Skip to content
Snippets Groups Projects
Commit f673a0eb authored by Florian Solbach's avatar Florian Solbach
Browse files

Create README

parents
No related branches found
No related tags found
No related merge requests found
# Let's FAIRify Reaction Mechanisms
goal: design and establish a standard for sharing reaction mechanism data in a FAIR way
## strategies
- low activation energy
- design for extendability
- allow distribution but central index?
- pro distribution: do not insist on platform or way to publish (esp. if data is already published somewhere else, this could not be included)
- pro centrality: findability
- pro distribution: allow to hide some data behind authentication/authorization
- science is done on the shoulders of giants
- use existing infrastructure, standards and software
## FAIR principles
| principle | subgoal | description |
| -------------- | :------ | --------------------------------------------------------------------------------------------------------- |
| findable | F1 | (Meta) data are assigned globally unique and persistent identifiers |
| | F2 | Data are described with rich metadata |
| | F3 | Metadata clearly and explicitly include the identifier of the data they describe |
| | F4 | (Meta)data are registered or indexed in a searchable resource |
| accessible | A1 | (Meta)data are retrievable by their identifier using a standardised communication protocol |
| | A1.1 | The protocol is open, free and universally implementable |
| | A1.2 | The protocol allows for an authentication and authorisation procedure where necessary |
| | A2 | Metadata should be accessible even when the data is no longer available |
| interoperatble | I1 | (Meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation |
| | I2 | (Meta)data use vocabularies that follow the FAIR principles |
| | I3 | (Meta)data include qualified references to other (meta)data |
| reusable | R1 | (Meta)data are richly described with a plurality of accurate and relevant attributes |
| | R1.1 | (Meta)data are released with a clear and accessible data usage license |
| | R1.2 | (Meta)data are associated with detailed provenance |
| | R1.3 | (Meta)data meet domain-relevant community standards |
### General Measures
- define standard
- store info in efficient way
- maybe define "levels of FAIRness" for a mechanism
- e.g. minimum: license + provenance data for mechanism as a whole, i.e., who created it
- build tools
- tools to help add metadata to mechanisms
- need to be able to deal with fact that DOI become available much later than data
- need to be able to allow bulk edits -> assign the same provenance info to a lot of parameters
- compatible with existing data (e.g. output of ChemTraYzer; in first step, probably not fully automatically)
- tools for searching and indexing
- ability to do some inference -> e.g. parameter in mech1 was generated by activity that used paremeter in mech2 => mech1 was derived from mech2
- tools for visualization
- visualize provenance info?
- build community
### Our measures to achieve FAIRness
- F1
- publish each dataset with a DOI and give each parameter a local id
- e.g. for reaction mechanisms: DOI + species/reaction/reaction_class (i.e. concrete model instance) + model (e.g. Arrhenius eqn) + parameter name (e.g. E_a)
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment