BMB Resource Integration Workshop
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The document summarizes a workshop aimed at integrating resources between several bioinformatics standards registries. The workshop agenda includes presentations from Identifiers.org, BioSharing, BMB Service Registry, EDAM ontology, and the BMB standards registry. Breakout sessions will identify overlaps and potential synergies between the registries, and define areas for collaboration. The goal is to reduce duplication of efforts and develop a common integration and development strategy across registries.
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BMB Resource Integration Workshop
- 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
Editor's Notes
- #4: Standards and data harmonisation is a prerequisite for data integration, a primary aim to the BioMedBridges project to achieve exchange and integrate data in a meaningful way there needs to be agreement on how data is annotated, formatted and organised.
- #8: BioMedBridges Standards Registry aims to facilitate syntactic operability across research infrastructures so that samples and data can be integrated and analysed across biomedical science domains EDAM : ontology of bioinformatics types of data,data formats, operations (tool, application, or workflow functions) and topics (application domains).
- #17: Preparing for this workshop and, Being a non specialist of those technical questions, Rafael kindly took time to explore different way to integrate several resources together – I guess the take home message from this doodle is that there are many ways to integrate, and there are point to consider for integration (like schemas, backend, Apis, vocabularies, UI) – The right way must be the one which is achievable and agreed by all resources