1st October 2014, Hinxton

1. BMB Resource Integration
Workshop
1st October 2014, Hinxton
Nathalie Conte & Rafael Jimenez
BioMedBridges
Standard
Registry

2. Agenda proposal
09:45 - 10:00 Coffee available
10:00 - 10:15 Presentation: Aims of the workshop and re-cap of the last workshop
10:15 - 10:25 Presentation: Identifiers.org
10:25 - 10:35 Presentation: BioSharing
10:35 - 10:45 Presentation: BMB Service Registry
10:45 - 10:55 Presentation: EDAM ontology
10:55 - 11:05 Presentation: BMB standards registry (11:00 - Coffee)
11:05 - 12:30 Break-out session: Identify overlaps and potential synergies among our registries
12:30 - 13:30 Lunch
13:30 - 15:00 Break-out session: Define areas of collaboration
15:00 - 15:30 Coffee
15:30 - 16:45 Discussion: Future plans and funding strategies
16:45 - 17:00 Wrap-up

3. Standard Workshop update
June 2014, Amsterdam
 Workshop overview
1. Identifiers best practice (e.g. which identifiers are
recommended for which entities) and an identifier gap
analysis (e.g. which entities are not identified and need
to be)
2. Discuss BMB standards registry development, usage
gap analysis and integration with other tools (e.g.
review prototype software, discuss level of detail needed,
what standards should be covered, how this registry can
facility integration by matching data elements, and
potential for integration tools registry, BMB services,
biosharing.org and identifiers.org)
Workshop report

4. Action
Standards registry
 Integration of resources between: URGENT
discussion
 identifiers.org
 BioSharing
 BMB
 Tools registry
 Standards registry
 EDAM
 Alejandra, Nick, Jon, Julie, Rafael, Morris
 Nathalie to facilitate TC by END JULY

5. Workshop aims
Identify common goals shared among our
resources
Identify areas of duplication and gaps
Define a common integration and development
strategy

6. Personal wish list
More integration
 Content
 Software
 Interfaces, schema, vocabulary, API
Collaborative development
More quality (content, code, design)
More openness (user community contributions)
 Content
 Software

7. Registries and Resources
 BioMedBridges Standards Registry
Registry standard data models (formats) and content guidelines and
facilitate standards mapping between datasets.
 BioSharing
Registry of community standards, (guidelines, formats, terminology),
databases, data policies and the interrelations between them.
 Miriam & identifiers.org
Registry provides a set of online services (databases, tools) including
resolvable persistent identifiers.
 ELIXIR Tools and Data Services Registry
Registry of software (tools) and data services (databases) required by
bioinformatics and biomedical researchers.
 EDAM
Ontology of bioinformatics types of data (including identifiers), data
formats, operations (including tools) and topics.

8. Content type overlap
Databases
Tools
Formats
Guidelines
Terminology
BMB Standard registry x x
BioSharing x x x x
Miriam & identifiers.org x
ELIXIR Tools and Data Services
Registry
x x
EDAM x

9. Stakeholders issues
User
There are several registries with different interfaces and no clear
understanding about their differences. Moreover registries which
provide complementary functionality are not linking to each other.
Registries
There is duplication of efforts such as content curation, content
definition (schemas and vocabularies) and software maintenance
(front end back end).
Funders
It is very difficult to commit with so many repositories which do not
work together and have a high overlap in content and
functionality.

10. Registry proliferation
Several
registries
Different
interfaces
Variable
results
Redundancy
Duplication of efforts
Specificity

14. Joint effort
More competitive
Better solution
Less redundant
Better use of resources
More quality
More chances of funding

15. How
?

16. Many ways to integrate !
Common
UI?
Common
backend?
Link
Backend ?
Link
Ui ?
Common
Curation effort ?
APIs?
Common
Data
submission
Form ?
Schema
Vocabulary

17. Thanks

19. Software