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validation/ValidationConfiguration.md | 25 +- validation/ValidationReport.md | 22 +- validation/ValidationResult.md | 55 +- validation/ValidationResultType.md | 2 + validation/category.md | 12 + validation/confidence.md | 12 + validation/definition.md | 12 + validation/definition_source.md | 12 + validation/documentation_objects.md | 14 +- validation/dry_run.md | 12 + validation/http_response_code.md | 12 + validation/id.md | 12 + validation/info.md | 18 +- validation/instantiates.md | 15 +- validation/lookup_references.md | 12 + validation/max_number_results_per_type.md | 12 + validation/modified.md | 12 + validation/number_of_attempts.md | 12 + validation/object.md | 14 +- validation/object_id.md | 12 + validation/object_info.md | 12 + validation/object_str.md | 14 +- validation/predicate.md | 15 +- validation/predicate_id.md | 12 + validation/problem.md | 12 + validation/prompt_info.md | 12 + validation/proposed_new_definition.md | 12 + validation/repairs.md | 12 + validation/results.md | 16 +- validation/schema_path.md | 12 + validation/severity.md | 16 +- validation/source.md | 14 +- validation/subject.md | 14 +- validation/subject_id.md | 12 + validation/subject_info.md | 12 + validation/successful.md | 12 + validation/suggested_modifications.md | 12 + validation/suggested_predicate.md | 12 + validation/time_checked.md | 12 + validation/type.md | 16 +- validation/type_severity_map.md | 14 +- validation/url.md | 12 + validation/validation_configuration.md | 12 + 3330 files changed, 80192 insertions(+), 11350 deletions(-) create mode 100644 _modules/oaklib/converters/data_model_converter.html create mode 100644 _modules/oaklib/converters/obo_graph_to_cx_converter.html create mode 100644 _modules/oaklib/converters/obo_graph_to_fhir_converter.html create mode 100644 _modules/oaklib/converters/obo_graph_to_obo_format_converter.html create mode 100644 _modules/oaklib/implementations/funowl/funowl_implementation.html create mode 100644 _modules/oaklib/implementations/gilda.html create mode 100644 _modules/oaklib/implementations/obograph/obograph_implementation.html create mode 100644 _modules/oaklib/implementations/ols/ols_implementation.html create mode 100644 _modules/oaklib/implementations/ontobee/ontobee_implementation.html create mode 100644 _modules/oaklib/implementations/owlery/owlery_implementation.html create mode 100644 _modules/oaklib/implementations/pantherdb/pantherdb_implementation.html create mode 100644 _modules/oaklib/implementations/pronto/pronto_implementation.html create mode 100644 _modules/oaklib/implementations/simpleobo/simple_obo_implementation.html create mode 100644 _modules/oaklib/implementations/sparql/sparql_implementation.html create mode 100644 _modules/oaklib/implementations/sqldb/sql_implementation.html create mode 100644 _modules/oaklib/implementations/ubergraph/ubergraph_implementation.html create mode 100644 _modules/oaklib/interfaces/class_enrichment_calculation_interface.html create mode 100644 _modules/oaklib/interfaces/dumper_interface.html create mode 100644 _modules/oaklib/selector.html create mode 100644 _sources/datamodels/association/proportion_entity1_subjects_in_entity2.md.txt create mode 100644 _sources/datamodels/association/proportion_entity2_subjects_in_entity1.md.txt create mode 100644 _sources/packages/src/oaklib.utilities.table_filler.rst.txt create mode 100644 association/proportion_entity1_subjects_in_entity2.md create mode 100644 association/proportion_entity2_subjects_in_entity1.md create mode 100644 datamodels/association/proportion_entity1_subjects_in_entity2.html create mode 100644 datamodels/association/proportion_entity2_subjects_in_entity1.html create mode 100644 packages/src/oaklib.utilities.table_filler.html diff --git a/_modules/index.html b/_modules/index.html index bc40ecef6..e1ed93e6b 100644 --- a/_modules/index.html +++ b/_modules/index.html @@ -14,7 +14,7 @@ - + @@ -82,12 +82,30 @@

All modules for which code is available

- -
  • Commands
    • +
  • Cache Control +
    • +
  • Commands +
  • Datamodels
    • @@ -119,9 +204,9 @@

    General Guidelines
    alias uberon='runoak -i obo:sqlite:uberon'
-alias cl='runoak -i obo:sqlite:cl'
-alias obi='runoak -i obo:sqlite:obi'
+
    alias uberon='runoak -i sqlite:obo:uberon'
+alias cl='runoak -i sqlite:obo:cl'
+alias obi='runoak -i sqlite:obo:obi'
 
    
 
    
 
    You can specify further implementations with -a which will create an aggregator implementation that wraps
@@ -171,6 +256,93 @@ 
    Predicates
+
    Cache Control
    
+
    OAK may download data from remote sources as part of its normal operations. For
+example, using the sqlite:obo:... input selector will cause OAK to
+fetch the requested Semantic-SQL database from a centralised repository.
+Whenever that happens, the downloaded data will be cached in a local directory
+so that subsequent commands using the same input selector do not have to
+download the file again.
    
+
    By default, OAK will refresh (download again) a previously downloaded file if
+it was last downloaded more than 7 days ago.
    
+
    The behavior of the cache can be controlled in two ways: with an option on the
+command line and with a configuration file.
    
+
    
+
    Controlling the cache on the command line
    
+
    The global option --caching gives the user some control on how the
+cache works.
    
+
    To change the default cache expiry lifetime of 7 days, the --caching
+option accepts a value of the form ND, where N is a positive integer
+and D can be either s, d, w, m, or y
+to indicate that N is a number of seconds, days, weeks, months, or years,
+respectively. If the D part is omitted, it defaults to d.
    
+
    For example, --caching=3w instructs OAK to refresh a cached file if it
+was last refreshed 21 days ago.
    
+
    The --caching option also accepts the following special values:
    
+
      
+
    • refresh to force OAK to always refresh a file regardless of its age;
      • 
+
    • no-refresh to do the opposite, that is, preventing OAK from
+refreshing a file regardless of its age;
      • 
+
    • clear to forcefully clear the cache (which will trigger a refresh as
+a consequence);
      • 
+
    • reset is a synonym of clear.
      • 
+
    
+
    Note the difference between refresh and clear. The former will
+only cause the requested file to be refreshed, leaving any other file that may
+exist in the cache untouched. The latter will delete all cached files, so that
+not only the requested file will be downloaded again, but any other
+previously cached file will also have to be downloaded again the next time they
+are requested.
    
+
    In both case, refreshing and clearing will only happen if the OAK command in
+which the --caching option is used attempts to look up a cached file.
+Otherwise the option will have no effect.
    
+
    To forcefully clear the cache independently of any command, the
+cache-clear command may be used. The contents of the cache may be
+explored at any time with the cache-ls command.
    
+
    
+
    
+
    Controlling the cache with a configuration file
    
+
    Finer control of how the cache works is possible through a configuration file
+that OAK will look up for at the following locations:
    
+
      
+
    • under GNU/Linux: in $XDG_CONFIG_HOME/ontology-access-kit/cache.conf;
      • 
+
    • under macOS: in $HOME/Library/Application Support/ontology-access-kit/cache.conf;
      • 
+
    • under Windows: in %LOCALAPPDATA%\ontology-access-kit\ontology-access-kit\cache.conf.
      • 
+
    
+
    The file should contain lines of the form pattern = policy, where:
    
+
      
+
    • pattern is a shell-type globbing pattern indicating the files that will be
+concerned by the policy set forth on the line;
      • 
+
    • policy is the same type of value as expected by the --caching
+option as explained in the previous section.
      • 
+
    
+
    Blank lines and lines starting with # are ignored.
    
+
    If the pattern is default (or *), the corresponding policy
+will be used for any cached file that does not have a matching policy.
    
+
    Here is a sample configuration file:
    
+
    # Uberon will be refreshed if older than 1 month
+uberon.db = 1m
+# FBbt will be refreshed if older than 2 weeks
+fbbt.db = 2w
+# Other FlyBase ontologies will be refreshed if older than 2 months
+fb*.db = 2m
+# All other files will be refreshed if older than 3 weeks
+default = 3w
+
    
+
    
+
    Note that when looking up the policy to apply to a given file, patterns are
+tried in the order they appear in the file. This is why the fbbt.db
+pattern in the example above must be listed before the less specific
+fb*.db pattern, otherwise it would be ignored. (This does not apply to
+the default pattern – whether it is specified as default or as
+* – which is always tried after all the other patterns.)
    
+
    The --caching option described in the previous section always takes
+precedence over the configuration file. That is, all rules set forth in the
+configuration will be ignored if the --caching option is specified on
+the command line.
    
+
    
+
 
    
 
    Commands
    
 
    The following section is autogenerated from the inline docs.
@@ -182,6 +354,6092 @@ 
    Commands
 
    runoak viz --help
 
    
 
    
+
    
+
    runoak
    
+
    Run the oaklib Command Line.
    
+
    A subcommand must be passed - for example: ancestors, terms, …
    
+
    Most commands require an input ontology to be specified:
    
+
    
+
    runoak -i <INPUT SPECIFICATION> SUBCOMMAND <SUBCOMMAND OPTIONS AND ARGUMENTS>
    
+
    
+
    Get help on any command, e.g:
    
+
    
+
    runoak viz -h
    
+
    
+
    runoak [OPTIONS] COMMAND [ARGS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-v, --verbose
    
+
    
+
+
    
+
    
+-q, --quiet, --no-quiet
    
+
    
+
+
    
+
    
+--stacktrace, --no-stacktrace
    
+
    If set then show full stacktrace on error
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--save-as <save_as>
    
+
    For commands that mutate the ontology, this specifies where changes are saved to
    
+
    
+
+
    
+
    
+--autosave, --no-autosave
    
+
    For commands that mutate the ontology, this determines if these are automatically saved in place
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--named-prefix-map <named_prefix_map>
    
+
    the name of a prefix map, e.g. obo, prefixcc
    
+
    
+
+
    
+
    
+--prefix <prefix>
    
+
    prefix=expansion pair
    
+
    
+
+
    
+
    
+--metamodel-mappings <metamodel_mappings>
    
+
    overrides for metamodel properties such as rdfs:label
    
+
    
+
+
    
+
    
+--import-depth <import_depth>
    
+
    Maximum depth in the import tree to traverse. Currently this is only used by the pronto adapter
    
+
    
+
+
    
+
    
+-g, --associations <associations>
    
+
    Location of ontology associations
    
+
    
+
+
    
+
    
+-G, --associations-type <associations_type>
    
+
    Syntax of associations input
    
+
    
+
+
    
+
    
+-l, --preferred-language <preferred_language>
    
+
    Preferred language for labels and lexical elements
    
+
    
+
+
    
+
    
+--other-languages <other_languages>
    
+
    Additional languages for labels and lexical elements
    
+
    
+
+
    
+
    
+--requests-cache-db <requests_cache_db>
    
+
    If specified, all http requests will be cached to this sqlite file
    
+
    
+
+
    
+
    
+-W, --wrap-adapter <wrap_adapter>
    
+
    Wrap the input adapter using another adapter (e.g. llm or semsimian).
    
+
    
+
+
    
+
    
+-i, --input <input>
    
+
    input implementation specification. This is either a path to a file, or an ontology selector
    
+
    
+
+
    
+
    
+-I, --input-type <input_type>
    
+
    Input format. Permissible values vary depending on the context
    
+
    
+
+
    
+
    
+-a, --add <add>
    
+
    additional implementation specification.
    
+
    
+
+
    
+
    
+--merge, --no-merge
    
+
    Merge all inputs specified using –add
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--profile, --no-profile
    
+
    If set, will profile the command
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--caching <caching>
    
+
    Set the cache management policy
    
+
    
+
+
    
+
    aliases
    
+
    List aliases for a term or set of terms.
    
+
    Example:
    
+
    
+
    runoak -i ubergraph:uberon aliases UBERON:0001988
    
+
    
+
    TERMS should be either an explicit list of terms or queries, or can be a selector query,
+such as ‘.all’ to fetch all terms in the ontology
    
+
    Show all aliases:
    
+
    
+
    runoak -i db/envo.db aliases .all
    
+
    
+
    Currently the core behavior of this command assumes a simple datamodel for aliases, where an aliases
+is a simple property-value tuples, with the property being from some standard vocabulary (e.g. skos:altLabel,
+oboInOwl, etc)
    
+
    If you know the synonyms follow the OBO/oboInOwl datamodel you can pass –obo-model, this will give back
+richer data if present in the ontology, including synonym categories/types, synonym provenance
    
+
    In future, this may become the default
    
+
    runoak aliases [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+--obo-model, --no-obo-model
    
+
    If true, assume the OBO synonym datamodel, including provenancem synonym types
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    ancestors
    
+
    List all ancestors of a given term or terms.
    
+
    Here ancestor means the transitive closure of the parent relationship, where
+a parent includes all relationship types, not just is-a.
    
+
    Example:
    
+
    
+
    runoak -i cl.owl ancestors CL:4023094
    
+
    
+
    This will show ancestry over the full relationship graph. Like any relational
+OAK command, this can be filtered by relationship type (predicate), using –predicate (-p).
+For example, constrained to is-a and part-of:
    
+
    
+
    runoak -i cl.owl ancestors CL:4023094 -p i,BFO:0000050
    
+
    
+
    Multiple backends can be used, including ubergraph:
    
+
    
+
    runoak -i ubergraph: ancestors CL:4023094 -p i,BFO:0000050
    
+
    
+
    Search terms can also be used:
    
+
    
+
    runoak -i cl.owl ancestors ‘goblet cell’
    
+
    
+
    Multiple terms can be passed:
    
+
    
+
    runoak -i sqlite:go.db ancestors GO:0005773 GO:0005737 -p i,p
    
+
    
+
    Python API:
    
+
    
+
    
+
    runoak ancestors [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+-M, --graph-traversal-method <graph_traversal_method>
    
+
    Whether formal entailment or graph walking should be used.
    
