Every class of error <code> is defined in the error-codes.properties as follows:
| Code | Category | Common Message | Details (template) |
|---|---|---|---|
| ambiguous.feature | information | Since the PhysicalEntity (being a component of a complex) does not have bindingFeature defined, it is not clear how it participates in the conversion (as a component of a complex or separately?) | {0} |
| cardinality.violated | specification | Cardinality violation | property: {0} requires exactly {1} value(s) |
| cloned.utility.class | recommendation | Two or more BioPAX objects are equivalent. Equivalence is based on their key BioPAX properties. Key properties for these two objects are either empty or exactly match to each other | equivalent elements: {0} (utility class: {1}) |
| complex.incomplete | specification | Complex has no components, or the one without properly defined stoichiometry | {0} |
| complex.stoichiometry.notcomponent | specification | The value (Stoichiometry) of the componentStoichiometry property refers to a physical entity that is not among the components of the complex | stoichiometry: {0}, phys.entity: {1}, whereas component: {2} |
| component.different.location | information | Complex components span multiple cellular locations. This is only valid for complexes that span multiple connected compartments, e.g cytosol and cytoplasmic membrane. Please check if this is the case | complex location: {0}, component(s): {1} |
| component.no.location | information | A component does not have any cellular location specified, whereas the complex does. | complex location: {0}, component(s): {1} |
| component.not.found | information | PathwayStep has a step process that is not a component of the same pathway. This means that pathway steps connect more than one different pathways, which could make pathways harder to work with | this pathway: {1}, step process: {0} |
| cyclic.inclusion | information | An object contains itself (either directly or indirectly). This might be biologically valid, but graph traversal algorithms must be aware of this | property: {0} |
| db.name.spelling | recommendation | The 'db' property value uses a variant name of the database | db: {0}, recommended name: {1} |
| denied.xref | recommendation | Database value of the UnificationXref (of a BioPAX element) does not apply (prohibited) for this type of element | element: {1}, xref.db: {0} (unification xrefs of: {2} cannot use: {3}) |
| diff.kind.same.name | information | Different physical entities of the same class but with different entityReference value have the same name. This may indicate that the wrong entity reference is linked to the physical entity. (All duplicates up to a limit are listed below) | physical entities: {0} |
| direction.conflict | recommendation | An illegal value or a conflict between related "direction" properties | {0} |
| duplicate.id.ignoringcase | recommendation | Several BioPAX elements have "almost the same ID", i.e., when they're compared ignoring case. This may cause trouble for software systems that ignore case (e.g. primary keys in MySQL) | ID equals ignoring case to: {0} |
| duplicate.names | recommendation | The same name is repeated multiple times. There is no need to duplicate information in the name properties | name: {0} |
| empty.biopax.model | information | No objects were recognized in the input document. This might be due to syntax errors in the OWL/XML header, such as namespace declarations, or could represent a syntactically valid, but empty file | level: {0} |
| empty.participants.intersection | information | This (next) step has no participants that were used in the previous step. This could indicate an error, or simply a valid pathway 'hole' | previous step: {0} |
| illegal.conversion | information | A bio-polymer (i.e., not a complex or small molecule) is either missing or "becomes" another type on the other side of the same Conversion interaction (except for Degradation and ComplexAssembly) | conversion: {0} |
| illegal.cv.term | specification | Term is not found in the recommended controlled vocabulary (- wrong name/spelling or the identifier/accession is used instead of the term) | Illegal term(s): {0}; {1} |
| illegal.cv.xref | specification | Unification xref cannot be resolved to a recommended term for the controlled vocabulary | Illegal xref(s): {0}; info: {1} |
| illegal.property.value | recommendation | Data property value might be wrong | property: {0}, value: {1} |
| improper.feature.use | specification | The EntityFeature is associated with the PhysicalEntity but not with its EntityReference | {0} is not a feature of Entity Reference {1} |
| invalid.id.format | recommendation | Xref 'id' value does not match the standard pattern for this type of db identifier. If this is due to the version of the object is embedded into the id, please use the idVersion property instead. If the database was not properly recognized (and the pattern is wrong), consider using standard name. | db: {0} (recognized as: {1}), id: {2}, pattern: {3} |
| invalid.rdf.id | syntax | Error in the BioPAX element ID, which must be a valid URI, i.e., only certain characters and a specific format are allowed | problem: {0} |
| inverse.functional.violated | specification | Different objects have the same value for the inverse functional property | {1} is a value of the inverse functional property {0}, but it is also {0} of {2} |
