Barend Mons slides from #ISMB 2014: Trends in data publishing

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Barend Mons slides from #ISMB 2014: Trends in data publishing. Talk 3 in the "What Bioinformaticians need to know about digital publishing beyond the PDF2" workshop at ISMB 2014, Boston, 16th July 2014

Ciencias

Simplified eScience
RO’s
All Core Legacy
Information +
WorkFlows
User
New
dataset
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

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)
Findable
Usable 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

3 tissues
Heart muscle
Skeletal muscle
Cerebral Cortex
RNA detected
In many more
tissues
25 TSS
???

Repositories
Data Owners
(supp)
data
Data
bases
ELIXIR FAIR Data Search Index
End-users
FAIR L2
ELIXIR semantic data repository
ELIXIR
Data
FAIR
Port
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
Elixir
Fin.
Elixir
Esp.
Elixir
Nor.
Elixir
UKElixir
SWEElixir
NL..
Elixir
Fin.
Elixir
Esp.
Elixir
Nor.
Elixir
UKElixir
SWEElixir
NL..
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

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