com/
• Try	to	input	the	following	phrases	and	submit:
• KEGG
• PubMed
• Papilio xuthus
• Useful	to	find:
• Images,	pictures	by	words
• Images,	pictures	similar	to	those	you	have
• Picture	theft
42018/7/10
Google	Scholar
• https://scholar.google.co.jp
• Try	to	input	the	following	phrases	and	submit:
• KEGG	Kotera
• Masaaki	Kotera
• metabolic	pathway	reconstruction
• Look	up	some	literatures
• Look	up	some	people
• Use	Google	Alerts	&	Google	Scholar	Alerts
52018/7/10
NIH	と NLM	と NCBI
• National	Institutes	of	Health (NIH)	-アメリカ国立衛生研究所
• 合衆国で最も古い医学研究の拠点機関。
• National	Library	of	Medicine	(NLM)
• NIHの一部門。世界最大の医学図書館。医学及び関連科学に関する700万冊以
上の書籍、学術雑誌、技術報告書、写本、マイクロフィルム、写真、画像を所有。
• National	Center	for	Biotechnology	Information	(NCBI)
• NLMの一部門。分子生物学やバイオインフォマティクスのデータベースの構築・
運営、ソフトウェア開発を行う。配列データベースGenBank 、一塩基多型 (SNP)	
データベース dbSNP、ESTデータベースdbEST、文献データベース MEDLINE、
PubMedなどを運営。
• 各研究者が発表したゲノムデータのリアノテーションを NCBI	で独自に行っており、
その結果をRefseq として公開。
• BLAST による相同性検索サービスの提供。
• 公開されているデータは基本的に無償で利用可能。
2018/7/10 6
NCBI	Pubmed
•https://www.ncbi.nlm.nih.gov/pubmed/
• Try	to	input	the	following	phrases	and	submit:
• Kotera,	Kotera M,	Kotera Masaaki
• Kotera 2014	
• E	coli
• E	coli	O157	genome	complete	
• P xuthus
• perhexiline
72018/7/10
NCBI	Pubmed
• https://www.ncbi.nlm.nih.gov/pubmed/
• Useful	options	to	check:
• Left	column
• Article	types,	Text	availability,	Publication	
dates,	Species
• Right	column
• PMC	image	search,	Find related data,	Search
details,	Recent Activity
• Top
• Format,	Sort	by,	Per	page
82018/7/10
Free	full-text	archives
• PMC	(PubMed	Central)
• https://www.ncbi.nlm.nih.gov/pmc/
•Europe	PMC
http://europepmc.org/
• arXiv.org e-Print	archive
• https://arxiv.org/
92018/7/10
NCBI-Nucleotide/Protein
• http://www.ncbi.nlm.nih.gov/
• Select	“Nucleotide”	or	“Protein”	and	search	for	the	
following	words:
• contig
• NSP
• LXR
• PXR
• PPAR
• terpineol
• Learn	how	to	limit	the	organism	and	obtain	a	FASTA-
format	file.
102018/7/10
NCBI-BLAST
• http://blast.ncbi.nlm.nih.gov/Blast.cgi
• Learn	how	to	BLAST	using	your	
nucleotide/protein	sequence.
• Try	to	use	PSI-BLAST	and	PHI-BLAST
• BLAST	is	also	provided	by	other	databases	such	
as	GenomeNet.
