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VEuPathDB-ontology / VEuPathDB-ontology

The VEuPathDB ontology is an application ontology developed to encode our understanding of what data is about in the public resources developed and maintained by the Eukaryotic Pathogen, Host & Vector Genomics Resource (VEuPathDB; https://veupathdb.org).
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data item related to microbiome detection #423

Open zhengj2007 opened 1 year ago

zhengj2007 commented 1 year ago

Describe the bug no Plasmodium by microscopy Definition: a data item that is the specified output of a microscopy assay that has a sample of blood as specified input and indicates that the sample does not contain Plasmodium

Is it a child of EUPATH_0027009 'presence of Plasmodium in blood by microscopy assay'? Shall indicate sample type in the label, such as 'no Plasmodium in blood by microscopy'

parasite species information Definition: A data item of which parasite species detected in a blood specimen. Parent: 'presence of organism in specimen' Value of 'presence of organism in specimen' should be boolean. So, I think 1). the parent of the term is not correct. 2). The label should be improved, such as 'parasite species in blood datum'

johnwjudkins commented 1 year ago

parasite species information New label: Plasmodium species in blood by microscopy datum New definition: A Plasmodium in blood by microscopy datum that specifies the species detected. New subclass: Plasmodium in blood by microscopy datum

no Plasmodium by microscopy New label: no Plasmodium in blood by microscopy New definition: A Plasmodium in blood by microscopy datum that specifies no Plasmodium detected. New subclass: Plasmodium in blood by microscopy datum

zhengj2007 commented 1 year ago

related issue: https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/issues/480

zhengj2007 commented 1 year ago

The labels and definitions look good to me. But it might be better after discuss the design patterns of organism detection data.