TAIR/Gramene/SGN Workshop I ASPB Meeting July 08, 2007 Chicago, IL
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Transcript of TAIR/Gramene/SGN Workshop I ASPB Meeting July 08, 2007 Chicago, IL
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TAIR/Gramene/SGN Workshop I
ASPB MeetingJuly 08, 2007Chicago, IL
Metabolic Databases
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MetaCyc and AraCyc: Curation of Plant
Metabolism
Hartmut FoersterCarnegie Institution
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Outline MetaCyc
Goals and application Curation Progress MetaCyc – main functions Pathway tools
AraCyc Build of AraCyc Curation progress Introduction to the database Omics viewer
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MetaCyc
http://www.metacyc.org
Caspi R, Foerster H, Fulcher CA, Hopkinson R, Ingraham J, Kaipa P, Krummenacker M, Paley S, Pick J, Rhee SY, Tissier CP, Zhang P, Karp PDMetaCyc: a multiorganism database of metabolic pathways and enzymesNucleid Acids Res., 34, D511- 516 (2006)
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What is MetaCyc ?
MetaCyc is a multi-organism database that collects any known pathways across all kingdoms
MetaCyc is a curated, literature-based biochemical pathways database
Collaboration between SRI International and Carnegie Institution
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Goal and ApplicationsGoal
Universal repository of metabolic pathways Up-to-date, literature-curated catalogue of
commented enzymes and pathways for use in research, metabolic engineering and education
Applications Database of reference used to generate
predicted Pathway/Genome DataBases (PGDBs)
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The Content of MetaCyc
Pathways from primary and secondary (specialized) metabolism Reactions with compound structures
Proteins Genes
Does not contain sequence information
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Curation Team
PhD-level curators
Extract data from literature experimentally verified data ideally protein information
Follow MetaCyc Curator’s guide http://bioinformatics.ai.sri.com/ptools/curatorsguide.pdf
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MetaCyc Version 11.1released May 25th, 2007
Note: The statistics for each year pertain to the last MetaCyc version released in that year
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The Taxonomic Distribution in MetaCyc
Mostly from microorganism and plant kingdoms, and several animal pathways
Plants: 219 species from 69 plant families
Share about 220 pathways involved in primary metabolism and 180 pathways of secondary (specialized) metabolism
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Taxonomy/Metabolism Ratio in MetaCyc
Plant families with the highest number of annotated pathways:Brassicaceae (Arabidopsis thaliana)
Legumes (Glycine max)
Poaceae (Zea mays)
Solanaceae (Solanum tuberosum, Nicotiana tabacum)
Plant families with the highest number of contributing species: Legumes (36) Solanaceae (16)
Poaceae (12) Brassicaceae (10)
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MetaCyc – Browse the Database
Explore class hierarchy of pathways, compounds, reactions,
genes and cell components
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MetaCyc – Browse the Database (cont’d)
Explore class hierarchy of pathways, compounds, reactions,
genes and cell components
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MetaCyc – Discover the Metabolic Universe
Query the database (pathways, reactions, compounds, genes)
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MetaCyc – Query Page
Type your search term
and click submit
Molybdenum
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MetaCyc – Query Result Page
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MetaCyc – Pathway Detail Page - Part I
The pathway diagram shows compounds,
reactions and metabolic links
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MetaCyc – Pathway Detail Page - Part II
Pathway commentary comprises general and
specific information about the pathway
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MetaCyc – More Detail
Extend or collapse the detail level of the pathway detail page
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MetaCyc – More Detail (cont’d)
In depth information about reaction, EC number, enzymes, genes, regulatory
aspects, and metabolic links to related
pathways
+
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MetaCyc – More Detail (cont’d)
EXP
COMP
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MetaCyc – More Detail (cont’d)
More detail reveals structural information about
compounds
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MetaCyc – Reaction Detail Page
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MetaCyc – Enzymes and Genes
Contains enzyme commentary,
references, and physico-chemical properties of the
enzyme
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MetaCyc – Enzymes and Genes (cont’d)
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Variants, Related Pathways and Links
Pathway variants are created as separate pathways
IAA biosynthesis I (tryptophane-dependent) IAA biosynthesis II (tryptophane-independent)
Links are added between interconnected pathways
Related pathways are grouped into superpathways
e.g.superpathway of choline biosynthesis
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Creation of a Superpathway
L-serine
ethanolamine
phosphoryl-ethanolamine
N-methylethanolamine phosphate
N-dimethylethanolamine phosphate
phosphoryl-choline
cholinecholine
biosynthesis III
Choline biosynthesis
II
ethanolaminephosphoryl-choline
CDP-choline-choline
a phosphatidylcholine
choline biosynthesis III choline biosynthesis IIcholine biosynthesis I
N-monomethylethanolamine
N-dimethylethanolamine
choline
choline
Superpathway choline biosynthesis
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Applications: Pathways Prediction
Goal Universal repository of metabolic pathways
Up-to-date, literature-curated catalogue of commented enzymes and pathways for use in research, metabolic engineering and education
Applications Database of reference used to generate
predicted Pathway/Genome DataBases (PGDBs)
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Pathway Tools Software Suite
Software for generating, curating, querying, displaying PGDBs
Developed by Peter Karp and team PathoLogic – Infers pathways from genome or transcripts
sequencing Pathway/Genome Editors – Curation interface Pathway/Genome Navigator – Query, visualization,
analysis and Web publishing OMICS Viewer
