1. Semantics &
Interoperability

2. Science process
Hypothesis + Data = Knowledge

3. Knowledge Semantics
Hypothesis + Data = Knowledge
Objects genes, proteins, cells, tissues, ...
Gene Ontology (GO)
Infectious Disease Ontology (IDO)
Ontologies Foundation Model of Anatomy (FMA)
Environment Ontology (EnvO)
....
Tools Datasets & Repositories

4. Process Semantics
Hypothesis + Data = Knowledge
article database
InputData + Workflow + Tool ...
Objects
(Material + Method + Instrument) refs
... authors
keywords
...
Ontologies EXPO, OBI, ??
MyExperiment, LaBLog,
Mendeley,
Tools InkSpot, OWW,
Papers
UsefulChem

5. Material = [Raw]Material + Method + Instrument
In more general terms:
Stuff(instrument) does Stuff(method) to Stuff(raw material)
to produce new Stuff (material). © Cameron N
Examples:
Material [Raw]Material Method Instrument
(Output Data) (Input Data) (Workflow) (Hard/Software)
Imaging device +
Phenotype Transgenic mouse Imaging + analysis
expert (author)
Chemical Structure Sample NMR Spectrometer
PubMed
Literature references Search PubMed, Google
(literature DB)
Data references UniProt Search Built-in engine
Remarks:
- Several [Raw]Materials can be fused to produce one output Material.
- [Raw]Materials can be subject to chains of transformations, commonly referred to as Protocols.
- Sometimes it might be impossible to split Method from Instrument.

6. Process Semantics
Hypothesis + Data = Knowledge
article database
InputData + Workflow + Tool ...
Objects
(Material + Method + Instrument) refs
... authors
keywords
...
Ontologies EXPO, OBI, ??
MyExperiment, LaBLog,
Mendeley,
Tools InkSpot, OWW,
Papers
UsefulChem

7. Semantic Science Web
Upper level BFO (Basic Formal Ontology)
Knowledge level GO, IDO, FMA, ...
(?) Open Science Ontology
Process level
EXPO, OBI, ...
MyExperiment, LaBLog, Mendeley PDB
Tools level InkSpot, OWW, Papers PubMed UniGene
UsefulChem ... arXiv ...
...
Hypothesis + Data = Knowledge