| max.cardinality.violated | specification | Maximal cardinality violation | property: {0} requires {1} value(s) at most |
| min.cardinality.violated | specification | Minimal cardinality violation | property: {0} requires at least {1} value(s). |
| multi.organism.pathway | recommendation | Different organism references are found in a pathway and/or its members (excl. evidence). Is this indeed a multi-organism pathway? | BioSources (unification xref IDs): {0} (names: {1}) |
| multiple.location | information | Participants span multiple cellular locations. This may be an error e.g. if the cellular locations do not connect to each other. Check that this information makes sense | participants: {0}, {1} |
| no.xref.cv.terms | recommendation | Controlled vocabulary(-ies) without unification xrefs for some of the (valid) terms | terms: {0}; info: {1} |
| not.allowed.element | specification | Direct instances of this class should not be used. A more specific class should be used instead | class: {0} |
| not.allowed.xref | recommendation | Database name in the UnificationXref (of a BioPAX element), probably, does not make sense for this type of element | element: {1}, xref.db: {0} (unification xrefs of: {2} are limited to: {3}) |
| not.specific.element | recommendation | Use of a more specific type (subclass) is recommended | class: {0} |
| null.entity.reference | recommendation | A Protein, SmallMolecule, etc. (but not a complex) has neither 'entityReference' (highly recommended) nor 'memberPhysicalEntity' values set | entityReference (range: {0}) is null, and memberPhysicalEntity is empty |
| participant.location.changed | recommendation | Physical entity changes its cellular location (either it is different on the left and right sides of the reaction or not specified on one side). Consider using a TransportWithBiochemicalReaction instead | left: {0}, right: {1} |
| range.violated | specification | BioPAX property range violation (illegal value type) | property: {0}, value: {1}; {2} is not {3} |
| same.state.entity | recommendation | Two physical entities of this reference type have exactly the same entityFeatures and cellular location. Consider merging them as they are in the same state. If they are not equivalent but the actual features that differentiate them is not known, consider defining a tagger entityFeature such as 'active' | entity: {0} is equivalent to: {1} |
| same.state.participant | recommendation | One of the participants of a conversion did not change as a result of the conversion. If this participant is a catalyst, consider defining it as a controller using a Control class or one of its subclasses. If the actual features that has changed is not known, consider defining a tagger entityFeature such as 'active' | left: {0}, right: {1} |
| shared.unification.xref | recommendation | Two or more elements share the same unification xref. Please note that defining a UnificationXref to an external resource implies that this object and external resource are identical. Therefore, elements that share the same unification xref must also be identical. Please consider merging these elements if they are identical, otherwise please consider converting this external reference to a RelationshipXref | is the xref of: {0} |
| stoichiometry.mismatch | information | The stoichiometries of the left and the right participants do not match | Left stoichiometry: {0}, right stoichiomtry: {1} |
| symmetric.violated | specification | 'Symmetric' constraint violated. The entity's property has an object value that does not refer back to this entity | this entity has {1} as its {0} but {1} does not have this entity as its {0} |
| syntax.error | syntax | Syntax error. This is usually caused by XML/RDF/OWL syntax problems found while reading the input BioPAX document | {0} |
| too.long.display.name | recommendation | 'displayName' exceeds the recommended maximum. These names should be kept short so they can easily be displayed, e.g., in a pathway diagram | {0}, length={1} exceeds {2} |
| too.long.id | information | Too long IDs (URIs) are allowed but not desirable, for it may cause various performance issues and errors in software that consumes BioPAX data. Also, if we look beyond a trivial data exchange use case, it is generally more difficult for a pathway data provider to support such verbose URIs, to keep it consistent from one release to another (note: ideally, a URI would be possible to resolve to a URL, with some data or summary - on that page) | length={0} (exceeds {1}) |
| transport.location.same | specification | Participant cannot be in the same cellular location on the left and right sides of a Transport interaction | left: {0}, right: {1} |
| unknown.class | specification | Unknown (or prohibited) class, not defined in the BioPAX specification (or only its subclasses are allowed) | could not add element: {0} |
| unknown.db | recommendation | Unknown database identifier. For Xref 'db' property and Provenance standard/display name properties, please use the official database name/prefix or synonym. MI "database citation" and child terms are also allowed but deprecated. Please use Bioregistry. | db name: {0} |
| unknown.property | specification | Unknown property (not defined in the BioPAX specification) | could not set property: {0} |
| wrong.conversion.class | information | There is no modification to the reaction participants, and a complex seems to be formed | conversion class: {0} |