+
    
+
    Options:
    
+
    HOP | ENTAILMENT
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+--statistics, --no-statistics
    
+
    For each ancestor, show statistics.
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    annotate
    
+
    Annotate a piece of text using a Named Entity Recognition annotation.
    
+
    Some endpoints such as BioPortal have built-in support for annotation;
+in these cases the endpoint functionality is used:
    
+
    Example:
    
+
    
+
    runoak -i bioportal: annotate “enlarged nucleus in T-cells from peripheral blood”
    
+
    
+
    For other endpoints, the built-in OAK annotator is used. This currently uses a basic
+algorithm based on lexical matching.
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:cl annotate “enlarged nucleus in T-cells from peripheral blood”
    
+
    
+
    Using the builtin annotator can be slow, as the lexical index is re-built every time.
+To preserve this, use the --lexical-index-file (-L) option to specify a file to save.
+On subsequent iterations the file is reused.
    
+
    You can also use --text-file to pass in a text file to be parsed one line at a time
    
+
    If gilda is installed as an extra, it can be used,
+but --matches-whole-text (-W) must be specified,
+as gilda only performs grounding.
    
+
    Example:
    
+
    
+
    runoak -i gilda: annotate -W BRCA2
    
+
    
+
    Aliases can be listed in the output by setting the flag
+–include-aliases to true (default: false).
    
+
    Example (using the plugin oakx-spacy):
    
+
    
+
    runoak -i spacy:sqlite:obo:bero annotate Myeloid derived suppressor cells. –include-aliases
    
+
    
+
    will yield:
    
+
    
+
    confidence: 0.8
+object_aliases:
+- Myeloid-Derived Suppressor Cells
+- MDSCs
+- mdscs
+- myeloid-derived suppressor cells
+object_id: obo:MESH_D000072737
+object_label: Myeloid-Derived Suppressor Cells
+subject_end: 30
+subject_start: 0
    
+
    
+
    Python API:
    
+
    
+
    
+
    Data model:
    
+
    
+
    
+
    runoak annotate [OPTIONS] [WORDS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-W, --matches-whole-text, --no-W, --no-matches-whole-text
    
+
    if true, then only show matches that span the entire input text
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--include-aliases, --no-include-aliases
    
+
    Include alias maps in output.
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--text-file <text_file>
    
+
    Text file to annotate. Each newline separated entry is a distinct text.
    
+
    
+
+
    
+
    
+-L, --lexical-index-file <lexical_index_file>
    
+
    path to lexical index. This is recreated each time unless –no-recreate is passed
    
+
    
+
+
    
+
    
+-A, --match-column <match_column>
    
+
    name of column to match on (if the input is tsv/csv)
    
+
    
+
+
    
+
    
+-m, --model <model>
    
+
    Name of trained model to use for annotation, e.g. ‘en_ner_craft_md’.
    
+
    
+
+
    
+
    
+-x, --exclude-tokens <exclude_tokens>
    
+
    Text file or list of tokens to filter from input prior to annotation.        If passed as text file, each newline separated entry is a distinct text.
    
+
    
+
+
    
+
    
+-R, --rules-file <rules_file>
    
+
    path to rules file. Conforms to https://w3id.org/oak/mapping-rules
    
+
    
+
+
    
+
    
+-C, --configuration-file <configuration_file>
    
+
    path to config file. Conforms to https://w3id.org/oak/text-annotator
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    Arguments
    
+
    
+
    
+WORDS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    apply
    
+
    Applies a patch to an ontology. The patch should be specified using KGCL syntax, see
+https://github.com/INCATools/kgcl
    
+
    Example:
    
+
    
+
    runoak -i cl.owl.ttl apply “rename CL:0000561 to ‘amacrine neuron’”  -o cl.owl.ttl -O ttl
    
+
    
+
    On an obo format file:
    
+
    
+
    runoak -i simpleobo:go-edit.obo apply “rename GO:0005634 from ‘nucleus’ to ‘foo’” -o go-edit-new.obo
    
+
    
+
    With URIs:
    
+
    
+
    runoak -i cl.owl.ttl apply           “rename <http://purl.obolibrary.org/obo/CL_0000561> from ‘amacrine cell’ to ‘amacrine neuron’”            -o cl.owl.ttl -O ttl
    
+
    
+
    Warning:
    
+
    This command is still experimental. Some things to bear in mind:
    
+
      
+
    • for some ontologies, CURIEs may not work, instead specify a full URI surrounded by <>s
      • 
+
    • only a subset of KGCL commands are supported by each backend
      • 
+
    
+
    runoak apply [OPTIONS] [COMMANDS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    
+
+
    
+
    
+--changes-output <changes_output>
    
+
    output file for KGCL changes
    
+
    
+
+
    
+
    
+--changes-input <changes_input>
    
+
    Path to an input changes file
    
+
    
+
+
    
+
    
+--changes-format <changes_format>
    
+
    Format of the changes file (json or kgcl)
    
+
    
+
+
    
+
    
+--dry-run, --no-dry-run
    
+
    if true, only perform the parse of KCGL and do not apply
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--expand, --no-expand
    
+
    if true, expand complex changes to atomic changes
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+--ignore-invalid-changes, --no-ignore-invalid-changes
    
+
    if true, ignore invalid changes, e.g. obsoletions of dependent entities
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--contributor <contributor>
    
+
    CURIE for the person contributing the patch
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+--overwrite, --no-overwrite
    
+
    If set, any changes applied will be saved back to the input file/source
    
+
    
+
+
    Arguments
    
+
    
+
    
+COMMANDS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    apply-obsolete
    
+
    Sets an ontology element to be obsolete
    
+
    Example:
    
+
    
+
    runoak -i my.obo apply-obsolete MY:0002200 -o my-modified.obo
    
+
    
+
    Multiple terms can be passed, as labels, IDs, or using OAK queries:
    
+
    
+
    runoak -i my.obo apply-obsolete MY:1 MY:2 MY:3 … -o my-modified.obo
    
+
    
+
    This may be chained, for example to take all terms matching a search query and then
+obsolete them all:
    
+
    
+
    runoak -i my.db search ‘l/^Foo/` | runoak -i my.db –autosave apply-obsolete -
    
+
    
+
    This command is partially redundant with the more general “apply” command
    
+
    runoak apply-obsolete [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    
+
+
    
+
    
+--expand, --no-expand
    
+
    if true, expand complex changes to atomic changes
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+--ignore-invalid-changes, --no-ignore-invalid-changes
    
+
    if true, ignore invalid changes, e.g. obsoletions of dependent entities
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    apply-taxon-constraints
    
+
    Test candidate taxon constraints
    
+
    Multiple candidate constraints can be passed as arguments. these are in the form of triples
+separated by periods.
    
+
    Example:
    
+
    
+
    runoak  -i db/go.db apply-taxon-constraints -p i,p GO:0005743 only NCBITaxon:2759
+never NCBITaxon:2 . GO:0005634 only NCBITaxon:2
    
+
    
+
    The –evolution-file (-E) option can be used to pass in a file of candidates.
+This should follow the format used in https://arxiv.org/abs/1802.06004
    
+
    E.g.
    
+
    
+
    GO:0000229,Gain|NCBITaxon:1(root);>Loss|NCBITaxon:2759(Eukaryota);
    
+
    
+
    Example:
    
+
    
+
    runoak  -i db/go.db eval-taxon-constraints -p i,p -E tests/input/go-evo-gains-losses.csv
    
+
    
+
    More examples:
    
+
    
+
    
+
    runoak apply-taxon-constraints [OPTIONS] [CONSTRAINTS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-E, --evolution-file <evolution_file>
    
+
    path to file containing gains and losses
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+-M, --graph-traversal-method <graph_traversal_method>
    
+
    Whether formal entailment or graph walking should be used.
    
+
    
+
    Options:
    
+
    HOP | ENTAILMENT
    
+
    
+
    
+
    
+
+
    Arguments
    
+
    
+
    
+CONSTRAINTS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    associations
    
+
    Lookup associations from or to entities.
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:hp -g test.hpoa -G hpoa associations
    
+
    
+
    The above will show all associations
    
+
    To query using an ontology term, including is-a closure, specify one or more
+terms or term queries, plus the closure predicate(s), e.g.
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:hp -g test.hpoa -G hpoa associations -p i HP:0001392
    
+
    
+
    This shows all annotations either to “Abnormality of the liver” (HP:0001392), or
+to is-a descendants.
    
+
    Using input specifications:
    
+
    It can be awkward to specify both input ontology and association path and format. You
+can use input specifications to bundle common combinations of inputs together.
    
+
    For example, the go-dictybase-input-spec combines go plus dictybase associations.
    
+
    Example:
    
+
    
+
    runoak –i src/oaklib/conf/go-dictybase-input-spec.yaml associations -p i,p GO:0008104
    
+
    
+
    More examples:
    
+
    
+
    
+
    runoak associations [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+--if-absent <if_absent>
    
+
    determines behavior when the value is not present or is empty.
    
+
    
+
    Options:
    
+
    absent-only | present-only
    
+
    
+
    
+
    
+
+
    
+
    
+-S, --set-value <set_value>
    
+
    the value to set for all terms for the given property.
    
+
    
+
+
    
+
    
+--add-closure-fields, --no-add-closure-fields
    
+
    Add closure fields to the output
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--association-predicates <association_predicates>
    
+
    A comma-separated list of predicates for the association relation
    
+
    
+
+
    
+
    
+-Q, --terms-role <terms_role>
    
+
    How to interpret query terms.
    
+
    
+
    Default:
    
+
    'object'
    
+
    
+
    Options:
    
+
    subject | object | both
    
+
    
+
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    associations-counts
    
+
    Count associations, grouped by subject or object
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:hp -g test.hpoa -G hpoa associations-counts
    
+
    
+
    This will default to summarzing by objects (HPO term), showing the number
+of associations for each term.
    
+
    This will be direct counts only. To include is-a closure, specify
+the closure predicate(s), e.g.
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:hp -g test.hpoa -G hpoa associations -p i
    
+
    
+
    You can also group by other fields
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:hp -g test.hpoa -G hpoa associations-counts –group-by subject
    
+
    
+
    This will show the number of associations for each disease.
    
+
    OAK also includes a number of specialized adapters that implement this method
+for particular databases.
    
+
    For example, to get the number of IEA associations for each GO term:
    
+
    
+
    runoak -i amigo: associations-counts  –limit -1 -F evidence_type=IEA –no-autolabel
    
+
    
+
    This can be constrained by species:
    
+
    
+
    runoak -i amigo:NCBITaxon:9606 associations-counts  –limit -1 -F evidence_type=IEA –no-autolabel
    
+
    
+
    Other options:
    
+
    This command accepts many of the same options as the associations command, see
+the docs for this command for details.
    
+
    runoak associations-counts [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+--add-closure-fields, --no-add-closure-fields
    
+
    Add closure fields to the output
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--association-predicates <association_predicates>
    
+
    A comma-separated list of predicates for the association relation
    
+
    
+
+
    
+
    
+-Q, --terms-role <terms_role>
    
+
    How to interpret query terms.
    
+
    
+
    Default:
    
+
    'object'
    
+
    
+
    Options:
    
+
    subject | object | both
    
+
    
+
    
+
    
+
+
    
+
    
+-L, --limit <limit>
    
+
    Limit the number of results
    
+
    
+
    Default:
    
+
    10
    
+
    
+
    
+
    
+
+
    
+
    
+-F, --filter <filter>
    
+
    Additional filters in K=V format
    
+
    
+
+
    
+
    
+--min-facet-count <min_facet_count>
    
+
    Minimum count for a facet to be included
    
+
    
+
    Default:
    
+
    1
    
+
    
+
    
+
    
+
+
    
+
    
+--group-by <group_by>
    
+
    Group by subject or object
    
+
    
+
    Default:
    
+
    'object'
    
+
    
+
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    associations-matrix
    
+
    Co-annotation matrix query.
    
+
    This queries for co-annotations between pairs of terms.
    
+
    See: Wood V., Carbon S., et al, https://royalsocietypublishing.org/doi/10.1098/rsob.200149
    
+
    Example:
    
+
    
+
    runoak  -i amigo:NCBITaxon:9606 associations-matrix -p i,p GO:0042416 GO:0014046
    
+
    
+
    This results in a 2x2 matrix (shown as a long table)
    
+
    As a heatmap:
    
+
    
+
    runoak  -i amigo:NCBITaxon:9606 associations-matrix -p i,p GO:0042416 GO:0014046 -O heatmap > /tmp/heatmap.png
    
+
    
+
    By default the heatmap will show the percentage of overlap between the two terms. To change this
+to be either the percentage of the first term in the second, or the percentage of the second term in the first,
+use the –main-score-field (-S) option, with “1” or “2”.
    
+
    You can plug in as many terms as you like, it will perform an all-by-all
    
+
    To compare one set with another, use the “@” separator.
    
+
    You can also substitute OAK expression language query terms
    
+
    
+
    runoak –stacktrace  -i amigo:NCBITaxon:9606 associations-matrix -p i,p .idfile cp.txt @ .idfile ct.txt
    
+
    
+
    runoak associations-matrix [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+--association-predicates <association_predicates>
    
+
    A comma-separated list of predicates for the association relation
    
+
    
+
+
    
+
    
+-Q, --terms-role <terms_role>
    
+
    How to interpret query terms.
    
+
    
+
    Default:
    
+
    'object'
    
+
    
+
    Options:
    
+
    subject | object | both
    
+
    
+
    
+
    
+
+
    
+
    
+--include-entities, --no-include-entities
    
+
    Include entities (e.g. genes) in the output, otherwise just the counts
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-S, --main-score-field <main_score_field>
    
+
    Score used for summarization
    
+
    
+
    Default:
    
+
    'proportion_subjects_in_common'
    
+
    
+
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    axioms
    
+
    Filters axioms
    
+
    Example:
    
+
    
+
    runoak -i cl.ofn axiom
    
+
    
+
    The above will write all axioms.
    
