Scripts, data files and ontologies for the FLOPO project
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flora-central-africa
flora-gabon
flora-malesiana
floras-other
floras-small
floras
glossary
models
ont
ontology
tbl
AddLabelToAnnotations.groovy
DeprecateDumbClasses.groovy
EntityQuality.groovy
EntityQuality.groovy~
ExtractLabels.groovy
FindEnrichedCategoriesInFuncOutput.groovy
GenFeaturesFromCooccurrences.groovy
GenFeaturesFromCooccurrencesFrench.groovy
GenerateLuceneIndex.groovy
GenerateLuceneIndexEnglish.groovy
GenerateLuceneIndexEnglishSolana.groovy
GenerateLuceneIndexFrench.groovy
GenerateOntologyIndex.groovy
LICENSE
LICENSE-ontology.txt
MakeFuncInput.groovy
MakeMakeNexusFileInput.groovy
MakeNexusFile.groovy
MakePlantPhenotypeOntology.groovy
ParseFloraFile.groovy
ParseFloraFile.groovy~
QueryLuceneIndex.groovy
QueryLuceneIndexEnglish.groovy
QueryLuceneIndexEnglishSolana.groovy
QueryLuceneIndexFrench.groovy
README.md
SpeciesID.groovy
en-sent.bin
en-token.bin
eq.txt
fdac.backup
flopo-classified.owl
flopo-unclassified.owl
missing-entities.txt
missing-parts-generated-from-glossary.txt
missing-qualities-from-glossary.txt
missing-qualities.txt
missing-types.txt
neotropikeycharacters.xls
plantphenotype.owl

README.md

Project to identify phenotypes occurring in flora files.

There are three components:

  1. ParseFloraFile is the original piece of code generated at the pro-iBiosphere Hackathon in Leiden. It will find PO and PATO terms in flora gabon and malaysia.
  2. Lucene-based indexing: this is a refactoring of the original code that uses the Lucence indexes and analyzers.
  3. MakePlantPhenotypeOntology generates a phenotype ontology from the generated descriptions.
  4. DeprecateDumbClasses deprecates all unsatisfiable classes; this script needs to be run after adding axioms (e.g., a GCI) that makes classes that could not exist in FLOPO unsatisfiable. Useful when adding has-part some (owl:Thing and has-quality some 'process quality') SubClassOf: owl:Nothing or similar axioms.

The resulting ontology is available under a CC-0 license in the ontology folder. All code is available under the BSD license.