• http://www.genome.jp/tools/blast/
112018/7/10
ExplorEnz	– The	Enzyme	Database
• http://enzyme-database.org
• A	dictionary	of	enzymes,	necessary	for	the	systematic	
nomenclature	provided	by	NC-IUBMB/IUPAC
• Try	to	input	the	following	phrases	and	submit:
• decarboxylase
• transporting
• terpineol
• Useful	options	to	check:
• Enzymes	by	Class
• Information/Glossary
122018/7/10
Gene	Ontology	(GO)
• http://geneontology.org/
• A	dictionary	of	gene	names,	necessary	for	the	
systematic	nomenclature	provided	by	Gene	Ontology	
Consortium
• Try	to	input	the	following	phrases	and	submit:
• methyl
• MECP2
• heterocyclic	compound	binding
• Useful	options	to	check:
• Tools/Enrichment	analysis
132018/7/10
Gene	Expression	Omnibus	(GEO)
• http://www.ncbi.nlm.nih.gov/geo/
• Try	to	input	the	following	phrases	and	submit:
• colorectal	cancer
• liver	toxicity
• dieldrin
• Useful	options	to	check:
• Organism,	Top	Organisms
• Study	type
• GEO	BLAST	(Gene	Expression	Omnibus	Nucleotide	
BLAST)
142018/7/10
PDBj
• http://pdbj.org/
• Try	to	input	the	following	phrases	and	submit:
• 1HTB
• aspartic	proteinase
• 酵素 (in	Japanese)
• Useful	options	to	check:
• 巨大構造エントリー
• 化合物一覧
• 今月の分子
152018/7/10
ChEBI
• https://www.ebi.ac.uk/chebi/
• Try	to	input	the	following	phrases	and	submit:
• liver	toxicity
• breast	cancer
• P450
• synephrine
• Useful	options	to	check:
• Advanced	search
• Browse	/	Entity	of	the	Month
162018/7/10
ChEMBL
• https://www.ebi.ac.uk/chembl/
• Try	to	input	the	following	phrases	and	submit:
• PXR for	Targets
• AhR for	Targets
• Mitochondrial	disruption	for	Assays
• Mitochondrial	disruption	for	Documents
• Dantrolene for	Compounds	
• Tamoxifen for	Compounds
172018/7/10
ChemIDplus
•https://chem.nlm.nih.gov/chemidplus/
•Try	to	search	for	the	compounds	having	
the	following	properties:
•LD50	:	100	~	200	mg/kg
•Molecular	Weight	:	201.2	~	201.7
•Search	for	the	relevant	literatures.
182018/7/10
PubChem
• https://pubchem.ncbi.nlm.nih.gov/
• Try	to	input	the	following	phrases	and	submit:
• cyclopentanone
• crotonic acid
• liver	toxicity	
• diabetes
• Find	some	relevant	information	and	their	data	
sources
192018/7/10
DBCLS	services
• https://dbcls.rois.ac.jp/services-en.html
• Some	useful	tools:
• TogoGenome
• DBCLS	SRA
• RefEx,	AOE
• GGRNA,	GGGenome
• Gendoo
• CRISPRdirect
• 新着論文レビュー、領域融合レビュー、統合TV
• BodyParts3D/Anatomography
• Available	in	Japanese	in	most	tools.
2018/7/10 20
KEGG database
http://www.kegg.jp/
Universe of biosystems
Universe of life science databases and tools
Universe of Internet
http://www.genome.jp/GenomeNet
2018/7/10 21
KEGG	and	GenomeNet
KEGG	(Kyoto	Encyclopedia	of	Genes	and	Genomes)	
• http://www.kegg.jp/
• Look	up	the	following	proteins	in	human:
• Bax
• FAS
• CASP10
• TP53
• BCL2
• KEGG	Mapper
• Add	“hsa:”	for	each	of	the	gene	names	above	and	
submit.
222018/7/10
KEGG	MEDICUS	/	KEGG	DRUG
• https://www.kegg.jp/kegg/medicus/
• Try	to	input	the	following	phrases	and	submit:
• penicillin
• tetracycline
• Try	to	find	the	following	relevant	information:
• pharmaceutical	activity
• DDI	search	(drug-drug	intereaction)
• Drug	development	(構造マップ)
232018/7/10
KEGG	DISEASE	/	KEGG	Cancer
• https://www.kegg.jp/kegg/disease/
• Try	to	input	the	following	phrases	and	submit:
• breast	cancer
• diabetes
• Useful	options	to	check:
• Human	diseases	[+	gene]
• Infectious	diseases	[+	genome]
• KEGG	Cancer	
https://www.kegg.jp/kegg/disease/cancer.html
242018/7/10
KEGG	BRITE
• https://www.kegg.jp/kegg/brite.html
• Try	to	input	the	following	phrases	and	submit:
• insulin
• angiotensin
• dihydrofolate
• Useful	options	to	check:
• Codes	and	Abbreviations
252018/7/10
GenomeNet
• https://www.genome.jp/
• Try	some	tools:
• Sequence	analysis
• BLAST,	MOTIF,	MAFFT	etc
• Genome	analysis:
• KAAS,	GENIES	etc
• Chemical	analysis:
• SIMCOMP,	PathPred,	E-zyme etc
262018/7/10
Short	Quiz	for	Today
• Choose	5	websites	and	
describe	their	usages.	
• Deadline:	The	end	of	
this	lecture.
1. Google
2. NCBI	PubMed
3. ExplorEnz
4. GO
5. GEO
6. PDBj
7. ChEBI
8. ChEMBL
9. ChemIDplus
10. PubChem
11. DBCLS
12. KEGG
272018/7/10
https://www.slideshare.net/maskot3/presentations

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