+
    You can filter by axiom type:
    
+
    Example:
    
+
    
+
    runoak -i cl.ofn axiom –axiom-type SubClassOf
    
+
    
+
    Note this currently only works with the funowl adapter, on functional syntax files
    
+
    runoak axioms [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+--axiom-type <axiom_type>
    
+
    Type of axiom, e.g. SubClassOf
    
+
    
+
+
    
+
    
+--about <about>
    
+
    CURIE that the axiom is about
    
+
    
+
+
    
+
    
+--references <references>
    
+
    CURIEs that the axiom references
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    cache-clear
    
+
    Clear the contents of the pystow oaklib cache.
    
+
    runoak cache-clear [OPTIONS]
+
    
+
    
+
    Options
    
+
    
+
    
+--days-old <days_old>
    
+
    Clear anything more than this number of days old
    
+
    
+
    Default:
    
+
    100
    
+
    
+
    
+
    
+
+
    
+
    
+
    cache-ls
    
+
    List the contents of the pystow oaklib cache.
    
+
    runoak cache-ls [OPTIONS]
+
    
+
    
+
    
+
    
+
    definitions
    
+
    Show textual definitions for term or set of terms
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:envo definitions ‘tropical biome’ ‘temperate biome’
    
+
    
+
    You can use the “.all” selector to show all definitions for all terms in the ontology:
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:envo definitions .all
    
+
    
+
    You can also include definition metadata, such as provenance and source:
    
+
    
+
    runoak -i sqlite:obo:cl definitions –additional-metadata neuron
    
+
    
+
    Python API:
    
+
    
+
    
+
    runoak definitions [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-D, --display <display>
    
+
    A comma-separated list of display options. Use ‘all’ for all
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
    Options:
    
+
    obo | obojson | ofn | rdf | json | yaml | fhirjson | csv | tsv | nl
    
+
    
+
    
+
    
+
+
    
+
    
+--if-absent <if_absent>
    
+
    determines behavior when the value is not present or is empty.
    
+
    
+
    Options:
    
+
    absent-only | present-only
    
+
    
+
    
+
    
+
+
    
+
    
+--additional-metadata, --no-additional-metadata
    
+
    if true then fetch additional metadata about statements stored as OWL reification
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+-S, --set-value <set_value>
    
+
    the value to set for all terms for the given property.
    
+
    
+
+
    
+
    
+-P, --lookup-references, --no-lookup-references
    
+
    Lookup references for each term, e.g. PMIDs
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    descendants
    
+
    List all descendants of a term
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:obi descendants assay -p i
    
+
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:uberon descendants heart -p i,p
    
+
    
+
    This is the inverse of the ‘ancestors’ command; see the documentation for
+that command. But note that ‘descendants’ commands have the potential to be more
+“explosive” than ancestors commands, especially for high level terms, and for when
+predicates are not specified
    
+
    Python API:
    
+
    
+
    
+
    runoak descendants [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+-M, --graph-traversal-method <graph_traversal_method>
    
+
    Whether formal entailment or graph walking should be used.
    
+
    
+
    Options:
    
+
    HOP | ENTAILMENT
    
+
    
+
    
+
    
+
+
    
+
    
+-D, --display <display>
    
+
    A comma-separated list of display options. Use ‘all’ for all
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    diff
    
+
    Compute difference between two ontologies.
    
+
    Example:
    
+
    
+
    runoak -i foo.obo diff -X bar.obo -o diff.yaml
    
+
    
+
    This will produce a list of Changes that are required to go from the main input ontology (–input)
+to the other ontology (–other-ontology, or -X).
    
+
    The output follows the KGCL data model.
+See https://incatools.github.io/ontology-access-kit/datamodels/kgcl/index.html
    
+
    You can use –output-type to control the output format.
    
+
    KGCL controlled natural language:
    
+
    
+
    runoak -i foo.obo diff -X bar.obo -o diff.txt –output-type kgcl
    
+
    
+
    KGCL JSON:
    
+
    
+
    runoak -i foo.obo diff -X bar.obo -o diff.json –output-type json
    
+
    
+
    YAML (default):
    
+
    
+
    runoak -i foo.obo diff -X bar.obo -o diff.yaml –output-type yaml
    
+
    
+
    The –statistics option can be used to generate summary statistics for the changes.
+These are grouped according to the –group-by-property option. For example,
+the GO uses the oio:hasOBONamespace property to partition classes into 3 categories.
    
+
    Example:
    
+
    
+
    runoak -i go.obo diff -X go-new.obo -o diff.yaml –statistics –group-by-property oio:hasOBONamespace
    
+
    
+
    This will produce a YAML dictionary, with outer keys being the values of the oio:hasOBONamespace property,
+and inner keys being the change types.
    
+
    If –group-by-property is not specified, or there is no value for this property, then the outer key
+will be “__RESIDUAL__”
    
+
    For summary statistics, you can also specify –output-type csv, to get a tabular out
    
+
    Limitations:
    
+
    This does not do a diff over every axiom in each ontology. For a complete OWL diff, you should
+use ROBOT.
    
+
    runoak diff [OPTIONS]
+
    
+
    
+
    Options
    
+
    
+
    
+-X, --other-ontology <other_ontology>
    
+
    other ontology
    
+
    
+
+
    
+
    
+--simple, --no-simple
    
+
    perform a quick difference showing only terms that differ
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--statistics, --no-statistics
    
+
    show summary statistics only
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--change-type <change_type>
    
+
    filter by KGCL change type (e.g. ‘ClassCreation’, ‘EdgeDeletion’)
    
+
    
+
+
    
+
    
+--group-by-property <group_by_property>
    
+
    group summaries by a metadata property, e.g. rdfs:isDefinedBy
    
+
    
+
+
    
+
    
+--group-by-obo-namespace, --no-group-by-obo-namespace
    
+
    shortcut for –group-by-property oio:hasOBONamespace (note this is distinct from the ID namespace)
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--group-by-defined-by, --no-group-by-defined-by
    
+
    shortcut for –group-by-property rdfs:isDefinedBy. This may be inferred from prefix if not set explicitly
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--group-by-prefix, --no-group-by-prefix
    
+
    shortcut for –group-by-property sh:prefix. Groups by the prefix of the CURIE
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+
    diff-associations
    
+
    Diffs two association sources.
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:go  -G gaf  diff-associations            –old-date ${date1} –new-date ${date2}            -g  “${download_dir}/${group}-${date1}.gaf”            -X “${download_dir}/${group}-${date2}.gaf”            –group-by publications -p i,p            -o “${group}-diff-${date1}-to-${date2}.tsv
    
+
    
+
    See https://w3id.org/oak/association for the diff data model.
    
+
    NOTE: This functionality may move out of core
    
+
    runoak diff-associations [OPTIONS]
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+--old-date <old_date>
    
+
    Old date, in YYYY-MM-DD format
    
+
    
+
+
    
+
    
+--new-date <new_date>
    
+
    Old date, in YYYY-MM-DD format
    
+
    
+
+
    
+
    
+-g, --associations <associations>
    
+
    associations
    
+
    
+
+
    
+
    
+-X, --other-associations <other_associations>
    
+
    other associations
    
+
    
+
+
    
+
    
+--group-by <group_by>
    
+
    One of: publications; primary_knowledge_source
    
+
    
+
+
    
+
    
+
    diff-terms
    
+
    Compares a pair of terms in two ontologies
    
+
    EXPERIMENTAL
    
+
    runoak diff-terms [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+--other-ontology <other_ontology>
    
+
    other ontology
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    diff-via-mappings
    
+
    Calculates cross-ontology diff using mappings
    
+
    Given a pair of ontologies, and mappings that connect terms in both ontologies, this
+command will perform a structural comparison of all mapped pairs of terms
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:uberon diff-via-mappings –other-input sqlite:obo:zfa  –source UBERON –source ZFA -O csv
    
+
    
+
    Note the above command does not have any mapping file specified; the mappings that are distributed within
+each ontology is used (in this case, Uberon contains mappings to ZFA)
    
+
    If the mappings are provided externally:
    
+
    
+
    runoak -i ont1.obo diff-via-mappings –other-input ont2.obo –mapping-input mappings.sssom.tsv
    
+
    
+
    (in the above example, –source is not passed, so all mappings are tested)
    
+
    If there are no existing mappings, you can use the lexmatch command to generate them:
    
+
    
+
    runoak -i ont1.obo diff-via-mappings -a ont2.obo lexmatch -o mappings.sssom.tsv
    
+
    runoak -i ont1.obo diff-via-mappings –other-input ont2.obo –mapping-input mappings.sssom.tsv
    
+
    
+
    The output from this command follows the cross-ontology-diff data model
+(https://incatools.github.io/ontology-access-kit/datamodels/cross-ontology-diff/index.html)
    
+
    This can be serialized in YAML or TSV form
    
+
    runoak diff-via-mappings [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-S, --source <source>
    
+
    ontology prefixes  e.g. HP, MP
    
+
    
+
+
    
+
    
+--mapping-input <mapping_input>
    
+
    File of mappings in SSSOM format. If not provided then mappings in ontology(ies) are used
    
+
    
+
+
    
+
    
+-X, --other-input <other_input>
    
+
    Additional input file
    
+
    
+
+
    
+
    
+--other-input-type <other_input_type>
    
+
    Type of additional input file
    
+
    
+
+
    
+
    
+--intra, --no-intra
    
+
    If true, then all sources are in the main input ontology
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+--include-identity-mappings, --no-include-identity-mappings
    
+
    Use identity relation as mapping; use this for two versions of the same ontology
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--filter-category-identical, --no-filter-category-identical
    
+
    Do not report cases where a relationship has not changed
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--bidirectional, --no-bidirectional
    
+
    Show diff from both left and right perspectives
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    disjoints
    
+
    Show all disjoints for a set of terms, or whole ontology.
    
+
    Leave off all arguments for defaults - all terms, YAML OboGraph model
+serialization:
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:uberon disjoints
    
+
    
+
    Note that this will include pairwise disjoints, setwise disjoints,
+disjoint unions, and disjoints involving simple class expressions.
    
+
    A tabular format can be easier to browse, and includes labels by default:
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:uberon disjoints –autolabel -O csv
    
+
    
+
    To perform this on a subset:
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:cl disjoints –autolabel -O csv  .desc//p=i “immune cell”
    
+
    
+
    Data model:
    
+
    
+
    
+
    runoak disjoints [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+--named-classes-only, --no-named-classes-only
    
+
    Only show disjointness axioms between two named classes.
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    dump
    
+
    Exports (dumps) the entire contents of an ontology.
    
+
    Example:
    
+
    
+
    runoak -i pato.obo dump -o pato.json -O json
    
+
    
+
    Example:
    
+
    
+
    runoak -i pato.owl dump -o pato.ttl -O turtle
    
+
    
+
    You can also pass in a JSON configuration file to parameterize the dump process.
    
+
    Currently this is only used for fhirjson dumps, the configuration options are specified here:
    
+
    https://incatools.github.io/ontology-access-kit/converters/obo-graph-to-fhir.html
    
+
    Example:
    
+
    
+
    runoak -i pato.owl dump -o pato.ttl -O fhirjson -c fhir_config.json -o pato.fhir.json
    
+
    
+
    Currently each implementation only supports a subset of formats.
    
+
    The dump command is also blocked for remote endpoints such as Ubergraph,
+to avoid killer queries.
    
+
    Python API:
    
+
    
+
    
+
    runoak dump [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Path to output file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-c, --config-file <config_file>
    
+
    Config file for additional params. Presently used by  fhirjson only.
    
+
    
+
+
    
+
    
+--enforce-canonical-ordering, --no-enforce-canonical-ordering
    
+
    Forces the serialization to be in canonical order, which is useful for diffing
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    enrichment
    
+
    Run class enrichment analysis.
    
+
    Given a sample file of identifiers (e.g. gene IDs), plus a set of associations (e.g. gene to term
+associations, return the terms that are over-represented in the sample set.
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:uberon -g gene2anat.txt -G g2t enrichment -U my-genes.txt -O csv
    
+
    
+
    This runs an enrichment using Uberon on my-genes.txt, using the gene2anat.txt file as the
+association file (assuming simple gene-to-term format). The output is in CSV format.
    
+
    It is recommended you always provide a background set, including all the entity identifiers
+considered in the experiment.
    
+
    You can specify –filter-redundant to filter out redundant terms. This will block reporting
+of any terms that are either subsumed by or subsume a lower p-value term that is already
+reported.
    
+
    For a full example, see:
    
+
    
+
    
+
    Note that it is possible to run “pseudo-enrichments” on term lists only by passing
+no associations and using –ontology-only. This creates a fake association set that is simply
+reflexive relations between each term and itself. This can be useful for summarizing term lists,
+but note that P-values may not be meaningful.
    
+
    runoak enrichment [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-T, --ontology-only, --no-ontology-only
    
+
    If true, perform a pseudo-enrichment analysis treating each term as an association to itself.
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--cutoff <cutoff>
    
+
    The cutoff for the p-value; any p-values greater than this are not reported.
    
+
    
+
    Default:
    
+
    0.05
    
+
    
+
    
+
    
+
+
    
+
    
+-U, --sample-file <sample_file>
    
+
    file containing input list of entity IDs (e.g. gene IDs)
    
+
    
+
+
    
+
    
+-B, --background-file <background_file>
    
+
    file containing background list of entity IDs (e.g. gene IDs)
    
+
    
+
+
    
+
    
+--association-predicates <association_predicates>
    
+
    A comma-separated list of predicates for the association relation
    
+
    
+
+
    
+
    
+--filter-redundant, --no-filter-redundant
    
+
    If true, filter out redundant terms
    
+
    
+
+
    
+
    
+--allow-labels, --no-allow-labels
    
+
    If true, allow labels as well as CURIEs in the input files
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    expand-subsets
    
+
    For each subset provide a mapping of each term in the ontology to a subset
    
+
    Example:
    
+
    
+
    runoak -i db/pato.db expand-subsets attribute_slim value_slim
    
+
    
+
    runoak expand-subsets [OPTIONS] [SUBSETS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    Arguments
    
+
    
+
    
+SUBSETS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    extract
    
+
    Extracts a sub-ontology.
    
