Download pdf - List of Public Databases

8/13/2019 List of Public Databases

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Canadian Bioinformatics

Workshopswww.bioinformatics.ca


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2Module #: Title of Module


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Module 4

Databases for Chemical, Spectral and

Biological Data

David Wishart


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Two Solitudes

B

ioinformatics

Ch

eminformatic

s


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Cheminformatics vs.Bioinformatics

Established in the1960s

Designed for the

needs of organicchemists

User-pay, limitedpublic access

Funded by largecompanies (MDL,Bielstein, Sigma,

CAS)

Established in the1990s

Designed for needs

of molecularbiologists

Web-based, openaccess model

Funded by largegovt agencies

(NCBI, EBI, NIH, GC)


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Whats A Database For?

Information consolidation & linkage Information retrieval (query matching)

Reference values, reference data,

reference sequences, reference images

Data for training/testing algorithms

Similarity searching (image, spectra,structure, sequence, text)

Prediction (structure, function, property,phylogeny, activity, relationship)


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Database Evolution

Hobby database(flatfile)

Limited coverageLimited depth

Greater coverageGreater depth

Extensive coverageModest depth

In

creasingCost+

Resources

Sizeofuserco

mmunity

Curated,non-redundant(relational, warehouse)

Archived, open deposit,redundant

(relational, distributed)


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Database Evolution

Hobby database(flatfile)

N

eedforstandar

dization

Curated,non-redundant(relational, warehouse)

Archived, open deposit,redundant

(relational, distributed)

D

ependenceonautomation

Queryingcap

abilities


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The Problem with Metabolomics

?

Genomics

Proteomics

Metabolomics

Gene IDs +

Transcript

Abundance

Protein IDs +

Concentrations

Metabolite IDs +

Concentrations


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Metabolomics Databases

Most data for metabolomics is still in texbooksor print journals (100+ years of clinicalchemistry, 75 years of classic biochemistry)

Field lags behind genomics/proteomics by about20 years

Challenge is to appeal to different usercommunities (metabolomics researchers,

analytical chemists, plant chemists, clinicalchemists, physicians, drug researchers, NMRspecialists, MS specialists, bioinformaticians,standards setters, etc.)


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Databases for Metabolomics

NMR spectral databases

Primarily small molecule spectra, not all metabolites

MS or MS/MS spectral databases

Primarily small molecule spectra, not all metabolites

Compound databases

Mostly compound names, structures, IDs, physprops

Pathway databases Mix of metabolite, drug, protein, signaling pathways

Comprehensive metabolomic databases

Combines most/all of the above, focus on metabolites


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NMR Spectral DBsSBDS NMRShiftDB

MMCD BMRB


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SDBS

http://riodb01.ibase.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi


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SDBS

Maintained in Japan by AIST (since1970s)

Includes 24,700 MS spectra, 15,400 1HNMR spectra, 13,600 13C NMR spectra,52,500 FT-IR spectra on 34,000 cmpds

Extensive suite of spectral search tools

Most compounds are not metabolites,but still very useful for manyresearchers


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BioMagResBank

http://www.bmrb.wisc.edu/metabolomics/


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BioMagResBank

868 reference metabolites

5-6 NMR spectra (1H, 13C, 1D, 2D) percompound

Search by name, synonyms, InChI,formula, SMILES

Focus primarily on plant metabolites

(Arabidopsis) although now includesother mammalian metabolites

No assignments available


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NMRShiftDB

46,606 1H/13C

NMR Spectra

38,802 structures

http://www.ebi.ac.uk/nmrshiftdb/


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NMRShiftDB

Database developed by ChristophSteinbeck (who also leads ChEBI)

Not restricted to metabolites, includes

many organic compounds Supports chemical shift prediction

Can search by name, structure or

chemical shifts (peaks and Jcamp file)

Includes chemical shift assignments(but in organic solvents)


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MMCD

http://mmcd.nmrfam.wisc.edu/

20,306 cmpds

791 1H NMR

791 13C NMR791 TOCSY

791 13C HSQC

300 1H NMR (Lit)

907 13C NMR (Lit)

525 HSQC (Lit)

2021 MS (Lit)


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MMCD

Supports structure, name, NMR (shifts),MS (peaks) searches

Data includes chemical formula, namesand synonyms, structure, physical andchemical properties, NMR and MS data,NMR chemical shifts, species

associations and extensive links toimages, references, and other publicdatabases


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MS Spectral DBsNIST/AMDIS Metlin

GolmDB MassBank


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MassBank

http://www.massbank.jp/


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MassBank

Very nicely maintained and easilysearchable collection of mostlymetabolite MS spectra

Includes ESI-QTOF, ESI-QqQ, GC-EI-TOF, EI, ESI-FTICR, Ion-trap, etc.

