H O W O P E N I S O P E N ?

A N E V A L U AT I O N R U B R I C F O R P U B L I C

K N O W L E D G E B A S E S

MELISSA HAENDEL

MARCH 28TH, 2017

@ontowonka

THERE ARE OVER 1500 PUBLIC DATABASES IN NUCLEIC ACIDS RESEARCH DATABASE COLLECTION

https://doi.org/10.1093/nar/gkw1188

HOW MANY OF THESE ARE TRULY OPEN?

OPENNESS IS AN NARREQUIREMENT, BUT …

WHY ARE WE STILL FAILING?

OPEN DATA IS FAIR DATA

http://www.nature.com/articles

/sdata201618

Findable Accessible Interoperable Reusable

ANATOMY OF FAIR: FINDABLE

persistent identifier

rich metadata

registered or indexed in a searchable resource

McMurry et al Identifiers for the 21st century

bit.ly/identifiers-2017

ANATOMY OF FAIR: ACCESSIBLE

(meta) data are openly retrievable by their

identifier using a standardized

communications protocol

Metadata are accessible, even when the data

are no longer available

http://api.monarchinitiative.org/api/

ANATOMY OF FAIR: INTEROPERABLE

Use a formal, accessible, shared, and broadly

applicable language for knowledge

representation

Define semantics of all relationships, including

cross references (hint: use the Relations

Ontology!)

ANATOMY OF FAIR: INTEROPERABLE

Picking on the Personal Genome Project (thanks Sasha!)

Do you have a severe genetic disease or rare genetic trait? If so, you can add a description for your public profile.

1. Extreme susceptibility to motion sickness. - answers pertain to this trait2. Pyloric stenosis3. Unusually small feet for my height

ANATOMY OF FAIR: REUSABLE

Meta(data) are described with a plurality of

accurate and relevant attributes

Detailed provenance and use of community

standards

www.obofoundry.orghttps://www.w3.org/TR/hcls-dataset/

https://peerj.com/articles/2331.pdf

A RUBRIC FOR EVALUATION

bit.ly/eval-rfi

Findable Accessible Interoperable Reusable

FAIR-TLC

Traceable Licensed Connected

FAIR-TLC: TRACEABILITY

Provenance is documented and attributed

Contributions to the content (data, tools,

algorithms, sources, etc.) are declared

Documentation on how to cite a record from a

source or the whole resource

FAIR-TLC: LICENSURE

http://peterdesmet.com/posts/analyzing-gbif-data-licenses.html

Not all data resources are free to use, derive, and

redistribute, even if they are publicly funded and

seemingly publicly available.

FAIR-TLC: LICENSURE

http://peterdesmet.com/posts/analyzing-gbif-data-licenses.html

Standard

license171

Non-standar

d license1069

No license10734

NON-STANDARD LICENSES BURDEN SCIENCE bit.ly/reusabledata-forum

FAIR-TLC: CONNECTEDBECAUSE AGGREGATED != INTEGRATED

FAIR-TLC: CONNECTEDBECAUSE AGGREGATED != INTEGRATED

192K datasets….probably more than 38 are relevant to diabetes

FAIR-TLC: CONNECTEDBECAUSE AGGREGATED != INTEGRATED

Similarly, clouds do not integrate data.

http://stonebond.com/wp-content/uploads/2015/05/cloud-data-bullet-points-img.jpg

EVALUATING THE OPEN SCIENCE CANDIDATES Room for

improvement

bit.ly/open-science-prize

Open imaging

DISCUSSION: HOW DO WE DO BETTER?

Make the right thing the easy thing:

- Carrots:

- Tenure & promotion cycles

- Dedicated funding for increasing FAIR-

TLC

- Sticks:

- Publication requirements

- Funding requirements

- Tools:

- Tracking tools

- Documentation tools

- Social tools

ARE JOURNAL DATA SHARING POLICIES HITTING THE MARK ?

Vasilevsky et al.

https://doi.org/10.7287/peerj.preprints.2588v1

TOO TINY A STICK?

Vasilevsky et al.

https://doi.org/10.7287/peerj.preprints.2588v1

REUSABLEDATA.ORG

Curate, evaluate, and provide guidance on

legal and effective data reuse and redistrubiton

Wanna help? Join the google group at:

Seth Carbonbit.ly/reusabledata-forum

T H A N KS T O :

JULIE MCMURRY

ANDREW SU

SETH CARBON