+
    Simple example:
    
+
    
+
    runoak -i cl.db extract neuron
    
+
    
+
    This will extract a single node for “neuron”. No relationships will be included,
+as –no-dangling is the default
    
+
    To include edges even if dangling:
    
+
    
+
    runoak -i cl.db extract neuron –dangling
    
+
    
+
    A subset of relationship types (predicates):
    
+
    
+
    runoak -i cl.db extract neuron –dangling -p i
    
+
    
+
    If you wish to get a fully connected is-a graph for all is-a ancestors:
    
+
    
+
    runoak -i cl.db extract .anc//p=i neuron –dangling -p i
    
+
    
+
    If you prefer, you can split this into 2 commands:
    
+
    
+
    runoak -i cl.db ancestors -p i neuron > seed.txt
    
+
    
+
    Then:
    
+
    
+
    runoak -i cl.db extract .idfile seed.txt –dangling -p i
    
+
    
+
    You can specify different output types and output paths:
    
+
    
+
    runoak -i cl.db extract .idfile seed.txt -O owl -o neuron.owl.ttl
    
+
    
+
    Allowed formats include: obo, obographs, owl/ttl, fhirjson
    
+
    runoak extract [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Path to output file
    
+
    
+
+
    
+
    
+--dangling, --no-dangling
    
+
    If True, allow dangling edges in the output
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--include-metadata, --no-include-metadata
    
+
    If True, include term metadata such as definitions, synonyms
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    fill-table
    
+
    Fills missing values in a table of ontology elements
    
+
    See https://incatools.github.io/ontology-access-kit/src/oaklib.utilities.table_filler
    
+
    Given a TSV with a populated ID column, and unpopulated columns for definition, label, mappings, ancestors,
+this will iterate through each row filling in each missing value by performing ontology lookups.
    
+
    In some cases, this can also perform reverse lookups; i.e given a table with labels populated and blank IDs,
+then fill in the IDs
    
+
    In the most basic scenario, you have a table with two columns ‘id’ and ‘label’. These are the “conventional” column
+headers for a table of ontology elements (see later for configuration when you don’t follow conventions)
    
+
    Example:
    
+
    
+
    runoak -i cl.owl.ttl fill-table my-table.tsv
    
+
    
+
    (any implementation can be used)
    
+
    The same command will work for the reverse scenario - when you have labels populated, but IDs are not populated
    
+
    By default this will throw an error if a lookup is not successful; this can be relaxed
    
+
    Relaxed:
    
+
    
+
    runoak -i cl.owl.ttl fill-table –allow-missing my-table.tsv
    
+
    
+
    In this case missing values that cannot be populated will remain empty
    
+
    To explicitly populate a value:
    
+
    
+
    runoak -i cl.owl.ttl fill-table –missing-value-token NO_DATA my-table.tsv
    
+
    
+
    Currently the following columns are recognized:
    
+
      
+
    • id – the unique identifier of the element
      • 
+
    • label – the rdfs:label of the element
      • 
+
    • definition – the definition of the element
      • 
+
    • mappings – mappings for the element
      • 
+
    • ancestors – ancestors for the element (this can be parameterized)
      • 
+
    
+
    The metadata inference procedure will also work for when you have denormalized TSV files
+with columns such as “foo_id” and “foo_name”. This will be recognized as an implicit normalized
+label relation between id and name of a foo element.
    
+
    You can be more explicit in one of two ways:
    
+
    
+
      
+
    1. Pass in a YAML structure (on command line or in a YAML file) listing relations
      2. 
+
    2. Pass in a LinkML data definitions YAML file
      3. 
+
    
+
    
+
    For the first method, you can pass in multiple relations using the –relation arg. For example,
+given a TSV with columns cl_identifier and cl_display_label you can say:
    
+
    Example:
    
+
    
+
    runoak -i cl.owl.ttl fill-table           –relation “{primary_key: cl_identifier, dependent_column: cl_display_label, relation: label}”
    
+
    
+
    You can also specify this in a YAML file
    
+
    For the 2nd method, you need to specify a LinkML schema with a class where (1) at least one field is annotated
+as being an identifier (2) one or more slots have slot_uri elements mapping them to standard metadata elements
+such as rdfs:label.
    
+
    For example, my-schema.yaml:
    
+
    
+
    
+
    classes:
    
+
    Person:
    
+
    attributes:
    
+
    id:
    identifier: true
    
+
    
+
    name:
    slot_uri: rdfs:label
    
+
    
+
    
+
    
+
    
+
    
+
    
+
    
+
    
+
    
+
    This is a powerful command with many ways of configuring it - we will add separate docs for this soon,
+for now please file an issue on github with any questions
    
+
      
+
    • TODO: allow for an option that will perform fuzzy matches of labels
      • 
+
    • TODO: reverse lookup is not provided for all fields, such as definitions
      • 
+
    • TODO: add an option to detect inconsistencies
      • 
+
    • TODO: add logical for obsoletion/replaced by
      • 
+
    • TODO: use most optimized method for whichever backend
      • 
+
    
+
    runoak fill-table [OPTIONS] TABLE_FILE
+
    
+
    
+
    Options
    
+
    
+
    
+--allow-missing, --no-allow-missing
    
+
    Allow some dependent values to be blank, post-processing
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--missing-value-token <missing_value_token>
    
+
    Populate all missing values with this token
    
+
    
+
+
    
+
    
+--schema <schema>
    
+
    Path to linkml schema
    
+
    
+
+
    
+
    
+--delimiter <delimiter>
    
+
    Delimiter between columns in input and output
    
+
    
+
    Default:
    
+
    '\t'
    
+
    
+
    
+
    
+
+
    
+
    
+--comment <comment>
    
+
    Comment indicator at the beginning of a row.
    
+
    
+
    Default:
    
+
    '#'
    
+
    
+
    
+
    
+
+
    
+
    
+--relation <relation>
    
+
    Serialized YAML string corresponding to a normalized relation between two columns
    
+
    
+
+
    
+
    
+--relation-file <relation_file>
    
+
    Path to YAML file corresponding to a list of normalized relation between two columns
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    Autolabel columns
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    Arguments
    
+
    
+
    
+TABLE_FILE
    
+
    Required argument
    
+
    
+
+
    
+
    
+
    generate-definitions
    
+
    Generate definitions for a term or terms.
    
+
    Currently this only works with the llm extension.
    
+
    Example:
    
+
    
+
    runoak -i llm:sqlite:obo:foodon generate-definitions FOODON:03315258
    
+
    
+
    The –style-hints option can be used to provide hints to the definition generator.
    
+
    Example:
    
+
    
+
    runoak -i llm:sqlite:obo:foodon generate-definitions FOODON:03315258           –style-hints “Write the definition in the style of a pretentious food critic”
    
+
    
+
    Generates:
    
+
    
+
    “The pancake, a humble delight in the realm of breakfast fare,
+presents itself as a delectable disc of gastronomic delight…”
    
+
    
+
    runoak generate-definitions [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+--style-hints <style_hints>
    
+
    Description of style for definitions
    
+
    
+
+
    
+
    
+--apply-patch, --no-apply-patch
    
+
    Apply KGCL syntax.
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--patch <patch>
    
+
    Path to where patch file will be written.
    
+
    
+
+
    
+
    
+--patch-format <patch_format>
    
+
    Output syntax for patches.
    
+
    
+
+
    
+
    
+--exclude-defined, --no-exclude-defined
    
+
    Exclude terms that already have definitions
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    generate-disjoints
    
+
    Generate candidate disjointness axioms.
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:iao generate-disjoints -O obo
    
+
    
+
    To generate spatial disjointness axioms:
    
+
    
+
    runoak -i sqlite:obo:zfa generate-disjoints -O obo p i,p
    
+
    
+
    runoak generate-disjoints [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-M, --min-descendants <min_descendants>
    
+
    Minimum number of descendants for a class to have to be considered a candidate.
    
+
    
+
    Default:
    
+
    3
    
+
    
+
    
+
    
+
+
    
+
    
+--exclude-existing, --no-exclude-existing
    
+
    Do not report duplicates with existing disjointness axioms.
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    generate-lexical-replacements
    
+
    Generate lexical replacements based on a set of synonymizer rules.
    
+
    If the –apply-patch flag is set, the output will be an ontology file with the changes
+applied. Pass the –patch argument to lso get the patch file in KGCL format.
    
+
    Example:
    
+
    
+
    runoak -i foo.obo generate-lexical-replacements -R foo_rules.yaml           –patch patch.kgcl –apply-patch -o foo_syn.obo
    
+
    
+
    If the apply-patch flag is NOT set then the main input will be KGCL commands
    
+
    Example:
    
+
    
+
    runoak -i foo.obo generate-lexical-replacements -R foo_rules.yaml -o changes.kgcl
    
+
    
+
    You can also pass the expressions directly as YAML
    
+
    Example:
    
+
    
+
    runoak -i foo.obo generate-lexical-replacements           -Y ‘{match: “nuclear (w+)”, replacement: “1 nucleus”}’ .all
    
+
    
+
    see https://github.com/INCATools/kgcl.
    
+
    Note: this command is very similar to generate-synonyms, but the main use case here
+is replacing terms, and applying rules to other elements such as definitions
    
+
    runoak generate-lexical-replacements [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-R, --rules-file <rules_file>
    
+
    path to rules file. Conforms to rules_datamodel.        e.g. https://github.com/INCATools/ontology-access-kit/blob/main/tests/input/matcher_rules.yaml
    
+
    
+
+
    
+
    
+-Y, --rules-expression <rules_expression>
    
+
    YAML encoding of a rules expression
    
+
    
+
+
    
+
    
+--apply-patch, --no-apply-patch
    
+
    Apply KGCL syntax generated based on the synonymizer rules file.
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--patch <patch>
    
+
    Path to where patch file will be written.
    
+
    
+
+
    
+
    
+--patch-format <patch_format>
    
+
    Output syntax for patches.
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    generate-logical-definitions
    
+
    Generate logical definitions based on patterns file.
    
+
    runoak generate-logical-definitions [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-P, --patterns-file <patterns_file>
    
+
    path to patterns file
    
+
    
+
+
    
+
    
+--show-extract, --no-show-extract
    
+
    Show the original extracted object.
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--parse, --no-parse
    
+
    Parse the input terms according to the patterns.
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+--fill, --no-fill
    
+
    If true, fill in descendant logical definitions.
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--analyze, --no-analyze
    
+
    Analyze consistency of logical definitions (in progress).
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--unmelt, --no-unmelt
    
+
    Use a wide table for display.
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    generate-synonyms
    
+
    Generate synonyms based on a set of synonymizer rules.
    
+
    If the –apply-patch flag is set, the output will be an ontology file with the changes
+applied. Pass the –patch argument to lso get the patch file in KGCL format.
    
+
    Example:
    
+
    
+
    runoak -i foo.obo generate-synonyms -R foo_rules.yaml –patch patch.kgcl –apply-patch -o foo_syn.obo
    
+
    
+
    If the apply-patch flag is NOT set then the main input will be KGCL commands
    
+
    Example:
    
+
    
+
    runoak -i foo.obo generate-synonyms -R foo_rules.yaml -o changes.kgcl
    
+
    
+
    see https://github.com/INCATools/kgcl.
    
+
    runoak generate-synonyms [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-R, --rules-file <rules_file>
    
+
    Required path to rules file. Conforms to rules_datamodel.        e.g. https://github.com/INCATools/ontology-access-kit/blob/main/tests/input/matcher_rules.yaml
    
+
    
+
+
    
+
    
+--apply-patch, --no-apply-patch
    
+
    Apply KGCL syntax generated based on the synonymizer rules file.
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--patch <patch>
    
+
    Path to where patch file will be written.
    
+
    
+
+
    
+
    
+--patch-format <patch_format>
    
+
    Output syntax for patches.
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    info
    
+
    Show information on term or set of terms
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:cl info CL:4023094
    
+
    
+
    The default output is minimal, showing only ID and label
    
+
    The –output-type (-O) option can be used to specify other formats for the output.
    
+
    Currently there are only a few output types are supported. More will be provided in future.
    
+
    In OBO format:
    
+
    
+
    runoak -i cl.owl info CL:4023094 -O obo
    
+
    
+
    As CSV:
    
+
    
+
    runoak -i cl.obo info CL:4023094 -O csv
    
+
    
+
    The info output format can be parameterized with –display (-D)
    
+
    With xrefs and definitions:
    
+
    
+
    runoak -i cl.owl info CL:4023094 -D x,d
    
+
    
+
    With all information:
    
+
    
+
    runoak -i cl.owl info CL:4023094 -D all
    
+
    
+
    Like all OAK commands, input term lists can be multivalued, a mixture of IDs and labels, as well
+as queries that can be combined using boolean logic
    
+
    Info on two STATO terms:
    
+
    
+
    runoak -i ontobee:stato info STATO:0000286 STATO:0000287 -O obo
    
+
    
+
    All terms in ENVO with the string “forest” in them:
    
+
    
+
    runoak -i sqlite:obo:envo info l~forest
    
+
    
+
    Info on all subtypes of “statistical hypothesis test” in STATO:
    
+
    
+
    runoak -i sqlite:obo:stato info .desc//p=i ‘statistical hypothesis test’
    
+
    
+
    runoak info [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-D, --display <display>
    
+
    A comma-separated list of display options. Use ‘all’ for all
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    information-content
    
+
    Show information content for term or list of terms
    
+
    Example:
    
+
    
+
    runoak -i cl.db information-content -p i .all
    
+
    
+
    Like all OAK commands that operate over graphs, the graph traversal is controlled
+by the –predicates option. In the above case, the frequency of each term is equal to
+the number of reflexive is-a descendants of the term divided by total number of terms
    
+
    By default, the ontology is used as the corpus for computing term frequency.
    
