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Intro to the InterMine Infrastructure - LegFed Meeting

Intro to the InterMine Infrastructure - LegFed Meeting

Overview of InterMine infrastructure, presented at the Legume Federation Project Meeting

Presented by Vivek Krishnakumar

Vivek Krishnakumar

April 28, 2015
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  1. Introduction to InterMine
    Infrastructure
    Vivek Krishnakumar
    LF Meeting 04/28/2015

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  2. InterMine in a nutshell
    • Open-source data warehouse software
    • Integration of complex biological data
    • Parsers for common biological data formats
    • Extensible framework for custom data
    • Cookie-cutter interface, highly customizable
    • Interact using sophisticated web query tools
    • Programmatic access using web-service API

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  3. Open-source Project
    • Source code available online
    • Distributed with the GNU
    LGPL license
    • GitHub Repo:
    https://github.com/intermine/int
    ermine
    • GitHub Organization:
    https://github.com/intermine
    intermine / intermine
    > bio
    > biotestmine
    > config
    > flymine
    > humanmine
    > imbuild
    > intermine
    > testmodel
    .gitignore
    .travis.yml
    LICENSE
    LICENSE.LIBS
    README.md
    RELEASE_NOTES

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  4. Richard N. Smith et al. Bioinformatics 2012;28:3163-3165
    InterMine system architecture

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  5. InterMine system architecture
    Web Application
    • Java Server Pages (JSP), HTML, JS, CSS
    • Interfaces with Java Servlets and IM web-services
    Web Server
    • Tomcat 7.0.x, serves Web application ARchive file
    • ant based build system using Java SDK
    Database Server
    • PostgreSQL 9.2 or above
    • range query, btree, gist enabled (refer docs here)
    http://intermine.readthedocs.org/en/latest/system-requirements/

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  6. Data Model Overview
    • Object-oriented data model
    • Divided into classes, their attributes and
    their relationships; defined in XML
    • Represented as Java classes (pure Java
    beans); auto-generated from XML,
    automatically map to tables in schema
    • Core data model; based on Sequence
    Ontology (SO); refer: bio/core/core.xml
    and bio/core/genomic_additions.xml
    http://intermine.readthedocs.org/en/latest/data-model/overview/

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  7. Data Model Overview













    Model expects standard Java names for classes and attributes
    • classes: start with an upper case letter and be CamelCase, no underscores or spaces.
    • fields (attributes, references, collections): should start with a lower case letter and be
    lowerCamelCase, no underscores or spaces.
    http://intermine.readthedocs.org/en/latest/data-model/model/

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  8. Creating & configuring a mine
    • Build out scaffold for mine
    $ cd git/intermine
    $ bio/scripts/make_mine legumine
    • Configure data to load and
    post-processing steps to
    run by customizing
    project.xml
    • Data elements
    correspond to directory
    under bio/sources/*;
    defines parsers to retrieve
    data and encodes rules for
    integration
    intermine / intermine
    > bio
    > biotestmine
    > config
    > flymine
    > legumine
    >
    dbmodel
    >
    integrate
    >
    postprocess
    >
    webapp
    >
    default.intermine.integrate.properties
    >
    default.intermine.webapp.properties
    >
    project.xml
    > humanmine
    > imbuild
    > intermine
    > testmodel
    .gitignore
    .travis.yml
    LICENSE
    LICENSE.LIBS
    README.md
    RELEASE_NOTES
    http://intermine.readthedocs.org/en/latest/get-started/tutorial/#creating-a-new-mine

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  9. Creating & configuring a mine















    :
    :





    :
    :


    project.xml
    http://intermine.readthedocs.org/en/latest/get-started/tutorial/#project-xml

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  10. Data Sources and Sets
    • InterMine provides a vast library of data source parsers and
    loaders, covering data types not restricted to:
    genome sequence (fasta)
    annotation (gff)
    ontology (go, so)
    proteins (uniprot)
    interactions (psi-mi)
    pathway (kegg, reactome)
    homologs (panther, compara, homologene)
    publications (pubmed)
    chado (sequence, stock)
    • Custom sources can be written by following the tutorial:
    http://intermine.readthedocs.org/en/latest/database/data-
    sources/custom/ or by referring to code from other mines
    http://intermine.readthedocs.org/en/latest/database/data-sources/library/

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  11. Building a mine
    • Each InterMine instance requires 3
    PostgreSQL databases:
    ¡
    legumine: core db mapping to data model
    ¡
    items-legumine: db for storing intermediate Items during load
    ¡
    userprofile-legumine: db for storing user specific data
    • Running build requires special config file in
    the users’ home area, containing db
    connection params and other mine
    specific configs to override
    ${HOME}/.intermine/legumine.properties
    http://intermine.readthedocs.org/en/latest/get-started/tutorial/#properties-file

