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Niall (minuting), Terri, Milo, Carole



  • BD2K-ELIXIR Training collaboration planning

  • Bioportal annotator vs EdamMap

  • API documentation

  • Latest TeSS developments

BD2K-ELIXIR Training collaboration planning

Collaboration between BD2K and ELIXIR for training so far has been sporadic e-mails, private conversations, and skype calls. Very difficult to review what's been discussed and with who. So I've created a handy fact sheet

It doubles as a planning document. The last table is a series of suggestions on points we can collaborate when we go to the US for a deep collab. The ideas have been extracted from e-mails.

We want to prioritise amongst the ELIXIR Reps which ones we should work on first, and circulate to the US contingent to do the same, then see if there's any clear winners. Should help push this collab forward.

Decide on common schema. There's is more semantic whereas ours is more discoverable. With Bioschemas hat on – We should assess theres create a mapping between the two and fold in values from theres if appropriate and defendable. 


Bioportal Annotator vs EdamMap

 Discussion started today on the tools registry mailing list. Discovered the userful web service bioportal annotator. Lots of discussion previously about EdamMap. EdamMap doesn't look well supported - very few recent commits, no installation instructions, burden of ownership unclear. Whereas bioportal annotator looks quite good.

This would be used for suggesting EDAM categories for materials. Already have category annotation mechanism in TeSS - this would plug in to that so no dependecy issues - just need to choose what suggestion mechanism.

Carole: Also ZOOMA  - Need to create a list of functional and non-functional requirements about what this annotation suggestor should be, do, look like etc. Then assess each of the available ones. This will then be a justifiable and accessible decision if you need to defend choices. 

Action Niall: Create (non/)functional requirements form to do assessment with

Planning on prototyping using the web service before EuBIC Semmering Winter School.

Carole: Also need gold standard to benchmark against. Could also have a bakeoff - trying each of them. 


API Documentation

Finally got round to writing up API documentation for TeSS in SWAGGER - some issues with consistency in API responses that are now in Github issues.

Lots of advantages to SWAGGER that I'm very excited about. Aside from being clear documentation about requests and responses - can test API interactively in browser, can download client code to interface, can even download server implementing the specification. 

Carole: Very useful for joining up the interoperability workpackage to other platforms. 

Action niall: Write post for interoperability knowledge hub about SWAGGER - experience, advice for implementing, pros/cons

Could also join up with the tools registry - may be interested in using the autogenerated client for their interactions with TeSS API 

Latest TeSS Developments

Not many new updates this week

Finn added numbers on filters to improve UI and sorted some background issues out.

Content provider status becoming unweildly. Dealing with dozens of content providers asking for information and not responding - need to create a list so I can prompt, keep track of promises and status.

Action Niall: create spreadsheet about this

For example SIB said in March they would implement Bioschemas - had technical discussion with Vassilious, agreed to implement, no response, prodded, will do in 2 weeks, no response yet 4 weeks on. 

Action Terri: Prod patricia about SIB content

Spanish Oscar Torreno and acanada working on exporting as ICS



Action Niall: Create (non/)functional requirements form to do assessment with

Action Niall: Write post for interoperability knowledge hub about SWAGGER - experience, advice for implementing, pros/cons

Action Terri: Prod patricia about SIB content

Action Niall: create spreadsheet about Content provider status'

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