+
    You can use an association file as the corpus:
    
+
    
+
    runoak -g hpoa.tsv -G hpoa -i hp.db information-content -p i –use-associations .all
    
+
    
+
    runoak information-content [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+--use-associations, --no-use-associations
    
+
    Use associations to calculate IC
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    labels
    
+
    Show labels for term or list of terms
    
+
    Example:
    
+
    
+
    runoak -i cl.owl labels CL:4023093 CL:4023094
    
+
    
+
    You can use the “.all” selector to show all labels:
    
+
    Example:
    
+
    
+
    runoak -i cl.owl labels .all
    
+
    
+
    (this may be blocked for remote endpoints)
    
+
    You can query for terms that have either no label, or to include only ones with labels:
    
+
    Nodes with no labels:
    
+
    
+
    runoak -i cl.owl labels .all –if-absent exclude
    
+
    
+
    Multilingual support: if the adapter supports multilingual querying
+(currently only SQL) and the ontology has multilingual support, you can restrict results to
+a particular language.
    
+
    Example:
    
+
    
+
    runoak –preferred-language fr -i sqlite:obo:hpinternational labels .ancestors HP:0020110
    
+
    
+
    You can also query for all languages, and see these pivoted:
    
+
    Example:
    
+
    
+
    runoak  -i sqlite:obo:hpinternational labels .ancestors HP:0020110 –pivot-languages
    
+
    
+
    Python API:
    
+
    
+
    
+
    runoak labels [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-D, --display <display>
    
+
    A comma-separated list of display options. Use ‘all’ for all
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
    Options:
    
+
    obo | obojson | ofn | rdf | json | yaml | fhirjson | csv | tsv | nl
    
+
    
+
    
+
    
+
+
    
+
    
+--pivot-languages, --no-pivot-languages
    
+
    include one column per language
    
+
    
+
+
    
+
    
+--all-languages, --no-all-languages
    
+
    if source is multi-lingual, show all languages rather than just default
    
+
    
+
+
    
+
    
+--if-absent <if_absent>
    
+
    determines behavior when the value is not present or is empty.
    
+
    
+
    Options:
    
+
    absent-only | present-only
    
+
    
+
    
+
    
+
+
    
+
    
+-S, --set-value <set_value>
    
+
    the value to set for all terms for the given property.
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    languages
    
+
    Show available languages
    
+
    Example:
    
+
    
+
    runoak languages
    
+
    
+
    runoak languages [OPTIONS]
+
    
+
    
+
    
+
    
+
    leafs
    
+
    List all leaf nodes in the ontology
    
+
    Like all OAK relational commands, this is parameterized by –predicates (-p).
+Note that the default is to return the roots of the relation graph over all predicates
    
+
    Example:
    
+
    
+
    runoak -i db/cob.db leafs
    
+
    
+
    This command is a wrapper onto the “leafs” command in the BasicOntologyInterface.
    
+
+
    runoak leafs [OPTIONS]
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+--filter-obsoletes, --no-filter-obsoletes
    
+
    If set, results will exclude obsoletes
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+
    lexmatch
    
+
    Performs lexical matching between pairs of terms in one more more ontologies.
    
+
    Examples
+-
    
+
    
+
    runoak -i foo.obo lexmatch -o foo.sssom.tsv
    
+
    
+
    In this example, the input ontology file is assumed to contain all pairs of terms to be mapped.
    
+
    It is more common to map between all pairs of terms in two ontology files. In this case,
+you can merge the ontologies using a tool like ROBOT; or,  to avoid a merge
+preprocessing step, use the –addl (-a) option to specify a second ontology file.
    
+
    
+
    runoak -i foo.obo –add bar.obo lexmatch -o foo.sssom.tsv
    
+
    
+
    By default, this command will compare all terms in all ontologies. You can use the OAK
+term query syntax to pass in the set of all terms to be compared.
    
+
    For example, to compare all terms in union of FOO and BAR namespaces:
    
+
    
+
    runoak -i foo.obo –add bar.obo lexmatch -o foo.sssom.tsv i^FOO: i^BAR:
    
+
    
+
    All members of the set are compared (including FOO to FOO matches and BAR to BAR
+matches), omitting trivial reciprocal matches.
    
+
    Use an “@” separator between two queries to feed in two explicit sets:
    
+
    
+
    runoak -i foo.obo –add bar.obo lexmatch -o foo.sssom.tsv i^FOO: @ i^BAR:
    
+
    
+
    ALGORITHM: lexmatch implements a simple algorithm:
    
+
      
+
    • create a lexical index, keyed by normalized strings of labels, synonyms
      • 
+
    • report all pairs of entities that have the same key
      • 
+
    
+
    The lexical index can be exported (in native YAML) using -L:
    
+
    
+
    runoak -i foo.obo lexmatch -L foo.index.yaml -o foo.sssom.tsv
    
+
    
+
    Note: if you run the above command a second time it will be faster as the index
+will be reused.
    
+
    RULES: Using custom rules:
    
+
    
+
    runoak  -i foo.obo lexmatch -R match_rules.yaml -L foo.index.yaml -o foo.sssom.tsv
    
+
    
+
    Full documentation:
    
+
+
    module-oaklib.utilities.lexical.lexical_indexer
    
+
    runoak lexmatch [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-R, --rules-file <rules_file>
    
+
    path to rules file. Conforms to rules_datamodel.        e.g. https://github.com/INCATools/ontology-access-kit/blob/main/tests/input/matcher_rules.yaml
    
+
    
+
+
    
+
    
+--add-labels, --no-add-labels
    
+
    Populate empty labels with URI fragments or CURIE local IDs, for ontologies that use semantic IDs
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+-L, --lexical-index-file <lexical_index_file>
    
+
    path to lexical index. This is recreated each time unless –no-recreate is passed
    
+
    
+
+
    
+
    
+--recreate, --no-recreate
    
+
    if true and lexical index is specified, always recreate, otherwise load from index
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+--ensure-strict-prefixes, --no-ensure-strict-prefixes
    
+
    Clean prefix map and mappings before generating an output.
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--exclude-mapped, --no-exclude-mapped
    
+
    Return only mappings for subjects that have not been mapped
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    lint
    
+
    Lints an ontology, applying changes in place.
    
+
    The current implementation is highly incomplete, and only handles
+linting of syntactic patterns (chains of whitespace, trailing whitespace)
+in labels and definitions.
    
+
    The output is a list of changes, in a KCGL-compliant syntax.
    
+
    By default, changes will be applied
    
+
    Example:
    
+
    
+
    runoak -i my.obo lint
    
+
    
+
    This can be executed in dry-run mode, in which case changes are not applied:
    
+
    
+
    runoak -i my.obo lint –dry-run
    
+
    
+
    One common workflow is to emit the changes to a KCGL file which is manually checked,
+then applied as a separate step.
    
+
    Example workflow:
    
+
    
+
    runoak -i my.obo lint –dry-run -o changes.kgcl
+# examine and edit changes.kgcl
+runoak -i my.obo apply –changes-input changes.kgcl
    
+
    
+
    runoak lint [OPTIONS]
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    
+
+
    
+
    
+--report-format <report_format>
    
+
    Output format for reporting proposed/applied changes
    
+
    
+
+
    
+
    
+--dry-run, --no-dry-run
    
+
    If true, nothing will be modified by executing command
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+
    logical-definitions
    
+
    Show all logical definitions for a term or terms.
    
+
    To show all logical definitions in an ontology, pass the “.all” query term
    
+
    Example; first create an alias:
    
+
    
+
    alias pato=”runoak -i obo:sqlite:pato”
    
+
    
+
    Then run the query:
    
+
    
+
    pato logical-definitions .all
    
+
    
+
    By default, “.all” will query all axioms for all terms including merged terms;
+to restrict to only the current terms, use an ID query:
    
+
    
+
    pato logical-definitions i^PATO
    
+
    
+
    You can also restrict to branches:
    
+
    
+
    pato logical-definitions .desc//p=i “physical object quality”
    
+
    
+
    By default, the output is a subset of OboGraph datamodel rendered as YAML, e.g.
    
+
    
+
    
+
    definedClassId: PATO:0045071
    genusIds:
+- PATO:0001439
+restrictions:
+- fillerId: PATO:0000461
    
+
    
+
    propertyId: RO:0015010
    
+
    
+
    
+
    
+
    
+
    You can also specify CSV to generate a flattened form of this.
    
+
    Example:
    
+
    
+
    pato logical-definitions .all –output-type csv
    
+
    
+
    You can optionally choose to “–matrix-axes” to transform the output to a matrix form.
+This is a comma-separated pair of axes, where each element is a logical definition element
+type: “f” for filler, “p” for predicate, “g” for genus, “d” for defined class.
    
+
    Example:
    
+
      
+
    • Each property/predicate is a column
      • 
+
    • For repeated properties, columns of the form prop_1, prop_2, … are generated
      • 
+
    
+
    Example:
    
+
    
+
    pato logical-definitions .all  –matrix-axes d,p –output-type csv
    
+
    
+
    This will generate a row for each defined class with a logical definition, with columns
+for each predicate (“genus” is treated as a predicate here).
    
+
    Limitations:
    
+
    Currently this only works for definitions that follow a basic genus-differentia pattern,
+which is what is currently represented in the OboGraph datamodel.
    
+
    Consider using the “axioms” command for inspection of complex nested OWL axioms.
    
+
    More examples:
    
+
    
+
    
+
    Python API:
    
+
    
+
    
+
    Data model:
    
+
    
+
    
+
    runoak logical-definitions [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+--unmelt, --no-unmelt
    
+
    Flatten to a wide table
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--matrix-axes <matrix_axes>
    
+
    If specified, transform results to matrix using these row and column axes. Examples: d,p; f,g
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+--if-absent <if_absent>
    
+
    determines behavior when the value is not present or is empty.
    
+
    
+
    Options:
    
+
    absent-only | present-only
    
+
    
+
    
+
    
+
+
    
+
    
+-S, --set-value <set_value>
    
+
    the value to set for all terms for the given property.
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    mappings
    
+
    List all mappings encoded in the ontology
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:envo mappings
    
+
    
+
    The default output is SSSOM YAML. To use the (canonical) csv format:
    
+
    
+
    runoak -i sqlite:obo:envo mappings -O sssom
    
+
    
+
    By default, labels are not included. Use –autolabel to include labels (but note
+that if the label is not in the source ontology, then no label will be retrieved)
    
+
    
+
    runoak -i sqlite:obo:envo mappings -O sssom
    
+
    
+
    To constrain the mapped object source:
    
+
    
+
    runoak -i sqlite:obo:foodon mappings -O sssom –maps-to-source SUBSET_SIREN
    
+
    
+
    Python API:
    
+
    
+
    
+
    Data model:
    
+
    
+
    
+
    More examples:
    
+
    
+
    
+
    runoak mappings [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-M, --maps-to-source <maps_to_source>
    
+
    Return only mappings with subject or object source equal to this
    
+
    
+
+
    
+
    
+--mapper <mapper>
    
+
    A selector for an adapter that is to be used for the main lookup operation
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    migrate-curies
    
+
    Rewires an ontology replacing all instances of an ID or IDs
    
+
    Note: the specified ontology is modified in place
    
+
    The input for this command is a list equals-separated pairs, specifying the
+source and the target
    
+
    Example:
    
+
    
+
    runoak -i db/uberon.db migrate-curies –replace SRC1=TGT1 SRC2=TGT2
    
+
    
+
    This command is a wrapper onto the “migrate_curies” command in the PatcherInterface
    
+
+
    oaklib.interfaces.patcher_interface.PatcherInterface.migrate_curies
    
+
    runoak migrate-curies [OPTIONS] [CURIE_PAIRS]...
+
    
+
    
+
    Options
    
+
    
+
    
+--replace, --no-replace
    
+
    If true, will update in place
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    Arguments
    
+
    
+
    
+CURIE_PAIRS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    normalize
    
+
    Normalize all input identifiers.
    
+
    Example:
    
+
    
+
    runoak -i translator: normalize HGNC:1 HGNC:2 -M NCBIGene
    
+
    
+
    Python API:
    
+
    
+
    
+
    Data model:
    
+
    
+
    
+
    runoak normalize [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-M, --maps-to-source <maps_to_source>
    
+
    Required Return only mappings with subject or object source equal to this
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    obsoletes
    
+
    Shows all obsolete entities.
    
+
    Example:
    
+
    
+
    runoak -i obolibrary:go.obo obsoletes
    
+
    
+
    To exclude merged terms, use the --no-include-merged flag
    
+
    Example:
    
+
    
+
    runoak -i obolibrary:go.obo obsoletes –no-include-merged
    
+
    
+
    To show migration relationships, use the --show-migration-relationships flag
    
+
    Example:
    
+
    
+
    runoak -i obolibrary:go.obo obsoletes –show-migration-relationships
    
+
    
+
    You can also specify terms to show obsoletes for:
    
+
    Example:
    
+
    
+
    runoak -i obolibrary:go.obo obsoletes –show-migration-relationships GO:0000187 GO:0000188
    
+
    
+
    More examples:
    
+
    
+
    
+
    Python API:
    
+
    
+
    
+
    runoak obsoletes [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+--include-merged, --no-include-merged
    
+
    Include merged terms in output
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+--show-migration-relationships, --no-show-migration-relationships
    
+
    Show migration relationships (e.g. replaced_by, consider)
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
    Options:
    
+
    obo | obojson | ofn | rdf | json | yaml | fhirjson | csv | tsv | nl
    
+
    
+
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    ontologies
    
+
    Shows all ontologies
    
+
    If the input is a pre-merged ontology, then the output of this command is trivially
+a single line, with the name of the input ontology
    
+
    This command is more meaningful when the input is a multi-ontology endpoint, e.g
    
+
    
+
    runoak -i ubergraph ontologies
    
+
    
+
    In future this command will be expanded to allow showing more metadata about each ontology
    
+
    Python API:
    
+
    
+
    
+
    runoak ontologies [OPTIONS]
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+
    ontology-metadata
    
+
    Shows ontology metadata
    
+
    Example:
    
+
    
+
    runoak -i bioportal: ontology-metadata obi uberon foodon
    
+
    
+
    Use the --all option to show all ontologies
    
+
    Example:
    
+
    
+
    runoak -i bioportal: ontology-metadata –all
    
+
    
+
    By default the output is YAML. You can get the results as TSV:
    
+
    Example:
    
+
    
+
    runoak -i bioportal: ontology-metadata –all -O csv
    
+
    
+
    
+
    Warning
    
+
    The output data model is not yet standardized – this may change in future
    
+
    
+
    Python API:
    
