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Biological Databases_May2023

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5 views

Biological Databases_May2023

Uploaded by

my jw
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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Biological Databases

What is a database?
⚫ A collection of data that needs to be:
⚫ Structured
⚫ Searchable
⚫ Updated (periodically)
⚫ Cross referenced

⚫ Challenge:
⚫ To change “meaningless” data into useful
information that can be accessed and analysed
the best way possible.
Making biological data
available
Bioinformatics centres of
excellence
⚫ The EMBL-European Bioinformatics Institute
(EMBL-EBI)
⚫ The US National Center for Biotechnology
Information (NCBI)
⚫ The National Institute of Genetics in Japan
(NIG)
Raw Biological data
Nucleic Acids (DNA)
Curated Biological data
3D Structures, folds
Accessing database
information
⚫ A request for data from a database is called a
query

⚫ Queries can be of three forms:


⚫ Common mode of search are keywords with
modifiers or identifiers
Cross-references link the information of different
databases
⚫ Query by example (QBE)
⚫ Query language
Limitations
⚫ There is no standard format
⚫ Every database or program has its own format

⚫ There is no standard nomenclature


⚫ Every database has its own names

⚫ Data is not fully optimized


⚫ Some datasets have missing information without
indications of it
⚫ Data errors
⚫ Data is sometimes of poor quality, erroneous,
misspelled
⚫ Error propagation resulting from computer
annotation
What are the ethical, legal and social
implications (ELSI) in biomedical
data sharing?
A few biological databases
⚫ Nucleotide Databases
Alternative Splicing, EMBL-Bank, Ensembl, Genomes Server, Genome,
MOT, EMBL-Align, Simple Queries, dbSTS Queries, Parasites,
Mutations, IMGT
⚫ Genome Databases
Human, Mouse, Yeast, C.elegans, FLYBASE, Parasites
⚫ Protein Databases
Swiss-Prot, TrEMBL, InterPro, CluSTr, IPI, GOA, GO, Proteome
Analysis, HPI, IntEnz, TrEMBLnew, SP_ML, NEWT, PANDIT
⚫ Structural Databases
PDB, MSD, FSSP, DALI
⚫ Microarray Database
ArrayExpress
⚫ Literature Databases
MEDLINE, Software Biocatalog, Flybase Archives
⚫ Alignment Databases
BAliBASE, Homstrad, FSSP
Pathway databases - Kegg
Disease databases - TCGA
Data sharing collaborations
GenBank Statistics
Hands on session 1

Explore the range of ressources of NCBI Databases at


http://www.ncbi.nlm.nih.gov/guide/all/#databases_
NCBI-Entrez retrieval system

https://www.ncbi.nlm.nih.gov/search/
Hands on session 2
⚫ http://www.nlm.nih.gov/bsd/disted/pubmedtuto
rial/cover.html
⚫ Save Searches and Set E-mail Alerts

https://www.youtube.com/watch?v=WbFjV91YNNY
⚫ How to: Find articles about a topic similar to
that in a given article
https://www.ncbi.nlm.nih.gov/guide/howto/find-
articles-similar/
https://medlineplus.gov/medlineplus-connect/
References
⚫ NAR Database issue
https://academic.oup.com/nar/issue/51/D1
⚫ NCBI

https://www.ncbi.nlm.nih.gov
⚫ EMBL-EBI

https://www.ebi.ac.uk/
⚫ AI and data resources

https://www.ebi.ac.uk/about/our-
impact/ai-and-machine-learning

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