Mondo Externally Managed Content
Automatic Mondo Quality Control Checks for Externally Managed Content¶
A subset of the extensive Mondo QC checks are automatically run on the externally managed content (EMC). To limit delay due to QC failure, any content from external providers that does not pass these QC checks is not included in Mondo until the content is updated by the data providers and passes the QC checks. Reports of these QC checks will be available for review of any errors so that any needed changes can be made.
QC Checks for Externally Managed Content¶
Error | Description | SPARQL Query |
---|---|---|
duplicate_scoped_synonym | The synonym from the external source is the same as a synonym already reported on the Mondo term, but the synonym scope is not the same. For example, the synonym from the source is "exact", and the synonym in Mondo is "broad". | duplicate scoped synonym |
invalid_xref | A database_cross_reference in the EMC file is not in CURIE format. | invalid xref |
qc-duplicate-exact-synonym-no-abbrev | An exact synonym, excluding abbreviations, or label in the EMC file duplicates an existing exact synonym or label for a different Mondo term/entity. | duplicate synonyms |
qc-syn-source-not-xref | A synonym in the EMC file does not have a database cross reference as the source of the synonym. | missing synonym source |
qc-trailing-whitespace.sparql | An entity contains a leading or trailing whitespace. | trailing whitespace |
qc-animal-disease-rare | An animal disease is contained within a rare disease subset. | animal disease rare |
qc-proxy-merges | A mapping in the EMC file caused two different Mondo classes to have a mapping to the same external source term. See proxy merges for more information. | proxy merge |
Example Report for QC Check¶
# QC Failure Report for nord.robot.tsv
## Removed from the resource
| mondo_id | report_ref | report_ref_source | preferred_name | preferred_name_source | synonym_type | subset | subset_source | subset_source2 | Source | Check |
|:--------------|:-------------|:--------------------|:---------------------------|:------------------------|:---------------|:---------|:----------------|:-----------------|:---------------|:----------------------------------------------------|
| MONDO:0001280 | | | Posterior Uveitis | | | | | | nord.robot.tsv | duplicate_scoped_synonym (oboInOwl:hasExactSynonym) |
| MONDO:0002119 | | | Juvenile Ossifying Fibroma | | | | | | nord.robot.tsv | duplicate_scoped_synonym (oboInOwl:hasExactSynonym) |
| MONDO:0005731 | | | Acanthocheilonemiasis | | | | | | nord.robot.tsv | duplicate_scoped_synonym (oboInOwl:hasExactSynonym) |
| MONDO:0005761 | | | Elephantiasis | | | | | | nord.robot.tsv | duplicate_scoped_synonym (oboInOwl:hasBroadSynonym) |
| MONDO:0007030 | | | Aarskog Syndrome | | | | | | nord.robot.tsv | duplicate_scoped_synonym (oboInOwl:hasExactSynonym) |
| MONDO:0007306 | | | Klippel-Feil Syndrome | | | | | | nord.robot.tsv | duplicate_scoped_synonym (oboInOwl:hasBroadSynonym) |
| MONDO:0007389 | | | Spondylothoracic Dysplasia | | | | | | nord.robot.tsv | duplicate_scoped_synonym (oboInOwl:hasExactSynonym) |