+
    
+
    
+
    runoak ontology-metadata [OPTIONS] [ONTOLOGIES]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+--all, --no-all
    
+
    If true, show all ontologies. Use in place of passing an explicit list
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    Arguments
    
+
    
+
    
+ONTOLOGIES
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    ontology-versions
    
+
    Shows ontology versions
    
+
    Currently only implemented for BioPortal
    
+
    Example:
    
+
    
+
    runoak -i bioportal: ontology-versions mp
    
+
    
+
    All ontologies:
    
+
    
+
    runoak -i bioportal ontology-versions –all
    
+
    
+
    Python API:
    
+
    
+
    
+
    runoak ontology-versions [OPTIONS] [ONTOLOGIES]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+--all, --no-all
    
+
    If true, show all ontologies. Use in place of passing an explicit list
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    Arguments
    
+
    
+
    
+ONTOLOGIES
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    paths
    
+
    List all paths between one or more start curies.
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:go paths  -p i,p ‘nuclear membrane’
    
+
    
+
    This shows all shortest paths from nuclear membrane to all ancestors
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:go paths  -p i,p ‘nuclear membrane’ –target cytoplasm
    
+
    
+
    This shows shortest paths between two nodes
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:go paths  -p i,p ‘nuclear membrane’ ‘thylakoid’ –target cytoplasm ‘thylakoid membrane’
    
+
    
+
    This shows all shortest paths between 4 combinations of starts and ends
    
+
    You can also use “@” to separate start node list and end node list. Like most OAK commands,
+you can pass either explicit terms, or term queries. For example, if you have two files of IDs,
+then you can do this:
    
+
    
+
    runoak -i sqlite:obo:go paths  -p i,p .idfile START_NODES.txt @ .idfile END_NODES.txt
    
+
    
+
    You can also pass in weights for each predicate, used when calculating shortest paths.
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:go paths  -p i,p ‘nuclear membrane’ –target cytoplasm                 –predicate-weights “{i: 0.0001, p: 999}”
    
+
    
+
    This shows all shortest paths after weighting relations
    
+
    (Note: you can use the same shorthands as in the –predicates option)
    
+
    This command can be combined with others to visualize the paths.
    
+
    Example:
    
+
    
+
    alias go=”runoak -i sqlite:obo:go”
+go paths  -p i,p ‘nuclear membrane’ –target cytoplasm –narrow | go viz –fill-gaps -
    
+
    
+
    This visualizes the path by first exporting the path as a flat list, then passing the
+results to viz, using the fill-gaps option.
    
+
    More examples:
    
+
    
+
    
+
    runoak paths [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+--target <target>
    
+
    end point of path
    
+
    
+
+
    
+
    
+--narrow, --no-narrow
    
+
    If true then output path is written a list of terms
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--viz, --no-viz
    
+
    If true then generate a path graph from output
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+--exclude-predicates <exclude_predicates>
    
+
    A comma-separated list of predicates to exclude
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+--directed, --no-directed
    
+
    only show directed paths
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--include-predicates, --no-include-predicates
    
+
    show predicates between nodes
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--predicate-weights <predicate_weights>
    
+
    key-value pairs specified in YAML where keys are predicates or shorthands and values are weights
    
+
    
+
+
    
+
    
+-S, --stylemap <stylemap>
    
+
    a json file to configure visualization. See https://berkeleybop.github.io/kgviz-model/
    
+
    
+
+
    
+
    
+-C, --configure <configure>
    
+
    overrides for stylemap, specified as yaml. E.g. `-C “styles: [filled, rounded]” `
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Path to output file
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    prefixes
    
+
    Shows prefix declarations.
    
+
    All standard prefixes:
    
+
    
+
    runoak prefixes
    
+
    
+
    Specific prefixes:
    
+
    
+
    runoak prefixes GO CL oio skos
    
+
    
+
    By default, prefix maps are exported as simple pairwise TSVs.
    
+
    Prefixes can also be exported in different formats, such as YAML and JSON, where they are
+simple dictionaries:
    
+
    In yaml:
    
+
    
+
    runoak prefixes –O yaml
    
+
    
+
    In turtle:
    
+
    
+
    runoak prefixes –O rdf
    
+
    
+
    For RDF exports, the prefix declaration should appear in BOTH prefix declarations, AND also as
+instances of SHACL PrefixDeclarations, e.g.
    
+
    
+
    @prefix CL: <http://purl.obolibrary.org/obo/CL_> .
+…
+[] a sh:PrefixDeclaration ;
    
+
    
+
    sh:namespace CL: ;
+sh:prefix “CL” .
    
+
    
+
    
+
    The default prefixmap is always used, unless options are passed specifying additional
+prefix maps.
    
+
    Example:
    
+
    
+
    runoak –named-prefix-map prefixcc prefixes
    
+
    
+
    If an ontology is loaded, then –used-only can be used to restrict to
+prefixes for entities in that ontology
    
+
    
+
    runoak -i sqlite:obo:cl prefixes –used-only
    
+
    
+
    runoak prefixes [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    
+
+
    
+
    
+--used-only, --no-used-only
    
+
    If True, show only prefixes used in ontology
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    query
    
+
    Execute an arbitrary query.
    
+
    The syntax of the query is backend-dependent.
    
+
    runoak query [OPTIONS]
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-q, --query <query>
    
+
    Main query, specified in adapter-specific language (SQL, SPARQL)
    
+
    
+
+
    
+
    
+-L, --label-fields <label_fields>
    
+
    Comma-separated list of fields to use as labels
    
+
    
+
+
    
+
    
+-P, --prefixes <prefixes>
    
+
    Comma-separated list of prefixes to expand
    
+
    
+
+
    
+
    
+
    relationships
    
+
    Show all relationships for a term or terms
    
+
    By default, this shows all relationships where the input term(s) are the subjects
    
+
    Example:
    
+
    
+
    runoak -i cl.db relationships CL:4023094
    
+
    
+
    Like all OAK commands, a label can be passed instead of a CURIE
    
+
    Example:
    
+
    
+
    runoak -i cl.db relationships neuron
    
+
    
+
    To reverse the direction, and query where the search term(s) are objects, use the –direction flag:
    
+
    Example:
    
+
    
+
    runoak -i cl.db relationships –direction down neuron
    
+
    
+
    Multiple terms can be passed
    
+
    Example:
    
+
    
+
    runoak -i uberon.db relationships heart liver lung
    
+
    
+
    And like all OAK commands, a query can be passed rather than an explicit term list
    
+
    The following query lists all arteries in the limb together which what structures they supply
    
+
    Query:
    
+
    
+
    runoak -i uberon.db relationships -p RO:0002178 .desc//p=i “artery” .and .desc//p=i,p “limb”
    
+
    
+
    More examples:
    
+
    
+
    
+
    Python API:
    
+
    
+
    
+
    runoak relationships [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+--direction <direction>
    
+
    direction of traversal over edges, which up is subject to object, down is object to subject.
    
+
    
+
    Options:
    
+
    up | down | both
    
+
    
+
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+--if-absent <if_absent>
    
+
    determines behavior when the value is not present or is empty.
    
+
    
+
    Options:
    
+
    absent-only | present-only
    
+
    
+
    
+
    
+
+
    
+
    
+-S, --set-value <set_value>
    
+
    the value to set for all terms for the given property.
    
+
    
+
+
    
+
    
+--include-entailed, --no-include-entailed
    
+
    Include entailed indirect relationships
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--non-redundant-entailed, --no-non-redundant-entailed
    
+
    Include entailed but exclude entailed redundant relationships
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--include-tbox, --no-include-tbox
    
+
    Include class-class relationships (subclass and existentials)
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+--include-abox, --no-include-abox
    
+
    Include instance relationships (class and object property assertions)
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+--include-metadata, --no-include-metadata
    
+
    Include metadata (axiom annotations)
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    rollup
    
+
    Produce an association rollup report.
    
+
    The report will list associations where the subject is one of the terms provided. The
+associations will be grouped by any provided –object-group options. This option can be
+provided multiple times. If the value is a comma separated list of object IDs, the first
+will be used as a primary grouping dimension and the remainder will be used to create
+sub-groups.
    
+
    Example:
    
+
    
+
    runoak -i sqlite:go.db -g wb.gaf -G gaf rollup             –object-group GO:0032502,GO:0007568,GO:0048869,GO:0098727             –object-group GO:0008152,GO:0009056,GO:0044238,GO:1901275             –object-group GO:0050896,GO:0051716,GO:0051606,GO:0051606,GO:0014823             –object-group=GO:0023052             –output rollup.html             WB:WBGene00000417 WB:WBGene00000912 WB:WBGene00000898 WB:WBGene00006752
    
+
    
+
    By default, is-a relationships between association objects are used to perform the rollup.
+Use the -p/–predicates option to change this behavior.
    
+
    runoak rollup [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+--object-group <object_group>
    
+
    An object ID to group by. If a comma separated list of IDs is provided, the first one is interpreted as a top-level grouping and the remaining IDs are interpreted as sub-groups within.
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    roots
    
+
    List all root nodes in the ontology
    
+
    Like all OAK relational commands, this is parameterized by –predicates (-p).
+Note that the default is to return the roots of the relation graph over all predicates.
+This can sometimes give unintuitive results, so we recommend always being explicit
+and parameterizing
    
+
    Example:
    
+
    
+
    runoak -i db/cob.db roots
    
+
    
+
    This command is a wrapper onto the “roots” command in the BasicOntologyInterface.
    
+
+
    runoak roots [OPTIONS]
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+-P, --has-prefix <has_prefix>
    
+
    filter based on a prefix, e.g. OBI
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-A, --annotated-roots, --no-annotated-roots, --no-A
    
+
    If true, use annotated roots, if present
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
+
    
+
    set-apikey
    
+
    Sets an API key
    
+
    Example:
    
+
    
+
    oak set-apikey -e bioportal MY-KEY-VALUE
    
+
    
+
    This is stored in an OS-dependent path
    
+
    runoak set-apikey [OPTIONS] KEYVAL
+
    
+
    
+
    Options
    
+
    
+
    
+-e, --endpoint <endpoint>
    
+
    Required Name of endpoint, e.g. bioportal
    
+
    
+
+
    Arguments
    
+
    
+
    
+KEYVAL
    
+
    Required argument
    
+
    
+
+
    
+
    
+
    siblings
    
+
    List all siblings of a specified term or terms
    
+
    Example:
    
+
    
+
    runoak -i cl.owl siblings CL:4023094
    
+
    
+
    Note that siblings is by default over ALL relationship types, so we recommend
+always being explicit and passing a predicate using -p (–predicates)
    
+
    runoak siblings [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
    Options:
    
+
    obo | obojson | ofn | rdf | json | yaml | fhirjson | csv | tsv | nl
    
+
    
+
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    similarity
    
+
    All by all similarity.
    
+
    This calculates a similarity matrix for two sets of terms.
    
+
    Input sets of a terms can be specified in different ways:
    
+
      
+
    • via a file
      • 
+
    • via explicit lists of terms or queries
      • 
+
    
+
    Example:
    
+
    
+
    runoak -i hp.db similarity -p i –set1-file HPO-TERMS1 –set2-file HPO-TERMS2 -O csv
    
+
    
+
    This will compare every term in TERMS1 vs TERMS2
    
+
    Alternatively standard OAK term queries can be used, with “@” separating the two lists
    
+
    Example:
    
+
    
+
    runoak -i hp.db similarity -p i TERM_1 TERM_2 … TERM_N @ TERM_N+1 … TERM_M
    
+
    
+
    The .all term syntax can be used to select all terms in an ontology
    
+
    Example:
    
+
    
+
    runoak -i ma.db similarity -p i,p .all @ .all
    
+
    
+
    This can be mixed with other term selectors; for example to calculate the similarity of “neuron”
+vs all terms in CL:
    
+
    
+
    runoak -i cl.db similarity -p i,p .all @ neuron
    
+
    
+
    An example pipeline to do all by all over all phenotypes in HPO:
    
+
    Explicit:
    
+
    
+
    runoak -i hp.db descendants -p i HP:0000118 > HPO
    
+
    runoak -i hp.db similarity -p i –set1-file HPO –set2-file HPO -O csv -o RESULTS.tsv
    
+
    
+
    The same thing can be done more compactly with term queries:
    
+
    
+
    runoak -i hp.db similarity -p i .desc//p=i HP:0000118 @ .desc//p=i HP:0000118
    
+
    
+
    Python API:
    
+
    
+
    
+
    Data model:
    
+
    
+
    
+
    runoak similarity [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+--set1-file <set1_file>
    
+
    ID file for set1
    
+
    
+
+
    
+
    
+--set2-file <set2_file>
    
+
    ID file for set2
    
+
    
+
+
    
+
    
+--min-jaccard-similarity <min_jaccard_similarity>
    
+
    Minimum value for jaccard score
    
+
    
+
+
    
+
    
+--min-ancestor-information-content <min_ancestor_information_content>
    
+
    Minimum value for information content
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    path to output
    
+
    
+
+
    
+
    
+--main-score-field <main_score_field>
    
+
    Score used for summarization
    
+
    
+
    Default:
    
+
    'phenodigm_score'
    
+
    
+
    
+
    
+
+
    
+
    
+--information-content-file <information_content_file>
    
+
    File containing information content for each term
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    similarity-pair
    
+
    Determine pairwise similarity between two terms using a variety of metrics
    
+
    NOTE: this command may be deprecated, consider using similarity
    
+
    Note: We recommend always specifying explicit predicate lists
    
+
    Example:
    
+
    
+
    runoak -i ubergraph: similarity-pair -p i,p CL:0000540 CL:0000000
    
+
    
+
    You can omit predicates if you like but be warned this may yield
+hard to interpret results.
    
+
    E.g.
    
+
    
+
    runoak -i ubergraph: similarity-pair CL:0000540 GO:0001750
    
+
    
+
    yields “fully formed stage” (i.e these are both found in the adult) as
+the MRCA
    
+
    For phenotype ontologies, UPHENO relationship types connect phenotype terms to anatomy, etc:
    
+
    
+
    runoak -i ubergraph: similarity-pair MP:0010922 HP:0010616  -p i,p,UPHENO:0000001
    
+
    
+
    Python API:
    
+
    
+
    
+
    Data model:
    
+
    
+
    
+
    runoak similarity-pair [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    singletons
    
+
    List all singleton nodes in the ontology
    
+
    Like all OAK relational commands, this is parameterized by –predicates (-p).
+Note that the default is to return the singletons of the relation graph over all predicates
    
+
    Obsoletes are filtered by default
    
+
    Example:
    
+
    
+
    runoak -i db/cob.db singletons
    
+
    
+
    This command is a wrapper onto the “singletons” command in the BasicOntologyInterface.
    
+
+
    runoak singletons [OPTIONS]
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+--filter-obsoletes, --no-filter-obsoletes
    
+
    If set, results will exclude obsoletes
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+
    statistics
    
+
    Shows all descriptive/summary statistics
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:pr statistics
    
+
    
+
    By default, this will show combined summary statistics for all terms
    
+
    You can also break down the statistics in two ways:
    
+
      
+
    • by a collection of branch roots
      • 
+
    • by a metadata property (e.g. oio:hasOBONamespace, rdfs:isDefinedBy)
      • 
+
    • by prefix (e.g. GO, PR, CL, OBI)
      • 
+
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:pr statistics -p oio:hasOBONamespace
    
+
    
+
    Note: the oio:hasOBONamespace is not the same as the ID prefix, it is
+a field that is used by a subset of ontologies to partition classes into
+broad groupings, similar to subsets. Its use is non-standard, yet a lot
+of ontologies use this as the main partitioning mechanism.
    
+
    A note on bundled ontologies:
    
+
    The standard release many OBO ontologies “bundles” parts of other ontologies
+(formally, the release product includes a merged imports closure of import
+modules). This can complicate generation of statistics. A naive count of
+all classes in the main OBI release will include not only “native” OBI classes,
+but also classes from other ontologies that are bundled in the release.
    
+
    For bundled ontologies, we recommend some kind of partitioning, such as via
+defined roots, or via the CURIE prefix, using the --group-by-prefix option.
    
+
    Output formats:
    
+
    The recommended output types for this command are yaml, json, or csv.
+The default output type is yaml, following the SummaryStatistics data model.
+This is naturally nested, as the statistics includes faceted groupings
+(e.g. edge counts are broken down by predicate). When specifying a flat
+format like csv, this is flattened into a single table, with dynamic
+column names.
    
+
    Change statistics:
    
+
    You can optionally combine the ontology statistics with a change
+summary relative to another ontology, using the --compare-with
+option.
    
+
    Example:
    
+
    
+
    runoak -i v2.obo statistics –group-by-obo-namespace –compare-with v1.obo
    
+
    
+
    This will also include change stats broken down by KGCL change types. If
+a group-by option is specified, these will be grouped accordingly.
    
+
    Python API:
    
+
    
+
    
+
    Data model:
    
+
    
+
    
+
    runoak statistics [OPTIONS] [BRANCHES]...
+
    
+
    
+
    Options
    
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
    Options:
    
+
    obo | obojson | ofn | rdf | json | yaml | fhirjson | csv | tsv | nl
    
+
    
+
    
+
    
+
+
    
+
    
+--group-by-property <group_by_property>
    
+
    group summaries by a metadata property, e.g. rdfs:isDefinedBy
    
+
    
+
+
    
+
    
+--group-by-obo-namespace, --no-group-by-obo-namespace
    
+
    shortcut for –group-by-property oio:hasOBONamespace (note this is distinct from the ID namespace)
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--group-by-prefix, --no-group-by-prefix
    
+
    shortcut for –group-by-property sh:prefix. Groups by the prefix of the CURIE
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--group-by-defined-by, --no-group-by-defined-by
    
+
    shortcut for –group-by-property rdfs:isDefinedBy. This may be inferred from prefix if not set explicitly
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--include-residuals, --no-include-residuals
    
+
    If true include an OTHER category for terms that do not have the property
    
+
    
+
+
    
+
    
+-X, --compare-with <compare_with>
    
+
    Compare with another ontology
    
+
    
+
+
    
+
    
+-P, --has-prefix <has_prefix>
    
+
    filter based on a prefix, e.g. OBI
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    Arguments
    
+
    
+
    
+BRANCHES
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    subsets
    
+
    Shows information on subsets
    
+
    Example:
    
+
    
+
    runoak -i obolibrary:go.obo subsets
    
+
    
+
    Example:
    
+
    
+
    runoak -i cl.owl subsets
    
+
    
+
    For background on subsets, see https://incatools.github.io/ontology-access-kit/concepts.html#subsets
    
+
    Note you can use subsets in selector queries for other commands; e.g. to fetch all
+terms (directly) in goslim_generic in GO:
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:go info .in goslim_generic
    
+
    
+
    Python API:
    
+
    
+
    
+
    See Also:
+-
    
+
    
+
    term-subsets command, which shows relationships of terms to subsets
    
+
    
+
    runoak subsets [OPTIONS]
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+
    synonymize
    
+
    Deprecated: use generate-synonyms
    
+
    runoak synonymize [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-R, --rules-file <rules_file>
    
+
    path to rules file. Conforms to rules_datamodel.        e.g. https://github.com/INCATools/ontology-access-kit/blob/main/tests/input/matcher_rules.yaml
    
+
    
+
+
    
+
    
+--apply-patch, --no-apply-patch
    
+
    Apply KGCL syntax generated based on the synonymizer rules file.
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--patch <patch>
    
+
    Output patch file containing KGCL commands.
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    taxon-constraints
    
+
    Compute all taxon constraints for a term or terms.
    
+
    This will apply rules using the inferred ancestors of subject terms, as well as inferred
+ancestors/descendants of taxon terms.
    
+
    The input ontology MUST include both the taxon constraint relationships AND the relevant portion
+of NCBI Taxonomy
    
+
    Example:
    
+
    
+
    runoak -i db/go.db taxon-constraints GO:0034357 –include-redundant -p i,p
    
+
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:uberon taxon-constraints UBERON:0003884 UBERON:0003941 -p i,p
    
+
    
+
    More examples:
    
+
    
+
    
+
    This command is a wrapper onto taxon_constraints_utils:
    
+
+
    runoak taxon-constraints [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+-M, --graph-traversal-method <graph_traversal_method>
    
+
    Whether formal entailment or graph walking should be used.
    
+
    
+
    Options:
    
+
    HOP | ENTAILMENT
    
+
    
+
    
+
    
+
+
    
+
    
+-A, --all, --no-A, --no-all
    
+
    if specified then perform for all terms
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--include-redundant, --no-include-redundant
    
+
    if specified then include redundant taxon constraints from ancestral subjects
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--direct, --no-direct
    
+
    only include directly asserted taxon constraints
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    term-categories
    
+
    List categories for a term or set of terms.
    
+
    runoak term-categories [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+--category-system <category_system>
    
+
    Example: biolink, cob, bfo, dbpedia, …
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    term-metadata
    
+
    Shows term metadata.
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:uberon term-metadata lung heart
    
+
    
+
    You can filter the results for only selected predicates:
    
+
    
+
    runoak -i sqlite:obo:uberon term-metadata lung heart -p id,oio:hasDbXref
    
+
    
+
    The default output is YAML documents, where each YAML document is a term, with
+keys representing selected predicates. Values are always lists of atoms, even
+when there is typically one value (e.g. rdfs:label)
    
+
    Python API:
    
+
    
+
    
+
    Data model:
    
+
    
+
    
+
    runoak term-metadata [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+--additional-metadata, --no-additional-metadata
    
+
    if true then fetch additional metadata about statements stored as OWL reification
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    term-subsets
    
+
    List subsets for a term or set of terms.
    
+
    Example:
    
+
    
+
    runoak -i sqlite:obo:uberon term-subsets heart lung
    
+
    
+
    Python API:
    
+
    
+
    
+
    runoak term-subsets [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    terms
    
+
    List all terms in the ontology
    
+
    Example:
    
+
    
+
    runoak -i db/cob.db terms
    
+
    
+
    All terms without obsoletes:
    
+
    
+
    runoak -i prontolib:cl.obo  terms –filter-obsoletes
    
+
    
+
    By default “terms” is considered to be any entity type in the ontology. Use –owl-type to constrain this:
    
+
    Classes:
    
+
    
+
    runoak -i sqlite:obo:ro terms –owl-type owl:Class
    
+
    
+
    Relationship types (Object properties):
    
+
    
+
    runoak -i sqlite:obo:ro terms –owl-type owl:ObjectProperty
    
+
    
+
    Annotation properties:
    
+
    
+
    runoak -i sqlite:obo:omo terms –owl-type owl:AnnotationProperty
    
+
    
+
    runoak terms [OPTIONS]
+
    
+
    
+
    Options
    
+
    
+
    
+--filter-obsoletes, --no-filter-obsoletes
    
+
    If set, results will exclude obsoletes
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+--owl-type <owl_type>
    
+
    only include entities of this type, e.g. owl:Class, rdf:Property
    
+
    
+
+
    
+
    
+
    termset-similarity
    
+
    Termset similarity.
    
+
    This calculates a similarity matrix for two sets of terms.
    
+
    Example:
    
+
    
+
    runoak -i go.db termset-similarity -p i,p nucleus membrane @ “nuclear membrane” vacuole -p i,p
    
+
    
+
    Python API:
    
+
    
+
    
+
    Data model:
    
+
    
+
    
+
    runoak termset-similarity [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+--information-content-file <information_content_file>
    
+
    File containing information content for each term
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    transform
    
+
    Applies a defined transformation to an ontology (EXPERIMENTAL).
    
+
    Transformations include:
    
+
      
+
    • SEPTransform: implements Structured-Entities-Parts (SEP) design pattern
      • 
+
    • EdgeFilterTransformer: filters edges based on a predicate
      • 
+
    
+
    Note that for most transformation operations, we recommend using ROBOT
+and commands such as remove, filter, query.
    
+
    Example:
    
+
    
+
    runoak -i xao.obo transform -t SEPTransform -o xao.sep.obo
    
+
    
+
    Removes all P part-of Ws from XAO and replaces occurrences with triads of the form:
    
+
      
+
    • W subClassOf W-structure
      • 
+
    • W subClassOf W-structure
      • 
+
    • W-Part subClassOf W-structure
      • 
+
    • P subClassOf W-Part
      • 
+
    
+
    runoak transform [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Path to output file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-c, --config-file <config_file>
    
+
    Config file for additional transform params.
    
+
    
+
+
    
+
    
+-t, --transform <transform>
    
+
    Required Name of transformation to apply.
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    tree
    
+
    Display an ancestor graph as an ascii/markdown tree.
    
+
    For general instructions, see the viz command, which this is analogous too.
    
+
    Example:
    
+
    
+
    runoak -i envo.db tree ENVO:00000372 -p i,p
    
+
    
+
    This produces output like:
    
+
    .packages:
    
+
    * [i] ENVO:00000094 ! volcanic feature
+    * [i] ENVO:00000247 ! volcano
+        * [i] ENVO:00000403 ! shield volcano
+            * [i] **ENVO:00000372 ! pyroclastic shield volcano**
+
    
+
    
+
    Note: for many ontologies the tree view will explode, especially if no predicates are specified.
+You may wish to start with the is-a tree (-p i).
    
+
    You can use the –gap-fill option to create a minimal tree:
    
+
    Example:
    
+
    
+
    runoak -i envo.db tree –gap-fill ‘pyroclastic shield volcano’ ‘subglacial volcano’ volcano -p i
    
+
    
+
    This will show the tree containing only these terms, and the most direct inferred relationships between them.
    
+
    You can also give a list of leaf terms and specify –add-mrcas alongside –gap-fill to fill in
+the most informative intermediate classes:
    
+
    Example:
    
+
    
+
    runoak -i envo.db tree –add-mrcas –gap-fill ‘pyroclastic shield volcano’            ‘subglacial volcano’ ‘mud volcano’ -p i
    
+
    
+
    This will fill in the term “volcano”, as it is the most recent common ancestor of the specified terms
    
+
    The –max-hops option can control the distance
    
+
    
+
    runoak -i envo.db tree ‘pyroclastic shield volcano’ ‘subglacial volcano’ –max-hops 1 -p i
    
+
    
+
    This will generate:
    
+
    
+
      
+
    • 
+
      [] ENVO:00000247 ! volcano
        
+
      • 
+
        [i] ENVO:00000403 ! shield volcano
          
+
        • [i] ENVO:00000372 ! pyroclastic shield volcano
          • 
+
        
+
        
+
        
+
        • 
+
      • [i] ENVO:00000407 ! subglacial volcano
        • 
+
      
+
      
+
      
+
      • 
+
    
+
    
+
    Note that ‘volcano’ is the root, even though it is 2 hops from one of the terms, it can be connected
+to at least one of the seeds (highlighted with asterisks) by a path of length 1.
    
+
    Python API:
    
+
    
+
    
+
    Data model:
    
+
    
+
    
+
    runoak tree [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+--down, --no-down
    
+
    traverse down
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--gap-fill, --no-gap-fill
    
+
    If set then find the minimal graph that spans all input curies
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--add-mrcas, --no-add-mrcas
    
+
    If set then extend input seed list to include all pairwise MRCAs
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+-S, --stylemap <stylemap>
    
+
    a json file to configure visualization. See https://berkeleybop.github.io/kgviz-model/
    
+
    
+
+
    
+
    
+-C, --configure <configure>
    
+
    overrides for stylemap, specified as yaml. E.g. `-C “styles: [filled, rounded]” `
    
+
    
+
+
    
+
    
+--max-hops <max_hops>
    
+
    Trim nodes that are equal to or greater than this distance from terms
    
+
    
+
+
    
+
    
+--skip <skip>
    
+
    Exclude paths that contain this node
    
+
    
+
+
    
+
    
+--root <root>
    
+
    Use this node or nodes as roots
    
+
    
+
+
    
+
    
+-D, --display <display>
    
+
    A comma-separated list of display options. Use ‘all’ for all
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    usages
    
+
    List usages of a term or set of terms.
    