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  12. Model Merging & Data Integration
    Model Merging
    • Each source contributes
    towards the data model
    • bio/core/core.xml is
    always used as the base
    for model merging
    • The ant build-db
    command consumes the
    SOURCE_additions.xml
    • Model is used to generate
    tables, Java classes and
    the webapp
    http://intermine.readthedocs.org/en/latest/database/database-building/model-
    merging/
    Data Integration
    • Key(s) for class of object
    defines equivalence for
    objects of that class
    • Primary key defines
    field(s) used to search for
    equivalence
    • For objects which share
    same primary key, fields
    are merged and stored as
    single object
    http://intermine.readthedocs.org/en/latest/database/database-building/primary-keys/

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  13. Post processing
    • Operations are
    performed on
    integrated data
    • Calculate/set fields
    difficult to work with
    while data loading,
    because they require 2
    or more sources to be
    loaded already
    • Order of steps is
    somewhat important
















    http://intermine.readthedocs.org/en/latest/database/database-building/post-processing/

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  14. Building & deploying a mine
    Two types of build mechanisms:
    • Manual:
    $ cd dbmodel && ant clean build-db ## initialize db
    $ ant -Dsource=legumine-gff ## load data sources
    $ ant -Dsource=legumine-chr-fasta ## load more sources
    $ cd ../postprocess && ant ## run post-process steps
    $ cd ../webapp ## build mine webapp
    $ ant clean remove-webapp default release-webapp
    • Automated:
    $ ../bio/scripts/project_build -b -v localhost ~/legumine-dump
    http://intermine.readthedocs.org/en/latest/database/database-building/build-script/

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  15. Lucene based search index
    • Post-process "create-search-index" runs the
    database indexing, zips and stores in db
    • On webapp (first) load, index is unpacked
    • By default, all id and text fields are ignored by the
    indexer
    • Uses the Apache Lucene whitespace analyzer to
    identify word boundaries
    • Control temp directory and classes/fields to be
    ignored by altering
    MINE_NAME/dbmodel/resources/keyword_sear
    ch.properties file
    http://intermine.readthedocs.org/en/latest/webapp/keyword-search/

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  16. Alex Kalderimis et al. Nucl. Acids Res. 2014;42:W468-W472
    InterMine web services
    http://iodocs.labs.intermine.org

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  17. Federated Authentication
    • Apart from the standard login scheme
    (username/password), InterMine supports industry
    standard OAuth2 based login flows, implemented
    by Google, GitHub, Agave, etc.
    • ThaleMine relies on this infrastructure to
    authenticate users against the araport.org tenant
    registered within the Agave infrastructure
    • Documentation available here:
    http://intermine.readthedocs.org/en/latest/webapp/
    properties/web-properties/#openauth2-settings-
    aka-openid-connect

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  18. Friendly reference mines
    • FlyMine: https://github.com/intermine/intermine/
    • ThaleMine: https://github.com/Arabidopsis-
    Information-Portal/intermine/
    • MedicMine: https://github.com/jcvi-plant-
    genomics/intermine/
    • PhytoMine:
    https://github.com/JoeCarlson/intermine/

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  19. Summary
    • Advantages
    ¡
    InterMine is a powerful biological data warehouse
    ¡
    Performs complex data integration
    ¡
    Allows fast and flexible querying
    ¡
    Well documented programmatic interface
    ¡
    Cookie-cutter, user-friendly web interface
    ¡
    Facilitates cross-talk between “mines”
    • Caveats
    ¡
    Adding more data requires a full database rebuild (incremental loading
    is not possible) because of the integration step
    • About InterMine:
    ¡
    Developed by the Micklem Lab at the University of Cambridge, UK
    ¡
    Written in Java, backed by PostgreSQLdb, deployed under Tomcat.
    Documentation and downloads available at http://www.intermine.org

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  20. Acknowledgments
    • InterMine Team
    ¡
    Gos Micklem
    ¡
    Julie Sullivan
    ¡
    Alex Kalderimis
    ¡
    Richard Smith
    ¡
    Sergio Contrino
    ¡
    Josh Heimbach
    ¡
    et al.
    • Araport Team
    ¡
    Chris Town
    ¡
    Jason Miller
    ¡
    Matt Vaughn
    ¡
    Maria Kim
    ¡
    Svetlana
    Karamycheva
    ¡
    Erik Ferlanti
    ¡
    Chia-Yi Cheng
    ¡
    Benjamin Rosen
    ¡
    Irina Belyaeva

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