Covers 30,857 MS spectra from

approximately 14,500 compounds Archives data from ~20 different

sources (Japan, Germany, US, etc)


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Compound DBsChEBI PubChem

ChemSpider Ligand Expo


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ChEBI

Pronounced KEBEE

Chemical Entities of Biological Interest

Contains 25,518 3 star compounds Most compounds are from KEGG,

LipidMaps, DrugBank, Patents

Most data is on names, ontology,synonyms, MW, formula and structure

Searchable by name, formula, structure


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PubChem

NIH database of 31 million compounds and 75million substances, 1644 HT screens of compounds

Compound must have


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ChemSpider

Contains 25 million compounds from 400data sources

Searchable by name, synonym, InChi,

structure, registry #, SMILES, calculatedproperties (but not by formula or mass)

Data includes names, synonyms, wikipediaarticles, descriptions, data sources,suppliers, patents, articles, properties, MESHheadings, pharmacology links, spectra (UV,IR, NMR, MS) sourced from other sites


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Ligand Expo

Contains the small molecules in thePDB

Useful because it links

chemicals/metabolites/drugs to theirtargets

Also provides 3D structure coordinates

Searchable via 3-letter chemicalidentifier code, molecular name,molecular formula, SMILES description,

InChi, 3D structure


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Other Compound DBs3DMet KNApSAcK

ZINC LipidMaps


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Other DBs 3DMet

3D structure database of natural metabolites

KNApSAcK

Database of 50,000 plant metabolites linked to

species information ZINC

Database of 2.7 million commercially available

chemicals (mostly drug-like compounds)

LipidMaps Database with 30,000 lipids (Fatty acyls,

glycerolipids, glycerophospholipids, sphingolipids,

sterols, prenols, saccharolipids, polyketides)


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Pathway DBsKEGG SMPDB

BioCyc/MetaCyc Reactome


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Pathway DBs

Rich source of biological data thatrelates metabolites to genes, proteins,diseases, signaling events and

processes

Provide various tools to permitvisualization and gene/metabolite

mapping Often cover multiple species


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KEGG Kyoto Encyclopediaof Genes and Genomes

http://www.genome.jp/kegg/


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The Small Molecule

Pathway Database (SMPDB)

http://www.smpdb.ca


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SMPDB

350 hand-drawn pathways relevant tohuman/mammalian metabolism

155 drug pathways

72 disease pathways

12 signalling pathways

70 standard metabolic pathways

Searching and browsing capabilities

Metabolite mapping capabilities

Captures structure, organelle,

cellular and organ information


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Exploring Pathways withSMPDB


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Mapping Metabolites withSMPDB


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Mapping MetaboliteConcentrations with SMPDB


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HMDB Features/Content

7969 metabolites

120 bacterial (gutmicrobe) metabolites

Normal/abnormalconcentrations

700+ disease links

1700 NMR spectra

2600 MS spectra

310 GC-MS spectra

Sequence search tools

Spectral search tools

Extensive browsing

tools Pathway search tools

Structure searches

Biofluid browsing

Text search tools

Full data downloads


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The Human Metabolome Project

$7.5 million Genome Canada Project launched in Jan.2005 - Based at the University of Alberta

Mandate to quantify and identify all metabolites inbiofluids such as urine, CSF and blood as well as

tissues using HT experiments and text analysis (~8000cmpds to date)

Associate metabolite concentrations to ~500 diseasesor conditions

Make all data freely and electronically accessible(HMDB, DrugBank, FooDB, T3DB)

Develop novel technologies and software to improvemetabolome coverage and metabolomic throughput


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The Human Metabolomes

M mM M nM pM fM

Endogenous metabolites

Drugs

Food additives/Phytochemicals

Drug metabolites

Toxins/Env. Chemicals3100 (T3DB)

500 (DrugMet)

30,000 (FooDB)

1450 (DrugBank)

8000 (HMDB)


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Meet the Metabolomes

http://www.foodb.ca http://www.drugbank.ca

http://www.hmdb.ca http://www.T3DB.org


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Inside the HMDB


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Inside the HMDB

HMDB Databrowser

102 data fields


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HMDB Spectral Searching


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HMDB: Pathway Tools

-Enter metabolites-Link to metabolic pathways-Explore pathway images


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The HMDB Biofluid Database

Reference metaboliteconcentrations for >450different diseases &conditions

Abnormal and normalmetaboliteconcentrations for >15biofluids and >4500different metabolites

Designed for clinicalchemists & physicians

Largest & most completeresource of its kind


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Inside DrugBank

http://www.drugbank.ca


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Query Tools

PharmaBrowse

ChemQuery


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Query Tools

SeqSearch

DataExtractor


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Database Comparison

HMDB

KEGGPubChem

MMCD

ChEBI

SDBS

Reactome

Metlin

Cyc DBs

MSSpectra

NMR

Spectra

Pathways

Structures

Description

s

ChemP

rops

Physiol.da

ta

Nomenclat.

Links+Re

fs