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The Family of Species-specific Databases
Annotated GenomeArabidopsis thaliana
PathoLogic
SoftwareReference PathwayDatabase (MetaCyc)
Reactions
Pathways
compounds
Gene products
genes
Pathway/Genome Database (AraCyc)
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AraCyc: The Arabidopsis thaliana
specific metabolic database
http://www.arabidopsis.org/tools/aracyc
Zhang P, Foerster H, Tissier CP, Mueller L, Paley S, Karp PD, Rhee SYMetaCyc and AraCyc. Metabolic pathway databases for plant researchPlant Phys., 138(1), 27-37 (2005)
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AraCyc – Birth of the A. thaliana Specific Database
AraCycinitial build
Databasecleaning
Datavalidation
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The Computational Build of AraCyc
In 2004, the Arabidopsis genome contained 7900 genes annotated
to the GO term ‘catalytic activity’
4900 loci in small molecule metabolism (19% of the total genome)
PathoLogic inferred 219 pathways and mapped 940 (19% enzyme-coding)
genes to the pathways
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Cleaning of a Newborn Database
PathoLogic errs on the side of over-prediction
First round of curation to remove false-positives
Add missing pathways
Improve the quality of information Introduce new pathways Increase number of pathway and protein comments Refine computational assignment of protein
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Pathway Validation Criteria
A pathway that is described in the Arabidopsis literature
A pathway whose crucialmetabolites are described in the Arabidopsis literature
A pathway that contains unique reactions and having genes assigned to those unique reactions
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Validation Procedure
Delete non-plant pathways: Pathway variants of bacteria-origin Pathways not operating in plants at
all (e.g. glycogen biosynthesis)
Add new plant-specific pathways: Pathway variants of plant-origin Plant-specific metabolites
(e.g. plant hormones)
Plant-specific metabolism (e.g. xanthophyll cycle)
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AraCyc - Curation Progress
AraCyc (2.1)April2005
AraCyc (2.5)
October 2005
AraCyc (2.6) May 2006
AraCyc (3.5)
February 2007
AraCyc (4.0) July
2007
Total pathways
221 197 228 262 285
New - 37 35 51 50
Updated - 0 4 37 42
Deleted - 61 6 12 16
Pathways manually reviewed
71 (32%)
170 (86%)
201 (88%)
233 (89%)
285(100%)
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How to Link to AraCycFrom the TAIR
home page click on the link to AraCyc
pathways
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AraCyc – The Home Page
Browse pathways,
enzymes, genes, compounds
Display of the Arabidopsis
metabolic network
Paint data from high-throughput experiments on the metabolic
map
User submission
form
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AraCyc – All the Help you Can Get
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AraCyc’s ContentAraCyc Pathway: flavonol biosynthesis
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Evidence Codes
Intuitive icons
Pathway Level
Evidence codes provide assessment of data quality, i.e. the affirmation for the existence of an pathway
Evidence codes provide assessment of data quality, i.e. the affirmation for the catalytic activity of an enzyme
Enzyme Level
Inferred by curator. An assertion was inferred by a curator from relevant information such as other assertions in a database
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Evidence Codes (cont’d)
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AraCyc: Pathway Detail Page
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AraCyc: Metabolic Map
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AraCyc: Metabolic Map (cont’d)
related pathways are grouped together
Generation of precorsur metabolites and energy>Calvin cycle
Compound: GA9Reaction: GA12 + O2 + NADPH = GA9 + CO2 + NADP+
Degradation/Utilization/Assimilation>C1 compounds
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AraCyc: OmicsViewer
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OMICS Viewer
Part of the Pathway Tools Software Suite
Displays bird-eye view of the Metabolic Overview diagram for a single organism KEGG pathways are ‘superpathways’ without
consideration of species specificity and pathway variants
Allows to paint data values from the user's high-throughput onto the Metabolic Overview diagram
Microarray Expression Data Proteomics Data Metabolomics Data
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OmicsViewer Submission Page
Step 1
Step 2
Load sample file and provide information
about your data
Sample data file(text tab-delimited)
0 1 2 3 4
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OmicsViewer Submission Page (cont’d)
Step 3
Step 6
Step 4
Step 5
Choose relative or absolute valuesCheck the box if
you have log values or
negative fold change numbers
Choose to display a single or
multiple step experiment
Select the type of data you want to display (refers to your loading
file)
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OmicsViewer Submission Page (cont’d)
For single/multiple or the ratio of time points add the corresponding
column number(s)
Step 7
0 1 2 3 4
111
123
1234
112
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Step 8
Step 9
OmicsViewer Submission Page (cont’d)
Choose your cutoff to
visualize your expression
values
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The Omics Viewer Result Page
reactions (lines) arecolor-coded accordingto the gene expression level
compounds (icons) are color-coded according to the concentration of compounds
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The Omics Viewer Result Page (cont’d)
The statistics for the expression map
(single time points only) is provided at the bottom of the
page
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Saving Results
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Acknowledgements TAIR
- Sue Rhee (PI)- Peifen Zhang (curator)- Christophe Tissier (curator)- Hartmut Foerster (curator)- Tom Walk (post doctoral researcher)
SRI - Peter Karp (PI)- Ron Caspi (curator)- Carol Fulcher (curator)- Suzanne Paley (software developer)- Pallavi Kaipa (programmer)- Markus Krummenacker (programmer)
NIH, NSF, Pioneer Hi-Bred
Previous contributers- Lukas Müller
- Aleksey Kleytman (curator assistant – TAIR)- Thomas Yan (programmer – TAIR)- Joe Filla (sysadmin - TAIR)
- Mary Montoya (software developer - NCBR)- John Pick (software developer - SRI)- Mario Latendresse (programmer - SRI)