Download Introduction - Bioinformatics Research Group at SRI International

Administering Pathway Tools
Obtaining Pathway Tools
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Free to non-commercial organizations
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To obtain license agreement go to BioCyc.org and click on
Software/Database Download
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Follow Installation Guide
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ptools-local directory
 Locate in common directory
 PGDBs created by all users who use this ptools installation
 PGDBs downloaded via the registry
 ptools-init.dat for this ptools installation
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Reporting Pathway Tools Problems
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E-mail to [email protected]
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Include:
 Error message
 Result of
[1] EC(2) :zoom :count :all
 error.tmp
 What version and platform you are running
 What operation were you performing when the error occurred?
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New patches automatically downloaded and loaded with
PTools starts up
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Auto-Patch
 Tools -> Instant Patch -> Download and Activate All Patches
New Pathway Tools Releases
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Major releases = External software releases
 Twice per year
 Announced on ptools-users mailing list
Minor releases twice per year affect only our BioCyc.org
Web site and flatfile distributions
We support one prior release only
Releases announced on [email protected]
Read release notes at
 http://brg.ai.sri.com/ptools/release-notes.html
Install process:
 Renames your old software directory tree out of the way
 Creates new directory tree for new version
 Upgrade schema of your DB (software assisted)
PGDB Storage:
File or Relational Database
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File storage:
 Advantages:
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Disadvantages:
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No RDBMS installation and configuration
Must be loaded and saved in its entirety
No transaction history
No concurrent access for multiple users
Oracle/MySQL storage:
 Advantages:
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Faster read access, faster saves
Concurrent update access for multiple users
Stores history of all PGDB updates
Disadvantages:
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RDBMS must be installed and configured
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Multiuser Access to PGDBs
 PGDB
 Each
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stored within one Oracle or MySQL server
curator installs PTools on their workstation
 Different curators can use different software
platforms
 Workstations query RDBMS server via internet
 Local disk cache speeds access
 For each frame access, PTools queries
 In-memory cache, disk cache, RDBMS server
 After curator saves changes, all changes made by
other users are loaded into curator’s session
How to Release a PGDB?
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Decide on release frequency and schedule
 Don’t wait until it’s perfect to release it!
Freeze curation for 1 week
Quality assurrance
 Run consistency checker
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Tools -> Consistency Checker
Also updates organism-summary statistics
Update publications, authors in organism frame
 Update via Organism editor
Create new version of PGDB
 ptools-local/pgdbs/yeastcyc/1.0/kb/yeastbase.ocelot
 Edit against the new version, release the old version
Author release notes
Register PGDB in SRI PGDB registry
 Will allow SRI to include it in BioCyc
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Pathway Tools Data Import/Export
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File->Export
File->Import
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Export/import to/from tab-delimited files
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Export to Genbank, SBML, BioPAX
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Export to attribute-value files
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Attribute-value files can be imported into BioWarehouse
 Relational database system for bioinformatics database integration
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Napster Comes to Bioinformatics
 Public
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sharing of Pathway/Genome Databases
PGDB registry maintained by SRI at URL
http://biocyc.org/registry.html
 Registry
operations
 List contents of registry
 Download PGDBs listed in the registry
 Register PGDBs you have created
Registry Details
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Why register your PGDB?
 Declare existence of your PGDB in a central location
 Facilitate its download by other scientists
 Facilitate its inclusion in BioCyc.org
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Why download a PGDB?
 Desktop Navigator provides more functionality than Web
 Comparative operations
 Programmatic querying and processing of PGDB
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Registration process
 Registered PGDBs have open availability by default
 Authors can provide their own license agreements
 Registered PGDBs reside in authors’ FTP site or HTTP server
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New Pathway Tools Features Coming
Soon
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Improvements to electron transport
Include updates to genome annotation in a PGDB
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Ability to manage more types of regulation
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Better support for signaling pathways
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Find dead-end metabolites
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Improve accuracy of pathway predictor
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Web login/preferences system
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Graph tracks for displaying ChIP/Chip data against genome
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Why Create a PGDB?
 Perform
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pathway analyses as part of a genome
project
 Analyze
omics data
 Create
a central information resource for the
organism
 Lay
the foundation for creating a FBA model
 Perform
comparative analyses
Model Organism Databases
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DBs that describe the genome and other information about
an organism
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Curated by experts for that organism
 No one group can curate all the world’s genomes
 Distribute workload across a community of experts to create a community
resource
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Every sequenced organism with an active experimental
community requires a MOD
 Integrate genome data with information about the biochemical and genetic
network of the organism
 Integrate literature-based information with computational predictions
Rationale for MODs
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 Each
“complete” genome is incomplete in several
respects:
 40%-60% of genes have no assigned function
 Roughly 7% of those assigned functions are incorrect
 Many assigned functions are non-specific
 MODs
are platforms for global analyses of an
organism
 Interpret omics data in a pathway context
 In silico prediction of essential genes
 Characterize systems properties of metabolic and genetic
networks
What is Curation?
 Ongoing
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updating and refinement of a PGDB
 Correct false-positive and false-negative
predictions
 Incorporate information from experimental
literature
 Update genome sequence
 Update gene functions, gene positions, gene names
 Author comments and citations
 Add new pathways, modify existing pathways
 Enter information about regulatory networks
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Issues in Creating Public MODs
 Obtaining
funding
 Scoping the project
 Identify user community
 Obtain buy-in and help from scientific community
 IT: Set up database server, Web server
 Hire and train curators
Questions
 Do
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you intend to make your PGDB public and to
update it on an ongoing basis?
 To
create a Model Organism Database?
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 Desktop
vs Web functionality in Pathway Tools
 http://biocyc.org/desktop-vs-web-mode.shtml