project.conf

#
# The settings in this file configure the ontology build process.  The only
# setting that is absolutely required to build an ontology is "ontology_file"
# in the "Ontology" section.  However, most ontology projects will eventually
# need to customize the settings "dev_base_IRI" and "release_base_IRI", in the
# "IRIs" section, and "entity_sourcefiles", in the "Ontology" section.
#


[IRIs]
#--------
# Settings for customizing IRI management.
#
# IMPORTANT: Virtually all projects will eventually need to customize the
# "dev_base_IRI" and "release_base_IRI" settings in this section.  However,
# none of these are required to get started with a new ontology project.
#--------

# The base IRI for compiled, non-released ontology documents and imports
# modules.  This can be either an IRI pointing to a folder on the local
# filesystem, or an IRI pointing to a folder at a remote location (e.g., a
# remote git repository).  Unless you are using an unusual project layout, this
# folder should correspond with the main project folder.  The value of this
# setting will be used to form the complete IRIs for generated ontology files
# and imports modules.  For example, if dev_base_iri is
# "http://dev.location/for/project/", then a compiled ontology file would have
# an IRI like "http://dev.location/for/project/ontology/demo-merged.owl".  If
# this setting is undefined, then a suitable base IRI will be generated from
# the project path in the local file system.
dev_base_IRI = 

# The base IRI for released versions of the ontology documents and imports
# modules.  As with dev_base_IRI, the release base IRI should usually point to
# a location that corresponds with the main project folder.  The value of this
# setting is used in the same manner as dev_base_IRI.  So, for example, if
# release_base_iri is "http://release.location/for/project/", then a compiled
# ontology file would have an IRI like
# "http://release.location/for/project/demo-merged.owl", and it would have a
# version IRI like
# "http://release.location/for/project/releases/YYYY-MM-DD/demo-merged.owl".
# If this setting is undefined, then the value of dev_base_IRI will be used.
release_base_IRI =

# The IRI of released versions of the main ontology document, if it needs to be
# different from that specified by release_base_IRI.  If this setting is
# undefined, the value of release_base_IRI will be used to generate a suitable
# IRI.
release_ontology_IRI =


[Ontology]
#--------
# Settings for customizing ontology compilation.  Note that relative file paths
# will be interpreted relative to the location of this configuration file.
#
# IMPORTANT: Virtually all projects will eventually need to customize the
# "ontology_file" and "entity_sourcefiles" settings in this section.  However,
# "ontology_file" is the only setting that is absolutely required to build an
# ontology.
#--------

# The local location and base name of the compiled ontology OWL file
# (REQUIRED).  This file name will be modified depending on the features of the
# compiled ontology file, and it will also be used for released ontology files.
# For example, if ontology_file is "ontology/demo.owl", compiled ontology files
# will have names like "ontology/demo-raw.owl", "ontology/demo-merged.owl",
# etc.  Can be either a relative or an absolute path.  Either way, it must be
# located inside of the main project folder (as determined by the location of
# the project configuration file).
ontology_file = ontology/blato

# Ontology entity source files.  These are the names of the entity source files
# that should be compiled into the final ontology, specified as a
# comma-separated list. Shell-style wildcards are supported.  As long as your
# project follows the suggested folder structure, you only need to provide the
# names of the files here, not full filesystem paths.  If your source files are
# in a non-standard location, you can set the value of the variable
# "entity_sourcedir", below, to specify the folder in which the source files
# are located.
#
# Example: entity_sourcefiles = ont_main_classes.ods, ont_extra_classes.ods,
#                               ont_properties.xlsx
# Example: entity_sourcefiles = *_classes.ods, ont_properties.xlsx
#
entity_sourcefiles = blato_*.csv, blato_*.ods, blato_*.xls, blato_*.xlsx


#--------
# NOTE: You should not need to modify anything else in the rest of this
# configuration file unless you have a non-standard source structure (e.g., you
# are not following the suggested directory structure), or you want to modify
# the build process (e.g., change from in-source to out-of-source builds or
# customize reasoner parameters).
#--------

# The location and name of the base ontology file.  By default, the location
# will be inferred from the path to the project configuration file and the file
# name will be generated from the ontology file name.  For example, if the
# ontology file name is "ppo.owl", the base ontology file will be called
# "ppo-base.owl".  If you have a non-standard project folder structure or
# source naming conventions, you might need to customize the value of this
# variable.  Can be either a relative or an absolute path.
#
# Example: base_ontology_file = src/ontology-base.owl
#
base_ontology_file = 

# The location of the ontology entities/terms source files.  Be default, the
# location will be inferred from the location of this configuration file.  Can
# be either a relative or an absolute path.
#
# Example: enitity_sourcedir = src/entities
#
entity_sourcedir = src/entities/


[Reasoning]
#--------
# Settings for customizing the process of running a reasoner to add inferred
# axioms to the compiled ontology.
#--------

# The reasoner to use when generating inferred ontology axioms.  Currently,
# "ELK", "HermiT", "Pellet", and "JFact" are the supported options.  If no
# reasoner is specified, HermiT will be used by default.  This setting is not
# case sensitive (e.g., either "HermiT" or "hermit" is fine.)
reasoner = HermiT

# The kinds of inferred axioms to generate when running a reasoner on an
# ontology.  This should be a comma-separated list of one or more of the
# following values:
#
#   "subclasses" (infer the class hierarchy)
#   "subdata properties" (infer the data property hierarchy)
#   "subobject properties" (infer the object property hierarchy)
#   "types" (infer individual types / class assertions)
#   "equivalent classes" (infer class equivalency axioms)
#   "disjoint classes" (infer class disjointness axioms)
#   "inverse object properties" (infer object property inverse relationships)
#   "property values" (infer property assertions for individuals)
#
# If no inference types are specified, the default is
# "subclasses, equivalent classes, types, subdata properties, subobject properties".
#
# This setting is not case sensitive (e.g., either "types" or "Types" is fine).
inferences = subclasses, equivalent classes, types, subdata properties,
             subobject properties

