EDAM Verification Utility Suite : edamverify

edamverify is a utility suite for verification of the EDAM ontology. It implements a set of quality control (QC) checks based upon:

• Guidelines from the Developers Guide for
  • adding concepts
  • hierarchy structure
  • deprecating concepts
• Rules of thumb for EDAM development from the Editors Guide

edamverify implement all checks previously implemented in edamxpathvalidator.

edamverify is invoked whenever the development copy of EDAM (EDAM_dev.owl) is changed, using the EDAM Travis CI system.

NB Current status: edamverify is fully specified - implementation is ongoing.

EDAM QC implementation

EDAM QC consists of:

• invocation of the report utility from the ROBOT ontology verification suite. This runs a series of basic quality control SPARQL queries, such as duplicated labels or synyonms, missing ontology metadata, references to deprecated concepts etc.
• invocation of edamverify which runs a series of SPARQL and SHACL queries, defined in the queries/ folder (see below) which are tailored specifically to EDAM. The SPARQL queries are invoked using the ROBOT verify utility. The SHACL queries are invoked directly.

Each query has a logging level (based on ROBOT report) which defines the severity of the issue:

• ERROR: Must be fixed before releasing EDAM. These issues will cause problems for users, such as classes with multiple labels.
• WARN: Should be fixed as soon as possible. These will not cause problems for all users, but may not be what they expect. For example, a class that is inferred to be equivalent to another named class.
• INFO: Should be fixed if possible. These are for consistency and cleanliness, such as definitions that do not start with an uppercase character.
• NOERR: No error found.

The problems detected by each query and its remedy are documented in the docs folder.

Report format

The QC check results are written to the last cell [1] of the Jupyter notebook in a consistent JSON format, for example:

[1] as required by the script which invokes and parses these notebooks in Travis CI

{
    "test_name": "fileExtensionBadCharacter",
    "reason": [
        "Bad characters found in <file_extension> property of these concepts:",
        "http://edamontology.org/format_3556 (MHTML): mhtml|mht|eml",
        "http://edamontology.org/format_3682 (imzML metadata file): imzML",
        "http://edamontology.org/format_3789 (XQuery): xq|xqy|xquery",
        "http://edamontology.org/format_3475 (TSV): tsv|tab",
        "http://edamontology.org/format_3750 (YAML): yaml|yml"
    ],
    "status": "WARN"
}

Tests

Test	Level	Docs	Issue	Solution [1]	File	Status
Omission of properties required for deprecated concepts	INFO - ERROR	docs	3	IPYNB	annotationDeprecationOmission.ipynb	DONE
Misuse of properties intended for deprecated concepts only	ERROR	docs	2	IPYNB	annotationDeprecationMisuse.ipynb	DONE
Ontology max depth exceeded	WARN	docs	6	SPARQL	maxDepthExceeded.sparql	todo
Singleton leaf node	WARN	docs	7	SPARQL	singletonLeaf.sparql	todo
Subset misuse	ERROR	docs	14, 17, 25, 27, 28	IPYNB	subsetMisuse.ipynb	DONE
Disallowed synonym	ERROR	docs	11	IPYNB	disallowedSynonym.ipynb	DONE
Placeholder chain too long	ERROR	docs	8	SPARQL	placeholderChainTooLong.sparql	todo
Unexpected multiple parents	WARN	docs	9	SPARQL	unexpectedMultipleParents.sparql	todo
Possible spelling mistake	INFO	docs	10	SPARQL	spellingMistake.sparql	todo
Bad EDAM URI reference	ERROR	docs	12	SPARQL	badEdamUriReference.sparql	todo
Bad non-boolean value	WARN	docs	13	IPYNB	badNonBooleanValue.ipynb	DONE
Mandatory property missing	ERROR	docs	8	IPYNB	mandatoryPropertyMissing.ipynb	DONE
Format property missing	INFO - WARN	docs	9, 11	IPYNB	formatPropertyMissing.ipynb	DONE
Identifier property missing	INFO	docs	10	IPYNB	identifierPropertyMissing.ipynb	DONE
Wikipedia link missing	INFO	docs	24	IPYNB	wikipediaLinkMissing.ipynb	DONE
Leaf concept is placeholder	WARN	docs	12	SPARQL	placeholderLeafConcept.sparql	todo
isIdentifierOf redundancy	WARN	docs	13	SPARQL	isIdentifierOfRedundancy.sparql	todo
Identifier relation missing	ERROR	docs	14	SPARQL	identifierRelationMissing.sparql	todo
Format relation missing	ERROR	docs	26	SPARQL	formatRelationMissing.sparql	todo
Redundant subclass relation	WARN	docs	15	SPARQL	redundantSubclassRelation.sparql	todo
Deprecated concept with disallowed annotations or axioms	WARN	docs	16	IPYNB	disallowedDeprecatedContent.ipynb	DONE
Concept ID numerical duplication	ERROR	docs	18	IPYNB	idNumericalDuplication.ipynb	DONE
File extension lacks synyonm	WARN	docs	19	SPARQL	fileExtensionMissingSynonym.ipynb	DONE
File extension bad characters	WARN	docs	19, 20	IPYNB	fileExtensionBadCharacter.ipynb	DONE
Misuse of Wikipedia links	WARN	docs	23	IPYNB	wikipediaMisuse.ipynb	DONE

[1] things labellled as "SPARQL" are implemented purely in SPARQL. "SHACL" is another possibility. Failing that "IPYNB" (Juypter notebook with SPARQL and Python code) or "Python" (in later two cases the links under "File" will be replaced with links to the relevant notebook or Python script).

General queries (from ROBOT report)

Query	Description	Level
annotation whitespace	link	WARN
deprecated boolean datatype	link	ERROR
deprecated class reference	link	ERROR
deprecated property reference	link	ERROR
duplicate definition	link	ERROR
duplicate exact synonym	link	WARN
duplicate label synonym	link	WARN
duplicate label	link	ERROR
duplicate scoped synonym	link	WARN
equivalent pair	link	WARN
invalid xref	link	WARN
label formatting	link	ERROR
label whitespace	link	ERROR
lowercase definition	link	INFO
missing definition	link	WARN
missing label	link	ERROR
missing obsolete label	link	WARN
missing ontology description	link	ERROR
missing ontology license	link	ERROR
missing ontology title	link	ERROR
missing superclass	link	INFO
misused obsolete label	link	ERROR
multiple definitions	link	ERROR
multiple equivalent classes	link	ERROR
multiple labels	link	ERROR

Files

File	Description
src/edamverify.py	edamverify utility
queries/	Queries in SPARQL query language and SHACL constraint language format
docs/	Query documentation (the problem detected by the query and its remedy)
reports/	Reports from running edamverify on EDAM_dev.owl
README.md	This file