24 September 2013

1. ELIXIR
Technical Coordinator
Rafael C Jimenez
2013 - 09 - 24
“Before, no one cared about standards. Now, people are very
aware of their importance, so everyone is developing their own”
ELIXIR WP12 report - Preparatory phase.

2. Mission
• Ensure implementation of services
• Forge collaborative development
• Execute the ELIXIR technical strategy

3. ELIXIR technical strategy
Compute
Data
Standards
Tools
Access
Search
Analysis
Formats
Ontologies
Guidelines
Privacy
Optimization
Integration
Storage
Network
Computing
e-infrastructure for Biological data

4. How?
Federative infrastructure based on
collaboration and share resources
National coordination

5. Specialization
Task forces coordination
• Database
• Computational
• Biological domain
• Standards
• Tools
• Training
Do what you do best!

6. Compute
Data
Standards
Tools
Technical coordination
• Nodes
• Task forces
• Central management
BioMedBridges
Research Infrastructures
Technological infrastructures
EMBRC, INSTRUCT, Eurobioimagining,
Infrafrontier, ERINHA, EUOpenScreen,
EATRIS, BBMRI, ECRINm, LifeWatch, …
EUDAT, PRACE, GEANT, EGI, JISC, …

7. Timeline2007
2008
2009
2010
2011
2012
2013
2018
2014
2015
2016
2017
CTO
Permanent phaseConstruction phasePreparatory phase
2021
2019
2020
2022
When

8. 1997
2001
2004
2005
2006
2007
2008
2013
2009
2010
2011
2012
UPV
CIPFEMBL-EBIEMBL-EBINBT
EMBL-EBI
NBN
UKZNIE
Functional
genomics
Phylogenetics
Proteomics
Genome
variation
Molecular
interactions
Mass
spectrometry
Web
Development
Visualization
Standards
Integration
Analysis
Web Services
Databases
Server
administration
Best practices
Training
Collaborative
Software
development
Software
Project
Management
PHP
Perl
Python
R
JavaScript
Java
Molecular
Biology
Computer
Science
Bioinformatics
Teaching
Systems
Biology

9. Projects & experience
Standards, reusability, data integration,
discoverability, community development,
open source.

10. More data coverage
Consortiums for data exchange
Nucleotide sequences
INSDC
ENA
DDBJ
NCBI
Molecular interactions
IMEx
IntAct
InnateDB
DIP
MINT
…
Protein indentifications
ProteomeXchange
PRIDE
PeptideAtlas
GPMDB
Tranche
…
Replication Federation Centralization
Proteomics data exchange and storage: the need for common
standards and public repositories. Jiménez RC, Vizcaíno JA.
Better data management
Less redundancy
Agreement on data standards and data integration
Less inconsistency

11. Schema
Interfaces
Guidelines
Ontologies Format
Identifiers
Data
Definition Representation Access
Federation
PublishFind
Registry
DAS ClientsDAS Clients
Clients
PSICQUIC
sources
PSICQUIC
sourcesServices
query
format
DAS
PSICQUIC
Service Oriented Architecture
Standards
PSICQUIC and PSISCORE:
accessing and scoring
molecular interactions.
Aranda B, Jimenez RC, et
all.
Integrating biological data-
-the Distributed
Annotation System.
Jenkinson AM, Jimenez RC,
et all
Teaching the fundamentals of biological data integration using classroom games.
Schneider MV, Jimenez RC.

12. Components Web applications
reuse
share
BioJS
BioJS: an open source JavaScript framework for biological data visualization. Gómez J, García
LJ, Salazar GA, Villaveces J, Gore S, García A, Martín MJ, Launay G, Alcántara R, Del-Toro N,
Dumousseau M, Orchard S, Velankar S, Hermjakob H, Zong C, Ping P, Corpas M, Jiménez RC.

13. Biologists &
Developer
Design
Requirements
13.12.2018
BioJS Best practices
Developer
BioJS component
BioJS
Coding
Developer
Registry
Source code
Release
API doc
Specification
Guidelines & tutorials

14. Unifying components
13.12.2018
• Represent the same type of information in different
projects using the same graphical component
1 2 3
Graphical representation
Developer
1 2 3 *
Type of representation
Website
Implementation a b c d

15. EMBL-EBI integration projects
EBI search / S4
• Summaries from
different sources
• Links to the original data
• “Just enough” just “in
time”
13.12.2018 15
Biosapiens
• Comparable annotations
from different sources
• Common control
vocabulary
• Links to the original data

16. Improving Links Between the Human Protein Atlas
(HPA) and EMBL-EBI’s resources
13.12.2018 16
DASS4
HP-WSBioJS
Summary data Details
Standards

17. molecular interactions
integration
molecular interaction
databases
organellar proteomics
datasets
analysisorganellar
interactomes
interactome
data
visualization
+
interactome
query
PSICQUIC
MISCORE
MICLUSTER
INTERACTOME
BUILDER
BIOJS
PSICQUIC integrated
resource
Organellar
interactomes
Interactome
context
Cellular location
evidence
Stats/Analysis
Proteomics interactome project
+
EMBL-EBI

18. PSICQUIC
MISCORE
MICLUSTER
INTERACTOME
BUILDER
BIOJS
PSICQUIC integrated
resource
Organellar
interactomes
Interactome
context
Cellular location
evidence
Stats/Analysis
Services
APID
API WS WEB
API WS
DB API
WEB
API
DB
WEBWS
WS
FW
API
FW
WEB
EMBL-EBI

19. Publications
PSICQUIC
MISCORE
MICLUSTER
INTERACTOME
BUILDER
BIOJS
PSICQUIC integrated
resource
Organellar
interactomes
Interactome
context
Cellular location
evidence
Stats/Analysis
BioJS: An Open Source
JavaScript Framework for
Biological Data Visualization
Apr 2013, 23435069
A New Reference
Implementation of the
PSICQUIC web service
July 2013, 23671334
Clustering and scoring molecular
interactions relying on community
standards
Aiming to submit in Sept
Integration and visualization of
protein interactions in context
with organelle protein
identifications.
Aiming to submit before Dec
EMBL-EBI

20. iAnn
Curation Centralization Distribution Integration
Registry
Input
form
Web
sites
Visualization
ModulesWeb
services
Editor Web services Viewer
Open source community-driven platform
for dissemination of life science events
iAnn: an event sharing platform for the life sciences.
Jimenez RC, Albar JP, Bhak J, Blatter MC, Blicher T, Brazas MD, Brooksbank C, Budd A, De Las Rivas J, Dreyer J, van
Driel MA, Dunn MJ, Fernandes PL, van Gelder CW, Hermjakob H, Ioannidis V, Judge DP, Kahlem P, Korpelainen E,
Kraus HJ, Loveland J, Mayer C, McDowall J, Moran F, Mulder N, Nyronen T, Rother K, Salazar GA, Schneider R, Via
A, Villaveces JM, Yu P, Schneider MV, Attwood TK, Corpas M.

21. Format
Ontology
Minimum
Information
guideline
Standards to exchange announcements among bioinformatics societies
More data coverage, less redundancy, less inconsistency, better data management
Integration
Access
Exchange
Sharing
Portability
Interoperability
Annotation
Comparison
Verification
Reusability
Representation

22. Conclusions
• Be realistic about what you can achieve
• Keep it simple
• Open the project to external contributions
• Let the community decide
• Purpose-driven requirements
• Fail early

