Command Line Interface
pyobo automatically installs the command pyobo. See pyobo --help for usage
details.
pyobo
CLI for PyOBO.
pyobo [OPTIONS] COMMAND [ARGS]...
Options
- --version
Show the version and exit.
clean
Delete all cached files.
pyobo clean [OPTIONS]
Options
- --remove-obo
database
Build the PyOBO Database.
pyobo database [OPTIONS] COMMAND [ARGS]...
alts
Make the prefix-alt-id dump.
pyobo database alts [OPTIONS]
Options
- --zenodo
Automatically upload to zenodo
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- --directory <directory>
Build location. Defaults to /home/docs/.data/pyobo/database/<today>
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --skip-pyobo
Skip prefixes whose ontologies are implemented as PyOBO sources
- --skip-below <skip_below>
Skip prefixes lexically sorted below the given one
build
Build all databases.
pyobo database build [OPTIONS]
Options
- --zenodo
Automatically upload to zenodo
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- --directory <directory>
Build location. Defaults to /home/docs/.data/pyobo/database/<today>
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --skip-pyobo
Skip prefixes whose ontologies are implemented as PyOBO sources
- --skip-below <skip_below>
Skip prefixes lexically sorted below the given one
definitions
Make the prefix-identifier-definition dump.
pyobo database definitions [OPTIONS]
Options
- --zenodo
Automatically upload to zenodo
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- --directory <directory>
Build location. Defaults to /home/docs/.data/pyobo/database/<today>
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --skip-pyobo
Skip prefixes whose ontologies are implemented as PyOBO sources
- --skip-below <skip_below>
Skip prefixes lexically sorted below the given one
edges
Make the edges dump.
pyobo database edges [OPTIONS]
Options
- --zenodo
Automatically upload to zenodo
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- --directory <directory>
Build location. Defaults to /home/docs/.data/pyobo/database/<today>
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --skip-pyobo
Skip prefixes whose ontologies are implemented as PyOBO sources
- --skip-below <skip_below>
Skip prefixes lexically sorted below the given one
mappings
Make the SSSOM dump.
pyobo database mappings [OPTIONS]
Options
- --zenodo
Automatically upload to zenodo
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- --directory <directory>
Build location. Defaults to /home/docs/.data/pyobo/database/<today>
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --skip-pyobo
Skip prefixes whose ontologies are implemented as PyOBO sources
- --skip-below <skip_below>
Skip prefixes lexically sorted below the given one
metadata
Make the prefix-metadata dump.
pyobo database metadata [OPTIONS]
Options
- --zenodo
Automatically upload to zenodo
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- --directory <directory>
Build location. Defaults to /home/docs/.data/pyobo/database/<today>
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --skip-pyobo
Skip prefixes whose ontologies are implemented as PyOBO sources
- --skip-below <skip_below>
Skip prefixes lexically sorted below the given one
names
Make the prefix-identifier-name dump.
pyobo database names [OPTIONS]
Options
- --zenodo
Automatically upload to zenodo
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- --directory <directory>
Build location. Defaults to /home/docs/.data/pyobo/database/<today>
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --skip-pyobo
Skip prefixes whose ontologies are implemented as PyOBO sources
- --skip-below <skip_below>
Skip prefixes lexically sorted below the given one
properties
Make the properties dump.
pyobo database properties [OPTIONS]
Options
- --zenodo
Automatically upload to zenodo
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- --directory <directory>
Build location. Defaults to /home/docs/.data/pyobo/database/<today>
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --skip-pyobo
Skip prefixes whose ontologies are implemented as PyOBO sources
- --skip-below <skip_below>
Skip prefixes lexically sorted below the given one
relations
Make the relation dump.
pyobo database relations [OPTIONS]
Options
- --zenodo
Automatically upload to zenodo
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- --directory <directory>
Build location. Defaults to /home/docs/.data/pyobo/database/<today>
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --skip-pyobo
Skip prefixes whose ontologies are implemented as PyOBO sources
- --skip-below <skip_below>
Skip prefixes lexically sorted below the given one
species
Make the prefix-identifier-species dump.
pyobo database species [OPTIONS]
Options
- --zenodo
Automatically upload to zenodo
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- --directory <directory>
Build location. Defaults to /home/docs/.data/pyobo/database/<today>
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --skip-pyobo
Skip prefixes whose ontologies are implemented as PyOBO sources
- --skip-below <skip_below>
Skip prefixes lexically sorted below the given one
synonyms
Make the prefix-identifier-synonym dump.
pyobo database synonyms [OPTIONS]
Options
- --zenodo
Automatically upload to zenodo
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- --directory <directory>
Build location. Defaults to /home/docs/.data/pyobo/database/<today>
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --skip-pyobo
Skip prefixes whose ontologies are implemented as PyOBO sources
- --skip-below <skip_below>
Skip prefixes lexically sorted below the given one
typedefs
Make the typedef prefix-identifier-name dump.
pyobo database typedefs [OPTIONS]
Options
- --zenodo
Automatically upload to zenodo
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- --directory <directory>
Build location. Defaults to /home/docs/.data/pyobo/database/<today>
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --skip-pyobo
Skip prefixes whose ontologies are implemented as PyOBO sources
- --skip-below <skip_below>
Skip prefixes lexically sorted below the given one
xrefs
Make the prefix-identifier-xref dump.
pyobo database xrefs [OPTIONS]
Options
- --zenodo
Automatically upload to zenodo
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- --directory <directory>
Build location. Defaults to /home/docs/.data/pyobo/database/<today>
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --skip-pyobo
Skip prefixes whose ontologies are implemented as PyOBO sources
- --skip-below <skip_below>
Skip prefixes lexically sorted below the given one
lookup
Lookup resources.
pyobo lookup [OPTIONS] COMMAND [ARGS]...
alts
Page through alt ids in a namespace.
pyobo lookup alts [OPTIONS] PREFIX
Options
- -i, --identifier <identifier>
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --version <version>
Explicit version of the data. If not given, the most recent will be looked up.
