Table 1 Ontology classes used in the three use cases (note: instances are not included):

administering substance in vivo

OBI: OBI_0600007

material combination

2

assay

OBI: OBI_0000070

planned process

1,3

caudate nucleus

NeuroLex: birnlex_1373

anatomical entity

1

conclusion textual entity

IAO: IAO_0000144

textual entity

3

data set

IAO: IAO_0000100

data item

3

evaluant role

OBI: OBI_0000067

role

3

extracellular electrophysiology recording

OBI: OBI_0000454

assay

1

function

snap#Function

realizable entity

1,2

host role

OBI: OBI_0000725

role

2

hypothesis driven investigation

OBI: OBI_0000355

planned process

3

hypothesis textual entity

IAO: IAO_0000415

textual entity

3

independent continuant

snap#IndependentContinuant

continuant

injection function

OBI:OBI_0005246

function

2

interpreting data

OBI: OBI_0000338

process

3

investigation

OBI: OBI_0000066

planned process

3

light source

OBI: OBI_0400065

processed material

1

Macaca fuscata

NCBI_Taxon: NCBITaxon_9542

organism

1

material combination

OBI: OBI_0000652

planned process

2

material to be added role

OBI: OBI_0000319

role

2

material entity

snap#MaterialEntity

Independent continuant

1,2,3

measure function

OBI: OBI_0000453

function

1

measurement device

OBI: OBI_0000832

processed material

1

measurement datum

IAO: IAO_0000109

data item

1,2

measuring neural activity in the caudate nucleus

OBI: OBI_0000812

extracellular electrophysiology recording

1

micro electrode

OBI: OBI_0000816

processed material

1

neuron

FMA: FMA:54527

anatomical entity

1

objective specification

IAO: IAO_0000005

directive information entity

3

organism

OBI: OBI_0100026

material_entity

2

pathogen challenge

OBI: OBI_0000712

administering substance in vivo

2

pathogen role

OBI: OBI_0000718

role

2

plan specification

IAO: IAO_0000104

directive information entity

3

planning

OBI: OBI_0000339

planned process

3

presentation of stimulus

OBI: OBI_0000807

process

1

process

span#Process

processual entity

1,2,3

processed material

OBI: OBI_0000047

material entity

1,2,3

role

snap#Role

realizable entity

1,2,3

Saccharomyces cerevisiae

NCBI_Taxon: NCBITaxon_4932

organism

3

spike train datum

OBI: OBI_0000801

measurement datum

1

study subject role

OBI: OBI_0000097

role

1

survival assessment

OBI: OBI_0000699

assay

2

survival rate

OBI: OBI_0000789

measurement datum

2

syringe

OBI: OBI_0000422

processed material

2

target of material addition role

OBI: OBI_0000444

role

2

vaccination

VO: VO_0000002

administering substance in vivo

2

vaccine

VO: VO_0000001

material entity

2