RDFProjector
Synopsis
Projects OBO terms and synonyms on sections.
Description
RDFProjector reads source SKOS terminologies or OWL ontologies and searches for class and concept labels in sections.
The parameters allowJoined , allUpperCaseInsensitive , caseInsensitive , ignoreDiacritics , joinDash , matchStartCaseInsensitive , skipConsecutiveWhitespaces , skipWhitespace and wordStartCaseInsensitive control the matching between the section and the entry keys.
The subject parameter specifies which text of the section should be matched. There are two options:
- the entries are matched on the contents of the section, subject can also control if matches boundaries coincide with word delimiters;
- the entries are matched on the feature value of annotations of a given layer separated by a whitespace, in this way entries can be searched against word lemmas for instance.
RDFProjector creates an annotation for each matched entry and adds these annotations to the layer named targetLayer . The created annotations will have the feature uriFeature containing the URI of the matched class or concept. RDFProjector may also map property object values into features specified by labelFeatures .
Snippet
<rdfprojector class="RDFProjector">
<source></source>
<targetLayer></targetLayer>
<uriFeature></uriFeature>
</rdfprojector>
Mandatory parameters
source
Path to the source SKOS/OWL files.
targetLayer
Name of the layer that contains the match annotations.
uriFeature
Feature where to store the entry URI.
Optional parameters
constantAnnotationFeatures
Constant features to add to each annotation created by this module.
language
Specify the language of labels to project. If this parameter is not set then labels of any language are projected. Labels without a language qualifier are always projected regardless of the value of this parameter.
matchedLabelFeature
Feature where to store the matched label.
matchedLanguageFeature
UNDOCUMENTED
matchedPropertyFeature
Feature where to store the URI of the property of the matched label.
trieSink
If set, then RDFProjector writes the compiled dictionary to the specified file.
trieSource
If set, read the compiled dictionary from the specified file. Compiled dictionaries are usually faster for large dictionaries.
allUpperCaseInsensitive
If set to true , then allow case folding on all characters in words that are all upper case.
allowJoined
If set to true , then allow arbitrary suppression of whitespace characters in the subject. For instance, the contents aminoacid matches the key amino acid .
caseInsensitive
If set to true , then allows case folding on all characters.
documentFilter
Only process document that satisfy this expression.
ignoreDiacritics
If set to true , then allow dicacritic removal on all characters. For instance the contents acide amine matches the key acide aminé .
joinDash
If set to true , then treat dash characters (-) as whitespace characters with regard to allowJoined . For instance, the contents aminoacid matches the entry amino-acid .
labelFeatures
Mapping from feature names to property URIs. This parameter indicates the properties of the entry to record in features.
labelURIs
RDF properties whose object values that represent entry keys.
matchStartCaseInsensitive
If set to true , then allow case folding on the first character of the entry key.
multipleEntryBehaviour
Specifies the behavior if the lexicon contains several entries with the same key.
prefixes
Specify URI prefixes to be used in resourceTypeURIs , labelURIs , and labelFeatures
rdfFormat
Specify the RDF serialization format (xml, rdfxml, xmlrdf, turtle, ttl, n3, ntriples, ntriple, nt, jsonld, rdfjson, jsonrdf, json, trig, nquads, nq, nthrift, csv, tsv, trix).
resourceTypeURIs
Type of RDF resources that represent an entry.
sectionFilter
Process only sections that satisfy this expression.
skipConsecutiveWhitespaces
If set to true , then allow the insertion of consecutive whitespace characters in the subject. For instance, the contents amino acid matches the entry amino acid .
skipWhitespace
If set to true , then allow arbitrary insertion of whitespace characters in the subject. For instance, the contents amino acid matches the key aminoacid .
subject
Specifies the contents to match.
substituteWhitespace
If set to true , then all whitespace characters match each other (including ‘\n’, ‘\r’, ‘\t’, and non-breaking spaces).
wordStartCaseInsensitive
If set to true , then allow case folding on the first character of each word.
Deprecated parameters
targetLayerName
Deprecated alias for targetLayer .
uriFeatureName
Deprecated alias for uriFeature .