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FAIRplus / FAIRPlus_squad2

an internal issue tracker (=todo list) for Squad team 2
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Different representation of ontologies in different tools #17

Open mkoatwork opened 5 years ago

mkoatwork commented 5 years ago

Using BAO version 2.5 in NCBI Bioportal and EBi OLS (access both at 20.06.2019 10:00) gives a different representation: grafik

grafik

proccaserra commented 5 years ago

@mkoatwork as suspected, it seems that NCBO Bioportal loaded the unreasoned version -> only asserted classes: (BAO pulled from github repo https://raw.githubusercontent.com/BioAssayOntology/BAO/master/bao_complete_merged.owl (because the following owl file http://www.bioassayontology.org/bao/bao_complete.owl served by OLS and Bioportal does not load in Protege)

image

Getting the inferred hierarchy (running hermit reasoner in Protege) shows the following:

image

Pay attention to the Protege view Inferred / Asserted toggle box.

OLS is loading the complete-merge & reasoned version of BAO NCBO seems to be loaded the asserted version.

this would be my explanation to the difference you observed.

Good catch @mkoatwork

mkoatwork commented 5 years ago

@proccaserra: Thanks, that's a good explanation. There are also other differences e.g 'IC50' is found on Bioportal as subclass of 'concentration response endpoint' and on OLS as subclass of 'AC50' or GI50 is a subclass of IC50 in OLS and on the same level as IC50 in Bioportal. The problem I have now is: how can we improve the quality of these services or make users aware of these issues? I haven't check if the same problems occures for other ontologies.

proccaserra commented 5 years ago

@mcourtot @mkoatwork: Notification made to: