The document discusses InterMine, an open-source data warehouse software designed for the integration and management of diverse biological data. It outlines its architecture, features like web services, interoperability, and advantages of a common data model that fosters data mining and analysis across multiple biological datasets. Additionally, it highlights specific applications like ThaleMine and MedicMine, and provides recommendations and challenges for future development within the InterMine framework.

1. Interoperation between
InterMines
Legume Federation, June 22, 2015
Vivek Krishnakumar
Chris Town
J. Craig Venter Institute

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

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

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

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/

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

7. 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 (Arabidopsis) 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

8. Interoperability?
• Ability of InterMine instances to
communicate ‘automatically’ with each
other
• By way of leveraging web services
• Questions to be answered:
 What do they say to each other?
 How do they say it?
 What mechanisms are used?
 Enabling these mechanisms…

9. Data Model
• Data Model === Schema of InterMine
instance
• Defined in XML format
• Core data model (based on SO) can be
extended to suit requirements
• Access a mines data model in JSON format
http://MINE_URL/service/model/?format=json
• Compatibility of data models across mines
ensures interoperability

10. Advantages of common data
model
• Data mining scripts developed for one
mine immediately compatible with
others
• Promotes crowdsourcing
 one/more groups write
tools/widgets/parsers
 can be easily reused by others
• Enables cross species analysis

11. Available tools
• Multi-mine search tool
https://github.com/alexkalderimis/multimine-search-tool
 Based on InterMine Lucene-based search index
 Allows for interoperation when data models are different
• Integration based on Homologs:
 Ontology integration using `dagify`
https://github.com/intermine/dagify
 Pathway Integration by way of collating shared pathways
• InterMine Staircase
 Powerful client-side interface enabling data analysis
workflows and cross-mine integration via web services
http://staircase.herokuapp.com

12. InterMine Staircase

13. InterMine Staircase
Configure access to multiple mines

14. InterMine Staircase
Cross-mine search

15. InterMine Staircase
Filter results by facets

16. InterMine Staircase
Prepare and enrich lists

17. InterMine Staircase
Perform mine-to-mine list conversions

18. InterMine Staircase
App/tool compatibility

19. InterMine Staircase
Application model
MedicMine SoyMine....

20. Available Reference Mines
• ThaleMine: https://github.com/Arabidopsis-Information-Portal/intermine/
 Integrates variety of genomic datasets pertaining to Arabidopsis thaliana col-0
 Leverages both data warehousing and federation methods
 Represents wide variety of data: genes, proteins, function, expression, co-expression,
interactions, pathways, homologs, alleles, polymorphism, stocks, germplasm,
phenotypes
• MedicMine: https://github.com/jcvi-plant-genomics/intermine/
 Warehouse for Medicago truncatula A17 genomic data
 Houses variety of data: genes, proteins, function, expression
• PhytoMine: https://github.com/JoeCarlson/intermine/
 Warehouse for 47 different Angiosperm genomes
 Developed on a Chado  InterMine migration path
 Houses variety of data: genes, proteins, expression, homologs, protein families,
variation
• FlyMine: https://github.com/intermine/intermine/

21. Recommendations and Challenges
• Recommendations:
 Develop core plant InterMine model
 Follow InterMine guidelines
 Learn from prior initiatives - InterMOD
• Challenges
 Users/developers are used to current way of
doing things
 Time taken to adapt to common data model
and/or software stack
 Difficult to arrive at consensus with diverse group

22. 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