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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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Add annotation properties needed for EDA to VEuPathDB ontology #185

Open cstoeckert opened 3 years ago

cstoeckert commented 3 years ago

The Exploratory data analysis (EDA) workspace has led to changes in the way variables will be displayed on the ClinEpiDB and VEuPathDB web sites. Annotation properties describing default units and data ranges have been created for the web display owl files. We will add them to the VEuPathDB ontology so they can be properly defined and managed.

cstoeckert commented 3 years ago

From https://github.com/VEuPathDB-ontology/VEuPathDB-ontology/blob/master/src/ID_range.txt In-house annotation property: EUPATH_0001000- EUPATH_0001100

sweverschulman commented 3 years ago

need to add the follow to the above list

EUPATH_0001016 - mergeKey

Descriptions of the below annotation properties are found in SOP 2.05 Variable Processing defaultDisplayRangeMin defaultDisplayRangeMax defaultBinWidth

zhengj2007 commented 3 years ago
ID Label ontology label Definition
EUPATH:0001006 replaces replaces Annotation property that records ontology term IRI that original used in the study. (JZ)
EUPATH:0001008 unitLabel unit label Annotation property that specifies units that are associated with a variable (if any) in a human-readable format. Use abbreviations.
EUPATH:0001009 unitIRI unit IRI Annotation property that specifies the IRI of unit from the unit ontology (UO).
EUPATH:0001010 dataSet dataSet Annotation property that specifies dataset that a term belong to. (JZ)
EUPATH:0001011 repeated repeated Annotation property that indicates terms that were assessed longitudinally / repeatedly over time.
EUPATH:0001012 is_featured is featured Annotation property that specifies important terms to be highlighted.
EUPATH:0001013 hidden hidden Annotation property that indicates that to hide terms in the UI and also in the download files.
EUPATH:0001014 scale scale Annotation property that identifies terms that are on the log scale or natural log scale, as opposed to on the linear scale.
EUPATH:0001015 is_temporal is temporal Annotation property that specifies terms that are related to time, to be used in visualizations looking at data over time. Also to be used in subsetting tab histograms (to indicate that the data range should not include the origin)
EUPATH:0001016 mergeKey merge key Annotation property that specifies key terms with longitudinal/repeated measures in the studies .
EUPATH:0001017 defaultDisplayRangeMin default display range min Annotation property that specifies default minimum value for each term’s range. Useful to ensure that histograms for related terms have the same x-axis range
EUPATH:0001018 defaultDisplayRangeMax default display range max Annotation property that specifies the default maximum value for each term’s range. Useful to ensure that histograms for related terms have the same x-axis range
EUPATH:0001019 defaultBinWidth default bin width Annotation property that specifies the bin width for each term’s histogram.

Definitions based on description in file: ClinEpiDB_SOP2.05_VariableProcessing expect two tagged with (JZ)

cstoeckert commented 3 years ago

Go ahead and add these.

bobular commented 3 years ago

I imagine that use cases for defaultDisplayRangeMin and defaultDisplayRangeMax would be useful for other plots and axes too.

cstoeckert commented 3 years ago

The listed properties were confirmed at the July 1, 2021 ClinEpiDB meeting.

zhengj2007 commented 3 years ago

The outreach team request a new annotation property, 'force string type'.

EUPATH_0001020 'force string type' Proposed definition: Annotation property used to annotate numeric terms as strings. Numeric terms annotated as strings will ALWAYS be ordinal. Study specific.