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BioKC: a platform for quality controlled curation and annotation of systems biology models

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(1)

Dr. Carlos Vega

Bioinformatics Core

Luxembourg Centre for Systems Biomedicine

BioKC: a platform for quality controlled curation and

annotation of systems biology models

BioNetVisA, 2020 Workshop

4

th

of September

(2)

• The demand for systems biology knowledge increases with new

findings demonstrating elaborate relationships between molecules, pathways and cells.

• Currently, high quality curation efforts concentrate around

dedicated pathway databases, with a limited input from the

research community.

• There is a need for novel

collaborative tools and platforms allowing to improve the quality

and the output of the curation process.

Motivation

(3)

Traditional approach

Implicitly requires working on the layout since the beginning

Diagram Editors • Single user

• Standalone application

• Layout Editor

• Lack of review process

• No collaborative work

• Limited annotation features

BioModels

(4)

Traditional approach

Implicitly requires working on the layout since the beginning

Table from paper in progress

(5)

Traditional approach

Implicitly requires working on the layout since the beginning

Table from paper in progress

(6)

Traditional approach

Implicitly requires working on the layout since the beginning

Table from paper in progress

(7)

Traditional approach

Implicitly requires working on the layout since the beginning

Table from paper in progress

(8)

Traditional approach

Implicitly requires working on the layout since the beginning

Table from paper in progress

(9)

BioKC

Web platform for collaborative model curation and annotation

• Granular facts, encoded in SBML.

• Facts can be annotated with sentences and ontology terms from identifiers.org

• Sentences from BioKB or 3rd party sources.

• Collaborative and quality control features:

• Tasks

• Action log

• Comments

• Inter-annotator agreement.

Fact

Minimal piece of representative knowledge that can can be cited, referenced, attributed, and serialised to a common

format (e.g. SBML).

(10)

BioKC

• Role system similar to GitLab and GitHub.

• Group-level role system:

• Managers

• Administrators of the group.

• Curators

• Permission to change the elements that compose a fact.

• Annotators

• Permission to annotate the facts.

• Readers

• Read only access to facts.

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Web platform for collaborative model curation and

annotation

(11)

BioKC

Two workflows to start creating facts Gather evidence

♀ ‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍‍

Curate Model

BioKB

1

Evidence

from:

(12)

BioKC

Two workflows to start creating facts Gather evidence

♀

Curate Model

Evidence from:

Other

Text-Mining and Knowledge Bases

1

(13)

BioKC

Two workflows to start creating facts

Curate Model Elements

Gather evidence

♀

Curate Model

1

(14)

BioKC

Two workflows to start creating facts

Assign Gathered Evidence

Gather evidence

♀

Curate Model

1

(15)

BioKC

Two workflows to start creating facts

Model Curation

2

Curate Model

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Annotate Model

(16)

BioKC

Two workflows to start creating facts Curate Model

�‍ �

‍

Annotate Model

Model Annotation

2

(17)

BioKC

Roadmap

• Fact publishing workflow:

• Using stable identifiers to reference matured facts.

• Lock a release, but enable versions.

• Wider interoperability with external sources and tools.

Acknowledgements

Dr. Marek Ostaszewski

Dr. Piotr Gawron

Dr. Venkata Satagopam

Valentin Grouès

(18)

Questions

Register and share your thoughts

https://biokb.lcsb.uni.lu/

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