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

From: Modeling biomedical experimental processes with OBI

Classes Sources and term IDs Parent class Use cases
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