barend mons slides from #ismb 2014: trends in data publishing

Trends in Datapublishing

Barend Mons

Simplified eScience

RO’sAll Core Legacy Information +

WorkFlows

User

New datase

t

New Insights

X

AREAL SURVEY DEEP EXCAVATION

‘Why would I believe this association’???

2005, 6:142

Why I gave up spending most of my energy on text mining years ago

Data loss is real and significant…

Nature news, 19 December 2013

…and so is Data growth

The Data cycle in eScience

6

Prof. Carole Goble

www.datafairport.org

F

A

I

R

Findable:- PID for each concept used- PID assignment (authorities)- ARTA-service

Accessable:- Machines can Map (IMS-service)- License on data elements- Authentication/Authorization

Interoperable:- Machines understand data- Download-link-data formats - Workflows (Research Objects)

Re-usable:- Functionally Interlinked- Harmonized- Citable and available for...

PID

'provenance' (user defined)

Data (elements)

Metadata (intrinsic)

A simplified diagram of a Digital (data) Object irrespective of technological choices and naming

PID

'provenance' (user defined)

Data (elements)

Metadata (intrinsic)

Digital Object Architecture s are Digital Objects

Nanopublications are Research ObjectsSome Research Objects are

PID\\\

Metadata (intrinsic)'provenance' (user

defined)

Data (elements)

Totally UNFAIR

PID

Metadata (intrinsic)'provenance' (user

defined)

Data (elements)

FindableUsable for Humans

PID

Metadata (intrinsic)'provenance' (user

defined)

Data (elements)

FAIR metadata

PID

Metadata (intrinsic)

'provenance' (user defined)

Data (elements)

FAIR data-restricted access

PID

Metadata (intrinsic)

'provenance' (user defined)

Data (elements)

FAIR data-Open Access

PID

Metadata (intrinsic)

'provenance' (user defined)

Data (elements)

FAIR data-Open Access/Functionally Linked

Data as increasingly FAIR Digital Objects

BYOD-01

15

16

17

Combine FANTOM5

&LOVD

16 TSS 10 Tissues

3 tissuesHeart muscle

Skeletal muscleCerebral Cortex

RNA detectedIn many more

tissues

25 TSS???

Repositories

Data Owners

(supp)data

Databases

ELIXIR FAIR Data Search Index

End-users

FAIR L2

ELIXIR semantic data repository

ELIXIRDataFAIRPort

ELIXIR federated data

FAIR L1

Search for datasets

Download data (sub)

sets in many formats (xml, rdf, json etc)

FAIR L3

FAIR L4

ASPs, Inhouse IT, Bioinformatics

Etc..

Tools &Applications

ElixirFin.

ElixirEsp.

ElixirNor.ElixirUKElixir

SWEElixirNL..ElixirFin.

ElixirEsp.

ElixirNor.ElixirUKElixir

SWEElixirNL..

3

1

2

4

Develop ELIXIR-NL

Engage key data owners

Training & Education

Develop Infrastructure &

service

Sustainable funding

Policy Alignment

1

2

3

6

5

4