Arguments
- PREFIX
Required argument
ancestors
Look up ancestors.
pyobo lookup ancestors [OPTIONS] IDENTIFIER PREFIX
Options
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --version <version>
Explicit version of the data. If not given, the most recent will be looked up.
Arguments
- IDENTIFIER
Required argument
- PREFIX
Required argument
definitions
Page through the identifiers and definitions of entities in the given namespace.
pyobo lookup definitions [OPTIONS] PREFIX
Options
- -i, --identifier <identifier>
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --version <version>
Explicit version of the data. If not given, the most recent will be looked up.
Arguments
- PREFIX
Required argument
descendants
Look up descendants.
pyobo lookup descendants [OPTIONS] IDENTIFIER PREFIX
Options
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --version <version>
Explicit version of the data. If not given, the most recent will be looked up.
Arguments
- IDENTIFIER
Required argument
- PREFIX
Required argument
hierarchy
Page through the hierarchy for entities in the namespace.
pyobo lookup hierarchy [OPTIONS] PREFIX
Options
- --include-part-of
- --include-has-member
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --version <version>
Explicit version of the data. If not given, the most recent will be looked up.
Arguments
- PREFIX
Required argument
ids
Page through the identifiers of entities in the given namespace.
pyobo lookup ids [OPTIONS] PREFIX
Options
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --version <version>
Explicit version of the data. If not given, the most recent will be looked up.
Arguments
- PREFIX
Required argument
mappings
Page through mappings for the given namespace.
pyobo lookup mappings [OPTIONS] PREFIX
Options
- --include-names
- -t, --target <target>
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --version <version>
Explicit version of the data. If not given, the most recent will be looked up.
Arguments
- PREFIX
Required argument
metadata
Print the metadata for the given namespace.
pyobo lookup metadata [OPTIONS] PREFIX
Options
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --version <version>
Explicit version of the data. If not given, the most recent will be looked up.
Arguments
- PREFIX
Required argument
names
Page through the identifiers and names of entities in the given namespace.
pyobo lookup names [OPTIONS] PREFIX
Options
- -i, --identifier <identifier>
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --version <version>
Explicit version of the data. If not given, the most recent will be looked up.
Arguments
- PREFIX
Required argument
prefixes
Page through prefixes appearing in an ontology.
pyobo lookup prefixes [OPTIONS] PREFIX
Options
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --version <version>
Explicit version of the data. If not given, the most recent will be looked up.
Arguments
- PREFIX
Required argument
properties
Page through the properties for entities in the given namespace.
pyobo lookup properties [OPTIONS] PREFIX
Options
- -k, --key <key>
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --version <version>
Explicit version of the data. If not given, the most recent will be looked up.
Arguments
- PREFIX
Required argument
relations
Page through the relations for entities in the given namespace.
pyobo lookup relations [OPTIONS] PREFIX
Options
- --relation <relation>
CURIE for the relationship or just the ID if local to the ontology
- --target <target>
Prefix for the target
- --summarize
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --version <version>
Explicit version of the data. If not given, the most recent will be looked up.
Arguments
- PREFIX
Required argument
species
Page through the identifiers and species of entities in the given namespace.
pyobo lookup species [OPTIONS] PREFIX
Options
- -i, --identifier <identifier>
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --version <version>
Explicit version of the data. If not given, the most recent will be looked up.
Arguments
- PREFIX
Required argument
synonyms
Page through the synonyms for entities in the given namespace.
pyobo lookup synonyms [OPTIONS] PREFIX
Options
- -i, --identifier <identifier>
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --version <version>
Explicit version of the data. If not given, the most recent will be looked up.
Arguments
- PREFIX
Required argument
typedefs
Page through the identifiers and names of typedefs in the given namespace.
pyobo lookup typedefs [OPTIONS] PREFIX
Options
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --version <version>
Explicit version of the data. If not given, the most recent will be looked up.
Arguments
- PREFIX
Required argument
xrefs
Page through xrefs for the given namespace to the second given namespace.
pyobo lookup xrefs [OPTIONS] PREFIX
Options
- -t, --target <target>
- -v, --verbose
Enable verbose mode. More -v’s means more verbose.
- -f, --force
Force re-downloading and re-processing
- --force-process
Force re-processing, but not necessarily re-downloading
- --strict, --no-strict
Turn on or off failure on unparsable CURIEs
- Default:
False
- --version <version>
Explicit version of the data. If not given, the most recent will be looked up.
Arguments
- PREFIX
Required argument
ls
List how big all of the OBO files are.
pyobo ls [OPTIONS]