IRI updates:
- property IRIs have been reused wherever possible (i.e. SCDO IRI were replaced by those from existing ontologies)
- Terms that were annotated with “Sufficient” by the “existence in other ontologies” annotation property had their IRIs replaced by the term in the external ontology that it was cross referenced to using the “database cross reference” annotation property.
- Remaining SCDO-specific IRIs have been updated to the standard OBO prefix, e.g. the IRI of “Clinical or Research Assessment Answer” was changed from “http://scdontology.h3abionet.org/ontology/SCDO_1000473” to “http://purl.obolibrary.org/obo/SCDO_1000473”
Content updates:
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Ontology annotations updated (we just had “place-holder” text there before).
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Removed annotations that were automatically ascribed to the “created_by” and “creation_date” annotation properties on the creation of new terms within WebProtege.
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Additional ELSI/consent-related terms added (especially types of consent during emergencies).
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Addition of the “Complication” sub-class, and a number of sub-classes below it, to the “Abnormal Phenotype” class.
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Additional terms/classes included during the process of mapping SickleinArica data elements to the SCDO.
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Additional upper level “Data Standards” class, containing sub-classes for mapping SickleInAfrica (SIA) SCD data elements to the SCDO:
- Clinical or Research Assessment Answer
- Clinical or Research Assessment Data Element
- Clinical or Research Assessment Question Type
- Clinical or Research Assessment Questionnaire
- Unit of Measurement
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Additional properties for mapping SCD data elements to the SCDO:
- Object properties:
- is question type
- has answer option
- collects
- has answer standard unit
- has reference range standard unit
- has possible finding
- diagnosed using finding
- code requires phenotype
- is ICD-10-CM code type
- Data properties:
- maximum number of selections allowed
- minimum number of selections allowed
- has LLN
- has ULN
- has LLN male
- has ULN male
- has LLN female
- has ULN female
- has LLN pediatric
- has ULN pediatric
- Annotation properties:
- has sections
- has field label
- has redcap variable
- has answer options text
- has field note
- has field type
- In CRF section
- order in CRF section
- custom alignment
- has redcap validation
- has branching logic
- has redcap action tags
- has redcap max number validation
- has redcap min number validation
- has redcap field annotation
- has calculation equation
- has slider label
- show slider
- is identifier
- required field
- in matrix group
- requires additional code
- autocomplete
- Object properties:
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“Country” term deprecated and replaced by more specific “National Origin” (existing term in Personal Attributes class) and “Country of Data Collection” (new term in Research class).
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Associations between ICD-10-CM codes below D57 to relevant SCDO classes using the code requires phenotype object property.
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Removed old erroneous ICD10 associations made with the has clinical code object property.
Accompanying mappings files:
- SSSOM mappings file (scdo-sssom-xrefs.tsv) This file contains mappings of SCDO classes to classes in other OBO ontologies.
- SSSOM rename file (scdo-sssom-xrefs-rename.tsv) This file lists the SCDO IDs and corresponding OBO term IDs of SCDO terms that have had their URIs updated to that of their cross referenced term in an external OBO ontology.