24. Dasty3, a WEB framework for DAS
Integration of Cardiac Proteome
Biology and Medicine
iAnn: an event sharing
platform for the life sciences
A new reference
implementation of the PSICQUIC
web service
BioJS: an open source JavaScript framework
for biological data visualization
Best practices in bioinformatics
training for life scientists
Bioinformatics workflows and web
services for experimentalists
Proteomics data exchange and storage:
common standards and public repositories.
Teaching the fundamentals of biological
data integration using classroom games.
The IntAct molecular
interaction database in 2012
myKaryoView: a light-weight client for
visualization of genomic data
PSICQUIC and PSISCORE: accessing and
scoring molecular interactions.
MyDas, an extensible Java DAS server
Bioinformatics Training Network (BTN): a
community resource for bioinformatics trainers.
DAS writeback: a collaborative
annotation system
easyDAS: automatic
creation of DAS servers
The Protein Feature Ontology: a tool for the
unification of protein feature annotations
Dasty2, an Ajax protein DAS client
OntoDas - a tool for facilitating the
construction of complex queries to the GO.
Integrating biological data--the
Distributed Annotation System
2013
2009
2010
2011
2012
UPV
CIPFEMBL-EBIEMBL-EBI
Publications

25. How

26. Quotes
Good project management cannot guarantee success, but poor management on significant
projects always leads to failure. A.A.Puntambekar
The biggest single problem that afflicts software developing is that of underestimating resources
required for a project. Mike Wooldridge
Before, no one cared about standards. Now, people are very aware of their importance, so
everyone is developing their own. ELIXIR WP12. Preparatory phase report
Considerations for transitioning to open development (NCI):
• Keep it simple. Make barriers to entry as low as possible, and reuse available resources.
• Let the community decide. For an open-source development ecosystem to be successful, it
needs to be truly owned
• Purpose-driven requirements. The use of standards and any concept of “certification” should
be established based on real needs and use cases.
• Don’t over-think the process, and stop waiting to do something – fail early. Don’t wait for the
code or process to be perfect. Put the applications out there and let them fail or succeed, as
determined by the community.

27. What
How
When
Who
ELIXIR technical
coordination

28. Data integration problems
Many data resources
• Many to maintain
• Databases change
• New appearing
• Some disappearing*
• Not easy to find them
Different query interfaces
data integration?
Variable results
• Formats
• Schemas
• Controlled vocabularies
• Minimum information guidelines
* Merali Z. et all. Databases in peril. Nature 2005.
• Inconsistency
• Mapping problems
• Records with not enough information
• Redundancy

29. Data standards
13/12/2018 29
Integration
AccessExchange
Sharing
Portability
Interoperability
Annotation
Comparison
Verification
Reusability
Representation
Compliance
Consistency
Replication
Web service
API
Submission
Edition
Conversion
Comparison Visualization
Analysis
Integration
Validation
TOOLS

30. 1 3
5
Popular data integration approaches
4
6
2
...
Data centralization Data warehousing Dataset integration Hyperlinks
Federated databases View integration

31. Heterogeneous
data sources
Same data types
Homogeneous vs Heterogeneous
data integration
A B C
1
2
leverage
B
C
A
Teaching the fundamentals of biological data integration
using classroom games. Schneider MV, Jimenez RC.

32. 184 molecular interactions
Pathway resources
13 December 2018 32
132
9
43
73
62
51
38
20
14
Pathway resource list
Protein-Protein Interactions
Genetic Interaction Networks
Protein-Compound Interactions
Metabolic Pathways
Signaling Pathways
Gene Regulatory Networks
Pathway Diagrams
Protein Sequence Focused
Other
http://www.pathguide.org/
442 pathway

33. Expertise to do this job
• Software project management
• Collaborative software development
• Bioinformatics in multidisciplinary fields
• Biological science
• System administration
• Writing
• Interpersonal skills

34. Achievements (last 4 years)
• Definition and implementation of standards like DAS and PSI
• Start the BioJS community open source project
• Participate as a Researcher Co-Investigator in a BBSRC grant
proposal
• Publish 17 publication (6 as a first or last author)
• Write 2 book chapters
• Report more than 10 deliverables
• I supervised 5 students (3 of which are currently collaborating with
our team)
• Participate as speaker/trainer in almost 30 bioinformatics events
• Co-organise 6 workshops about web services and visualisation
• Participate in several projects including Biosapiends, ENFIN, COPa,
IntAct, IMEx, PRIDE, Affinomics, LARK2-LEAPS, ELIXIR,
BioMedBridges and AgedBrainSysBio

35. Reports preparatory phase