+
    Usages of neuron in GO:
    
+
    
+
    runoak -i sqlite:obo:go usages CL:0000540
    
+
    
+
    Association/annotations sources can also be used:
    
+
    
+
    runoak -i quickgo: usages GO:0031969
    
+
    
+
    Note this query may be slow - you can restrict to a species:
    
+
    
+
    runoak -i quickgo:NCBITaxon:9606 usages GO:0031969
    
+
    
+
    (this should return no results, as there should be no human proteins annotated
+to chloroplast membrane)
    
+
    Using amigo:
    
+
    
+
    runoak -i amigo: usages GO:0031969
    
+
    
+
    Using ubergraph:
    
+
    
+
    runoak -i ubergraph: usages CL:0000540
    
+
    
+
    This will include usages over multiple ontologies
    
+
    Using ontobee:
    
+
    
+
    runoak -i ubergraph: usages CL:0000540
    
+
    
+
    You can multiple queries over multiple sources (an AggregatorImplementation):
    
+
    
+
    runoak -i sqlite:obo:go -a ubergraph: -a amigo: -a quickgo: usages GO:0031969
    
+
    
+
    runoak usages [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-P, --used-by-prefix <used_by_prefix>
    
+
    
+
+
    
+
    
+--include-unused, --no-include-unused
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    validate
    
+
    Validate an ontology against ontology metadata
    
+
    Implementation notes: Currently only works on SQLite
    
+
    Example:
    
+
    
+
    runoak  -i db/ecto.db validate -o results.tsv
    
+
    
+
    The default validation performed is structural (conformance to the ontology_metadata schema)
    
+
    There is experimental support for additional ontology rules, which includes heuristic methods
+such as aligning text and logical definitions. These are off by default.
    
+
    To run these, pass –no-skip-ontology-rules
    
+
    Example:
    
+
    
+
    runoak -i db/uberon.db validate –skip-structural-validation –no-skip-ontology-rules
    
+
    
+
    For more information, see the OAK how-to guide:
    
+
+
    runoak validate [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+--cutoff <cutoff>
    
+
    maximum results to report for any (type, predicate) pair
    
+
    
+
    Default:
    
+
    50
    
+
    
+
    
+
    
+
+
    
+
    
+--skip-structural-validation, --no-skip-structural-validation
    
+
    If true, main structural validation checks are skipped
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--skip-ontology-rules, --no-skip-ontology-rules
    
+
    If true, ontology rules are skipped
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-R, --rule <rule>
    
+
    A rule to run. Can be specified multiple times. If not specified, all rules are run.
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    validate-definitions
    
+
    Checks presence and structure of text definitions.
    
+
    To run:
    
+
    
+
    runoak validate-definitions -i db/uberon.db -o results.tsv
    
+
    
+
    By default this will apply basic text mining of text definitions to check
+against machine actionable OBO text definition guideline rules.
+This can result in an initial lag - to skip this, and ONLY perform
+checks for presence of definitions, use –skip-text-annotation:
    
+
    Example:
    
+
    
+
    runoak validate-definitions -i db/uberon.db –skip-text-annotation
    
+
    
+
    Like most OAK commands, this accepts lists of terms or term queries
+as arguments. You can pass in a CURIE list to selectively validate
+individual classes
    
+
    Example:
    
+
    
+
    runoak validate-definitions -i db/cl.db CL:0002053
    
+
    
+
    Only on CL identifiers:
    
+
    
+
    runoak validate-definitions -i db/cl.db i^CL:
    
+
    
+
    Only on neuron hierarchy:
    
+
    
+
    runoak validate-definitions -i db/cl.db .desc//p=i neuron
    
+
    
+
    Output format:
    
+
    This command emits objects conforming to the OAK validation datamodel.
+See https://incatools.github.io/ontology-access-kit/datamodels for more
+on OAK datamodels.
    
+
    The default serialization of the datamodel is CSV.
    
+
    
+
    Notes:
    
+
    This command is largely redundant with the validate command, but is useful for
+targeted validation focused solely on definitions
    
+
    runoak validate-definitions [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+--skip-text-annotation, --no-skip-text-annotation
    
+
    If true, do not parse text annotations
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+-C, --configuration-file <configuration_file>
    
+
    Path to a configuration file. This is typically a YAML file, but may be a JSON file
    
+
    
+
+
    
+
    
+--adapter-mapping <adapter_mapping>
    
+
    Multiple prefix=selector pairs, e.g. –adapter-mapping uberon=db/uberon.db
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    
+
    validate-mappings
    
+
    Validates mappings in ontology using additional ontologies.
    
+
    To run:
    
+
    
+
    runoak validate-mappings -i db/uberon.db
    
+
    
+
    For sssom:
    
+
    
+
    runoak validate-mappings -i db/uberon.db -o bad-mappings.sssom.tsv
    
+
    
+
    By default this will attempt to download and connect to
+sqlite versions of different ontologies, when attempting to resolve a foreign
+subject or object id.
    
+
    You can customize this mapping:
    
+
    
+
    runoak validate-mappings -i db/uberon.db –adapter-mapping uberon=db/uberon.db             –adapter-mapping zfa=db/zfa.db
    
+
    
+
    This will use a local sqlite file for ZFA:nnnnnnn IDs.
    
+
    You can use “*” as a wildcard, in the case where you have an application ontology
+with many mapped entities merged in:
    
+
    
+
    runoak validate-mappings -i db/uberon.db –adapter-mapping “*”=db/merged.db”
    
+
    
+
    The default behavior for this command is to perform deterministic rule-based
+checks; for example, the mapped IDs should not be obsolete, and if the mapping
+is skos:exactMatch, then the cardinality is expected to be 1:1.
    
+
    Other adapters may choose to implement bespoke behaviors. In future there
+might be a boomer adapter that will perform probabilistic reasoning on the
+mappings. The experimental LLM backend will use an LLM to qualitatively
+validate mappings (see the LLM how-to guide for more details).
    
+
    runoak validate-mappings [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+--adapter-mapping <adapter_mapping>
    
+
    Multiple prefix=selector pairs, e.g. –adapter-mapping uberon=db/uberon.db
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-C, --configuration-file <configuration_file>
    
+
    Path to a configuration file. This is typically a YAML file, but may be a JSON file
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    validate-multiple
    
+
    Validate multiple ontologies against ontology metadata
    
+
    See the validate command - this is the same except you can pass a list of databases
    
+
    For more information, see the OAK how-to guide:
    
+
+
    runoak validate-multiple [OPTIONS] [DBS]...
+
    
+
    
+
    Options
    
+
    
+
    
+--cutoff <cutoff>
    
+
    maximum results to report for any (type, predicate) pair
    
+
    
+
    Default:
    
+
    50
    
+
    
+
    
+
    
+
+
    
+
    
+-s, --schema <schema>
    
+
    Path to schema (if you want to override the bundled OMO schema)
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    Arguments
    
+
    
+
    
+DBS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    validate-subset
    
+
    
+
    Validates term subsets.
    
+
    The default metrics used for evaluation involve calculating the degree of overlap between members of the
+subset. Subsets in general should partition the ontology into sets that overlap as little as possible.
    
+
    Different overlap metrics can be plugged in, see the information-content methods for more details.
    
+
    The simplest way to run this is to pass in a list of terms via a subset query
    
+
    
+
    runoak -i po.db validate-subset p i,p  .in Tomato
    
+
    
+
    You can also calculate IC scores for each term and pass them in via a file:
    
+
    
+
    runoak -i amigo:NCBITaxon:9606 information-content -o human-ic.tsv
    
+
    
+
    
+
    Then
    
+
    
+
    runoak -i go.db validate-subset p i,p  .in goslim_generic –information-content-file human-ic.tsv
    
+
    
+
    runoak validate-subset [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+--adapter-mapping <adapter_mapping>
    
+
    Multiple prefix=selector pairs, e.g. –adapter-mapping uberon=db/uberon.db
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+-X, --exclude-query <exclude_query>
    
+
    A query to exclude certain terms
    
+
    
+
+
    
+
    
+--information-content-file <information_content_file>
    
+
    File containing information content for each term
    
+
    
+
+
    
+
    
+--information-content-adapter <information_content_adapter>
    
+
    Adapter to use for information content scores
    
+
    
+
+
    
+
    
+--config-yaml <config_yaml>
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-C, --configuration-file <configuration_file>
    
+
    Path to a configuration file. This is typically a YAML file, but may be a JSON file
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    validate-synonyms
    
+
    Validates synonyms in ontology using additional ontologies.
    
+
    To run:
    
+
    
+
    runoak validate-synonyms -i db/uberon.db
    
+
    
+
    You can customize this mapping:
    
+
    
+
    runoak validate-synonyms -i db/uberon.db –adapter-mapping uberon=db/uberon.db             –adapter-mapping zfa=sqlite:obo:zfa
    
+
    
+
    This will use a remote sqlite file for ZFA:nnnnnnn IDs.
    
+
    You can use “*” as a wildcard, in the case where you have an application ontology
+with many mapped entities merged in:
    
+
    
+
    runoak validate-synonyms -i db/uberon.db –adapter-mapping “*”=db/merged.db”
    
+
    
+
    You can also pass synonymizer rules. For example:
    
+
    
+
    runoak -i sqlite:obo:go  validate-synonyms            -R go-strip-activity.synonymizer.yaml GO:0000010             –adapter-mapping ec=sqlite:obo:eccode
    
+
    
+
    In this case if the synonymizer rule file contains:
    
+
    
+
    
+rules:
    
+
    
+
      
+
    • match: ” activity”
+replacement: “”
      • 
+
    
+
    
+
    
    
+
    
+
    Then the GO synonyms will have the word “activity” stripped from them, prior to attempting
+to match with EC.
    
+
    The default behavior for this command is to perform deterministic rule-based
+checks; for example, the mapped IDs should not be obsolete, and if the mapping
+is skos:exactMatch, then the cardinality is expected to be 1:1.
    
+
    Other adapters may choose to implement bespoke behaviors. In future there
+might be a boomer adapter that will perform probabilistic reasoning on the
+mappings. The experimental LLM backend will use an LLM to qualitatively
+validate mappings (see the LLM how-to guide for more details).
    
+
    runoak validate-synonyms [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+--autolabel, --no-autolabel
    
+
    If set, results will automatically have labels assigned
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+--adapter-mapping <adapter_mapping>
    
+
    Multiple prefix=selector pairs, e.g. –adapter-mapping uberon=db/uberon.db
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Output file, e.g. obo file
    
+
    
+
+
    
+
    
+-C, --configuration-file <configuration_file>
    
+
    Path to a configuration file. This is typically a YAML file, but may be a JSON file
    
+
    
+
+
    
+
    
+-R, --rules-file <rules_file>
    
+
    path to rules file. Conforms to rules_datamodel.        e.g. https://github.com/INCATools/ontology-access-kit/blob/main/tests/input/matcher_rules.yaml
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
+
    viz
    
+
    Visualize an ancestor graph using obographviz
    
+
    For general background on what is meant by a graph in OAK,
+see https://incatools.github.io/ontology-access-kit/interfaces/obograph
    
+
    
+
    Note
    
+
    This requires that obographviz is installed.
    
+
    
+
    Example:
    
+
    
+
    runoak -i sqlite:cl.db viz CL:4023094
    
+
    
+
    Same query on ubergraph:
    
+
    
+
    runoak -i ubergraph: viz CL:4023094
    
+
    
+
    Example, showing only is-a:
    
+
    
+
    runoak -i sqlite:cl.db viz CL:4023094 -p i
    
+
    
+
    Example, showing only is-a and part-of, to include Uberon:
    
+
    
+
    runoak -i sqlite:cl.db viz CL:4023094 -p i,p
    
+
    
+
    As above, including develops-from:
    
+
    
+
    runoak -i sqlite:cl.db viz CL:4023094 -p i,p,RO:0002202
    
+
    
+
    With abbreviation:
    
+
    
+
    runoak -i sqlite:cl.db viz CL:4023094 -p i,p,d
    
+
    
+
    We can also limit the number of “hops” from the seed terms; for
+example, all is-a and develops-from ancestors of T-cell, limiting
+to a distance of 2:
    
+
    
+
    runoak -i sqlite:cl.db viz ‘T cell’ -p i,d –max-hops 2
    
+
    
+
    Python API:
    
+
    
+
    
+
    Data model:
    
+
    
+
    
+
    runoak viz [OPTIONS] [TERMS]...
+
    
+
    
+
    Options
    
+
    
+
    
+--view, --no-view
    
+
    if view is set then open the image after rendering
    
+
    
+
    Default:
    
+
    True
    
+
    
+
    
+
    
+
+
    
+
    
+--down, --no-down
    
+
    traverse down
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--gap-fill, --no-gap-fill
    
+
    If set then find the minimal graph that spans all input curies
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+--add-mrcas, --no-add-mrcas
    
+
    If set then extend input seed list to include all pairwise MRCAs
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+-S, --stylemap <stylemap>
    
+
    a json file to configure visualization. See https://berkeleybop.github.io/kgviz-model/
    
+
    
+
+
    
+
    
+-C, --configure <configure>
    
+
    overrides for stylemap, specified as yaml. E.g. `-C “styles: [filled, rounded]” `
    
+
    
+
+
    
+
    
+--max-hops <max_hops>
    
+
    Trim nodes that are equal to or greater than this distance from terms
    
+
    
+
+
    
+
    
+--meta, --no-meta
    
+
    Add metadata object to graph nodes, including xrefs, definitions
    
+
    
+
    Default:
    
+
    False
    
+
    
+
    
+
    
+
+
    
+
    
+-p, --predicates <predicates>
    
+
    A comma-separated list of predicates. This may be a shorthand (i, p) or CURIE
    
+
    
+
+
    
+
    
+-O, --output-type <output_type>
    
+
    Desired output type
    
+
    
+
+
    
+
    
+-o, --output <output>
    
+
    Path to output file
    
+
    
+
+
    Arguments
    
+
    
+
    
+TERMS
    
+
    Optional argument(s)
    
+
    
+
+
    
+
    
 
    
 
 
@@ -189,7 +6447,7 @@ 
    Commands