# If True, inferred axioms will be annotated as such when they are added to the
# compiled ontology.  If False or undefined, inferred axioms will not receive
# any annotations to indicate that they were inferred.
annotate_inferred = False

# Specifies the location of a file specifying classes to exclude from inferred
# class assertion axioms.  Inferred type assertions for individuals will
# typically include large numbers of assertions for high-level ontology
# classes, and these assertions are often neither very interesting nor very
# useful.  For large data sets, removing these assertions can save considerable
# space.  This setting should point to a file that contains a table with three
# columns: "ID", "Exclude class", and "Exclude superclasses".
excluded_types_file =

# If True, inverse object property assertion axioms and inverse negative object
# property assertion axioms will be directly materialized *prior* to running
# the reasoner, including assertions about symmetric properties.  This is
# useful for cases in which a reasoner that does not support inverses (such as
# ELK) must be used (e.g., for runtime considerations) on an ontology with
# inverse property axioms.  With this pre-reasoning step, many inferences that
# depend on inverse property pairs will still be correctly recovered even with
# a reasoner that does not support inverse properties.  However, it is very
# important to note that whether *all* inferences are recovered depends on the
# structure of the source ontology.  For example, inverse object property
# assertions will only be generated for object property assertions that are
# explicitly stated in the ontology; not for object property assertions that
# are implicit.  The default is False.
preprocess_inverses = False


[Build]
#--------
# Settings for customizing the build process for both import modules and the
# main ontology.  Note that relative file paths will be interpreted relative to
# the location of this configuration file.
#--------

# If True, the build system will do in-source builds, which means that all
# compiled files will be written directly to their final locations in the
# project.  If False or undefined, then all compiled files will be written to a
# separate build directory and will then need to be moved to their final
# locations by hand.
insource_builds = True

# The location of the build directory.  All output files will be written to
# this directory.  If the directory does not exist, it will be created as part
# of the initial build process.  By default, the build directory will be called
# "build" and will be located in the same place as this configuration file.
# Can be either a relative or an absolute path.
builddir = build/

# Whether to modify ontology entity text definition strings by adding the IDs
# of term labels referenced in the definitions.  The default is True.
expand_entity_defs = True

# The format in which to write output ontology files.  Supported values are
# "RDF/XML", "Turtle", "OWL/XML", and "Manchester" (values are not
# case-sensitive).  If undefined, the default value is "RDF/XML".
output_format = RDF/XML


[Imports]
#--------
# Settings for customizing the import module build process.  Note that relative
# file paths will be interpreted relative to the location of this configuration
# file.
#--------

# The location of the source files for the import modules.  By default, this
# will be inferred from the location of this configuration file, but you can
# customize it here if your project does not follow the standard folder
# structure.  Can be either a relative or an absolute path.
#
# Example: imports_src = src/imports
#
imports_src = src/imports/

# The location of the compiled import modules.  By default, this will be
# "imports/".  The default should be fine for most projects, but you can
# customize the location here if your project does not follow the standard
# folder structure.  Can be either a relative or an absolute path.  Either way,
# it must be located inside of the main project folder (as determined by the
# location of the project configuration file).
#
# Example: imports_dir = imports/
#
imports_dir = imports/

# The location and name of the top-level imports source file.  This is the file
# that lists the ontologies from which terms should be imported.  By default,
# the first file in the imports source folder that matches the pattern
# "imported_ontologies.*" will be used.  If no matching file is found,
# "imported_ontologies.csv" will be used.  Can be either a relative or an
# absolute path.
#
# Example: top_importsfile = src/imports/imported_ontologies.csv
#
top_importsfile = 

# The suffix to use for naming the import module OWL files.  By default, this
# will be generated from the name of the main ontology file.  For example, if
# the ontology file is "ppo.owl", the import module files will be named
# "*_ppo_import_module.owl".
import_mod_suffix = 

# If True, entities that are merged into the main ontology from an external
# ontology will be annotated with the 'imported from' (IAO:0000412) annotation
# property to indicate their origin.  This setting is True by default.
annotate_merged = True


[Documentation]
#--------
# Settings for customizing the documentation build process.  Note that relative
# file paths will be interpreted relative to the location of this configuration
# file.
#--------

# The location and name of a documentation specification file.  This file
# defines which ontology entities to include in the documentation and how they
# should be organized.  See the example specification file and online OntoPilot
# documentation for more information about the specification file format.  The
# default value for this setting is "src/doc_specification.txt".
doc_specification = src/doc_specification.txt

# The location and name to use for user documentation files.  By default, the
# location will be inferred from the path to the project configuration file and
# the documentation file names will be generated from the ontology file name.
# For example, if the ontology file name is "ppo.owl", the default value of
# this setting would be "documentation/ppo".  Then, HTML documentation, for
# instance, would be written to the file "documentation/ppo.html".  If you have
# a non-standard project folder structure or source naming conventions, you
# might need to customize the value of this variable.  Can be either a relative
# or an absolute path.
#
# Example: docs_file_path = documentation/ontology-docs
#
docs_file_path = 

# A comma-separated list of one or more output formats to use when generating
# ontology documentation.  Currently, the only supported formats are "HTML" and
# "Markdown".  If no format is specified, the default is "HTML".  This setting
# is not case sensitive (e.g., either "HTML" or "html" is fine).
doc_formats = HTML